DAT Biology BIG SET

Microscopy

Microscopy is an important tool in biology that allows us to view objects that could not be seen with the naked eye. In optical microscopy, visible light is focused on an object and then reflected back through lens to magnify the view of a sample. Electron microscopy is similar, but a focused beam of electrons is used rather than visible light. In general, electron microscopy allows for significantly higher magnification than light microscopy, but it cannot be used to view living specimens due to the necessary preparation steps ❖ Note that in the image above, cellular organelles (such as the mitochondria) are approximately the same size as bacteria. ❖ Most viruses are so small that they must be viewed using electron microscopy.

anamniotes

On the contrary, amphibians and fishes are anamniotes, meaning that their eggs do not contain an amnion. This is because fish and amphibian eggs are laid in water, which already acts like a cushion. The surrounding water also performs the process of nitrogenous waste removal for the embryo, via diffusion.

microvilli

On top of each villus, there are tiny projections known as *microvilli*. These further expands the surface area to help in nutrient absorption.

transcription stop point

Once bound, Rho moves along the RNA transcript in the 5' 3' direction, which is the same direction that RNA polymerase is extending the transcript. Eventually, Rho will catch up to RNA polymerase because a region of DNA, called the *transcription stop point*, forcing RNA polymerase to pause. When Rho catches up to RNA polymerase, it displaces the RNA transcript and transcription ends.

*Auto*crine

Secretes hormones to *itself*

hemorrhage and blood pressure

Blood pressure has fallen so the body wants to raise it. Thus the body, wants to increase cardiac output via an increase in heart rate and an increase in systemic vascular resistance.

Three Categories of Cleavage

1. Radial vs. Spiral cleavage 2. Determinate vs. Indeterminate cleavage 3. Holoblastic vs. Meroblastic cleavage

The embryo consists of four parts

1. Radicle 2. Hypocotyl 3. Plumule 4. Epicotyl

There are two main types of termination in bacteria

1. Rho independent termination 2. Rho-dependent termination

Earth and atmosphere formed through volcanoes. The atmosphere consisted of

CH4, NH3, CO, CO2, H2, N2, H20, S, HCl, HCN, little or no O2.

Multiple Alleles

Multiple alleles (more than two possibilities) exist for a given gene. ex) - ABO blood type: A, B, O allele possibilities - Rabbit coat color has four different allele possibilities

Mismatch repair

DNA polymerase can't catch all its mistakes - mismatch repair is a way for the cell to mark the uncaught errors so they can be replaced with the correct sequence.

ecological community

Encompasses *all of the populations* living in a certain area where the different species interact.

Estrogen and progesterone

Female sex hormones (although males do have varying levels of estrogen as well). They contribute to the menstrual cycle and reproduction, as well as female secondary sex characteristics (eg. breast development).

Flat bones

Flat bones are like Oreos, where cortical bone acts as the hard chocolate cookies and cancellous bone acts as the soft cream sandwiched between. ○ Some examples include the sternum and bones forming the skull.

Ganglia

Masses of nerve tissue, which may be strung together by thinner segments of nerve like beads on a string. Ganglia can fuse with each other to form 'mini brains' that are capable of controlling larger body structures.

Taxis

The directional movement in response to a stimulus. The movement is either toward or away from the stimulus. *Phototaxis* is the movement toward light. Examples of this include: ● Moths move in response to light. ● Sharks move in response to food odors. ● Mosquitos move in response to the CO2 and lactic acid produced by mammals.

immune system

The immune system is what protects us against the hostile microbes that we are in contact with everyday. It consists of a protective outer wall and a team of well-versed soldiers who fight together to protect their kingdom — our body.

The dermis has two layers.

The more superficial, thinner layer is the papillary dermis. The deeper and thicker layer is the reticular dermis.

Passive transport

The movement of molecules down a concentration gradient. This does not require energy input.

Isometric contractions

The muscular contractions that occur when the muscle does not change length and the angle across the joint between the muscle's origin and insertion does not change. These types of contraction occur because the tension on the muscle is equal to the load the muscle is contracting against. ● DAT Pro-Tip: Iso = same; metric = length

Chloroplast Thylakoid lumen

This is the interior of the thylakoid. H+ accumulates here.

Chloroplast Thylakoids

This phospholipid bilayer structured organelle is suspended within stroma (stacks). The individual membrane layers are thylakoids. An entire stack is called the *granum* membrane of thylakoids. It contains (PSI + PSII), cytochromes, and other e‐ carriers.

Large motor units

Those which have many muscle fibers innervated by one motor neuron. Powerful movements are created by large muscles with few motor units.

innate immune system

We can think of the innate immune system as our body's frontline soldiers. These soldiers attack whenever there is enemy invasion. They are quick to act but lack specificity.

Adrenal Gland

We have two adrenal glands sitting on top of each kidney. The gland can be divided into two main structures: the outer *cortex* and the inner *medulla*. The cortex and medulla of the adrenal gland each produce different hormones.

Fusion

Weakening of reproductive barriers- the two species fuse.

G protein

alpha (α), beta (β) and gamma (γ) subunits. Also known as a guanine nucleotide binding protein, are a category of proteins that activate other things. The three big components in a G protein are the alpha (α), beta (β) and gamma (γ) subunits.

protein denaturation

any secondary, tertiary, and quaternary structure is removed but the amino acid sequence (primary structure) remains intact.

Haldane effec

almost like a corollary to Bohr effect; deoxygenation of the blood increases hemoglobin's ability to carry CO2. It explains how CO2 affects the dissociation curve.

anaphase II

each chromosome is pulled into two separate chromatids and migrate to opposite poles of the cell

The bundles inside a muscle are called

fascicles

intermolecular bonds

hydrogen bonds

Lipids

hydrophobic molecules with multiple functions: insulation, energy storage, structure, and endocrine

The hypothalamus secretes a few hormones to control the anterior pituitary

hypothalamic-releasing hormones and hypothalamic-inhibiting hormones

The storage material in a seed provides

nutrients to the embryo.

Electromagnetic receptors

sense light.

Nociceptors

sense pain.

DNA forms two antiparallel strands of a double helix. The backbone is held together by

phosphodiester bonds

Lymph also transports absorbed fat from

small intestine to the blood.

pyrimidines

the nitrogenous bases *cytosine*, *thymine*, and *uracil*, which are single-ring nitrogen bases. Mnemonic: CUT the PY = Cytosine, Uracil, and Thymine are PYrimidines.

antibodies variable regions

the ones that bind to different antigens, that's why they have different amino acid sequences.

In eukaryotes, the rough ER is continuous with

the outer nuclear membrane. The rough ER tends to make proteins that are part of the membrane, or secreted by the cell.

Protobionts

the precursors of cells. They are metabolically active but unable to reproduce.

Ontogeny recapitulates phylogeny

the theory of recapitulation that states that embryological stages represent our past evolutionary ancestors. This is theory is now considered defunct.

atria

the upper chambers of the heart.

Chromosomes

tightly condensed chromatin that form when the cell is ready to divide.

Trypsin is secreted as

trypsinogen

operon

when a group of related genes are under the control of one promoter site

Gram stain

'Gram' refers to how the Eubacteria cell wall absorbs a *Gram stain* - whether the Eubacteria retains the purple-violet dye color of the Gram stain, or not. Eubacteria can be divided into Gram positive and Gram negative bacteria. Peptidoglycan thickness in the cell wall is one way that Gram-positive bacteria are differentiated from Gram-negative bacteria. *Gram positive* bacteria have a *thick peptidoglycan layer* within their cell wall, whereas *Gram negative* bacteria have a *thin peptidoglycan layer*. *Gram positive* bacteria stain *dark purple*, whereas Gram negative bacteria have the Gram stain washed away. *Gram negative* bacteria stain *pink* because part of the Gram staining protocol is to apply a counterstain. *Counterstain* is applied after Gram staining. It is important to counterstain, otherwise you wouldn't be able to visualize the Gram negative bacteria, which had the Gram stain washed away. Gram negative bacteria have a *second, outer membrane* outside of the bacterial cell wall, *which is absent in Gram positive bacteria*. *Gram negative* cells contain *lipopolysaccharide* (LPS) *endotoxin* while Gram positive bacteria do not. LPS is found within the outer membrane of Gram negative bacteria, and it is only released when the bacteria is destroyed. *Exotoxin* is a toxin that *both* Gram positive and Gram negative bacteria secrete. Contrast this with *endotoxin*, which is embedded within the outer membrane of Gram negative bacteria only. So, Gram negative bacteria produce both exotoxin and endotoxin (LPS), whereas Gram positive bacteria produce pathology through exotoxin only. *Teichoic* acids are acidic polysaccharides found only in *Gram positive* bacteria. They connect the cell wall peptidoglycan to the cell membrane providing significant rigidity and structure. The *capsule* cover both Gram negative and Gram positive bacterial cells. Essentially, the capsule act as shields that prevent bacteria from being eaten by eukaryotic immune cells - like macrophages. Capsules also contain moisture, which prevents the cells from drying out. Therefore, capsules are *virulence factors*.

Unsaturated fatty acid tails have double bonds that introduce

'bends' in the structure that prevent the molecules from packing as closely together

regeneration

(Also known as *fragmentation*) a piece of an organism 'breaks off'. The original organism regenerates the piece that broke off, and sometimes the fragment can regenerate into a completely new organism. Hydra and planarian flatworms demonstrate regeneration.

Erythrocytes

(RBCs) transport oxygen (up to 4) on hemoglobin. ▪ They catalyze the conversion of CO2 and H2O to H2CO3. ▪ They lack a nucleus or organelles to maximize hemoglobin content and do not undergo mitosis. Erythrocytes get energy from glycolysis since they lack organelles. This includes the mitochondria. If tissues do not receive enough oxygen, the kidneys can synthesize and secretes a hormone called *erythropoietin* (EPO) to stimulate generation of more erythrocytes in bone marrow. ▪ It is possible for yellow bone marrow to convert to red bone marrow if the blood cell supply is low. ▪ Erythrocyte resist strong shearing forces because they contain the protein *spectrin*.

Plant-like protists

(aka algae-like protists) are *photosynthetic*, and they are some of the most important primary producers in any ecosystem. Some examples of plant-like protists include Dinoflagellates, Diatoms, and Euglenoids.

Camouflage

(cryptic coloration) allows animals to avoid visual detection through matching of their appearance to the environment. An insect appearing stick-like is an example of this.

tumor suppressor genes

(e.g. p53) help prevent growth, and if mutated in a way that decreases their activity, can contribute to the onset of cancer.

Proto-oncogenes

(e.g. ras gene) stimulate normal growth, but if mutated they can become *oncogenes* (genes that can cause cancer).

Smooth ER

(no ribosomes) synthesizes lipids and steroid hormones for export. In liver cells, the smooth ER functions in the breakdown toxins, drugs, and toxic by-products from cellular respiration.

K-selected species

(or K-strategists) undergo long gestation periods to produce few, large offspring that take a relatively long time to mature. These animals provide significant parental investment and support. Therefore, a high percentage of the offspring survive to reproductive age. Examples include humans and most large mammals. Survival of K-selected species is demonstrated by a type I survivorship curve. This curve demonstrates a high rate of survival during early and middle age, with mortality increasing during old age.

R-selected species

(r-strategists) produce *abundant, small offspring* that *mature quickly.* These animals provide little to *no parental investment* or support. Therefore, a high percentage of the offspring *do not survive* to reproductive age; however, this is okay since so many offspring were produced. Examples include bacteria, insects, and species that produce many free-swimming larvae. Survival of r-selected species is demonstrated by a *type III survivorship curve*. Survival undergoes exponential decay with respect to age.

DNA polymerase

(the enzyme which adds new nucleotides) can only extend the 3' end of an existing strand. *DAT Pro-Tip*: several DNA polymerase enzymes have proofreading capabilities that allow them to 'double check' their work and correct errors whenever they add a non complementary base to the strand they are synthesizing.

Protozoans

(unicellular animal-like [due to movement] protists) move gas through simple diffusion within cell.

Aposematic coloration

(warning coloration) is a vibrant, bright coloration of poisonous animals, which warns predators that they are poisonous. An example of aposematic coloration is the bright coloring of poison dart frogs.

Rough ER

(with ribosomes) creates glycoproteins by attaching polysaccharides to polypeptides as they are assembled by ribosomes.

Rough ER

(with ribosomes) creates glycoproteins by attaching polysaccharides to polypeptides as they are assembled by ribosomes. In eukaryotes, the rough ER is continuous with the outer nuclear membrane. The rough ER tends to make proteins that are part of the membrane, or secreted by the cell. Neurons contain NISSL BODIES, granules of rough ER and free ribosomes that synthesize protein.

five signs associated with inflammation

*1. Heat* ○ Heat is a result of *dilation* of capillaries. When there is increased blood flow, the tissue gets warmer. *2. Redness* ○ Redness is also a result of *dilation* of capillaries. More blood = redder color. *3. Swelling* ○ Swelling is a result of *permeable* capillaries. When blood vessels become leaky, fluid starts accumulating in nearby tissues, causing swelling. *4. Pain* ○ There are two types of pain when you get hurt: a sharp pain that happens right at the time of injury caused by nerve endings, and a slower, throbbing pain that you feel afterwards, which is caused by inflammation. ○ For the pain from inflammation, it is because the swollen areas exert *pressure* on *free nerve endings*, which causes a continuous pain. (That's why it hurts even more when you press a swollen ankle!) *5. Loss of function* ○ This is more of an *indirect* outcome of inflammation. When there is swelling and pain, that part of the body becomes *less useable*. For example, when people suffer from arthritis (inflammation of joints), they can't really walk normally. This has a beneficial effect of causing disuse of the injured area, aiding in healing.

The posterior pituitary stores and releases two hormones:

*ADH (vasopressin)* and *oxytocin* produced by the hypothalamus. *Note: the posterior pituitary itself DOESN'T produce hormones because it is purely neuronal.

There are four codons you should memorize for the DAT

*AUG* represents the *start* codon, which corresponds to the amino-acid *methionine*. The ribosome will assemble around an mRNA transcript and begin scanning for the start codon. The start codon tells the ribosome where protein translation should initiate translation. ● Note: you should memorize for the DAT the start codon AUG = methionine. *Stop* codons do not code for amino acids. Rather, they tell ribosomes to disassociate from mRNA and end protein translation. The stop codons in mRNA are *UAA, UAG, and UGA*.

auditory communication

*Auditory* signals are sounds animals use to communicate over long distances, through water, and at night. It may be used to warn of danger, communicate reproductive readiness, species recognition, or warning against rivals. ● Examples of auditory communication include whale infrasound (can be heard for hundreds of miles by other whales), elephant infrasound, frog calls, cricket calls, and songs to male birds.

Properties of Hemoglobin

*Bohr effect*: hemoglobin O2 binding affinity decreases under conditions of low pH (high [CO2] and [H+]), causing oxygen loads to be released by hemoglobin because both O2 and H+ compete for binding at hemoglobin molecule. ❖ *Haldane effect*: almost like a corollary to Bohr effect; deoxygenation of the blood increases hemoglobin's ability to carry CO2. It explains how CO2 affects the dissociation curve. ● An increase in CO2 pressure will result in an increase in CO2 content in the blood. Deoxygenated blood carries an increasing amount of carbon dioxide. ● When hemoglobin is saturated by oxygen, its capacity to hold CO2 is reduced. ● In tissues, where CO2 concentration is high, O2 is released by hemoglobin and CO2 is picked up. ● At the lungs, where O2 concentration is high, hemoglobin releases the CO2 it picked up from the tissue and grabs oxygen again. ● Deoxygenated hemoglobin has a higher affinity for CO2 than does oxygenated hemoglobin. This is because hemoglobin without oxygen acts as a blood buffer by accepting H+. This reduced hemoglobin has a higher capacity to form *carbaminohemoglobin* rather than the oxygen carrying kind, explaining how the Haldane effect occurs.

Cilia: Motile vs Non-motile

*Cilia* are structures that extend outward from cells. *Motile* cilia help organisms to move substances around, whereas *non-motile* cilia act as cellular antennas for receiving signals from neighboring cells and the surrounding environment. ○ DAT Pro-Tip: flame cells have cilia, which helps them in the filtering process.

Summary of DNA Replication

*DNA helicase* Separates complementary strands at the replication fork. *Single strand binding proteins* Proteins that prevent the two strands from coming back together after they separate. *Topoisomerase (DNA gyrase)* Relaxes the DNA double helix from the tension the opening helix is creating . *Primase* Provides a 3' hydroxyl group for DNA polymerase to attach new nucleotides to. *DNA polymerases* The class of enzymes that extends DNA in the 5' 3' direction. Several have proofreading capabilities that allow them to catch synthesis errors. *DNA Sliding clamp* Helps to hold DNA polymerase to the template strand *DNA ligase* Glues together separate pieces of DNA. *Telomerase* Adds repetitive DNA to the ends of eukaryotic chromosomes, which prevents critical information from being lost.

Density dependent factors

*Dependent* on the *population density*; they become more significant as the population density increases. Examples include diseases and resource competition.

Cell Cycle Checkpoints

*End of G1 (Restriction Point)* ● The most important checkpoint. ● Cell growth is assessed and favorable conditions are checked. If checkpoint fails, cell enters G0. ● Some cells (liver, kidney) can be induced out of Go, some stay permanently (nerve and muscle cells). ● Cells can either never proceed or wait unl the cell is ready. *End of G2* ● The cell evaluates the accuracy of DNA replicaon and signal whether to begin mitosis. ● The cell checks for sufficient mitosis promong factor (MPF) levels to proceed. *M Checkpoint - during metaphase* ● Mitosis stops if the chromosomes are not aached to spindle fibers. ● If all are aached, cell is allowed to proceed with anaphase.

Nephron Excretion

*Excretion* is the removal from the body of whatever has ended up in the filtrate after the processes of reabsorption and secretion have occurred through the nephron tubules, as urine. After filtration, secretion, and reabsorption, the filtrate (now considered urine) in the kidneys is excreted. The filtrate from all the different nephrons flow into the *collecting duct*, which leads to the renal pelvis. From the renal pelvis, it goes to the ureter. The *ureter* is the connecting passageway between the kidneys and the urinary *bladder*. The bladder is where the urine is temporarily stored until the body signals for it to be excreted. When this signal comes, the fluid flows to the *urethra*. The urethra is where the urine is excreted and exits the body via either the penis or the vagina.

Summary of Digestive Hormones and Enzymes

*Gastrin* G cells of stomach 1. Stimulate parietal cells —> acid juice 2. Stimulate chief cells —> pepsinogen + gastric lipase *Secretin* Duodenum 1. Stimulate pancreas —> bicarbonate ions to neutralize acidic chyme *Cholecystokinin (CCK)* Duodenum 1. Slows gastric emptying 2. Stimulate pancreas —> digestive enzymes 3. Stimulate gallbladder —> bile

Spermatogenesis

*Germ cells* are the cells of the body that produce gametes. They're the only cells in the body that can undergo mitosis as well as meiosis. Spermatogonia are the male germ cells and oogonia are the female germ cells. *Spermatogonia* (plural of spermatogonium) are the primordial (earliest) sperm cells. They're replicated by mitotic division in the seminiferous tubules of the testicle. Some of these cells undergo completion of the first and second meiotic division to form *spermatids*. Differentiation of spermatids create *sperm*, which combine with various fluids (discussed below) to form semen. Semen is ejactulated out of the male penis to fertilize a female egg.

Hair

*Hair follicles* generate *hair* and keep it attached to the body surface. Essentially, hair is a *keratin protein filament* that protects mammals from UV radiation and hypothermia (the function of hair in humans is still under debate). Muscles attach to the hair follicle, and function to *erect the hair*. This results in "goosebumps," and in some mammals it plays a role in temperature regulation and scaring off predators.

Exploitation competition

*Indirect*, and it occurs when a common resource is *depleted*. For example, lions and cheetahs hunting for a common resource: the gazelle. If cheetahs are more successful and eat all the gazelles, the lions will suffer from depletion of this food resource.

The current system for taxonomic rank from the broadest to most specific group is:

*K*ingdom *P*hylum *C*lass *O*rder *F*amily *G*enus *S*pecies DAT Mnemonic: *K*ing *P*hillip *C*ame *O*ver *F*or *G*reat *S*oup

Arthropoda (Insecta) Characteristics

*Key Names and Examples* Ant, grasshopper *Symmetry of Body Plan* Bilateral *Tissue Organization* Triploblasts, eumetazoa *Coelom* Coelomate *Circulatory System* Open circulatory system, hemolymph *Nervous System* Fused ganglia, ventral nerve cord *Respiratory System* Spiracles and tracheal tubes *Digestive System* One-way digestion, some have salivary glands *Excretory System* Malpighian tubules *Embryonic Development* Protostome *General Characteristics*: Exoskeleton made of chitin, jointed appendages, coelomates, three pairs of legs, more species than any other phylum combined, metamorphosis

Mollusca Characteristics

*Key Names and Examples* Clam, snail, slug, squid, octopus, cephalopod, gastropod *Symmetry of Body Plan* Bilateral *Tissue Organization* Triploblasts, eumetazoa *Coelom* Coelomate *Circulatory System* Mainly open; hemocoel *Nervous System* Ventral nerve cords and brain *Respiratory System* Gills *Digestive System* Complete, mouth and anus, radula *Excretory System* Nephridia *Embryonic Development* Protostome *General Characteristics*: Visceral mass (mantle) that secretes calcium carbonate, tongue (radula), aquatic or land (terrestrial) habitats, have hemocoel.

Annelida Characteristics

*Key Names and Examples* Earthworm, leech *Symmetry of Body Plan* Bilateral *Tissue Organization* Triploblasts, eumetazoa *Coelom* Coelomate *Circulatory System* Closed circulatory system, multiple pairs of aortic arches, distinct arteries and veins *Nervous System* Ventral nerve cord, anterior ganglia (brain) *Respiratory System* None (diffusion) *Digestive System* Alimentary canal, mouth and anus *Excretory System* Most have metanephridia *Embryonic Development* Protostome *General Characteristics*: Segmented bodies, coelom is divided by septa, sexual (hermaphrodites) and asexual (regeneration) reproduction, longitudinal and circular muscles.

Platyhelminthes Characteristics

*Key Names and Examples* Flatworms, trematoda, flukes, tapeworm, planaria *Symmetry of Body Plan* Bilateral w/ cephalization *Tissue Organization* Triploblasts, eumetazoa *Coelom* Acoelomate *Circulatory System* None (diffusion) *Nervous System* Two nerve cords, anterior centralized ganglia (brain), some planarians have eyespots *Respiratory System* None (diffusion) *Digestive System* Gastrovascular cavity, two way digestion *Excretory System* Protonephridia and flame cells *Embryonic Development* - *General Characteristics*: Can reproduce sexually (hermaphrodites) or asexually (regeneration), mainly aquatic habitats, parasitic lifestyles, most primitive of triploblastic animals, has organs. Tapeworms specifically don't have a true digestive tract, they just absorb food around them.

Cnidaria Characteristics

*Key Names and Examples* Hydra, jellyfish, sea anemone, coral *Symmetry of Body Plan Radial *Tissue Organization* Diploblasts, true tissues (eumetazoa) *Coelom* n/a *Circulatory System* None (diffusion) *Nervous System* Nerve net, no brain *Respiratory System* None (diffusion) *Digestive System* Gastrovascular cavity, two way digestion *Excretory System* None (diffusion) *Embryonic Development* - *General Characteristics*: Aquatic habitats, some have stinging cells (nematocysts), some have life cycles that switch from polyp to medusa forms, sexual or asexual reproduction, gastrovascular cavity acts as hydrostatic skeleton to aid in movement.

Arthropoda (Crustacea) Characteristics

*Key Names and Examples* Lobster, crayfish, crab *Symmetry of Body Plan* Bilateral *Tissue Organization* Triploblasts, eumetazoa *Coelom* Coelomate *Circulatory System* Open circulatory system, hemolymph *Nervous System* Fused ganglia, ventral nerve cord *Respiratory System* Some have gills *Digestive System* One-way digestion, some have salivary glands *Excretory System* Aquatic - use green glands Terrestrial - use malpighian tubules *Embryonic Development* Protostome *General Characteristics*: Exoskeleton, jointed appendages, coelomates, aquatic and terrestrial habitats.

Rotifera Characteristics

*Key Names and Examples* Rotifers *Symmetry of Body Plan* Bilateral *Tissue Organization* Triploblasts, eumetazoa *Coelom* Pseudocoelomate *Circulatory System* None (diffusion) *Nervous System* Cerebral ganglia (brain) w/ some nerves extending through body *Respiratory System* None (diffusion) *Digestive System* Alimentary canal, mouth and anus *Excretory System* Protonephridia and flame cells *Embryonic Development* - *General Characteristics*: Not truly segmented, can reproduce sexually or parthenogenetically, mostly freshwater environments. Draw food and water into mouth by beating cilia.

Nematoda Characteristics

*Key Names and Examples* Round worm, hook worm, trichinella, C. elegans, ascarcis *Symmetry of Body Plan* Bilateral *Tissue Organization* Triploblasts, eumetazoa *Coelom* Pseudocoelomate (hydrostatic skeleton) *Circulatory System* None (diffusion) *Nervous System* Nerve cord and ring *Respiratory System* None (diffusion) *Digestive System* Alimentary canal, one way *Excretory System* None (diffusion) *Embryonic Development* - *General Characteristics*: Some have cuticle to prevent degradation by host digestive system, longitudinal muscles so they can get shorter - no circular muscles, parasitic, not segmented.

Arthropoda (Arachnida) Characteristics

*Key Names and Examples* Spider, scorpion *Symmetry of Body Plan* Bilateral *Tissue Organization* Triploblasts, eumetazoa *Coelom* Coelomate *Circulatory System* Open circulatory system, hemolymph *Nervous System* Fused ganglia, ventral nerve cord *Respiratory System* Trachea or book lungs *Digestive System* One-way digestion, some have salivary glands *Excretory System* Malpighian tubules and/or coxal glands *Embryonic Development* Protostome *General Characteristics*: Exoskeleton, jointed appendages, coelomates, four pairs of legs, land (terrestrial) habitats.

Porifera Characteristics

*Key Names and Examples* Sponge *Symmetry of Body Plan* Asymmetrical *Tissue Organization* No true tissues (parazoa) *Coelom* n/a *Circulatory System* None (diffusion) *Nervous System* None *Respiratory System* None (diffusion) *Digestive System* Intracellular digestion (via amoebocytes) *Excretory System* None (diffusion) *Embryonic Development* - *General Characteristics*: Sessile, suspension feeders, aquatic habitats, earliest animals, can reproduce asexually (budding) or sexually (hermaphrodites), used in production of antibiotics.

Echinodermata Characteristics

*Key Names and Examples* Starfish, sea urchin, sea cucumber *Symmetry of Body Plan* Bilateral (larvae), five fold radial (adult) *Tissue Organization* Triploblasts, eumetazoa *Coelom* Coelomate *Circulatory System* Open, no heart *Nervous System* Nerve ring and radial nerves *Respiratory System* None (diffusion) *Digestive System* Complete, mouth and anus *Excretory System* None (diffusion) *Embryonic Development* Deuterostome *General Characteristics*: Spiny, central disk, water vascular system, tube feet, sexual or asexual reproduction, closest related major phyla to chordates.

Chordata Characteristics

*Key Names and Examples* Vertebrates *Symmetry of Body Plan* Bilateral *Tissue Organization* Triploblasts, eumetazoa *Coelom* See below *Circulatory System* See below *Nervous System* See below *Respiratory System* See below *Digestive System* See below *Excretory System* See below *Embryonic Development* Deuterostome DAT Pro-Tip reminder: Echinoderms and Chordates are deuterostomes—all the other animal phyla from the mnemonic are protostomes. *Shared traits of all chordates:* *Chordata* are animals that contain notochords. *Notochords* are cartilaginous rods that support the body of all chordates when they are in the embryonic stage. Most chordates will lose their notochord as they mature; however, a select few will keep it into adulthood. In *chordates*, the notochord provides a flexible rod that functions as support, and is eventually replaced by bone in most vertebrates. The notochord is derived from the *mesoderm* and defines the primitive axis of the embryo. In chordates, it is the *dorsal hollow nerve cord* that eventually develops into the spinal cord (not the notochord). The dorsal hollow nerve cord goes on to form the basis of the nervous system, including the brain. In chordates, it is the *pharyngeal gill slits* that go on to form the pharynx, gills, or other feeding systems later in the animal's development. The pharyngeal gill slits provide a channel across the pharynx to the outside body. They can go on to form other structures or disappear entirely during embryonic development. In mammals, the gill pouch eventually forms the Eustachian tubes in the ears and various other head and neck structures. In chordates, the muscular tail extending behind the anus (sometimes referred to as a *muscular post-anal tail*) does not describe the *notochord* (a length of cartilage extending along the body that eventually forms part of the spinal discs). This tail is lost during the embryonic development of humans, and many other chordates.

Role of the Chloroplast

*Light-dependent* and *light-independent reactions* occur in this organelle. It has a double membrane like the mitochondria and nucleus.

scenarios that cause the opening or closing of the stomata

*Low [CO2]* inside plant This happens during daytime- light is available to carry out photosynthesis. Constant photosynthesis depletes [CO2] levels inside plant. Needs more [CO2] to carry out photosynthesis. Open stomata (to intake more [CO2]). *High [CO2]* inside plant This happens during *nighttime*- light is not available. Therefore, photosynthesis is halted. [CO2] levels inside plant build up. Does not need more [CO2] to carry out photosynthesis. Close stomata. *High temperature* Needs to prevent transpiration. Close stomata (to retain water in the plant). Note: Stomata opening is accompanied by diffusion of K+ ions into the guard cells. This creates a gradient that causes water to follow and flow into the guard cells, making them turgid. This turgidity changes the shape of the guard cells so that they reveal stomata (openings) and allow gas exchange to happen. If the guard cells are flaccid and limp, they cover the stomata, preventing gas exchange. Plants can minimize transpiration by closing their stomata, and therefore keep the water in. However when the stomata are closed, the plants are keeping CO2 out as much as they are keeping water in. CO2 is necessary to carry out photosynthesis, and photosynthesis is the source of food for plants. If the stomata stay closed for too long, the plant will essentially starve. When plants open their stomata, CO2 can enter into the leaves, and the plant can produce food via photosynthesis. But remember, if the stomata stay open for too long, the plant will dry up because of transpiration. Plants must be able to regulate the opening and closing of the stomata to achieve this tricky but necessary *balance* between the need for food and the need for water.

Macroevolution: Phyletic Gradualism and Punctuated Equilibrium

*Macroevolution* refers to the pattern of evolution of groups of species over long periods of time. There are two distinct theories of macroevolution. ● *Phyletic gradualism* is a model of evolution that theorizes that evolution occurs by gradual accumulation of small changes. This theory is unlikely to be valid because intermediate stages of evolution are missing (no fossils); fossils only reveals major changes in groups of organisms. ● *Punctuated equilibrium* is a model of evolution that theorizes that evolutionary development consists of geologically short periods of rapid evolution between geologically long periods of stasis (stability) with little or no evolution. Absence of fossils revealing intermediate stages of evolution is considered data that confirms rapid evolutionary events.

What can lead to more than one zygote developing?

*Monozygotic twins* are *identical* twins. In this case, one fertilization gives rise to one zygote, which then divides to form two separate embryos. The two embryos have the exact same genetic material, that's why they become identical twins. *Dizygotic twins* are *fraternal* twins. In this case, the mother ovulates two eggs and both eggs are individually fertilized by two different sperms. This leads to two different zygotes with slightly different genetic material (due to crossing over in meiosis).

Since the stomach is always under an acidic environment, there is a type of cell that functions to protect the stomach lining from the corrosive acid:

*Mucous cells*: secrete mucus to lubricate and protect the stomach lining.

Kidney Hormones

*Parathyroid* hormone (aka PTH) *increases calcium* levels in the blood. It does this in part by stimulating reabsorption of calcium in the tubules (as well as causing the bones to release calcium). *Calcitonin 'tones down calcium'* (lowers) calcium levels in the blood. It does this in part by inhibiting reabsorption of calcium from the tubules (as well as causing the bones to absorb calcium). *Note that PTH and calcitonin have opposite effects. *Aldosterone* is considered a *mineralocorticoid* hormone, and is produced by the adrenal cortex. Aldosterone functions to *increase salt and water reabsorption*, as well as potassium secretion in the distal tubules and collecting duct of the kidneys. *Antidiuretic* hormone (aka ADH or *vasopressin*) will prevent diuresis (production of urine). The hypothalamus will stimulate release of ADH from the *posterior pituitary* when extracellular fluid volume is low. It causes *aquaporins* (water channels) to insert into the collecting duct of the nephron and allows more water reabsorption (and therefore, less water is urinated).

Gastrulation

*Primitive streak* is an important structure to mark the beginning of *gastrulation*. Gastrulation refers to the formation of a *trilaminar* embryo. Recall that the embryo is at a *bilaminar* stage when the ICM is divided into the hypoblast and the epiblast. Afterwards, epiblast cells invaginate inwards through the primitive streak to form *three germ layers — endoderm, mesoderm, and ectoderm* through gastrulation. With these three germ layers formed, the embryo is considered to be at the *gastrula stage*. As cells invaginate inwards from the primitive streak, it creates an opening called the *blastopore*. The opening gradually deepens and forms a *center cavity* called the *archenteron*. The archenteron will eventually form the *digestive tract* (which is basically a hollow tube). The *opening of the archenteron (blastopore)* will become the *anus* in *deuterostomes*, and the *mouth* in *protostomes*. Mnemonic: in *deuter*ostomes the blastopore contributes to where you pass *'doody'* (ie. feces) through - the anus.

Nephron Reabsorption

*Reabsorption* is the removal of water and solutes from the filtrate back into the blood vasculature. This happens throughout the rest of the nephron- from the proximal convoluted tubule up to and including the collecting duct. However, certain parts of the nephron are specific in which substances they allow the body to reabsorb, most notably the two limbs of the loop of Henle. The filtrate flows from the Bowman's capsule to the proximal convoluted tubule, then into the loop of Henle. The *loop of Henle* is the part of the nephron that descends from the cortex of the kidney to the medulla. The *descending limb* has a high permeability to water and a low permeability to solutes. Therefore as the filtrate travels down, *water rushes out* of the loop of Henle (out of the filtrate) and is absorbed back into the blood supply by the *vasa recta*, blood capillaries that run adjacent and parallel to the loop of Henle. Because water is being removed from the filtrate, the filtrate becomes *more concentrated* as it travels down the descending limb. This is our body's way of reabsorbing and retaining water. Then the filtrate flows back up the *ascending limb* of the loop of Henle. The ascending limb is the opposite of the descending limb in that it has a high permeability to solutes and a very low permeability to water. Therefore as the filtrate travels up, *solutes flow out* of the loop of Henle (out of the filtrate) and are absorbed by the vasa recta. Because solutes are being removed from the filtrate, the filtrate becomes *less concentrated* as it travels up the ascending limb . This is our body's way of reabsorbing and retaining important salts.

DNA replication takes place during

*S phase* of the cell cycle

Enzymes to remember

*Salivary Amylase* Salivary glands in mouth Starch —> Maltose *Gastric Lipase* Chief cells in stomach Fats —> glycerol + fatty acid *Pepsinogen —> later activated to pepsin* Chief cells in stomach Proteins —> amino acids *Pancreatic Amylase* Pancreas Starch —> Maltose *Enteropeptidase* Duodenum Trypsinogen —> trypsin *Trypsinogen + Chymotrypsinogen* Pancreas Trypsin converts chymotrypsinogen —> chymotrypsin Both functions to cleave proteins —> amino acids

Nephron Secretion

*Secretion* is the transfer of solutions from the blood vasculature *directly* into the nephron tubule filtrate. After going up the ascending limb of the loop of Henle, the filtrate flows through the *distal convoluted tubule*. The distal convoluted tubule, as well as the proximal convoluted tubule (discussed previously) are the areas of secretion. Certain (usually harmful) substances are extracted from the blood (specifically from the peritubular capillaries) and taken up by the nephrons directly.

Accessory Glands

*Semen* is the combination of sperm and secretions from the *accessory glands*. There are three accessory glands in the male reproductive tract that contribute certain secretions to the sperm to form semen. These secretions aid sperm in achieving successful fertilization when ejaculated into the female reproductive tract. 1. seminal vesicles 2. prostate gland 3. bulbourethal glands

Structural Features: Archaea vs Eubacteria

*Similar*: Certain archaea and bacteria contain *pili*, which are basically 'feelers' that allow the cell to make contact with other cells. This type of contact allows cells to transfer plasmids between each other, which is known as *horizontal gene transfer*. Many eubacteria and archaea also contain *flagella*, which allows them to move about.

DNA Organization: Archaea vs Eubacteria

*Similar*: Many archaea and bacteria possess *plasmids*, which are segments of extrachromosomal DNA that may be passed horizontally between cells. *Differ*: Some Archaea possess *histone* proteins (DNA packaging) and Archaeal DNA contains *introns*. Eubacteria lack histones and introns.

Reproduction: Archaea vs Eubacteria

*Similar*: both eubacteria and archaea reproduce via binary fission. *Binary fission* occurs when a cell simultaneously grows, replicates its genome, and divides into two genetically identical cells.

Where are steroid hormones synthesized?

*Smooth ER*

Lichens

*Symbiotic autotrophs*, which means they are groups of different types of organisms that live together and make their own food. The two main types of lichen are fungi paired with either algae or cyanobacteria. Fungi are tasked with protecting the algae or cyanobacteria, as well as providing them with water and nutrients via breaking down decaying matter. Conversely, the algae or cyanobacteria produce food for the fungi via *photosynthesis*. In general, a lichen is *resistant* to adverse conditions; therefore, lichens can be found in almost all ecosystems. They grow and reproduce as their constituent organisms grow and reproduce; similarly, they may be found growing on rocks, tree bark, and even other lichen communities! Lichens are important to the ecosystems they are found in because they clean the air of pollutants. Therefore, lichens can serve as a signal that the whole ecosystem is healthy.

stem cells

*Undifferentiated* cells that can have the potential to give rise to many types of different cells.

Tracheophytes

*Vascular* plants, plants that contain *xylem* and *phloem* vessels. These vessels provide an effective means of transporting water and nutrients to different areas of the plant, allowing tracheophytes to grow *vertically* and *tall* (think of a tree). They also have a *root system* which anchors them in place. Tracheophytes spend most of their life cycle in the *sporophyte* stage. There are two types of vascular plants: those that are seedless and those that have seeds. The *presence of seeds* in a plant shows great evolutionary advancement. Seeds are more resilient and *durable* (remember the nutritious endosperm and the protective seed coat!), allowing them to disperse more effectively and get planted and grow into a mature plant more successfully.

purines

*adenine* and *guanine*, which are double-ringed nitrogen bases. Mnemonic: PUR As Gold = PURines are Adenine and Guanine

A fetus can be tested for genetic disorders via amniocentesis or chorionic villus sampling (CVS).

*amniocentesis* or *chorionic villus sampling* (CVS)

Within the structure of a villus, there are

*blood capillaries* and a *lymphatic capillary — lacteal*. They are both responsible for absorption of different nutrients.

exocrine

*digestive enzymes* through the *pancreatic duct* into the stomach.

After large meals,

*insulin* stores glucose as glycogen. *Glucagon* has the opposite effect and turns on glycogen degradation. Insulin activates the PFK enzyme, while glucagon inhibits it. Think about it this way: insulin says "hey, we've got a lot of glucose around, so let's chew up," whereas glucagon says "uh oh, not enough glucose around, don't chew it up- we need it for the brain, other tissues can use other energy sources."

Digestion can be divided into

*intracellular* and *extracellular* digestion Intracellular digestion happens *within* cells, whereas extracellular digestion happens *outside* of cells Humans mainly use extracellular digestion. This is because macromolecules are mainly broken down within our digestive tract, outside of cells. It is only after most digestion has taken place that our cells absorb the nutrients inside (which then can be further digested within the cell).

There are two types of embryonic ossification

*intramembranous* and *endochondral* ossification. DAT Pro-Tip: endochondral ossification is more common than intramembranous ossification.

Angiosperms can be further divided into two groups:

*monocotyledons* (often shortened to monocots) and *dicotyledons* (often shortened to dicots).

each single strand is made of a chain of nucleotides, which are linked together by

*phosphodiester bonds* this creates the negatively charged phosphate backbone

Some other forms of post-transcriptional gene regulation and mRNA processing in eukaryotes include

*siRNA's* (small interfering RNA) and *miRNA's* (microRNA), which are considered RNAi molecules. *RNAi molecules* (RNA interference molecules) silence certain gene expression. They interfere with mRNA via complementary base pairing; therefore, they prevent translation.

initiation site

-10 and -35 elements lie upstream of the *initiation site*. The initiation site is the +1 site; or, the first DNA nucleotide of the transcribed region. Therefore, all negative numbers refer to DNA nucleotides that are *upstream* of the initiation site, while all positive numbers refer to DNA nucleotides that are *downstream* of the initiation site.

Tundra

-Cold -Very little precipitation (mostly snow) -Mosses -Grasses -Lichens -Shrubs -Bears -Caribou -Wolves -Foxes -Rodents -Example: Iceland, northern Canada -Ground freezes during winters -Topsoil thaws during summer, but deeper soil (permafrost) stays frozen

Polar

-Cold -Precipitation is snow ]-Penguins -Polar bears -Example: Antarctica -Ice-covered for most of the year

Taiga (coniferous forest)

-Cold winters with snowfall -Warm, rainy summers -Coniferous trees (trees with needles, not leaves) -Bears -Otters -Wolves -Rabbits -Owls -Example: most of Canada and Alaska -Largest terrestrial biome

Tropical Rainforests

-Consistent, hot temperature -Consistent, heavy rainfall -Tall trees with most branches near the top -Vines -Ferns -Orchids -Reptiles -Amphibians -Insects -Small and large mammals (monkeys, elephants) -Colorful birds -Example: Amazon Rainforest -Biome with the greatest amount of diversity

Temperate Grasslands

-Cool winters -Hot summers -Seasonal rain (less rain than savannas) -Grasses -Small shrubs -Large, grazing mammals -Birds -Reptiles -Example: North American prairie -Fertile soils -Seasonal droughts and fires

Savannas

-High temperatures -Small amount of rainfall (seasonal) -Grasses -Scattered trees -Ungulates (large, hooved, plant-eating mammals), like giraffes -Example: "African safari" -Savannas are tropical grasslands with diffuse trees -Seasonal droughts and fires

Deserts

-Hot days -Cold nights -Extreme temperature fluctuations -Very little rain -Cacti -Rodents -Reptiles -Arachnids -Coyotes -Bobcats -Example: Arizona -Plant growth occurs after rainfall -Animals are often nocturnal and conserve water by not producing urine or producing very concentrated urine -Plants have leathery leaves or spines, to conserve water

Chaparral

-Mild winters -Hot, dry summers -Trees -Shrubs -Poison oak -Cacti -Foxes -Jackrabbits (hares) -Deer -Example: California's west coast, Mediterranean coast -Scattered vegetation, often with small, tough leaves to conserve water -Common droughts and fires

Temperate deciduous forests

-Warm summers -Cold winters -Moderate precipitation -Snows during winter -Hardwood, deciduous trees -Ferns -Mosses -Wildflowers -Rodents -Birds -Squirrels -Deer -Bears -Porcupines -Example: eastern North America -Trees shed their leaves in the winter due to poor growing conditions

There are three main types of mutations

1. *Base substitutions (point mutations)* 2. *Insertion* 3. *Deletion* ○ Note: insertion and deletion mutations can cause *frameshift mutations*, which we will also discuss in this section.

Chondroblasts secrete a cartilaginous matrix containing:

1. *Collagen*, which is important for resisting tension and is the most common protein in mammals. ■ Analogy: collagen provides cushioning and support, like a pair of really comfortable sneakers. 2. *Elastin*, which is important for its elastic properties. ■ DAT Pro-Tip: changing the amounts of collagen and elastin will change the type of cartilage.

Some key hypothalamic-releasing hormones to remember:

1. *GnRH* (gonadotropin-releasing hormone) a. Gn stands for gonads b. Tells the anterior pituitary to release *LH* and *FSH* to the gonads. 2. *TRH* (thyrotropin-releasing hormone) a. T stands for thyroid b. Tells the anterior pituitary to release *TSH* to our thyroid glands 3. *CRH* (corticotropin-releasing hormone) a. C stands for corticoids (discussed later on) b. Tells the anterior pituitary to release *ACTH* 4. *GRH* (growth hormone-releasing hormone) a. G stands for Growth Hormone b. Tells the anterior pituitary to release *GH* *Tip: All hormone with the letter "*R*" in their abbreviated names e.g. GRH, GnRH etc. are secreted from the *hypothalamus* because "R" stands for "releasing".

The small intestine uses two ways to protect itself from the highly acidic chyme:

1. *Goblet* cells: ○ Secretes *mucus* to protect the epithelial lining. 2. *Neutralization*: ○ The small intestine produces *secretin* (a hormone) in response to the entry of chyme from stomach. ○ Secretin stimulates the *pancreas* to secrete *bicarbonate ions* (HCO3-) into the duodenum via the pancreatic duct. ○ Bicarbonate is *basic*, and it neutralizes the acidic gastric juice that just entered the small intestine.

The *ICM* will form the *embryo* itself. It is further differentiated into two different layers, which is called the *bilaminar stage*:

1. *Hypoblast* ○ Will contribute *partially* to the *yolk sac*. ○ Remainder will go through *apoptosis* (controlled cell death) and degenerate 2. *Epiblast* ○ Will contribute to the *main embryo* ○ Epiblast cells will then thicken and form a structure called the *primitive streak*. ■ The primitive streak defines the left-right, top-bottom *axis* for the developing embryo. ■ The primitive streak is a crucial structure to begin the process of *gastrulation*. Mnemonic: We can think of the important structures (like the embryo) as being on the top of the list, hence belonging to the *epi*blast (epi- means above / on top of). In contrast, things that are not very important will go to the bottom, hence the *hypo*blast (hypo- means below).

The endocrine gland of the pancreas mostly works to balance the level of glucose in our blood. Glucose is our body's main source of energy. After we eat a carbohydrate-rich meal, our body immediately uses some of the glucose as fuel. The remaining glucose that's not used up are stored in 3 ways:

1. *Liver* stores glucose as *glycogen* 2. *Muscle* cells store glucose as *glycogen* 3. *Adipose (fat)* cells convert and store glucose as *triglycerides*

There are 3 main functions of the large intestine

1. *Water absorption* ○ The large intestine completes the water absorption process that began in the small intestine ■ Note: the small intestine absorbs about 95% of the water we ingest ○ If too much water is absorbed —> constipation ○ If too little water is absorbed —> diarrhea 2. *Mineral absorption* ○ Some salts are absorbed together with the water e.g. sodium chloride 3. *Vitamin production and absorption* ○ The large intestine contains a rich bacteria community that live in harmony ○ The bacteria produce *Vitamin B* and *Vitamin K* which are then absorbed into our body. ○ Some of them are also responsible for *metabolizing bile acid*, and *fermenting fiber* ■ This is a *mutualistic* relationship - the bacteria receive nutrients from our digestive system to consume, and they produce vitamins for our benefit

There are three main types of post-transcriptional modifications in eukaryotes:

1. 5' capping 2. Polyadenylation of the 3' end 3. Splicing out introns

A seed consists of

1. A seed coat 2. Storage material (usually food- either as endosperm or as cotyledons) 3. The embryo

After the peptide hormones binds to a cell surface receptor, there are two ways that signal can be passed down:

1. Activate intracellular secondary messengers 2. Cell surface receptors, which act as or activates another *ligand-gated ion channels*

There are three main functional groups of skeletal muscles, which work together to coordinate movement. They are:

1. Agonists (primary movers) 2. Antagonists 3. Synergists

There are three main types of cells contained in each islet (cluster of different cells)

1. Alpha (α) cells 2. Beta (β) cells 3. Delta (δ) cells

The six kingdoms are:

1. Archaea 2. Eubacteria 3. Protista 4. Fungi 5. Plantae 6. Animalia

Endoskeletons can be separated into:

1. Axial skeletons 2. Appendicular skeletons Analogy: If an endoskeleton were a tree, the axial skeleton would be the tree trunk and the appendicular skeleton would be all the branches coming off it.

Synovial joints contain:

1. Bones 2. Articular cartilage covering opposing epiphyses 3. Ligaments 4. Fibrous joint capsule 5. Synovial fluid lubricant within the joint cavity

The steps that led to the origins of life include:

1. Earth and atmosphere formed through volcanoes. The atmosphere consisted of CH4, NH3, CO, CO2, H2, N2, H20, S, HCl, HCN, little or no O2. 2. Primordial sea formation occurred as the earth cooled, leading to condensation of gases that created seas with water and minerals. 3. Complex molecules were synthesized. Inorganic molecules formed organic molecules via energy from ultraviolet light, lightening, heat and radiation. This led to the creation of acetic acid, formaldehyde, and amino acids. ●*Oparin and Haldane* formulated the organic "soup" theory. The theory states if there was O2 (very reactive) in the atmosphere, no organic molecules would have formed. Oparin's hypothesis was that the original Earth environment was reducing. This environment provided the chemical requirements needed to produce complex molecules from simple building blocks. In an oxidizing environment, complex molecules would have been broken apart. ● *Stanley Miller* tested the above theory and produced organic molecules. Miller & Urey used ammonia, methane, water, and hydrogen sealed in flask and stimulated lightning. They saw the formation of several organic molecules, amino acids, and starting materials but no nucleic acids! 4. Polymers and self-replicating molecules were created. Monomers form polymers via dehydration condensation reaction. ● *Proteinoids* are abiotically produced polypeptides. These can be formed in the lab by dehydrating amino acids on hot, dry substrates. 5. Organic molecules were concentrated/isolated into protobionts. ● *Protobionts* are the precursors of cells. They are metabolically active but unable to reproduce. ● Microspheres/liposomes and coacervates (spontaneously formed lipid or protein bilayer bubbles are experimentally (abiotically) produced protobionts that have some selective permeable qualities. ● Note: we can also produce *microsomes* in the lab: vesicle-like artifacts from reformed pieces of the ER if a cell is broken up in a lab. 6. Primitive heterotrophic prokaryotes obtained energy by consuming other organic substances. An example of this are pathogenic bacteria. 7. Primitive heterotrophic prokaryotes underwent mutations and gained the ability to produce its own food. Therefore, heterotrophs mutated to become *autotrophs*. An example of an autotrophic prokaryotic is cyanobacteria. 8. Oxygen and ozone layer formed and abiotic chemical evolution ended by production of photosynthetic activity of autotrophs. UV light and oxygen led to the formation of the ozone layer. After the formation fo this later, UV light was absorbed, blocking energy for abiotic synthesis of organic materials leading to the termination of primitive cells. 9. Eukaryotes formed. ● The *endosymbiotic theory* states that eukaryotic cells originated mutually among prokaryotes (mitochondria, chloroplasts establish resident inside another prokaryotes). ● Much evidence exists for theory. Some include: ▪ Thylakoid membranes of chloroplasts resemble photosynthetic membranes of cyanobacteria. ▪ Mitochondria and chloroplasts have their own circular DNA. It is not wrapped with histones (prokaryotic like). The ribosomes of these organelles resemble those of bacteria. They reproduce independently via processes similar to binary fission. They also have two membranes.

Factors influencing development

1. Embryonic Induction 2. Homeotic genes 3. Egg Cytoplasm Determinant 4. Apoptosis

There are five plant hormones you should know for the DAT

1. Ethylene 2. Auxins 3. Cytokinins 4. Gibberellins 5. Abscisic acid

There are many types of connective tissue holding our body together. Including:

1. Fibrous connective tissue 2. Cartilage 3. Joints

There are four main processes that occur in the nephron of the kidneys

1. Filtration 2. Reabsorption 3. Secretion 4. Excretion

The trophoblast has 3 main functions:

1. Forming the *extraembryonic membranes*, which are supportive structures to the main embryo. a. These are the amnion, yolk sac, chorion, and allantois (discussed later). 2. *Implanting* the embryo inside the uterus (as we said earlier) 3. Producing *HCG* to maintain the corpus luteum + uterine endometrium

five signs associated with inflammation

1. Heat 2. Redness 3. Swelling 4. Pain 5. Loss of function

Water (H2O) is a molecule with several important properties:

1. High Heat Capacity 2. Cohesion/Surface Tension 3. Adhesion 4. Unique solid density 5. Strong Solvent

There are three types of cartilage:

1. Hyaline cartilage 2. Fibrous cartilage 3. Elastic cartilage

DNA replication has three main parts

1. Initiation 2. Elongation 3. Termination

Vertebrate movement involves two main types of muscular contraction

1. Isotonic contractions 2. Isometric contractions

Microstructures in cortical bone include

1. Osteons 2. Haversian canals 3. Lamellae 4. Lacunae 5. Canaliculi 6. Volkmann's canals

There are six types of synovial joint:

1. Pivot 2. Hinge 3. Saddle 4. Plane 5. Condylar 6. Ball and Socket ■ Hint: this type of joint is unstable and accounts for many injuries.

Process of Blood Clotting

1. Platelets contact exposed collagen of damaged vessel and cause neighboring platelets to form a *platelet plug*. 2. Both the platelets and damaged tissue release tissue clotting factor: *thromboplastin*. 3. Thromboplastin converts inactive plasma protein *prothrombin* to active *thrombin*. 4. Thrombin converts *fibrinogen* into *fibrin*. 5. Fibrin threads coat the site of injury and trap blood cells to form a clot.

Roles of the pancreas

1. Secretes *bicarbonate* ions to neutralize stomach acid (as discussed before) 2. Secretes *pancreatic amylase* ○ Similar to salivary amylase (see section 2), pancreatic amylase breaks starch —> maltose 3. Secretes *pancreatic lipase* ○ Works together with *bile* to breakdown and digest fats ○ It digests the emulsified fats —> glycerol and fatty acids 4. Secretes *Trypsin* and *Chymotrypsin* ○ Digests proteins —> amino acids ○ Remember how pepsin from the stomach is first secreted as a *zymogen*, pepsinogen, as a form of protection? The same concept applies to trypsin and chymotrypsin, which are also *proteases*. ○ Trypsin is secreted as *trypsinogen* ○ Chymotrypsin is secreted as *chymotrypsinogen* ○ *See the similar pattern in their names compared to pepsin*ogen*? :) ○ When food enters the duodenum, glands in the duodenum release *enteropeptidase*. ■ Enteropeptidase is enzyme that activates trypsin which in turn activates chymotrypsin

list of barriers found in our body (innate immunity)

1. Skin 2. Cilia 3. Stomach Acid 4. Symbiotic bacteria

Types of Muscle

1. Smooth 2. Cardiac 3. Skeletal

Gastrin is a hormone with two main functions:

1. Stimulates parietal cells of the gastric gland to release gastric juice into the stomach. ○ Gastric juice is extremely acidic with a pH of 2 due to the high concentration of HCl 2. Stimulates chief cells of the gastric gland to secrete: ○ Gastric Lipase ■ Lipase is an enzyme that functions to break fats —> fatty acids + glycerol ○ Pepsinogen ■ Pepsinogen is a zymogen ● A zymogen is the inactive precursor of an enzyme. ■ Pepsinogen will be activated into pepsin (active form) when immersed in the acid of the stomach ● Pepsin is a protease that cleaves peptide bonds: Proteins —> amino acids

The thyroid gland manufactures and releases 3 main hormones into the blood, the first two are secreted in response to TSH coming from the anterior pituitary:

1. T3 - triiodothyronine (mnemonic: T3 corresponds with tri) 2. T4 - thyroxine 3. Calcitonin

Fibrous connective tissue includes things like:

1. Tendons 2. Ligaments 3. The periosteum and endosteum

there are two ways water can move between cells:

1. The *apoplastic pathway* is water movement outside the cell, with the cell wall. 2. The *symplastic pathway* is water movement through the cell's cytoplasm.

the trp operon is also controlled in two ways

1. The trp repressor protein 2. Attenuation

The lac operon is controlled in two ways

1. lac repressor protein 2. cAMP levels and catabolite activator protein (CAP)

The lac operon controls three genes:

1. lacZ 2. lacY 3. lacA These genes code for proteins that are used in the metabolism of lactose. Lactose can be digested to form glucose and galactose to power the cell's functions. However, lactose is not the preferred energy source for E. coli - glucose is. Glucose will always be used by E. coli whenever it is around; therefore, the lac operon is usually inactive.

Layers of the Epidermis

1. stratum *corneum* 2. stratum *lucidum* 3. stratum *granulosum* 4. stratum *spinosum* 5. stratum *basale* DAT Mnemonic: The epidermis from most superficial to deep: *C*ome *L*et's *G*et *S*ome *B*eers *C*orneum *L*ucidum *G*ranulosum *S*pinosum *B*asale *Corneum* *Corneocytes* (dead keratinocytes) form the outermost, protective layer. *Lucidum* *Dead keratinocytes* that are not yet fully differentiated into corneocytes. It's present in palms and soles. *Granulosum* Keratinocytes secrete *lamellar bodies* to form a water-barrier. *Spinosum* Important for strength (*desmosomes*) and immunity (*Langerhans cells*). *Basale* Precursor keratinocyte *stem cells* proliferate here. This is also where light touch sensation (*Merkel cells*) and melanin synthesis (*melanocytes*) occurs.

The final products of the Krebs cycle are

3 NADH, 1 FADH2, 1 ATP (via substrate level phosphorylation), 2 CO2.

Arthropods

80% of all living species- insects, spiders, crustaceans (crabs), etc Grasshopper: Series of chitin-lined respiratory tubules called *trachea* open to surface in opening called *spiracles* through with O2 enters, CO2 exits. No oxygen carrier is needed due to direct distribution and removal of respiratory gases between air and body cells; diffusion across moistened tracheal endings. Spider: *Book lungs*: stacks of flattened membranes enclosed in internal chamber. have an open circulatory system that pumps blood into an internal cavity called *hemocoel* (cavities called *sinus*), which bathe tissues in oxygen and nutrient containing fluid (*hemolymph*). This fluid returns to pumping mechanism (heart) through holes called *ostia*. ● Examples of arthropods include mostly insects and molluscs.

Ways to distinguish Animalia: Coelom

A *coelom* is a cavity found within certain organisms. This cavity lies between the *mesoderm* and *endoderm*. ● If there is no cavity between the mesoderm and endoderm, the organism is said to be a *acoelomate*. ● An organism will only qualify as a *coelomate* if the coelom is surrounded by mesoderm on all sides. ● If the coelom is only partially surrounded by mesoderm, the organism is said to be a *pseudocoelomate*. Everything before Nematoda is *acoelomate* (lack a coelom). Nematoda are considered pseudocoelomate ('fake" coelomate). This pseudocoelom helps with nematode motility; they use the pseudocoelom as a hydrostatic skeleton. ● A *hydroskeleton* (hydrostatic skeleton) provides rigidity through fluid pressure. Everything after Nematoda is *coelomate* (contains a coelom).

Cell Wall (Archaea vs Eubacteria)

A bacterial cell wall surrounds an inner cell membrane. In certain types of bacteria, the cell wall also contains another outer cell membrane. *Similar*: Both Eubacteria and Archaea *possess a cell wall*. The cell wall surrounds the cell membrane and offers protection and structural support to the cell. *Differ*: The cell wall of Eubacteria contains *peptidoglycan* whereas in Archaea it does not. The lipids in the cell wall of Eubacteria is linked via *esters*, whereas the lipids in the cell wall of Archaea is linked via *ethers*.

Spinal

A bundle of nerves located within the spinal column, which is formed by the vertebrae. In a cross-sectional view, white matter tracts form the peripheral region, which contain sensory and motor axons. More interior to this is the gray matter, which is composed of nerve cell bodies. Note that this orientation is opposite to that of the brain, where the cortex is made of gray matter and the medulla is made of white matter. In the spinal cord, the gray matter has a shape that resembles a butterfly, with two ventral horns and two dorsal horns. ❖ Sensory stimuli from the periphery, such as the arms and legs, enter the *dorsal* horns and travel to the somatosensory area of the cerebral cortex. ❖ Motor neurons travel from the brain's primary motor cortex to the *ventral horns*, where they are relayed to peripheral skeletal muscles. ❖ There are three layers of *meninges*, which protect and support the brain and spinal cord o The innermost layer is the *pia mater*, which is inseparable from the brain and spinal cord. o The *arachnoid mater* is the intermediate layer. It features a spider web-like appearance. ▪ The *subarachnoid space*, between the pia mater and arachnoid mater, contains cerebrospinal fluid, which provides buoyancy, support, and protection for the brain and spinal cord. o The thick, outermost layer is the *dura mater*.

stroke

A clot that causes death of nervous tissue in the brain.

thrombus

A clot that forms in a vessel abnormally and can cause a heart attack.

prosthetic group

A cofactor that binds tightly/covalently to an enzyme

biosphere

A combination of *all of the ecosystems on Earth*. It encompasses their interactions with each other and with the lithosphere, geosphere, hydrosphere, and atmosphere.

Peptidoglycan

A combination of carbohydrate and amino acids. A test that is used to determine the amount of peptidoglycan content in a Eubacteria cell wall is called a Gram stain.

Cartilage

A complex substance that is *avascular* (no blood supply) and *not* innervated. This means that the cells living in cartilage can only get their nutrition and immune support from the surrounding fluid.

epididymis

A duct that sits around the testes, and is the site of sperm *storage* before ejaculation. Sperm continue to mature while stored in the epididymis.

Parthenogenesis

A form of asexual reproduction where an unfertilized egg cell develops into an offspring. Recall that most animals are diploid; however, an unfertilized egg cell is only haploid. There are several mechanisms in place for restoring diploidy of the egg. *Half clones* have half of the mother's DNA due to chromosomal recombination during a mechanism that restores diploidy. If the egg retains all of the mother's DNA, it is said to be a *full clone*.

Artificial selection

A form of directional selection carried out by humans when they breed favorable traits. This is NOT natural selection.

Receptor-mediated

A form of pinocytosis triggered when specific molecules (ligands) bind to receptors ● Proteins that transport cholesterol in blood (LDL) and hormones target specific cells via this mechanism

Dominance hierarchies

A form of social structure between animals to create a ranking system. It minimizes fighting for food and mates. *Pecking order* describes the dominance hierarchy in chickens made up of a linear ranking system.

Ethylene

A gaseous hormone that increases the *ripening of fruit*. You may have heard the phrase that 'one rotten apple spoils the bunch' - it's because one rotten (overly-ripe) apple will release lots of ethylene. Because ethylene is a gas, it diffuses throughout the apple barrel and causes excess ripening of all the other apples.

periplasm

A gel located in the periplasmic space. The *periplasmic space* is located in between the inner plasma membrane and outer membrane of *Gram negative* bacteria. A much smaller periplasmic space exists outside the plasma membrane of *Gram positive* bacteria.

Testosterone

A gonadal steroid hormone. Functions in spermatogenesis to mature the sperm, and is responsible for contributing to male secondary sex characteristics (facial hair, lean muscle mass etc.).

population

A group of organisms of a *specific species* that live in a *given location*. An example is all of the koi fish living in a pond, or all of the oak trees in a forest.

Species

A group of organisms that is able to *interbreed* and have *viable, fertile offspring*. Thus, to be considered a species, the organisms' offspring must also have the capacity to reproduce. For example, all dog breeds are of the same species - a husky and golden retriever (different breeds but both dog species) can mate and produce viable, fertile offspring.

Clade

A group of species that includes a common ancestor and all of its descendants (aka monophylym).

vas deferens

A group of tubules that helps move sperm from the storage area in the epididymis towards the ejaculatory ducts. Again, peristalsis is the force that helps propel the sperm further along.

Imprinting

A highly specific type of learning that occurs in young animals only if the appropriate stimulus is experienced during *critical/sensitive period.* Once acquired, the trait is irreversible. It can influence sexual selection. ● A well-studied example of this are graylag goslings accepting any moving object as their mother during first day of life. ● Imprinting is also observed in salmons. Salmons return to their birthplace (freshwater) to breed based on the imprinted odors associated with their birthplace. ● Imprinting provides the animal with flexibility. For example, in chicks, if a mother is killed prior to hatching, the chicks can choose a new mother due to imprinting. They will likely choose the same species.

Protista

A kingdom of (usually unicellular) eukaryotic organisms, which means they contain membrane bound organelles - including a nucleus. Protists are not fungi, plants, or animals. There are several types of protists that are relevant for the DAT. These include fungus-, plant-, and animal-like protists.

biome

A large area of land or water defined by its biotic factors (*plant* and *animal* populations), which are adapted to the *climate* and *geography* (rainfall, temperature, soil, sunlight, etc.) of that region. Biomes exist on land (terrestrial biomes) and in water (aquatic biomes). All of the abiotic factors described above (soil, sunlight, temperature, and rainfall) affect ecosystem distribution. However, *rainfall* and *temperature* have the most important effect on *biome* distribution. This is because areas with similar *latitudes* can have radically different biomes, even though they receive about the same amount of *sunlight*. For example, areas of the Sahara Desert are located at similar latitudes, and thus receive similar amounts of sunlight, as lush tropical forests in Central America. Even mountainous, snowy biomes in Nepal are located at the same latitude! Hence, sunlight cannot be the determining factor of biome distribution. The main differences between these biomes are temperature (often due to differences in *altitude*) and rainfall. Keep climate in mind as you review the terrestrial and aquatic biomes.

negative feedback loop

A loop that inhibits the pathway to decrease production. An increase in A leads to a decrease in B, stopping the cycle. Here are some examples: During the menstrual cycle, *follicle stimulating hormone* (FSH) and *luteinizing hormone* (LH) cause an increase in progesterone and estrogen. The combination of *increasing progesterone and estrogen causes the levels of FSH and LH to drop*. This is negative feedback. As testosterone levels rise, the *high testosterone levels* will create a negative feedback loop on the hypothalamus and the pituitary. The hypothalamus will produce *less gonadotropin releasing hormone* (GnRH), and the pituitary gland will produce *less LH and FSH*. This results in *less testosterone*. This is because the hormones that create high testosterone are inhibited when testosterone increases- a negative feedback loop. The categorization of what type of feedback loop the hormone exhibits is dependent on the context. For example, *testosterone* stimulating sperm maturation is the effect of a hormone on its target. Mature sperm do not stimulate or inhibit further testosterone production. This is not an example of a feedback loop. Therefore, we cannot say testosterone exhibits negative feedback simply from the paragraph above, because that is specific to the context of testosterone's effect on GnRH, LH, and FSH.

positive feedback loops

A loop that ramps itself up, or stimulates the pathway to increase production. An increase in A leads to an increase in B, which leads to an increase in A... and so on. Prolactin and oxytocin are two hormones released by the posterior pituitary gland that exhibit a positive feedback loop. *Prolactin* functions to stimulate *lactation (milk production)* in female mammals in response to infant suckling. The more the infant suckles, the more prolactin is produced, leading to more milk production, which causes the infant to suckle more... a positive feedback loop. While prolactin produces the milk, *oxytocin releases the milk*. It helps perform the *milk let down reflex*, which increases contractions of smooth muscle in the breast to eject the milk. As the baby continues to suckle, prolactin and oxytocin work together to produce and release more milk. *Oxytocin* also functions to *increase contractions* in labor. During childbirth, this increase in contractions pushes the child out of the womb. The baby presses against the *cervix* of the *uterus*, and this stimulates a nerve. The nerve signals the hypothalamus and pituitary gland to *release more oxytocin*, which causes more contractions, which causes greater pressure on the cervix, which causes more oxytocin release, which causes more contractions...etc. —again, a positive feedback loop.

Sexual selection

A result of differential mating of males (or females) in a population. The female chooses superior males (intersexual selection) in order to increase fitness of offspring; they invest greater energy so they maximize quality of their offspring. Males, on the other hand, increase their fitness by maximizing quantity of offspring. ● Male competition (*intrasexual selection*) leads to fights. Mating opportunities are awarded to strongest male, and favors traits like musculature, horns, large stature, etc. ● Traits/behaviors in males that are favorable to the female result in *female choice*. Females favor traits like colorful plumage or elaborate mating behavior and this often leads to *sexual dimorphism* (differences in appearance of males and females). This is a form of disruptive selection.

vascular cambium

A ring of meristematic tissue located between the primary xylem (located closer to the center) and primary phloem (located closer to the edge). Cells of the vascular cambium divide to produce new cells. Cells that are produced on the inside of the vascular cambium ring become the secondary xylem, and cells produced on the outside of the ring become the secondary phloem.

cork cambium

A ring of meristematic tissue located beyond the phloem, closer to the edge. Cells of the cork cambium repeatedly divide to form the *cork*. The cork is the outermost layer of the bark and serves as a protective layer for the plant. It protects the plant from various things, such as water loss, animals, insects, and other environmental stresses.

Allantois

A sac that *buds off* from the *archenteron* (the digestive gut). This pouch *stores waste* for disposal.

endosteum

A single layer membrane that lies *between* cortical and cancellous bone. It is found lining the medullary cavity of a long bone, surrounding the cancellous bone of epiphyses, and lining the cavities of haversian and Volkmann's canals.

Deme

A small local population of the same species that regularly interbreed (e.g. all the beavers along a specific portion of a river).

detritivores

A subclass of decomposers. Examples include *worms and slugs*. These organisms do not actually break down organic matter; rather, they *consume detritus* (organic wastes), which helps expose additional organic matter for decomposition by fungi/bacteria.

Mantle

A thin layer of tissue found inside mollusks. It secretes calcium carbonate, which mollusks use to build their shells.

Intraspecific competition

A type of competition that occurs between members of the same species. An example is two rabbits competing for carrots.

Cast

A type of fossil that is formed when a mold is filled in.

Dopamine

AMINO ACID-DERIVED (biogenic amines) Excitatory NT of the brain involved in reward-motivated behavior.

Epinephrine

AMINO ACID-DERIVED (biogenic amines) Excitatory post-synaptic NT of the sympathetic nervous system.

Norepinephrine

AMINO ACID-DERIVED (biogenic amines) Excitatory post-synaptic NT of the sympathetic nervous system.

Serotonin (5HT)

AMINO ACID-DERIVED (biogenic amines) Inhibitory NT of the brain involved in mood, appetite, sleep, and learning. Increases contraction of the gastrointestinal tract in response to food intake.

Glycine

AMINO ACIDS Inhibitory NT of the CNS (spinal cord, brainstem, and retina).

Gamma-aminobutyric acid (GABA)

AMINO ACIDS Inhibitory NT of the brain.

Glutamate

AMINO ACIDS The main excitatory NT of the CNS; it is the most abundant NT of the vertebrate nervous system. NT of the neuromuscular junction in invertebrates.

biotic potential

Ability to undergo its highest possible birth rate and lowest possible death rate, resulting in maximal population growth. The biotic potential occurs when environmental conditions are ideal for that species.

secondary consumers

Above the primary consumers. Prey on primary consumers. They are also known as *primary carnivores*. The word *carnivore* means "meat eater." Hence, a carnivore is an organism that eats animal tissues. Compare that with an *omnivore*, which is an organism that consumes both plant and animal material to survive.

Active immunity

Active immunity is *developed* by the organism when a pathogen invades the body and prompts an innate or adaptive immune response. When we administer pathogens in vaccination, it provokes active immunity. The vaccination introduces a small amount of weakened or dead pathogen to our body (in a form that is not pathogenic, or disease causing), which stimulates an immune response. This type of active immunity is *artificially acquired*. Vaccines will induce the formation of memory B cells and T cells that remain in our body to protect us against future exposures of the real pathogen.

vagina

Acts as the opening between the uterus (and its contents) with the external environment. It is where sperm first enter the female body to fertilize eggs, and it is where newborn babies that were developing in the uterus exit the female body (*parturition*, ie. giving birth / delivery).

Telomerase

Adds repetitive DNA to the ends of eukaryotic chromosomes, which prevents critical information from being lost.

Catecholamines

Adrenal Medulla epinephrine and norepinephrine ○ They are the *"fight or flight"* hormones ○ Secreted when facing acute stresses ○ Key functions: ■ Quickly *breaks down glucose* —> ATP, this energizes the body ■ *Increases heart rate* ■ When binds to *beta receptors* causes *vasodilation* (dilation of blood vessels to allow more blood flow) and *bronchodilation* (opens up the bronchioles of the lungs to allow deeper breathing) ■ When binds to *alpha receptors* causes *vasoconstriction* (constriction of blood vessels which shunts blood away from unimportant areas to the important areas - constricting certain blood vessels helps get more blood to the brain and to the muscles) ● Mnemonic: AC/BD - alpha constriction, beta dilation ○ They act on any cells with complementary adrenergic receptors ■ Note: Epinephrine is also called *adrenaline*, hence acting on *adrenergic8 receptors.

Mineralocorticoids

Adrenal cortex (i.e. *aldosterone*) ○ Key function: ■ Increase blood volume and blood pressure ○ How it achieves this: ■ *Increases reabsorption* of sodium (Na+) and *excretion* of (K+) in our excretory system ● *Tip to remember: *K*, you're out! ■ The active reabsorption of Na+ will *passively* allow *reabsorption of water* into the blood ● Water follows salt! (Osmosis concept)

Glucocorticoids

Adrenal cortex (i.e. *cortisol*) ○ Key function: ■ During periods of long-term stress, it *prevents tissue build-up* of macromolecules and *breaks down storage molecules* to generate *immediate fuel*. ○ How it achieves this: ■ *Raises* blood glucose level (same effect as glucagon!) ● Targets muscle cells: break down muscles into amino acids, then the liver converts amino acids into glucose ● Targets liver cells: glycogen —> glucose ● Targets fat cells: fat —> glucose ○ It also *lowers our immune response*, thereby suppressing inflammation (one of the immune responses in our body) ■ This is why cortisol is prescribed to patients suffering from chronic inflammatory diseases like certain types of arthritis. It inhibits the immune response, reducing inflammation.

Gibberellins

Affect stem and shoot *elongation, elimination of dormancy* of a seed, *flowering*, production of *fruits*, as well as *leaf and fruit death*.

Motor unit summation

Affects force of contraction because action potentials are traveling to different motor units at different times. *Small motor units* with *small fibers* are innervated by the *most* excitable neurons. Conversely, *large motor units* with *large fibers* are innervated by the *least* excitable neurons. ● Main takeaway: we recruit small motor units first, then we recruit larger and larger motor units until we have achieved the tension we were aiming for. This is known as the *size principle of motor unit recruitment* and it helps us to avoid fatigue because different *motor units* within the same muscle are being stimulated at different *times*, giving them a chance to relax.

DNA ligase

After DNA polymerase has begun its extension, a different DNA polymerase (DNA polymerase I in bacteria and DNA polymerase β in eukaryotes) seeks out each RNA primer and replaces it with DNA nucleotides. However, these are separate, unconnected strands. *DNA ligase* solves this problem by ligating (gluing together) the separated strands.

So how do we get troponin to move tropomyosin off the actin binding site, so that actin and myosin can bind and the muscle can contract?

After an action potential and the release of *calcium* in our muscle cell, this release of calcium then encourages *troponin* to remove *tropomyosin* from the binding sites on *actin*, thereby allowing the two myofilaments to interact and slide over each other. Troponin has three binding sites: A, C, and T. The *A site* is where troponin holds onto *a*ctin. The *C site* is a site where troponin can bind to *c*alcium. The *T site* is where *t*roponin holds onto tropomyosin. When calcium is released from the sarcoplasmic reticulum into the sarcoplasm, it binds on the *C site* of *troponin*. When calcium binds to *troponin-C*, it alters the shape of troponin. Troponin can no longer hold *tropomyosin* in the proper location to prevent myosin binding to actin. Myosin now has the potential of binding to actin's exposed binding sites. Myosin heads are *ATPases*; when they hydrolyze an ATP molecule into ADP and inorganic phosphate (Pi), the myosin head cocks back into a *high energy state* and binds to actin, forming a complex called the *cross-bridge*. When the cross-bridge is formed, myosin releases ADP + Pi and a *'power stroke'* occurs. The power stroke is when the myosin head contracts from its high energy state and *pulls actin* towards the center of the sarcomere. This shortens the sarcomere and causes the muscle to contract. Now that the myosin is in its *low energy state* (not cocked back), it doesn't have the power to pull actin any closer to the center of the sarcomere. However, passing ATP binds to myosin, causing myosin to release its grasp from actin. ● DAT Pro-Tip: in the case of dead animals, *rigor mortis* occurs because no ATP is being produced to stimulate the release of myosin from actin. This results in muscle becoming "stiff" because the *resting state* of a muscle is contracted. Myosin's enzymatic function will then hydrolyze the new ATP into ADP + Pi, re-enter its high energy state, create a new cross-bridge, and release ADP + Pi to perform another power stroke. Contraction stops when the brain stops sending nerve impulses to the muscles. This allows the myosin heads to become saturated with ATP and disassociate from actin. Further, the *sarcoplasmic reticulum* recaptures calcium by pumping back inside via active transport. This allows *troponin* to return to its original shape and pull *tropomyosin* back over actin's binding site on myosin.

Glycogenesis

After eating, excess glucose we've consumed that isn't immediately needed is converted into *glycogen* that is stored in the liver.

Innate Immunity — Immune Cells and Molecules

After the capillaries become permeable under the influence of histamine, immune cells rush to the site of injury and begin the battle against pathogens. The process of cells moving from capillaries to tissues is called *diapedesis*. The process of moving to a location in response to a chemical signal is called *chemotaxis*. Chemo = chemicals, and taxis = movement. In the inflammatory response, many white blood cells are drawn to the site of injury via chemical signals to arrive.

diapedesis

After the capillaries become permeable under the influence of histamine, immune cells rush to the site of injury and begin the battle against pathogens. The process of cells moving from capillaries to tissues is called diapedesis.

colon

After the cecum, digested food passes through the colon where water absorption is completed. This gradually hardens the feces until it is stored in the rectum and eventually expelled through the anus.

cleavage

After the initial fertilization takes place, the zygote is ready for some growth. The first step of growth is *cleavage*. Cleavage is rapid cell division without changing the total mass of cells. This means that after each successive division, each daughter cell has less cytoplasm than the mother cell. Therefore, cleavage *increases the number of cells*, while the *total cell mass stays the same.*

Modes of Speciation

Allopatric Speciation Sympatric speciation ● Balanced polymorphism ● Polyploidy ● Hybridization - Reinforcement - Fusion - Stability Adaptive radiation

Porins

Allow passage of certain ions + small polar molecules. These tend not to be specific, they're just large passages. Molecules that fit will diffuse through.

Ion channels

Allow passage of ions across membrane. Called gated channels in nerve and muscle cells, respond to stimuli. These can be further classified: ● Voltage-gated: respond to difference in membrane potential ● Ligand-gated: chemical binds and opens channel ● Mechanically-gated: respond to pressure, vibration, temperature, etc.

skeletal muscles

Allow us to move about by inserting into bone, and pulling in different directions. Skeletal muscles are under *voluntary* control, meaning we must rely upon our somatic nervous system to use them. Skeletal muscle cells are long, *multinucleated*, and *striated*.

Anterior Pituitary

Also known as *adenohypophysis*. It begins with the prefix adeno- because the anterior pituitary is composed of *glandular* tissue (adeno- means relating to glands). In contrast with the posterior pituitary, the anterior pituitary actually produces its own hormones. The anterior pituitary is connected with the hypothalamus via a *hypophyseal portal system*.

Posterior Pituitary

Also known as *neurohypophysis*. It begins with the prefix neuro- because the posterior pituitary is composed of *neuronal* tissue. The posterior pituitary is actually a *direct* extension of neurons from the hypothalamus.

G protein

Also known as a guanine nucleotide binding protein, are a category of proteins that activate other things. The three big components in a G protein are the alpha (α), beta (β) and gamma (γ) subunits. When a molecule of GTP replaces the GDP molecule that was bound to the G protein, the beta and gamma subunits dissociate from the alpha subunit. This activates the G protein. The G protein in the activated GPCR will then activate some effector, which leads to some message being sent. For example, the G protein could activate *adenylyl cyclase* which in turn converts ATP cAMP, with cAMP acting as a secondary messenger that can then activate other proteins in the cell.

The Kidney

Although there are several major players in the excretory system, the most significant and prominent one is the kidney. Humans have two kidneys. The top, outer portion of the kidney is called the *cortex* (this is where the blood enters the kidneys). The middle portion is called the *medulla*. The very inner portion is called the *pelvis* (this is where the filtrate exits the kidneys).

Conjugated protein

Amino acids + non‐protein components. ex) glycoprotein (mucin), metalloprotein (hemoglobin), lipoprotein (HDL/LDL)

Complex reflex

An automatic response to significant stimulus that is controlled at the brain stem or even cerebrum. An example of this is the *startle response* which is controlled by the reticular activating system. It occurs in response to potential danger or to hearing one's name called.

unconditioned stimulus

An established innate reflex (food causing salivation). The natural response that occurs in response to the stimulus is called the *unconditioned response* (salivation). ▪ Association of the bell with food leads to it becoming *conditioned stimulus* that will elicit response even in absence of the unconditioned stimulus. Product of this conditioning experience is called the *conditioned reflex* (salivation). Remember: the new stimulus becomes the conditioned stimulus when paired with the unconditioned stimulus!

Sliding Filament Theory of Muscle Contraction

An even closer look at a myofibril would reveal many repeating units, called sarcomeres. *Sarcomeres* are the functional unit of muscle fibers, which *shorten* to facilitate muscle contraction. Sarcomeres contain an array of long, filament proteins, called *myofilaments*. For the purposes of the DAT, the most important myofilaments are THIN *actin* filaments and THICK *myosin* filaments. The *sliding filament model of muscle contraction* explains how myofilaments slide past one another to shorten the sarcomeres of a muscle cell, leading to contraction of the muscle as a whole. ● Note: The filaments of actin and myosin do not get shorter during a contraction: the sarcomere shortens because the filaments slide past each other. This is why this is referred to as the sliding filament model.

short-term biological interaction

An example of a short-term interaction is competition

long-term biological interaction

An example of long-term biological interactions is symbiosis.

prions

An exception to the central dogma of genetics. misfolded proteins that cause other proteins to misfold

Instinct

An inborn pattern of behavior that is distinct to a species. It is often in response to specific environmental stimuli. A common example is female mammals taking care of their offspring.

homozygous

An organism is considered to be *homozygous* for a given gene if an identical allele is present on each homologous chromosome. *Homozygous-dominant* individuals carry two copies of the dominant allele (e.g. BB), while *homozygous-recessive* individuals carry two copies of the recessive allele (bb).

autotroph

An organism that is able to produce energy (organic compounds) through sunlight, water, carbon dioxide, and other inorganic substances in its environment.

heterotroph

An organism that must ingest organic compounds to generate energy and survive.

budding

An outgrowth (a bud) forms on an organism (can be either unicellular or multicellular). The DNA of the organism is replicated and deposited into the bud, and the outgrowth buds off and separates from the original organism to form a new organism. Hydra (a Cnidaria) and yeast (a fungus) demonstrate budding.

Parthenogenesis (non-animal reproduction)

An unfertilized egg develops into a viable (living) organism. Many species that exhibit parthenogenesis can reproduce both sexually and asexually, but resort to sexual reproduction when the environmental conditions are not ideal and cannot sustain large populations. This is because sexual reproduction is slower and produce fewer offspring. Honeybees are a common example species that exhibits parthenogenesis. Offspring that arise from *unfertilized* eggs (parthenogenesis - asexual reproduction) are *females*. Offspring that arise from *fertilized* eggs (sexual reproduction) are *males*.

Animal Pole vs Vegetable Pole

Animal pole: ● Very active cleavage ● Little yolk Vegetal pole: ● Very slow cleavage ● Lots of yolk Mnemonic: Vegetables can't move while animals can jump around. So vegetal pole is less actively dividing, whereas animal pole has a lot of activity (division).

pheromones

Animals can communicate using *chemicals* called *pheromones*. These chemicals allow animals to attract their mates, mark their territory, and accelerate reproductive maturity. ● Chemicals that trigger reversible behavioral changes are called releaser *pheromones*. Those that cause long term physiological (and behavioral) changes are called *primer pheromones*. Some pheromones trigger response via smell, others when eaten. ● Releaser pheromones are released by a doe in heat, ants (formic acid) to mark a trail to food, and reproductively receptive moths. ● Queen bees and aunts secrete primer pheromones to prevent development of reproductive capability. ● Some pheromones are territorial. A well-known example of this is cats and dogs peeing on territory to mark it as claimed. ● Pheromones can act as alarm symbols. For example, when a pheromone recognized as an alarm substance is released among minnows, they all aggregate away from the substance and reduce their movement.

Animals

Animals share several general features. These include the fact that animals are eukaryotic, *diploid*, and multicellular. In addition, animals are *heterotrophic aerobes* meaning they cannot make their own food (they must consume it), and they depend on oxygen. Animals are usually motile at some point during their life, which also means that many have nervous and muscular systems. The most important phyla within the kingdom animalia for the DAT include: ● *P*orifera ● *C*nidaria ● *P*latyhelminthes ● *N*ematoda ● *A*nnelida ● *M*ollusca ● *A*rthropoda ● *E*chinodermata ● *C*hordata DAT Mnemonic: *P*rivileged *C*hildren *P*lay *N*icely *A*nd *M*aturely, Arthur Ensures Cooperation Anytime a letter occurs twice (like P, C, A), the word has a hint for the animal it represents. ● PR..ivileged... - PoRifera ● Ch...ildren - Cn...darian (Ch looks like Cn) ● PLAY - PLAtYhelminethes ● Nicely - Nematoda ● ANd - ANNelida ● Maturely - Mollusca ● ARTHur - ARTHropoda ● Ensures - Echninoderma ● COoperation - CHOrdata

Scavengers

Animals that decompose other *dead animals* (and sometimes dead plant matter). The scavenging process is done by both carnivores and herbivores. Examples of scavengers are vultures and some beetles.

amniotes

Animals that have an amnion (reptiles, mammals, birds).

insulin

Another example of a peptide hormone that acts through *secondary messenger*. Insulin binds to its receptor on cell surface (receptor tyrosine kinase = *RTK*). *Note: Kinases are enzymes that *phosphorylate* other substrates. Once insulin binds to monomeric RTK, it quickly *dimerizes* (forms a dimer) with a neighboring RTK. In addition, the binding of insulin stimulates both RTK to phosphorylate each other, hence *cross-phosphorylation* takes place. An interesting thing to take note is that the RTKs phosphorylate each other's *tyrosine* amino acid, that explains why the receptor is called *receptor tyrosine kinase*. Once RTKs are phosphorylated, it will result in effects such as *releasing of glucose transporter* to remove excess glucose swimming in our blood after a carb-rich meal. Insulin is *quick acting*. If you eat a carb rich meal, insulin is released to lower your blood sugar and prevents you from being *hyperglycemic* (high blood sugar). If insulin worked via the transcription factor method of steroid hormones, then the body would have to wait for DNA transcription, post-transcriptional modification, translation (and possibly post-translational modification) before glucose transporters would be available. That would be far too slow. Insulin wants to work quickly, and the insulin receptor tyrosine kinase permits that.

trial and error learning (operant conditioning)

Another form of associative learning. The animal learns a certain behavior based on the consequences or the *reward*. If the response is desirable (positive reinforcement), animal will repeat the behavior. If the response is negative and undesirable (painful e.g. punishment), the animal avoids the behavior. ▪ An example of this Skinner training rats to push a lever to avoid food or avoid painful shocks.

Spatial learning

Another form of associative learning. The animal encodes information about the their environment by associating parts of it with the reward of identifying and returning to that location. ▪ An example of this are wasps associating pinecones with location of their nest. They lose this ability upon removal of pinecones.

Liver Glucose Metabolism

Another important function of the liver is maintenance of the blood glucose level. It achieves this through: ● *Glycogenesis* ● *Glycogenolysis* ● *Gluconeogenesis* These three terminologies look very similar, but there is a tip to remember and differentiate them: Words ending in *-genesis* means to *create*, hence *glycogenesis = create glycogen*. Words ending in *-lysis* means to *break*, hence *glycogenolysis = break down glycogen*. Words containing *-neo-* means *new*, hence *gluconeogenesis = create new glucose*.

interferon

Another important molecule that links the innate and adaptive immune systems. Interferon is secreted by *virus-infected cells* to warn nearby non-infected cells. Interferon will act as a messenger and bind to non-infected cells to help them be prepared for a viral attack. Inteferons also help activate dendritic cells, which helps kickstart the adaptive immune response.

arthropoda examples

Ant, grasshopper

Antibodies

Antibodies are also known as *immunoglobulins*. ○ Antibodies circulate in the blood and lymph. Antibodies are typically *Y-shaped*, consisting of a *light chain* and a *heavy chain* linked through *disulphide bonds*. The constant regions have very similar amino acid coding sequence (antibody is a protein after all!) within a particular class of antibodies. The *variable regions* are the ones that bind to different antigens, that's why they have different amino acid sequences.

Prokaryotes: Archaea and Eubacteria

Archaea and Eubacteria are prokaryotes. *Prokaryotes* are organisms that *do not have membrane bound organelles*. *Word Origin* 'Pro' means before, 'karyon' means nucleus. A prokaryote is a cell that developed 'before the nucleus'. Both Eubacteria and Archaea are prokaryotic and therefore lack any membrane bound organelles. Lacking membrane bound organelles is a main feature Eubacteria and Archaea have in common and is why at one point both Eubacteria and Archaea were grouped together into one kingdom called Monera. However, further research of structure and biochemistry of these organisms proved that Eubacteria and Archaea were actually less related to each other than Archaea is related to Eukarya. For this reason, the kingdom Monera has been dropped, and Eubacteria and Archaea have been split into separate kingdoms. The prefix 'Eu-' in biology means true. Eubacteria turned out to be what the scientific community thought of as 'true' bacteria. Eubacteria fit the initial thoughts of what a bacteria was. The prefix 'Archae' means ancient. The first Archaea that were identified were methane producing and were thought to have played a role in primitive Earth.

Apical meristems

Are at the very tips of the roots and at the very tips of the shoots. Growth at the apical meristems cause the plant to grow *vertically*, increasing the height of the plant.

Meristems

Areas of a plant where growth takes place via repeated cell division/mitosis. There are two types of meristem: *apical* and *lateral*.

Mouth, Pharynx, Esophagus in Digestion

As food enters the *mouth*, both *mechanical* and *chemical* digestion take place. Chewing food physically breaks it down. This is mechanical digestion, as we are mechanically breaking down large food particles into smaller ones. *Saliva* is secreted within the oral cavity by salivary glands. Saliva contains an enzyme, *salivary amylase*, which will begin chemical digestion of carbohydrates in the mouth. In addition, saliva functions to lubricate the partially digested food and forms it into a *bolus* (small round mass) so it can be passed down the pharynx and esophagus. Salivary amylase: *Starch —> Maltose* Recall, maltose = glucose + glucose in a chain. Therefore, the mouth doesn't fully break down starch into glucose (simplest monomer of carbohydrates), the chemical digestion process begins in the mouth and is completed further down the digestive tract. When we swallow, food is moved to the back of the oral cavity, we reach an area called the *pharynx*. The pharynx is a special region common to the *respiratory system and digestive system* merge, which then *separate* into the trachea and esophagus. This is why we can breathe through our mouth, as well as eat! When we inhale air into our oral cavity, air travels through the pharynx into the trachea. When we swallow, there is a structure called the *epiglottis* that *blocks the opening* to the trachea, this is to ensure that solids and liquids can only enter the esophagus. However, sometimes the epiglottis doesn't close quick enough while we eat and talk at the same time, and this leads to *choking* as our body tries to expel the foreign material that just entered the trachea. Now that food passes through the mouth and the pharynx, it enters the *esophagus* — a tubular structure that guides the food into the stomach. An important thing to note is that the esophagus is made up of *smooth muscles*, hence we cannot control its contraction. It pushes the bolus of food via *peristalsis* (a rhythmic wave-like contraction) down to the stomach.

desiccation

As much as transpiration is helpful in delivering water from the roots to the rest of the plant, it also poses the threat of drying out the plant, called *desiccation*. Remember, transpiration is evaporation.

septa

As the individual hyphae of a mycelium grow, a wall often forms inside them. These walls are known as septas. A *septa* separates the hyphae into different sections, and the fungi that produce septa are said to have *septate hyphae.*

cohesion-tension theory

As water evaporates - because of cohesion - it pulls on the water column underneath it, and lifts the entire water column higher (bulk flow). This is known as the cohesion-tension theory, as tension (pulling) is causing via cohesion.

Movement of Food

As we now know, vascular tissues transport material (such as water and sugars) throughout the plant. Materials are transported *from the source* (where the material is generated) *to the sink* (where the material is used). We will call this the *source to sink theory.* For example, phloem transports sugars from the leaves (source) to the roots (sink). Related to the source to sink theory is the *pressure flow hypothesis*. This hypothesis explains the movement of sugar in the phloem in relation to the movement of water. Source cells in the leaves produce sugar and load the sugar into the phloem at the leaves. This increases the sugar concentration inside phloem cells, creating a gradient that pulls water (from the xylem which is nearby) into these phloem cells. This, in turn, creates a turgor pressure in the phloem, which results in a bulk flow movement of the sugar (and water) from the source (leaves) down to the sink (roots).

source to sink theory.

As we now know, vascular tissues transport material (such as water and sugars) throughout the plant. Materials are transported from the source (where the material is generated) to the sink (where the material is used).

Radial vs. Spiral cleavage

As you may recall from the diversity of life chapter, *deuterostomes* undergo *radial* cleavage, whereas *protostomes* undergo *spiral* cleavage. This category is based on the *axis of cleavage.* *Radial* cleavage results in cells *aligned* on the vertical axis, with the top cells directly overlap the bottom cells. *Spiral* cleavage results in *misaligned* cells that deviate away from the axis, meaning that if you look at it from a top-down view, you can see that the bottom cells are shifted compared to the top cells. *Tip to remembering: you can think of spiral cleavage like those spiral stairs you see in fancy mansions. If you look down from the top of the stairs, the stairs are not aligned on the same vertical axis.

Tertiary consumers

At a higher trophic level than the secondary consumers. *Tertiary consumers* (secondary carnivore) eat secondary consumers.

Chemistry of Gas Exchange Bigger Picture

At the tissues, a high concentration of carbon dioxide is present. It diffuses into the blood, and into the RBC. In the RBC: the carbonic anhydrase turns the CO2 into H2CO3, which then becomes bicarbonate and H+. ❖ The bicarbonate then travels out to the plasma, where it travels through the blood. ❖ A high concentration of CO2 results in a low pH because the formation of bicarbonate (done in the presence of high concentration of CO2) results in H+ creation as well. ❖ At the lungs, CO2 diffuses out of the plasma. The CO2 in the plasma is in bicarbonate form, so it has to re-enter the RBC where the carbonic anhydrase enzyme will catalyze the reverse reaction to turn it back into CO2. It will then diffuse out to the lungs. ❖ There is also hemoglobin to consider. The hemoglobin interacts with the H+ to form a more reduced version of hemoglobin that does not bind oxygen as well (and binds CO2 more). In the presence of high [CO2] and [H+], the hemoglobin structure is altered to the reduced form that will release its oxygen. ❖ The *Bohr effect* relates to how [CO2]/[H+] affects hemoglobin's affinity for O2. The Haldane effect relates how [O2] is affecting hemoglobin's affinity for CO2/H+. ● These two effects work in synchrony to facilitate O2 liberation and uptake of CO2 and H+.

Hypercholesterolemia

Autosomal Dominant Excess cholesterol in blood → Heart disease

Sickle-Cell Anemia

Autosomal Recessive Defective hemoglobin due to substitution

PKU

Autosomal Recessive Inability to produce proper enzymes for phenylalanine breakdown → degradation product phenylpyruvic acid accumulates → mental retardation

Tay-Sachs

Autosomal Recessive Lysosome defect: cannot breakdown lipids for normal brain function (fatal within the first 5 years of life)

General categories of living organisms

Autotrophic anaerobes Autotrophic aerobes Heterotrophic anaerobes Heterotrophic aerobes

Capacitation

Back to our dating example, you can think of capacitation as the final stage of puberty for boys. After this takes place, a boy matures into a man and is ready for romantic relationships. Likewise, capacitation is the *final maturation step* for the sperm prior to fertilization. After capacitation, the sperm is ready to fertilize! As the sperm is moving up in the female reproductive tract, secretions from *uterine wall* triggers capacitation. Capacitation will *destabilize* the sperm's plasma membrane proteins and lipids, leading to two main results: 1. *Prepares* the tip of the sperm for *acrosomal reaction* 2. *Increases* the *permeability* to *calcium* a. The increase in calcium influx put the sperm into a *hyperactive* state — the *flagellum* (tail) *beats harder* and it *swims faster*.

tryptophan

Bacteria require the amino acid tryptophan for their function; because of this, bacteria have the ability to use tryptophan from the environment or they can make their own when environmental levels are low. Using tryptophan from the environment is preferable because synthesizing tryptophan requires costly cell resources.

trp operon

Bacterial tryptophan production is managed by five structural genes in the *trp operon*, which code for *tryptophan synthetase*. The trp operon is an example of a *repressible operon*. This means the operon is always active, unless it is turned off somehow. In other words, bacterial cells always want to be making tryptophan. The presence of environmental tryptophan allows them to save their resources by repressing the tryptophan operon.

Basophils

Basophils are the least numerous kind of leukocytes. They only make up less than 1% of all leukocytes. Similar to eosinophils, basophils also contain granules that can be released to nearby tissues. Two important contents of the granules are histamine and heparin. We are familiar with the functions of histamine — vasodilation and making capillaries more permeable. Heparin, on the other hand, is a type of anticoagulant which prevents blood from clotting too quickly. Basophils are similar in function to mast cells, but they come from different cell lineages. The difference is that basophils leave bone marrow (site of blood cell production) as mature cells and remain circulating in the blood, whereas mast cells leave the bone marrow and circulate the blood as immature cells, only maturing when they enter the tissue.

Transmission Electron Microscopy (TEM)

Beam of electrons passed through a very thin secon of a sample to product a 2D image of the thin slice. Advantages: Can view internal structures, High resolution. Disadvantages: Costly, Extensive sample preparation (kills sample)

less biomass is stored at the higher trophic levels

Because only ~10% of energy stored in one trophic level can be converted into organic tissue in the next trophic level (consumption, digestion, and utilization are inefficient processes), *less biomass is stored at the higher trophic levels*. Hence, there must be more biomass in the lower trophic levels in order to support the higher trophic levels. This concept is demonstrated by a "food pyramid."

degeneracy

Because there are 64 codon combinations, there is a lot of redundancy, called *degeneracy*, in the amino-acid code. Degeneracy means that some codons will code for the same amino-acid, which helps to limit the damaging effects of a DNA mutation. For example, GGG and GGU both code for the amino-acid glycine. A change in that final nucleotide from G to U does not change the amino acid coded by the codon; therefore, the amino acid remains the same and the protein as a whole remains unchanged.

innate behavior

Behavior that is inherited through genes. It is influenced by natural selection and should increase fitness. Sometimes behaviors that are innate may appear to be learned. The innate behavior just requires *maturation*. An example of this is a bird flying. It seems like birds are learning to fly by trial and error or by observational learning. This is not the case as if a bird was raised in isolation, it will fly on the first try if physically capable. Therefore, the ability to fly is innate, it just requires maturation.

Invertebrate skeletons

Belong to organisms without bones, especially backbones. These types of animals possess a skeletal system on the outside of their body, known as an *exoskeleton*. ● DAT Pro-Tip: Think of *ex*oskeleton as *ex*it (outside)

disphotic zone

Below the euphotic zone. It is *semi-irradiated* with sun, but there is not sufficient sunlight for most plants to survive here. However some of the light in this zone is from *bioluminescent species* (you may have heard of Aequorea victoria, the bioluminescent jellyfish from which the famous green fluorescent protein was isolated).

Glycogenolysis

Between meals, when our body needs energy, the liver breaks down storage glycogen back into *glucose*.

Receptor proteins

Binding site for hormones and other trigger molecules.

Codominance

Both alleles are completely expressed. ex) - Blood Type: AB blood type expresses both A and B antigens on RBC surface - Flower petals: R red x W white = RW alternating patches of red and white

Ependymal Cells

CENTRAL NERVOUS SYSTEM Line the ventricles of the brain, circulating cerebrospinal fluid through sweeping motions of their ciliary projections (cilia).

Astrocytes

CENTRAL NERVOUS SYSTEM Physically, chemically, and energetically support neurons. Maintain the blood-brain barrier.

Microglia

CENTRAL NERVOUS SYSTEM Specialized macrophages capable of phagocytosis.

Oligodendrocytes

CENTRAL NERVOUS SYSTEM Wrap around axons to produce myelin sheaths. One oligodendrocyte can myelinate several neurons.

bulk flow of CO2

CO2 mainly transported as HCO3- ions in plasma, liquid portion of blood. produced by *carbonic anhydrase* in RBCs (CO2 + H2O --> H2CO3 --> H+ + HCO3-) CO2 can also directly mix with plasma (as CO2 gas), or bind hemoglobin inside RBCs (forming carbaminohemoglobin).

Seed-bearing tracheophytes

Can be further broken into two groups: *gymnosperms* and *angiosperms*. All seed-bearing tracheophytes are *heterosporous*.

Luteinizing Hormone (LH) in Females

Causes ovulation of an egg and formation of the corpus luteum. It also stimulates production of female sex hormones (progesterone and estrogen). Mnemonic: Follicle stimulating hormone stimulates the follicle to develop - this makes intuitive sense based on the name follicle stimulating hormone. Luteinizing hormone causes ovulation of the egg and formation of the corpus luteum - this makes intuitive sense based on the name luteinizing hormone.

cell fractionation

Cell fractionation separates cell components via centrifugation based on density, size and shape. From most dense to least dense: nuclei > mitochondria/chloroplast > ER fragments > ribosomes.

membrane fluidity

Cells are capable of changing membrane fatty acid composition. ● ↑ unsaturated fatty acids = ↑ membrane fluidity ▪ Unsaturated fatty acid tails have double bonds that introduce 'bends' in the structure that prevent the molecules from packing as closely together ▪ In response to cold temperature, a cell would ↑ unsaturated fatty acids in the membrane to maintain fluidity and avoid rigidity ● ↑ saturated fatty acids = ↓ membrane fluidity ▪ Saturated fatty acid tails lack double bonds and are straight chains that pack together closely In response to warm temperature, a cell would ↑ saturated fatty acids in the membrane to increase rigidity and avoid excess fluidity

Density‐dependent inhibition

Cells stop dividing when surrounding cell density reaches a maximum.

Amino acid structure

Central α-carbon bonded to H, NH2, COOH and a variable R group

Cri du Chat

Chromosomal Deletion on chromosome 5; causes mental retardation

Downs Syndrome

Chromosomal Trisomy 21; causes mental retardation

Turner Syndrome

Chromosomal XO; sterility; typically doesn't cause mental retardation

chromosome

Chromosomes are an even denser packaging of chromatin that are visible with a light microscope, particularly during metaphase. Chromosomes can exist in duplicated or unduplicated states. At the beginning of mitosis, for example, a chromosome consists of two sister chromatids - *chromatids*.

Protostomes

Classified as a group of animals where the blastopore forms the mouth (proto = first; stome = mouth). Protostomes have embryonic cleavages that are is spiral and determinate.

Embryogenesis in mammals

Cleavage will eventually result in a ball of cells (blastomeres) called the *morula*. While there is no hard definition of when a developing embryo is a morula, it usually is defined as being the *12-16 cell stage*. The morula will continue to divide. At around the *128 cell stage*, a *hollow cavity* begins to form in the center of the solid mass of dividing cells, known as the *blastocoel*. When the solid morula begins to develop a hollow, fluid filled center, the embryo is at the *blastula* stage. The cleavage stage officially ends once the blastocoel begins to form. The cells of the blastula will then divide and differentiate (a cell changing to a more specialized type of cell) to form two structures: 1. *Trophoblast:* the outer ring of single-layer cells. 2. *Inner cell mass* (ICM): the inner bulk of cells surrounded by the trophoblast. When the inner cell mass has occurred, the blastula is now referred to as a *blastocyst*. *Fertilization* usually takes place in the *oviduct*. As the fertilized egg travels down to the uterus, this is when cleavage happens. When the fertilized egg reaches the *uterus*, it will usually be at the *blastocyst* stage. The blastocyst is the one that *implants* into the uterine wall of the mother. Before the blastocyst can successfully implant into the uterine wall, it needs to *get rid of its zona pellucida* through a process called *zona hatching*. The zona pellucida will be replaced by a layer of trophoblast cells that can implant into the uterus. Let's go back and talk a little more about the different parts of a blastocyst. Since the cells of the trophoblast and inner cell mass (ICM) are differentiated cells, they are each responsible for forming different structures in the developmental process.

euphotic zone

Closest to the surface. It receives *strong irradiance* (and heat) from the sun - plants are able to survive and undergo photosynthesis. The *littoral zone* is the part of the euphotic zone where sunlight penetrates all the way down to the floor of the ocean.

Nematocysts

Cnidaria Cells that shoot poisonous barbes for protection and hunting.

Gastrovascular cavities

Cnidaria Digestive systems with just one opening. This means that both food and waste enter and exit the organism through the same opening. Recall that these cavities act as hydrostatic skeletons.

Hydrostatic skeletons

Cnidaria Use fluid pressure to provide structural support. Think of a fresh tube of toothpaste: if there weren't toothpaste inside, the container would lack its structure! Organisms with hydrostatic skeletons can contract *circular* muscles to get longer. Similarly, they can contract *longitudinal* muscles to get shorter.

Invertebrate Respiration Overview

Cnidaria: Protozoa and Hydra Annelids Arthropods: Grasshoppers and Spiders Fish

Sudoriferous (sweat) glands

Come in two types: *eccrine* and *apocrine*, which differ in their location and product.

Molds

Common *filamentous* fungi, and they are *aerobic*. They are multicellular and multinucleate (multiple nuclei per cell) because they form hyphae. *Hyphae* are the long, branching filaments that extend out and form a network with nearby fungi. All the hyphae together are known as *mycelium*. For example, when you see a mushroom in the forest, the mushroom top only represents one spore. Many spores in a patch of mushroom tops are all connected underground by hyphae. All the connected spores are collectively called the mycelium.

outer ear

Composed of auricle and the external auditory canal, and it functions to collect sound waves from the environment. The *auricle (pinna)* is the external portion of the ear. It is what one thinks of when they hear the word, "ear." The *external auditory canal (external acoustic meatus)* transmits sounds from the pinna to the tympanic membrane.

Parallel evolution

Concerns distinct species that share similar ancestry but occupy *separate (but similar) environments*. These species maintain a consistent level of similarity over time; hence they *independently* develop similar traits. An example of this is between placentals and marsupials. They have independently developed *similar traits* (hair, limbs), despite evolving on completely separate land masses.

Osteons

Considered the functional unit of cortical bone. They are multi-layered cylinders that extend parallel to the the bone's long axis. At the center of each of these cylinders is a canal, known as a *haversian canal*. For this reason, osteons are also referred to as *haversian systems*. ● Analogy: the cross section of an osteon looks a lot like a tree stump, due to the layers surrounding the haversian canal at the center. ● DAT Pro-Tip: The layers of an osteon are called *lamellae*. Each lamellar layer is made of cortical bone and *collagen* fibers, which help bones resist torsion strain.

Osteons

Considered the functional unit of cortical bone. They are multi-layered cylinders that extend parallel to the the bone's long axis. At the center of each of these cylinders is a canal, known as a haversian canal. For this reason, osteons are also referred to as haversian systems.

Haversian canals

Contain blood vessels, which supply nutrients to various types of bone cells living in *lacunae*.

Yolk Sac

Contains *yolk*, which functions to *provide nutrients* to the growing embryo. It is important to remember that the *yolk sac* (membrane) itself is an *extraembryonic* structure, whereas its content — the *yolk*, is actually *intraembryonic* (part of the embryo).

Aquatic biomes

Cover around 75% of the Earth and are therefore the *largest* of Earth's biomes. The vast amount of photosynthetic algae that live within these huge aquatic biomes *contribute most of the Earth's atmospheric oxygen*. These can be saltwater or freshwater.

root cap

Covers and protects the apical meristem, allowing it to continue to grow and deeper penetrate the soil.

After electrophoresis

DNA can be sequenced or probed to identify the location of a specific DNA sequence.

Recombinant DNA

DNA containing different segments from multiple sources. These DNA segments can be transferred from viral transduction, bacterial conjugation, transposons, or through artificial recombinant DNA technology. ❖ Recombinant DNA technology uses *restriction endonucleases* (aka restriction enzymes) to cut up specific segments of DNA. The cut ends of DNA are called *sticky ends*, and are left unpaired. These sticky ends allow for new DNA pieces (cut at the same points with the same restriction endonuclease) to bind, creating a DNA molecule from multiple sources. ● Restriction enzymes (e.g. EcoRI and BamHI) are normally used by bacteria to protect against viral DNA. Their own DNA is protected via DNA methylation. ● When restriction enzymes are applied to the DNA of individuals, fragments of different sizes are created due to individual differences in DNA. These fragments are called *restriction fragment length polymorphisms (RFLPs)*. RFLPs are inherited in a Mendelian fashion, and can be used in paternity suits or in crime scenes to match DNA to suspects (sometimes referred to as *DNA fingerprinting*). Recall that a *polymorphism* is when two or more different phenotypes exist for a trait - for example, there are multiple human blood types, and each is considered a different polymorphism). In RFLPs, the polymorphisms are the fragments of different length. Another aspect of DNA used to identify individuals in crime or paternity are *short tandem repeats* (STRs). These are repeats of 2-5 nucleotides that are different between all individuals except identical twins. This differs from RFLP analysis in that restriction enzymes aren't used. Instead, probes and PCR amplification are used to discover STR lengths

DAT Pro-Tip DNA vs RNA

DNA is called deoxyribonucleic acid, while RNA is called ribonucleic acid... DNA is missing the extra oxygen! DNA is de-oxygened.

nucleosome

DNA-histone complex. Each nucleosome contains nine histone proteins: eight in the central core and one keeping the DNA wrapped around the central core. The central core of histones are numbered H2A, H2B, H3 and H4. There are two sets of each type per nucleosome; so, while there are only four types of histone protein in the central core, there are actually eight histone proteins inhabiting the central core. Nucleosomes also contain another type of histone, called histone H1. *Histone H1* is essentially responsible for keeping the DNA wrapped around the central histone core. ● Note: histone proteins are not found in bacterial DNA.

Reticular Dermis

Deep to the papillary dermis, and it gets its name from its reticular fibers. However, collagen and elastic fibers are also present within this *dense irregular connective tissue*. These fibers are the reason why the dermis is so strong and elastic. Additionally, blood vessels, sensory receptors, hair follicles, nail beds, and glands are contained within this fibrous network.

TEMPORAL

Deep to the temples Contains the *auditory cortex*, which is important for processing and interpreting sounds and *Wernicke's* area, which is essential to understanding speech.

Hypertonic

Describes a solution in which there is a higher solute concentration than inside the cell. Cells in this solution undergo *plasmolysis* (shrinkage of cytoplasm from water loss away from the cell wall). Animal cells will shrivel due to water being pulled out of the cell.

Hypotonic

Describes a solution in which there is a lower solute concentration than inside the cell. Plant cells in hypotonic solutions will have their vacuoles swell, resulting in turgid cells ‐ this is their normal state.

Isotonic

Describes a solution in which there is an equal solute concentration with the environment inside the cell. In an isotonic solution, plant cells are laccid.

niche

Describes all the *biotic and abiotic* resources it uses. If a niche is occupied by two different species, competition for resources will ensue.

realized niche

Describes the environment where an organism *truly lives*.

Allopatric speciation

Describes the formation of a new species *with the presence of a geographic barrier*, which separates the population into separate groups. Interbreeding between the two split populations is prevented and gene frequencies can diverge due to natural selection, mutation, and genetic drift (genetic drift is a change in a population's frequency of genotypes due to organism disappearance, death, or lack of reproduction). If the gene pools become sufficiently divergent, speciation may occur.

Allopatric speciation

Describes the formation of a new species with the presence of a geographic barrier, which separates the population into separate groups.

contraction phase

Describes the period of time when calcium binds to *troponin-C*, triggering a shape change in troponin that causes it to pull *tropomyosin* away from actin's myosin binding sites. *Cross-bridges* are established and the *H zone* begins to shrink.

latent phase

Describes the period where an action potential spreads over the *sarcolemma* and down the *T-tubules*, signaling the *sarcoplasmic reticulum* to release its calcium ions into the *sarcoplasma*.

Degrees of Muscle Contraction

Despite the fact that a muscle fiber's *twitch* will always be the same size, the overall force of contraction *varies*. This is accomplished through *summation*, of which there are *two types*: 1. Wave summation (temporal summation) 2. Motor unit summation The two *summation* mechanisms support the idea that skeletal muscle contracts *voluntarily*. However, we never really think about standing straight or keeping our head upright. This is because all of our muscles have a resting *tone* that keeps them firm.

epicotyl

Develops into the very top region of the young shoot, or the shoot tip.

Steroid Hormones: Lipid-Soluble

Due to its lipid property, steroid hormones *cannot* travel freely in the bloodstream like peptide hormones. They require a *carrier* to help shield them from the water based blood. However, the plasma membrane loves these lipid-soluble friends. Unlike peptide hormones which cannot penetrate through the cell's membrane, lipid soluble hormones can diffuse through the membrane. Afterwards, steroid hormones can bind to receptors floating in the cytoplasm or directly to the receptors in the nucleus. Hence, steroid hormones *directly stimulate* receptor cells.

Muscle tone (or tonus)

Due to weak and *involuntary* twitches of small groups of motor units within a muscle, due to a continuous output of action potentials from the brain and spinal cord. We never feel fatigued by our *tonus* because different *motor units* of a muscle are being stimulated at different *times*. ● Note: resting *muscle tone* affects motor units in *smooth muscle* as well. This aids in digestion and the maintenance of things like blood pressure, for example. *Cardiac muscle* has no inherent muscle tone.

chromatin

During cell replication, the DNA is tightly packed into *chromosomes*. However, when the cell is not dividing, the DNA is packaged into one of two types of *chromatin*. This packaged DNA (chromatin), reduces the volume of the DNA allowing it to fit inside the nucleus, and helps control which genes are transcribed and translated.

X-inactivation

During embryonic development in female mammals, one of two X chromosomes does not uncoil. Instead, it forms a dark and coiled compact body chromosome (*Barr body*) that is not expressed. The genes on the other X chromosome will be expressed. ● The X chromosome that is inactivated can differ from cell to cell - as a result, not all cells in a female mammal are necessarily functionally identical. This phenomenon is why calico cats have multiple patches of different fur color, as their fur pigment is X-linked and subject to X-inactivation. Hemophilia is an X-linked recessive disease. A woman that is heterozygous for hemophilia (XHXh) is normally just a carrier for the disease, but if XH is inactivated, Xh can be expressed.

Barr body

During embryonic development in female mammals, one of two X chromosomes does not uncoil. Instead, it forms a dark and coiled compact body chromosome (Barr body) that is not expressed. The genes on the other X chromosome will be expressed.

annelida examples

Earthworm, leech

Ectoderm

Ecto- prefix = outside. Ectoderm is your outermost germ layer. *Ecto*derm is your *attracto*-derm. This is how you attract partners, which might eventually lead to sexual intercourse. Things like your *brain* and *nervous system* (you gotta be smart!), your *epidermis* (outer layer of skin), *nails* and *hair*, your *enamel* (pearly white teeth), your ability to get over your nervousness and ask the person out (lots of epinephrine and norepinephrine) produced by the *adrenal medulla*, and you hopefully aren't sweating too much and can keep these *sweat glands* in check, those mammary glands, and your *eyes* and *ears* (the sensory parts of them!) Here is a more comprehensive list of the tissues ectoderm develops into: ● CNS (brain and spinal cord) and PNS ● Sensory parts of the ear, eye, and nose ● Epidermis layer of skin, nails, and hair ● Mammary and sweat glands ● Pigmentation cells ● Jaws and teeth ● Adrenal medulla

vitreous humor

Eighty percent of the eye is composed of *vitreous humor*, a gelatinous substance that fills the space between the lens and retina. It maintains eye shape and holds the retina in place.

Directional selection

Eliminates one extreme of a range of traits. The trait at the opposite extreme are favored. After many generations, a change in allele frequency is observed (such as insecticide resistance). ● *Industrial melanism*: selection of dark-colored (melanic) varieties in various species of moths (peppered moth) as a result of industrial pollution.

Measuring Heart Contraction Overview

End diastolic volume End systolic volume Stroke volume Cardiac output Mean Arterial Pressure

Endoderm

Endo- prefix = inner. The endoderm is the innermost germ layer surrounding the archeteron. *End*-oderm are your endernals (internals) + PLTT. It gives rise to the *epithelial lining of the internal organs*, such as linings of the *digestive*, *respiratory*, and *excretory* systems. It also becomes the *PLTT*: Pancreas, Liver, Thyroid + Parathyroid, Thymus. Here is a more comprehensive list of the tissues mesoderm develops into: ● Lining of digestive, respiratory, and excretory system ○ Stomach, liver, pancreas, lungs, bladder etc. ● PLTT ○ Pancreas ○ Liver ○ Thyroid + Parathyroid ○ Thymus

Types of Bones and their Structure

Endoskeletal systems contain various types of bones. The types of bones are *long*, *short*, *flat*, *sesamoid*, and *irregular*.

Eosinophils

Eosinophils are also part of the innate response. Their cytoplasms are filled with granules which contain proteins that can be released into the surrounding tissue to kill pathogens. They are especially effective against parasites.

introns

Eukaryotic DNA and mRNA contain interruptions within the coding sequence for a gene. These interruptions are known as *introns*. The expressed, protein coding sequences are known as *exons*. ● Mnemonic: Introns = Interruptions. Exons = Expressed.

would a mutation in an intron that changes one DNA nucleotide for another lead to any issues or be silent (i.e. not seen)?

Even though introns are noncoding DNA, a mutation in an intron could lead to an effect in the protein if the mutation was in a part of the DNA that signals that the intron needs to be spliced out (i.e. the 'splice signal'). If there was a mutation here, the spliceosome might not recognize the 'splice site' and the intron may not be removed.

chyme

Eventually, the acidic, semi-digested food mixture, also known as *chyme*, leaves the stomach through the *pyloric sphincter* and enters the small intestine. *Note: cardiac sphincter is the sphincter that controls food entering the stomach, pyloric sphincter is the sphincter that controls food exiting the stomach.

Nitrogen Fixation

Every biogeochemical cycle has three main components: *reservoirs* that serve as major storage location for the element, *assimilation* that is responsible for the element being taken up by plants and animals, and a *release* process that returns the element back to its environment. We will walk through how these terms relate to the nitrogen cycle. Nitrogen is essential for plant growth and development, and there is plenty of nitrogen in the air. In fact, nitrogen makes up around *78% of the Earth's atmosphere*. The Earth's atmosphere can be considered one of the reservoirs for nitrogen. However plants can only use specific forms of nitrogen: ammonia and nitrate. Plants cannot convert nitrogen into these forms on their own- they acquire the help of nitrogen-fixing organisms. *Nitrogen fixing bacteria* in the root nodules of legumes can fix atmospheric nitrogen (N2) into ammonium NH4+. *Nitrifying bacteria* convert ammonium NH4+ into nitrites NO2- and nitrites into nitrates NO3-. Nitrates NO3- are taken up by plants (assimilation of nitrogen), and the plants incorporate the nitrogen into amino acids and into chlorophyll. This is a fundamental for plant growth. Plants are the producers of the biosphere and are eaten by consumers, which then utilize the nitrogen from the plants they have eaten (or a secondary consumer may eat a primary consumer and utilize the nitrogen the primary consumer obtained from the plant). These plants and animals eventually will die and decay, known as *detritus*. Detritus will decompose back into the soil to contribute a nitrogen source. And any nitrates NO3- that are not taken up by plant roots are released back into the atmosphere by *denitrifying bacteria* (release). Denitrifying bacteria convert nitrates NO3- into N2 *atmospheric nitrogen*. Plants and nitrogen-fixing organisms have a *symbiotic* (mutually beneficial) relationship. Plants give the bacteria carbohydrates produced from photosynthesis, while the bacteria "fix" the nitrogen in the soil into a form that the plants can use.

Dark field microscopy

Excludes light that is not reflected from the sample. Advantages: Excellent contrast on living samples. Disadvantages: Low light intensity.

Metanephridia

Excretory glands involved in invertebrate osmoregulation. Metanephridia are tubes with cilia that move fluids around. Ultimately, the tube empties into the coelom. Ducts between the coelom and body exterior allow the waste fluid to be removed from the animal.

density independent factors

Exert their effects *independent* of population density. Examples include weather and climate.

Glands

Exocrine glands are composed of specialized cells that create and secrete a product through a duct to an external surface, such as the skin or gastrointestinal tract (which can be considered an "external" tube from the mouth to the anus). There are several types of exocrine glands. The ones associated with the integumentary system are explained here. ● Sudoriferous (sweat) glands ○ Eccrine glands ■ Ceruminous glands ■ Mammary glands ● Sebaceous glands

arthropoda general characteristics

Exoskeleton made of chitin, jointed appendages, coelomates, three pairs of legs, more species than any other phylum combined, metamorphosis

Circulatory system

Extracellular circulation Complex animals with cells too far from external environment require one. Uses vessels (e.g. the *vascular system*).

Diffusion

Extracellular circulation If cells in close contact with external environment, diffusion can sufice for food and respiration needs. It is also used for transport of materials between cells and interstitial luid around cells in more complex animals.

process of acrosomal reaction

First, the *hyperactive* sperm dashes through the jelly-like corona radiata. When the sperm reaches the zona pellucida, *actin* filaments from the sperm extend out and bind to *ZP3*. The binding signals mutual recognition. Afterwards, the sperm's acrosome membrane fuses with the sperm head's plasma membrane. This exposes the *acrosomal enzymes* held within, and helps to digest through the zona pellucida. The sperm can now fuse with the egg's plasma membrane, and fertilization can occur. In mammals, the zona pellucida plays a key role to prevent fertilization between different species. For example, the sperm of a dog cannot recognize the zona pellucida of a cat's egg (no catdog for now...).

Hormones the anterior pituitary gland produces can be remembered with the acronym FLAT PiG. *FLAT are all tropic, and PiG are direct!

Follicle Stimulating Hormone (FSH) Leutinizing Hormone (LH) Adrenocorticotropic Hormone (ACTH) Thyroid Stimulating Hormone (TSH) Prolactin Ignore Growth Hormone

Hormones in Females Overview

Follicle Stimulating Hormone (FSH) Luteinizing Hormone (LH) Estrogen and progesterone

Hormones in Males Overview

Follicle Stimulating Hormone (FSH) Luteinizing Hormone (LH) Testosterone

Secondary succession

Follows a similar pattern to primary succession. However, unlike primary succession, secondary succession follows a *smaller disturbance*, such as a flood or fire. Hence, the succession process happens on terrain that has *already supported life*. Since soil is already present, this process *begins with the establishment of grasses and shrubs*, rather than pioneer species.

Stomach in Digestion

Food is emptied from the esophagus into the stomach via the cardiac sphincter. A sphincter is a ring of muscles that constricts and relaxes to control openings i.e. between esophagus and stomach. *Tip to remembering: you can think of the opening between esophagus and stomach is close to the heart, hence controlled by the cardiac sphincter. Similar to the mouth, both mechanical and chemical digestion take place in the stomach. Mechanical digestion: ● Churning of stomach by muscles to mix and break down the food Chemical digestion: ● Enzymatic digestion of proteins and fat The stomach's lining is filled with gastric pits that leads to gastric glands. Gastric glands are formed by multiple types of cells that altogether contribute to a healthy-working stomach. The lining is also made of lamina propria (connective tissue) and muscles. There is a chain of events that happens after the stomach senses food's entrance. It involves the collaboration between different cells, hormones, and enzymes. When a food bolus enters the stomach, the stomach is distended (stretched). This stretching is a signal for G cells of the stomach to release gastrin.

peristalsis

Food is then moved by *peristalsis*, from the duodenum to the jejunum and ileum where nutrients are absorbed.

origin of replication

For DNA replication to occur, the strands first need to be separated at a specific place, called an origin of replication. Here, proteins cause the two strands to 'bubble' away from each other. ● There is only one origin of replication in bacteria that have a circular chromosome; however, organisms with linear chromosomes (humans) can have several origins of replication bubbling out along a single chromosome, and archaea have multiple origins of replication along their single chromosome.

cardiac muscle

Found in the heart. This type of muscle also contracts and relaxes *involuntarily*, and has just *one nucleus* per cell. Cardiac muscle is *striated* (it contains sarcomeres). A helpful way to remember the way cardiac cells look is to remember that they resemble tunnels in an ant farm - highly branched. ● DAT Pro-Tip: Cardiac cells also contain something called intercalated discs. *Intercalated discs* contain a desmosome and a gap junction. The desmosome is a inter-cell connection that holds the cells tightly together. The gap junction is like a tube between heart muscle cells that lets the cells quickly pass key ions from cell to cell, allowing the heart tissue to depolarize and contract in unison.

smooth muscle

Found in the walls of our organs, airways, and blood vessels. It contracts and relaxes *involuntarily* (without us needing to consciously initiate the function).Imagine how overwhelming it would be to think about passing that last meal you ate through your digestive system, or thinking about every single breath you took! Smooth muscle is *not striated*, containing short tapered cells with only *one* nucleus. ● DAT Pro-Tip: It is *sarcomeres* that give certain muscles a striated appearance. We will talk about what a sarcomere is, as well as how they help muscles contract later in this chapter. Smooth muscle lacks sarcomeres, which is why it does not have a striated appearance.

Dermal tissue

Found on the *outer layer* of the plant. It provides *protection* to the insides of the plant and also helps *regulate* how the plant is affected by its *external* environment. *Epidermis*: a type of dermal tissue that covers the outside of a plant. The epidermis of the plant is covered by a waxy layer, known as the *cuticle*. The waxy cuticle "waterproofs" the plant (*limits evaporation* of water). This is especially found in plants found in hot climates as it helps them survive the high temperatures. *Root Hairs*: little structures that project out of the epidermis of root cells. They *increase the surface area* of the epidermis cells which allow for *greater water and nutrient uptake*. Larger surface area means larger amount of space where the plant is in contact with and can draw substances from the soil.

Abscisic acid

Functions in times of plant *stress*. It promotes dormant seeds (prevents premature opening), closes stomata (during drought), and inhibits growth. The dormancy caused by abscisic acid can be broken by gibberellin increase or environmental stimuli such as temperature or light.

Vascular tissue

Functions to *transport material* to different parts of the plant. Vascular tissue transport material *from the source* (where the material is generated) *to the sink* (where the material is used). There are two different types of vascular tissue: *phloem* and *xylem*.

middle ear

Functions to amplify sounds and transmit auditory information to the inner ear, and it consists of the tympanic membrane and the ossicles. ▪ The *tympanic membrane (eardrum)* vibrates at the same frequency as the sound waves and transmits these vibrations to the ossicles. ▪ The *Ossicles* are three small bones named the *malleus, incus, and stapes*, which vibrate and transmit auditory information to the inner ear.

Fungi

Fungi are heterotrophic *saprophytes*, which means they feed on dead and decaying matter. This is important because this process recycles organic matter within the biosphere. There are two main categories of fungi: nonfilamentous and filamentous.

key cells in stomach digestion

G cells - releases gastrin (hormone) — stimulates parietal and chief cells ○ Parietal cell - gastric juice (HCl) ○ Chief cells — pepsinogen and gastric lipase ○ Mucous cells — protection of mucus

Nitric Oxide

GASOTRANSMITTERS (GASES) Causes smooth muscle relaxation. In blood vessels, this results in vasodilation, which leads to decreased blood pressure. Unlike other NTs, it is synthesized and released on demand, rather than stored in vesicles.

HIV (human immunodeficiency virus)

HIV cDNA will then integrate into the host DNA, which begins the lysogenic cycle. When HIV enters the lytic cycle, it starts to destroy the host cells. The host cells affected by HIV are T *helper cells (CD4 cells)*. As CD4 cell counts decrease, the patient has decreasing immunity. The condition has progressed to *AIDS (acquired immune deficiency syndrome)* when the number of CD4 cells falls below a certain number.

Primary succession

Happens after a *large disturbance* (like a volcanic eruption) or on substrate that had *not previously supported life* (like a rocky terrain). It occurs on substrate that completely lacks plant and animal life. The process begins with *pioneer species* (lichen, algae, and fungi are classic examples), in combination with abiotic factors such as water and sunlight. Once a thin layer of soil has formed, vascular plants, like grasses and shrubs, join (or replace) the pioneer species. Eventually, the community may be able to support larger plants, like trees. And, as the community changes, more and more animals become attracted to and join this community. Eventually, a climax community may be established. A *climax community* results when the ecological succession process has reached a steady state and there is a balance in the prevalence of each species.

Monocots

Have a single cotyledon, parallel leaf venation, and flower organs in multiples of 3's. Their vascular bundles are scattered and their root system is fibrous (many fine roots rather than a single large root).

Osteoblasts

Have a single nucleus and primarily function to *build bone*. They secrete the proteins and collagen that make osteoid. Similarly, they make an enzyme that allows calcium, phosphate, and water to crystallize into hydroxyapatite. ● Hint: remember that osteo*b*lasts *b*uild bone. Eventually, osteoblasts secrete so much bone matrix that they get trapped by it, maturing into *osteocytes*. These are highly branched cells that communicate with other cells to maintain bone. They live in those little spaces (lacunae) in a haversian system (osteon).

Dicots

Have two cotyledons, netted/branching leaf venation, and have flower organs in multiples of 4's or 5's. Their vascular bundles are organized in a circle, and they have a taproot (a single large root).

Casparian strip

Helps *regulate* the type and amount of *substances* that can enter through the roots and travel to the rest of the plant (via the vascular tissues). It is made of a fatty, waxy substance that makes it impenetrable and is found inside the cell walls of plant roots. Therefore, all incoming substances that were travelling through the cell walls (which do not have a way of filtering substances) run into the impenetrable Casparian strip and are forced into the cytoplasm of the root cells. This way, the substances are forced to flow through the plasma membrane, which we know are semi-permeable and therefore do have a way of filtering substances.

DNA Sliding clamp

Helps to hold DNA polymerase to the template strand

adrenal cortex: stress

Helps us deal with *long-term stresses* such as prolonged dehydration or starvation. This is because the adrenal cortex is indirectly stimulated through the hypothalamus and the anterior pituitary, which takes longer, and also because the corticosteroids have a more prolonged effects on our body compared to catecholamines.

five main types of leukocytes

Here is an acronym for remembering the relative number of leukocytes circulating in the blood from highest number of cells to lowest number of cells in circulation: Never Let Monkeys Eat Bananas Never = Neutrophils Let = Lymphocytes Monkeys = Monocytes/Macrophages Eat = Eosinophils Bananas = Basophils

Histone and DNA binding

Histone proteins contain lots of *positively* charged amino acids, while DNA is a *negatively* charged molecule (because of the phosphate groups). The positively charged histones are electrostatically attracted to the negatively charged DNA. This is how histones and DNA bind to each other. Histone proteins can be *acetylated* and *deacetylated* to change how tightly the DNA binds.

Holoblastic vs. Meroblastic cleavage

Holoblastic vs meroblastic cleavage is based on the *evenness of embryo division*. *Holoblastic* cleavage refers to cleavage that happens *throughout the entire embryo*. It is a complete cleavage that *evenly divides* the entire embryo into distinct blastomeres. Typically this happens in embryos *without a lot of yolk*, such as humans, sea urchins, and frogs. *Meroblastic* cleavage refers to *partial cleavage* that happens in parts of the embryo. Therefore, the entire embryo *does not evenly divide*. This usually happens in embryos with *a lot of yolk*, such as birds, fish, and reptiles. When there is a lot of yolk present in an embryo, the embryo will exhibit *polarity* — divided into an *animal pole* and a *vegetal pole*. The vegetal pole contains mainly yolk. The animal pole will have very active cleavage, while the vegetal pole has slow / negligible division. DAT Pro-Tip: *frog* embryos *do contain yolk*, but they still undergo *holoblastic cleavage* (note that we said above holoblastic cleavage typically occurs in embryos with little yolk). For the purpose of the DAT, we don't need to go deep into specifics of why, but it's due to the amount of yolk the frog embryo contains. While the entire frog embryo goes through cleavage (holoblastic), it is notable that this holoblastic cleavage *is uneven* due to the presence of the animal and vegetal poles )unlike other animals that undergo holoblastic cleavage). Mnemonic: The latin prefix holo- refers to all, hence holoblastic cleavage means cleavage throughout the ENTIRE embryo. Mero- means partial, hence meroblastic cleavage means partial cleavage that is uneven.

Root pressure

How does water get into the root in the first place? *Root pressure* is a pressure that builds up in the roots of plants. Particularly in moist soils, there exists an *osmotic gradient* which drives water into the root. The osmotic pressure pushes the column of water in the xylem upwards.

Neurotransmission

How neurons communicate with each other, as well as with muscle cells and glands. *Neurotransmitters* are endogenous (created by the organism) chemical messengers used during chemical neurotransmission.

Adaptive Immunity

If innate immunity isn't sufficient to protect us from pathogens, the adaptive immunity joins the battle. The adaptive immunity is a specific immune response because it targets specific antigens. An antigen is a marker from a foreign molecule that is able to trigger an immune response. Antigens serve as a target, and our body will mark the cells bearing the antigen as non-self. Our immune system is normally programmed to recognize its own cells and not attack them. How does it distinguish between self and non-self cells? It accomplishes this through the major histocompatibility complex (MHC) molecule found on the surface of cells. All nucleated (cells with a nucleus) body cells bear MHC class I molecules on their cell surface. Every genetically-unique individual will have his/her own unique set of uniform MHC I molecules. This means that identical twins (which are genetically identical) will have the same MHC I expression on their cells. When our immune system sees its own MHC I molecules, it will recognize these cells as allies and spare them from death. In cases of organ transplantation, the donor organ will bear a different MHC I molecule which will be labelled as an antigen by our immune system. As a result, our immune system will attack the "enemy" organ. This will lead to organ failure and transplant rejection. This is why transplant patients need to take immunosuppressants on a life-long basis to lower/eliminate the immune system's response towards the foreign organ. However, lowering the immune system also makes these patients more susceptible to general infections. However, there are also cases of autoimmune diseases when the immune system mistakenly attack self cells, such as in type I diabetes when the pancreatic cells are destroyed by the immune system and lose their functions. Earlier, we talked about two kinds of antigen-presenting cells (APCs) that act as a bridge between the innate and adaptive response — macrophages and dendritic cells. In addition to MHC I molecules that all nucleated body cells bear, APCs specifically also have another type of MHC — MHC II on their cell surface. After APCs phagocytose the pathogen and break off the antigen, APCs will load the antigen on the MHC molecule and present it to immune cells. For example, an immature T cell can bind to the antigen on the MHC II of the APC via its T Cell Receptor (TCR), and become activated. Note here that antigens can be presented on either MHC I or MHC II, later we will see how that makes a difference. There is an important part of the antigen called the epitope. The epitope is important because it is the section of the antigen that is recognized by immune cells like B cells and T cells. Both B cells and T cells are lymphocytes, which means that they are produced from the bone marrow. Their differences is that afterwards B cells stay and mature in the bone marrow, while T cells go and mature in the thymus. Review: ● Adaptive immune response: *specific*, targeted protection ● Antigens: any molecule recognized as *'non-self'* and can trigger an immune attack ● MHC I: found on *all nucleated body cells* ○ Mark for *'self'* ○ Foreign MHC I molecules are deemed as antigens (i.e. organ donation) ● MHC II: found *only on APCs* ● APCs (macrophages + dendritic cells) present antigens on MHC to B cells and T cells ● Epitope: important part of the antigen that is recognized by immune cells ● Lymphocytes: ○ B cells —> born in bone marrow —> mature in bone marrow ○ T cells —> born in bone marrow —> mature in thymus ○ Natural killer cells —> born in bone marrow —> stay in bloodstream

coenocytic hyphae

If septa are not formed, the hyphae is one long and continuous tube of multinucleated cytoplasm. This is known as *coenocytic hyphae*. A *coenocyte* is a large multinucleate cell. This occurs when a fungal hyphae or Protista divides, but *cytokinesis* (cell splitting) does not occur. Therefore, the daughter cells of mitosis remain connected and the coenocyte is the remaining, multinucleated cell.

Innate Immunity — Inflammatory Responses

If the protective wall is penetrated, innate immunity continues with the inflammatory response. This is why when you accidentally cut yourself, the injury site reddens and swells up after a few minutes. The first part of the inflammatory response is rally signalling. The mast cells are responsible for this. Mast cells are a type of leukocyte that sits in tissues. As soon as there is an injury, the injured tissue and mast cells work together to release a substance called histamine. Histamine has two main functions: 1. Dilate nearby capillaries —> increase blood flow 2. Make capillary walls more permeable —> fluid and immune cells leak out to the site of injury. ● Mast cells release histamine 1. Dilate capillaries 2. Make capillaries more permeable ● There are 5 signs of inflammation: redness, heat, swelling, pain, loss of function

divergent evolution

If two *closely-related* species compete for the *same resources*, they may undergo *divergent evolution* (evolution to become less similar). During this process, the species become adapted to new habitats. If they fail to do this, they may face extinction.

Hormones

If we say the endocrine system plays the role of a communicator in our body, then *"hormones"* are the language it uses to communicate. While the nervous system uses *electrical* signals (action potentials), the endocrine system uses *chemical* signals (hormones). Here are a few characteristics that hormones have: 1. A small amount of hormones can have a large effect 2. Hormones bind to very specific receptors 3. A single type of hormone can elicit multiple different effects in the body (e.g. testosterone stimulates sperm maturation, hair growth, libido, and much more!) 4. Hormones are slower acting than electrical signals (compare how long it takes to go through puberty versus how long it takes to have a knee jerk)

antibody that Can give the newborn passive immunity through breastfeeding

IgA

antibody that Functions to bind and stop pathogens externally before they enter circulation

IgA

antibody that is Most abundant in body secretions e.g. breastmilk, tears, saliva

IgA

These are antigen receptors found on basophils and mast cells

IgE

Most abundant antibody found in circulation

IgG

● The ONLY antibody that can cross the placenta to give fetus passive immunity

IgG

anitbody that activates complement system (innate immunity)

IgM

first antibody to be produced in response to an antigen

IgM

the only pentamer out of the 5 classes of antibodies

IgM

the largest antibody

IgM Think of IgMost because IgM has the most number of Y shaped monomer forks

Osteoprogenitors

Immature precursor cells, which mature into osteoblasts.

differential fractionation

In *cell fractionation*, the process of differential *centrifugation* (spinning at high speeds) is used in order to separate the contents of cells based on density, size, and shape. ● First, cells must be broken apart to create cellular homogenate, which can be thought of as the contents of a cell without being contained in its membrane. ● The cell homogenate is passed through a filter, and then spun at a relatively lower speed, creating a dense pellet layer of nuclei. This layer appears the most quickly because nuclei are the most dense cell content. ● The remaining homogenate is then poured out and spun again at a higher speed. This creates the second most dense layer, containing mitochondria, chloroplast, lysosomes, and peroxisomes. ● The remaining homogenate is once again poured out and then spun at an even higher speed, creating the next most dense layer containing plasma membrane and endoplasmic reticulum fragments. ● The process repeats, creating a layer of ribosomes. The remaining homogenate contains only the cytosol (the aqueous portion of the cytoplasm).

primary growth

In a young, newly hatched seedling, growth first happens at the apical meristems (not at the lateral meristems). This vertical growth of the plant is called *primary growth*, because it happens first before the lateral growth (if any) of the plant.

Adaptive Immunity — B cells

In adaptive immunity, B cells are responsible for *antibody-mediated immunity*, which means that they control the production and release of antibodies. It is also called humoral immunity because humor = body fluid, and antibodies are found in various types of body fluids such as blood and lymph. B cells have *B cell receptors (BCR)* to bind to the epitope of the antigen. BCR can bind to free-floating antigens or antigens that is presented by APCs. After BCR binds to its antigen, the B cell becomes *activated*. Following activation, the B cell divides and make many copies of itself. Every B cell has a *unique and uniform* BCR that binds to one kind of antigen, which means that a single B cell cannot have different BCRs that bind to different antigens. This brings us to the *clonal selection model*. This theory states that since each B cell has a unique BCR, the antigen selects which BCR it can bind to, and which B cell to activate. Therefore, out of thousands of pre-existing B cells, only one specific B cell is selected to proliferate and make clones of itself. We have amplification of the B cell that is specific to the antigen that is present in the pathogen of attack.

density centrifugation

In contrast to differential centrifugation, *density centrifugation* only separates cell contents on the basis of density. Unlike the multiple spin steps of differential centrifugation, density centrifugation involves one spin step that creates multiple layers separated by density. ❖ Centrifugation can also be used to separate proteins based on solubility (insoluble proteins pellet out, soluble proteins remain in the supernatant).

eukaryotic ribosomes

In eukaryotes, ribosomes are composed of small (*40S*) and large (*60S*) subunits, which come together to form a *80S ribosome*. The *nucleolus* is a region of densely packed DNA inside the nucleus of a eukaryotic cell. rRNA is synthesized and attached to proteins at the nucleolus. The 40S and 60S subunits are assembled at the nucleolus as well.

Oogenesis

In females, *oogonia* are the primordial (earliest) egg cells. They are replicated by mitotic division in the ovaries. As many as 10 million oogonia can be produced in human females, however the large majority will apoptose and die; about 50,000 will remain (exact numbers aren't important - just know that *many oogonia are produced*, and there is *major apoptosis*, with only a *small fraction remaining*). These remaining cells will differentiate into *primary oocytes*, which will begin the first meiotic division, but will not complete meiosis I. *Meiosis I will be arrested* in prophase I *until puberty*. Once the female hits puberty, monthly one of these eggs will be stimulated to develop in the process of *ovulation*. This ovulated egg will complete the first meiotic division, producing a *large secondary oocyte* and a *polar body*. The secondary oocyte is large because it keeps most of the cytoplasm from this division. The polar body is a small daughter cell which lacks most organelles, and will atrophy away. This secondary oocyte will then *arrest in metaphase II*. Only if *fertilization occurs*, will the egg be stimulated to *complete meiosis II*. If the egg is fertilized and goes onto complete meiosis II, three polar bodies will have been produced. However, *only the oocyte can produce viable offspring* (not the polar bodies) because the vast majority of the nutrients and cytoplasm in the progenitor cells go into making the oocyte viable (the polar bodies receive very little cytoplasm from each division). Sperm contribute very little cytoplasm or nutrients to the fertilized egg, and it is the responsibility of the high-investment oocyte to provide enough for the offspring to survive.

Polyspermy Block

In fertilization, *polyspermy* would occur if more than one sperm were to penetrate into the egg. This would result in a *polyploidy* (more than two copies of chromosomes), and would not be a viable embryo. The body has developed *two* types of polyspermy block: the *fast block* and *slow block.*

prokaryotic ribosomes

In prokaryotes, ribosomes are composed of small (*30S*) and large (*50S*) subunits, forming a *70S ribosome*. rRNA is synthesized and attached to proteins in a region called the nucleoid. The *nucleoid* is the region within prokaryotic cells that contains most of the cell's genetic material. It is analogous to a eukaryotic nucleolus. DAT Pro-Tip: prokaryotes lack a nuclear membrane; both transcription and translation can occur in the cytosol at the same time. The prokaryotic ribosome can translate an mRNA transcript as RNA polymerase is continuing to transcribe it.

prokaryotic ribosomes

In prokaryotes, ribosomes are composed of small (30S) and large (50S) subunits, forming a 70S ribosome. rRNA is synthesized and attached to proteins in a region called the nucleoid.

Adaptive Immunity — T cells

In the adaptive immune response, T cells are responsible for *cell-mediated immunity*. Contrary to B cells which send out antibodies to do the job of killing enemies (humoral response), T cells do the work themselves (cell mediated response). Similar to B cells, T cells have *T cell receptors (TCR)* on their surfaces. Every T cell has a *unique and uniform* TCR that binds to only one kind of antigen. Hence, T cells also go through *clonal selection*. However, unlike B cells, T cells are more needy. T cells cannot recognize free floating antigens; they can ONLY bind to antigens presented by antigen presenting cells (APCs). The most common APCs that serve T cells are macrophages, dendritic cells, and B cells. Recall we mentioned that antigens can be presented on either MHC I or MHC II molecules. If an antigen is presented by *MHC I*: ● T cells activate and become *cytotoxic T cells*, also called *CD8 cells* However, if an antigen is presented by *MHC II*: ● T cells activate and become *helper T cells*, also called *CD4 cells* A third type of T cells that form after clonal selection is *memory T cells*. Review: ● T cells —> cell-mediated immunity ● TCR: ○ Can only detect antigens presented by APCs, NOT free floating antigens ○ Unique and uniform ● Cytotoxic T cells kill enemies in the same fashion as natural killer cells.

cell-mediated immunity.

In the adaptive immune response, T cells are responsible for cell-mediated immunity. Contrary to B cells which send out antibodies to do the job of killing enemies (humoral response), T cells do the work themselves (cell mediated response).

gel electrophoresis can also be applied to proteins

In the case of proteins, we must first add SDS (a compound that denatures, linearizes, and adds a negative charge to protein).

Innate Immunity — Complement system

In the last section, we focused on how individual *cells* contribute to the innate immune response. In this chapter, we will talk about *blood plasma proteins* that participate in the innate immune response. There are approximately *30* proteins included in the *complement system*. They are called the complement system because they are a system (group) of proteins that exist as a side-kick to the immune cell soldiers, helping the immune cells to make the battle against pathogens more effective. Although proteins are much smaller in size compared to cells, they can generate a big effect by 'turning each other on' through a *cascade series of activation*. They activate each other through the release of *cytokines* (intracellular signalling molecule). When activated, the complement system can do a lot of things, including: 1. Improves the 'eating' ability of phagocytosing cells (eg. macrophages) by binding complement protein C3b to antigens and tagging them for phagocytosis, a process called *opsonization* 2. Amplifying inflammatory responses a. Certain proteins can bind to *mast cells* to trigger a stronger *histamine* release. 3. Lyse pathogen membranes a. Some proteins can form a *membrane attack complex (MAC)* which specifically functions to poke holes in pathogen membranes. i. Once holes are created, fluid and salts can go into the pathogen and make the cell burst and die. Review: ● Complement system: a team of ~*30* blood plasma *proteins* (not cells) ● The complement system is part of *innate immunity* ● *Membrane attack complex (MAC)* —> poke holes on pathogen membranes —> cell lysis

tropomyosin

In the relaxed state, actin's binding site for myosin is covered by *tropomyosin*.

type II survivorship curves

In this case, the probability of survival remains relatively constant regardless of the organism's age. Some organisms that demonstrate this type of survivorship include the hydra (a genus of small, freshwater organisms), lizards, some birds, and some small mammals (mice and squirrels, for example).

Seedless tracheophytes

Include the phylums lycophytes and pterophytes. Common examples include club moss, quillworts, fern, and horsetail. Ferns formed the first forests during the Carboniferous period. Although most are found in moist habitats, their vascular system allows them to successfully grow in more dry climates as well. Most seedless tracheophytes are *heterosporous* (can produce both male and female spores). Seedless tracheophytes have *flagellated sperm*, meaning it can move on its own (does not travel via wind or animal).

Polygamy

Includes *polygyny* (one male with many females) and *polyandry* (one female with multiple males).

Lamarck's theory of evolution

Includes three important concepts. ● *Use and disuse*: organisms develop body parts that they use and if it is not used, it will deteriorate. This is correct in athletes. ● *Inheritance of acquired characteristics*: idea that the characteristics that an organism acquires throughout its lifetime can be passed to its offspring. This is incorrect as traits are only passed on to offspring via genetic material. ● *Natural transformation of species*: organisms produce offspring that are slightly more complex than the preceding generation. Organisms do not become extinct or split into more species. This is incorrect.

Darwin's theory of evolution

Includes two important concepts. ● *Natural selection*: better known as "survival of the fittest." This is known as Darwinism. The idea of the "survival of the fittest" was integrated with the idea of genetics as the method of biological inheritance to formulate a new theory called *neo-Darwinism* or the *synthetic theory of evolution*. ● *Descent with modification*: this is a concept coined by Darwin to describe that over time and generations, traits providing reproductive advantage become more common within the population vis natural selection.

Vitamin D

Increases calcium in the blood by increasing the number of *osteoclasts*. Additionally, it stimulates the secretion of more *PTH* from the parathyroid gland.

Changes in Allele Frequencies: Natural Selection

Increases or decreases allele frequency due to the environment.

Fixed action patterns (FAP)

Innate behaviors that follow a predictable series of actions. They are initiated by a specific stimulus called *sign stimuli* (*releaser* when between members of the same species). The behavior goes to completion, even if the stimulus is removed. Reflexes are technically FAPs. ● A well-known example of this is a graylag goose methodically rolling her egg back to the nest once if it slips away or is removed. The goose will follow very predictable movements when pushing the egg back to the nest. ● Another example of this is a male stickleback fish defending their territory against any object with red underside. ● Another example of this are animals that herd or flock together, such as swimming actions of fish or the flying actions of locusts. ● Innate behaviors (e.g. FAP) provide successful/dependable mechanism to an expected event. The challenge need not be resolved repeatedly by every new generation.

Somatic Nervous System

Innervates skeletal muscles. It consists of both afferent sensory nerves and efferent motor nerves. o The *neuromuscular junction* is where the efferent motor neuron directly synapses with the skeletal muscle. The neuron releases acetylcholine into the synaptic cleft to induce muscle contraction. This can be voluntary or involuntary. o An example of a voluntary muscle contraction is raising your hand. o Involuntary muscle contractions within the somatic nervous system are rarer, and they are rapidly induced by a *reflex arc*, such as the knee-jerk reflex. Rather than being integrated by the brain, the sensory neuron synapses in the spinal cord, which either directly or indirectly (via an interneuron) activates the motor neuron to cause movement. However, the brain will still receive the sensory stimulus, so one becomes aware of it after the reflex takes place.

Fibrous protein

Insoluble, long polymer ibers/sheets, form structural components of cells. ex) collagen

hypothalamic-releasing hormones

Instructing the anterior pituitary to release other hormones (it's a hormone that instructs a gland to release another hormone)

Chemical neurotransmission

Involves the release of neurotransmitters from the terminal bouton of one neuron, which travel through the synaptic space (or cleft) and bind to receptors on the dendrites of post-synaptic neuron. This results in either an EPSP or IPSP for the post-synaptic neuron. o The most typical form of neurotransmission in animals o Unidirectional - from pre- to post- synaptic neuron Steps 1. Neurotransmitters are synthesized and then stored in vesicles in the axon terminal of the presynaptic neuron 2. When an action potential reaches the axon terminal, voltage-gated Ca2+ channels open, allowing calcium to enter the axon terminal. 3. The increase in intracellular calcium induces the presynaptic vesicles to fuse with the pre-synaptic membrane, releasing neurotransmitter into the synaptic cleft. 4. The neurotransmitter molecules diffuse across the synapse and bind to postsynaptic receptors on the target cell, resulting in an EPSP or an IPSP. 5. The neurotransmitter molecules are deactivated through reuptake (recycling) into the presynaptic neuron, enzymatic degradation within the synaptic cleft, or diffusion away from the synapse.

Animal-like protists

Known as *protozoa* (proto = primitive; zoan = animal). They are unicellular, eukaryotic protists - so they have membrane bound organelles. Some of these organelles include food vacuoles, which stores food until the cell needs to use the energy it contains. Protozoa, including amoeba and paramecium, move about thanks to flagella and cilia. Since these cells can move, they are heterotrophic in nature. Moreover, they tend to be parasitic pathogens that infect and feed off a host organism.

Types of Chordata

Lancelets (also known as Amphioxus) Tunicates (also known as Urochordata) Fish (Jawless) Fish (Cartilaginous) Fish (Bony) Amphibia Mammalia (Monotremes) Mammalia (Marsupials) Mammalia (Placental) Reptilia Birds

Changes in Allele Frequencies: Mutations

Lead to changes in allele frequency that may be beneficial. However, most as harmful.

Leaf Structure

Leaves are also covered by an epidermis layer. As discussed in the plant tissues section, the epidermis is covered by a waxy layer, called the cuticle. The cuticle "waterproofs" the plant. Along the lower epidermis are several small openings called *stomata*. Stomata allow for *gas exchange* between the external environment and the plant, and *open and close* depending on the situation. The opening and closing of the stomata are *controlled by guard cells*, specialized epidermal cells that surround the stomata.

Diffusion system

Less Stable System (high G): Highly ordered molecules More Stable System (low G): Randomly dispersed molecules

Chemical Reaction system

Less Stable System (high G): Molecule of glucose More Stable System (low G): Breakdown products of glucose

Gravitational Motion system

Less Stable System (high G): Object at high altitude More Stable System (low G): Object at low altitude

CryoSEM

Like SEM, but sample is frozen rather than dehydrated to produce a 3D image of sample's surface. Advantages: High resolution. Sample presented in a more natural form. Disadvantages: Extensive sample preparation (kills sample). Freezing can cause artifacts.

Cytokinins

Like auxins regulate cell differentiation and division. The ratio of auxin:cytokinin affects cell growth. Cytokinins can prevent senescence (aging) of plants.

secondary messenger

Literally a 'second message'. The hormone was the first message, and it activates a second message to be sent. ○ Some common secondary messengers include: ■ *cAMP (cyclic AMP)* ■ *IP3 (inositol triphosphate)* ■ *DAG (diacylglycerol)* ■ *Calcium ions*

Biotic factors

Living elements in an ecosystem, like plants, animals, and microorganisms.

Primary producers

Located at the *lowest trophic level* (the bottom of the food chain). Most commonly, they are *autotrophs* that undergo photosynthesis to *generate the biomass of an ecosystem*.

Consumers

Located at the higher trophic levels, and they eat either *producers* or *other consumers* (located at lower trophic levels). Located one trophic level higher than producers is the *primary consumer*. This is an organism that solely consumes primary producers; primary consumers are often *herbivores* (an organism that derives its energy from plant matter).

Lateral meristems

Located on the plant so that growth in these areas cause the plant to grow laterally or *horizontally*, increasing the width/thickness of the plant.

Long bones

Long bones are longer than they are wide and are wide mainly out of *corticol* bone, with few "pockets" out of *cancellous* bone. Cortical bone is dense and *compact,* while cancellous bone is more *spongy.* Some examples of long bones include the femur, radius, and ulna. Long bones have several distinct features: 1. Epiphyses 2. The diaphysis 3. A medullary cavity 4. Metaphyses 5. Epiphyseal plates (growth plate)

spongy mesophyll

Loosely-packed, allowing for a lot of space between the cells (hence the name), and is found closer to the lower epidermis. The "sponginess" of the spongy mesophyll allow for *gas exchange* between the external environment and the leaf. This also explains why the spongy mesophyll would be found right next to the lower epidermis, where the stomata are located.

Lymphocytes

Lymphocytes are your artillery units, the ones who identify and acquire a target before killing it. The lymphocytes are B cells, T cells, natural killer cells. The B cells and T cells are part of the adaptive immune response, whereas the natural killer cells are part of the innate immune response. Natural killer (NK) cells attack and kill virus-infected cells or cancerous body cells. They are part of the innate response because they do not require activation, unlike B cells and T cells — they are always "on". NK cells fight enemies with two main weapons: ■ Perforin, which perforates (poke holes in) pathogenic cell membranes, causing cell lysis (cell breakdown). ■ Granzymes, a protease which stimulates a target cell to undergo apoptosis (programmed cell death)—useful for killing cancerous cells.

Epiphyseal Plates

Made of *hyaline cartilage*, which grows in response to growth factors. Epiphyseal plates *ossify* (become bone) when pubertal hormones signal for *calcification* and *apoptosis* (programmed cell death). Epiphyseal plates lie between an epiphysis and metaphysis. They grow in the direction of the *metaphyses*; however, they lengthen the *diaphysis*. ○ Extra info: Cartilage is *avascular* (lacks blood vessels) and is notoriously difficult to heal, which is why breaking a bone at the growth plate is such a big deal!

Elastic cartilage

Made of a matrix that is extremely similar to hyaline cartilage; however, it contains more elastin proteins. The greater amounts of elasting make this type of cartilage extremely flexible. ● Elastic cartilage is found in the ears and epiglottis. Unlike cartilage, joints *are* innervated and vascularized. There are several types of joints between our bones, including: 1. *Synarthroses*, which are dense, *fibrous joints* between bones that *do not* move. 2. *Amphiarthroses*, which are *cartilaginous joints* between bones that *partially* move. 3. *Diarthroses*, which are *synovial joints* between bones that are *fully* movable.

Agnostic behavior

Made up threats, aggression, and submission. This behavior is due to competition for food, mates, or territory. It is often ritualized, so injuries and time spent in contests are minimized.

Genetic Variation: Balanced polymorphism

Maintains different phenotypes in the population (one is usually the best and increased in allele frequency). However, polymorphisms (coexistence of two or more phenotypes within the members of a population) can exist and be maintained: ● *Heterozygote advantage* ● *Hybrid vigor (heterosis)* ● *Frequency-dependent selection (minority advantage)*

Mesoderm

Meso- prefix = middle. The mesoderm is the middle germ layer. *Meso*derm is your *means*-oderm. These derivatives are the means you require to have sex. Things like your *bones* and *skeleton*, your different *muscle* types (gotta be able to move!), your *blood* system (need that blood pumping!), your *gonads* (obvious reasons!), your *adrenal cortex* - which can produce some androgens (male sex hormones!). And *spleen* sounds like mean, from meansoderm. Here is a more comprehensive list of the tissues mesoderm develops into: ● Bone and skeleton ● Muscles ● Cardiovascular system ● Gonads ● Adrenal cortex ● Spleen ● *Notochord* ○ This is one that many students tend to forget. The notochord is derived from the mesoderm. The notochord *induces* the formation of the spinal cord from the ectoderm. But itself is derived from *mesoderm*! The notochord function will be discussed later on in this chapter.

There are 5 classes of antibodies that we need to know for the DAT:

Mnemonic: Me And Eve Don't Go Ig*M* ● *Pentamer* (the only pentamer out of the 5 classes of antibodies) — contains 5 Y-shaped forks in one IgM ○ Hence, IgM is the *largest* antibody! ○ Think of IgMost because IgM has the most number of Y shaped monomer forks ● *First* to be produced in response to an antigen ● Activates complement system (innate immunity) Ig*A* ● *Dimer* ○ *Tip: when you think of IgA, think of IgAnd, when there is this and that —> dimer ● Most abundant in *body secretions* e.g. breastmilk, tears, saliva ○ Can give the newborn *passive immunity* through breastfeeding ● Functions to bind and stop pathogens *externally* before they enter circulation Ig*E* ● *Monomer* ● These are antigen receptors found on *basophils* and *mast cells* ○ Whenever there is an *allergen*, IgE will bind and trigger the release of *histamine* from these two cells —> allergic reaction ● *Tip: IgE stands for IgEve, Eve is one girl (monomer) who is allergic to many things. Ig*D* ● *Monomer* ● The function is not well understood, and only a small amount is produced ● *Tip: IgD stands for IgDon't, as we don't know much about it! Ig*G* ● *Monomer* ● Most abundant antibody found in *circulation* e.g. blood, lymph ● The ONLY antibody that can *cross the placenta* to give fetus passive immunity ○ *Tip: IgG stands for IgGo, so it can go through the placenta! ● Triggers *opsonization* = Binds to antigen and triggers phagocytosis ● Also activates complement system

There are 5 classes of antibodies that we need to know for the DAT:

Mnemonic: Me And Eve Don't Go IgM IgA IgE IgD IgG

Cell Theory/Cell Doctrine

Modern cell theory covers several fundamental principles of biology: ● All living things are composed of one or more cells ● Cells are the basic unit of structure, function, and organization in all organisms ● All cells come from pre-existing, living cells ● Cells carry hereditary information ● Energy flow (e.g. metabolism) occurs within cells ● All cells have the same basic chemical composition

Monocytes/Macrophages

Monocytes are also part of the innate response. They are called monocytes when they are in their immature state in the blood vessels. After they cross into the infected tissue through diapedesis, monocytes mature into macrophages. They are similar to neutrophils in that they are also phagocytes. They also 'eat things' that should not be in the body in a nonspecific way. Later on, macrophages function as antigen-presenting cells to activate adaptive immunity. You can think of an antigen as the unique ID of the enemy. Macrophages act as messengers that carry vital information about the enemies from the frontline soldiers (innate immunity) to the backup troops (adaptive immunity).

IgE

Monomer Tip: IgE stands for IgEve, Eve is one girl (monomer) who is allergic to many things.

Anchorage dependence

Most cells only divide when aached to an external surface such as neighboring cells or a side of culture dish.

adrenal medulla: stress

Mostly responsible for fighting against *short-term stresses* like running away from a bear. This is because the adrenal medulla is directly stimulated by the sympathetic nervous system, and also because the catecholamines produced by the medulla have short-term effects.

Plasmolysis

Movement of water out of a cell that results in its collapse.

Osteoclasts

Multinucleated cells deriving from *monocytes*. The primary function of an osteoclast is to resorb bone. ● Hint: remember that osteoclasts chew through bone. ○ Extra info: osteoclasts can be found in *Howship's lacunae*, which are simply the little pits they create as they chew away at a bone.

Balanced polymorphism (sympatric speciation)

Multiple alleles exist in the population (polymorphisms). Those with alleles that impart a greater ability to survive and reproduce in a certain niche thrive, while the members with less beneficial alleles (of the same species in the same geographic area) for that niche do not. These less benefiting members may be more suited for another niche within which they can thrive. Eventually, this can result in a new species.

sarcoplasmic reticulum

Muscle cells have smooth ER's that store and release ions, (e.g. Ca2+).

Motor Units

Muscles are made up of *motor units*. A motor unit is *all* the muscle fibers innervated by one motor neuron.

Sources of Genetic Variation

Mutation Sexual reproduction Diploidy Outbreeding Balanced polymorphism Neutral variation Geographic variation

resting state

Myosin wants to pull actin toward the center of the sarcomere. In fact, a muscle's *resting state* is contracted. However, myosin cannot come into contact with actin when we are relaxed because certain proteins act as "bodyguards" for actin.

The Krebs Cycle produces

NADH and FADH2.

Short chain amino acids, such as substance P

NEUROPEPTIDES Diverse roles involved in a wide range of brain functions.

Neurons contain

NISSL BODIES, granules of rough ER and free ribosomes that synthesize protein.

It is important to note that unlike meiosis,

NO genetic variation occurs in mitosis.

Papillary Dermis

Named for its *dermal papillae*, small *nipple-like*, *upward projections* of the dermis towards the epidermis. These projections create our *fingerprints*, and they *increase the surface area* between the dermis and epidermis. This increases the capacity for delivery of oxygen and nutrients to the epidermis, which relies on the *blood vessels* of the papillary dermis for *nourishment* and *waste removal*. Its high surface area also increases the strength of the junction between the dermis and epidermis.

Causes of Changes in Allele Frequencies

Natural selection Gene Flow Genetic drift ● Founder effect ● Bottleneck Nonrandom ● Inbreeding ● Sexual selection Mutations

High temperature with plant

Needs to prevent transpiration. Close stomata (to retain water in the plant).

Nerve rings

Nematoda Rings of nerve tissue surrounding the esophagus of an animals.

Alimentary canals

Nematoda The entire passage between an animal's mouth and anus. This passage includes the esophagus, stomach, and intestines; however, the alimentary canal does not include the accessory digestive glands that you might find in an animal with a complete digestive system.

examples of invertebrate movement

Nematoda and annelida move via *hydrostatic skeletons*.

Symbiotic bacteria

Not all bacteria are bad! Symbiotic bacteria are our allies and out-compete their more hostile relatives. ○ We naturally have bacteria in our mouths (some of which are benign and don't cause issue). If you take a steroid inhaler that kills those naturally occurring bacteria, you can end up with an opportunistic yeast infection (oral thrush)

ribozymes

Not all enzymes are proteins - some RNA molecules can act as enzymes.

adrenal medulla

Not controlled by hormones from the anterior pituitary, it is *directly controlled* by the *sympathetic nervous system* (fight or flight response). The adrenal medulla secretes *only amino-acid derived* hormones. *Tip to remember: since adrenal medulla produce only amino-acid derived hormones, it produces catechol*amines*. ● *Catecholamines* ○ *Epinephrine* (aka. Adrenaline) ○ *Norepinephrine* (aka. Noradrenaline)

adrenal medulla

Not controlled by hormones from the anterior pituitary, it is directly controlled by the sympathetic nervous system (fight or flight response).

diffusion between blood and cells

O2 transported through body within hemoglobin containing red blood cells (RBCs).

OCCIPITAL

OCCIPITAL Posterior and inferior to the parietal lobe Houses the *visual cortex*, which is important for processing and interpreting visual stimuli.

Acetylcholine

OTHER Excitatory NT of the neuromuscular junction in vertebrates. Pre-synaptic NT of the sympathetic and parasympathetic nervous systems. Post-synaptic NT of the parasympathetic nervous system. Facilitates the opening of *ligand gated sodium channels* on the muscle fiber. This allows some sodium to enter the muscle fiber; therefore, creating a *graded potential*. This small *depolarization* opens nearby *voltage gated sodium channels*. When the voltage gated sodium channels open, we have successfully transferred an action potential from a neuron to a muscle!

Mutualism

Occurs when *both organisms benefit* from the the other's presence. An example is an oxpecker bird on a rhinoceros. The oxpecker eats ticks and parasites off of the rhinoceros. Hence, the oxpecker benefits from this food source, while the rhinoceros benefits from pest removal.

Commensalism

Occurs when *one organism benefits* and the *other organism is neither helped nor harmed* by the first organism's behavior. For example, the jackal eats food that the tiger left behind. In this instance, the jackal benefits, and the tiger is unaffected.

Observational/social learning

Occurs when an animal copies behavior of another without having experienced any feedback themselves. ● An example of this are monkeys following the lead of the first by washing potato in water.

Associative learning

Occurs when an animal recognizes or learns that events are connected. Associative learning allows animals to benefit from exposure to unexpected repeated events. It can be reversed in the absence of reinforcement. This is called *extinction*. The behavior no longer elicits the response. However, sometimes a behavior that was thought to be extinct can be recovered in a phenomenon called *spontaneous recovery*.

Associative learning

Occurs when an animal recognizes or learns that events are connected. Associative learning allows animals to benefit from exposure to unexpected repeated events. It can be reversed in the absence of reinforcement. This is called extinction.

Mate choice copying

Occurs when animals in a population copy the mate choice of others.

Mullerian mimicry

Occurs when different poisonous species that share a common predator evolve to resemble each other. This way, it is easier for the predator to learn to avoid these species. An example is of a stinging bee and a stinging wasp, which have evolved to share similar coloring and body size.

Metamorphosis

Occurs when immature animals completely alter their appearance as they mature into their adult forms. Metamorphosis occurs in distinct stages, whereas something like puberty tends to happen slowly over time.

Polyploidy

Occurs when more than the normal two sets of chromosomes are possessed. In plants we find 3n (triploid) and 4n (tetraploid). Non-disjunction of the chromosomes results in two viable diploid gametes and two sterile gametes with no chromosomes. When diploid gamete is fertilized by another diploid gamete, a tetraploid 4n zygote is formed. The zygote will continue to produce diploid gametes, resulting in reproductive isolation with normal gametes. Plants can be *autopolyploid* (having more than two haploid sets of chromosomes that are derived from the same ancestral species) or *allopolyploid* (having three or more complete sets of chromosomes derived from different species).

Apparent competition

Occurs when one predator preys on two species. For example, apparent competition would occur when an owl hunts both a spider species and a beetle species, and the beetle prevalence suddenly increases. Because of the increase in owl food resources (the beetle), there would be an increase in owl survival. This, in turn, could lead to a decrease in the number of spiders, because there would be more owls to prey on them.

Disruptive selection

Occurs when the common trait is selected against. The environment *favors extreme or unusual traits*. Short and tall are favored while average is selected against. A classic example is of a peppered moth population. These moths have a spectrum of color from white to grey to black, and they live in an area with white and black rocks. Predators are able to see the grey moths against the white and black rocks, and thus, they are more readily eaten. On the other hand, the white and black moths can blend in with the rocks and are less readily eaten. This results in disruptive selection- the moths at the ends of the spectrum (white and black) survive to pass on their genes with greater frequency.

Disruptive selection

Occurs when the common trait is selected against. The environment favors extreme or unusual traits. Short and tall are favored while average is selected against.

Hybridization (sympatric speciation)

Occurs when two different species reproduce, and it can result in a new species. An example is of the liger - a cross between a lion and a tiger.

Coevolution

Occurs when two or more species having a close ecological relationship evolve together in response to new adaptations that appear in another species (predator/prey). Camouflage, aposematic coloration, and mimicry are examples of coevolution.

semiconservative replication

Once each strand on the original DNA is exposed, proteins can swoop in and attach a new, complementary strand to them. Therefore, each of the two strands created through DNA replication contains one 'old' strand and one 'new' strand.

classical conditioning

One form of associative learning. It occurs when an animal performs behaviors in response to a new stimulus rather than the normal stimulus. A well-known example of this Pavlov conditioning dogs to salivate in response to a ringing bell. Dogs normally salivate in the presence of food. Pavlov would ring a bell prior to presenting the dogs with food. Eventually, he could stimulate salivation with ringing the bell (new stimulus) alone.

Epistasis

One gene affects the phenotypic expression of a second, separate gene. ex) Fur pigmentation: 1st gene controls (turns on/off) the production of pigment and the 2nd gene controls pigment color. If 1st gene codes for no pigment → 2nd gene has no effect, regardless of pigment color gene. CCBb → black fur ccBb → no fur pigment

Monogamy

One male mating with one female.

optic nerve

One of the twelve cranial nerves. It transmits visual information in the form impulses from the retina to the brain. o Each eye has a *blind spot*, which is the point at which the optic nerve comes into contact with the retina. Because the optic nerve is located in this area, it is not possible to have photoreceptors in this area, which leads to this phenomenon.

chondroblast

One type of cell living in cartilage. Chondro*b*lasts are responsible for *b*uilding cartilage. Extra info: chondroblasts mature into *chondrocytes* when they become trapped by the matrix they secrete. Chondrocytes are found in *cartilaginous lacunae* and are responsible for maintaining cartilage.

G protein coupled receptors (GPCRs)

One type of cell surface receptor that can bind a hormone and generate a second messenger response. A GPCR consist of *seven transmembrane domains* that pass back and forth through the cell membrane. They use many types of secondary messengers to propagate the signal into the cell. For example, activation of the GPCR can activate a G-protein.

keystone species

One which has a substantial effect on maintaining ecological balance in an environment despite a relatively low abundance. A *keystone predator* maintains this balance by hunting other species to prevent their overabundance (and subsequent damaging effects on other species present).

simple protein

Only amino acids. ex) albumin

splicing

Only eukaryotic cells contain introns for removal, or *'splicing'*. Introns are removed from the pre-mRNA during mRNA processing via the spliceosome. The *spliceosome* is a molecule found only in eukaryotic cells.

Homosporous plants

Only produce *one type* of spore, making it a *bisexual gametophyte*.

Mold

Organic matter that leaves an impression in rock or inorganic matter, later the organic matter decays and leaves a negative impression.

Heterotrophic anaerobes

Organisms that cannot make their own food and do not use oxygen for metabolism (e.g. yeast).

Heterotrophic aerobes

Organisms that cannot make their own food and use oxygen for metabolism (e.g. amoebas, earthworms, humans).

Autotrophic anaerobes

Organisms that make their own food from inorganic molecules and do not use oxygen for metabolism (e.g. chemosynthetic bacteria).

Autotrophic aerobes

Organisms that make their own food from inorganic molecules and use oxygen for metabolism (e.g. green plants, photoplankton).

Glycerol is converted into

PGAL, and then enters glycolysis. ● PGAL is an alternative name for glyceraldehyde 3-phosphate (G3P).

Mitochondria Outer Membrane

Phospholipid bilayer that encloses the organelle

Mitochondria Inner Membrane

Phospholipid bilayer that is folded into many folds called the cristae Location of the ETC (oxidative phosphorylation)

Amoebocytes

Phylum (Class): Porifera Cells that contribute to structure, digestion, reproduction, and regeneration of Porifera (sponges). These cells are totipotent, meaning they can give rise to any type of cell you might find in a sponge. Amoebocytes also move by extending their cytoplasm (aka pseudopodia aka false foot).

Parazoa

Phylum (Class): Porifera Describes animals without true tissues (tissues, organs, and a digestive cavity); such as, the Porifera (sponges).

Sessile

Phylum (Class): Porifera Fixed in one place; not moveable.

Hermaphroditism

Phylum (Class): Porifera When an organism has both male and female sexual structures and has the capability of producing both male and female gametes. These types of organisms can self-fertilize; or, they can fertilize gametes from another organism of the same species.

Budding

Phylum (Class): Porifera When an outgrowth from an old organism produces a new organism. The new organism will remain attached to the old organism until it is fully developed, at which point the two organisms separate.

Cell wall present only in

Plants (cellulose) and Fungi (chitin)

Saprophytes

Plants, fungi, and microorganisms that consume dead organic materials for survival. These *decomposers* work with scavengers to contribute to this organic recycling process. They are organisms that survive by *breaking down or consuming dead or decaying organic matter*, such as a fallen tree.

Plasma cells

Plasma cell release *antibodies*, also known as *immunoglobulins* Structurally, BCR and antibodies are *identical*. BCR is bound to B cell membrane, whereas they are called antibodies when they are freely secreted. Antibodies are also known as *immunoglobulins*. ○ Antibodies circulate in the blood and lymph

platelet plug

Platelets contact exposed collagen of damaged vessel and cause neighboring platelets

Protonephridia

Platyhelminthes Bundles of flame cells, which forms a structure that functions similarly to a kidney.

Nerve cords

Platyhelminthes Dense clusters of nerves that run the length of an invertebrates body - platyhelminthes have two.

Triploblastic organisms

Platyhelminthes Have three germ layers (from innermost to outermost): endoderm, mesoderm, and ectoderm.

Flame cells

Platyhelminthes Involved in osmoregulation and they filter harmful substances from the body.

Cephalization

Platyhelminthes Refers to organisms with a head. The head of a cephalic organism contains various sensory structures that connect to the central nervous system (brain).

Bilateral symmetry

Platyhelminthes Splits organisms into right and left halves; therefore, the plane of symmetry is along the organism's midline aka sagittal plane. An organism that is bilaterally symmetrical will have one of each sensory organ and one of each type of appendage on either side of the body. Internal organs are usually not bilaterally symmetrical.

Osmoregulation

Platyhelminthes The process of moving water across a semipermeable membrane due to the solute concentrations on either side of that same membrane. ○ Example: if you have an equal volume of water on either side of a membrane, but different concentrations of some solute (like salt), water will move from the low solute side to the high solute side. Therefore, the solute concentrations become equal on both sides, but the volumes of water has changed.

endocrine system

Plays a critical role as a *communicator* in our body. Our nervous system gives quick and rapid signals to our body, whereas our endocrine system monitors *slower acting responses* that may span over days or even years, such as growing taller and puberty.

Tactile communication

Plays a critical role in social relationships, such as social bonding, infant care, grooming, and mating. ● An example of this bees using the round dance and waggle dance to communicate food proximity.

Postzygotic isolating mechanisms

Prevent hybrids from passing on their genes. ● Hybrid invariability ● Hybrid sterility ● Hybrid breakdown

Prezygotic isolating mechanisms

Prevent the formation of a viable zygote. ● Habitat isolation ● Temporal isolation ● Behavioral isolation ● Mechanical isolation ● Gametic isolation

Reproductive isolation

Prevents gene flow when species are not physically separated by a geographic barrier. These evolutionary mechanisms may appear randomly or may be a result of natural selection.

Heterosporous plants

Produce *two types* of spores, both male and female. *Micro*spores are *male* gametophytes. *Mega*spores are *female* gametophytes. I remember this by thinking about human eggs and sperm. Human eggs are larger (more mega) than human sperm (more micro). Megaspores are plant 'eggs' (female), microspores are plant 'sperm' (male).

bulbourethral glands

Produce a viscous mucus that helps clean and lubricate the urethra.

seminal vesicles

Produce secretions containing *fructose* which provides the sperm with nutrients to produce ATP for motility. The seminal vesicles also secrete a *viscous mucus*, which cleans and lubricates the urethra. They also secrete *prostaglandins* which stimulates contraction of the urethra. Contractions further help the sperm move through the urethra.

Liver Roles

Producing bile is only one of the functions of the liver. Let's go through some of its other important roles: 1. Blood Maintenance 2. Glucose Metabolism 3. Protein Metabolism

Eukaryotic Transcriptional Control

Prokaryotes do not have membrane bound organelles; so, transcription of their DNA into mRNA has to occur in the cytosol. Eukaryotes do have membrane bound organelles. Transcription of eukaryotic DNA into mRNA occurs in the nucleus. ● DAT Pro-Tip: there are three classes of RNA polymerase in eukaryotes. *RNA polymerase II* is the one responsible for transcribing most eukaryotic genes. In eukaryotic cells, RNA polymerases cannot directly detect and bind to the promoter region. They require the binding of transcription factors. *Transcription factors* are regulatory proteins that bind to promoter DNA and affect the recruitment of RNA polymerases. Eukaryotic promoter sequences tend to contain a region known as the *TATA box*. TATA boxes are recognized by transcription factors. Transcription factors can either increase rates of transcription (*upregulation*) or decrease rates of transcription (*down-regulation*). In addition to transcription factors binding at the promoter site, eukaryotic DNA also contain enhancer sites and silencer sites that transcription factors can bind to. These sites can be upstream, downstream or within the gene. *Activator* proteins bind *enhancers*. These elements will increase transcription. *Repressor* proteins bind *silencers*. These elements will decrease transcription. Because enhancers and silencers can be far upstream or downstream from a gene, the DNA is thought to loop around so that the enhancer/silencer can *colocalize* with RNA polymerase. Enhancers and silencers work even if the sequence of nucleotides is excised and flipped or if they are excised and moved to a different location within the nucleotide sequence. This is what makes them different than promoters, which have a very specific location and orientation. In eukaryotes, the terminator sequence for protein coding genes involves a *poly A signal*. This signal tells certain enzymes to cut the transcript away from RNA polymerases, so transcription can be terminated. Additionally, the poly A signal in the mRNA stimulates *polyadenylation* of the transcript, where 50-300 adenine nucleotides are added to the 3' end. These adenine nucleotides are added after termination. ● Polyadenylation is poly = many, adenylation = adenine nucleotides.

Prokaryotic Transcriptional Control

Prokaryotes do not have membranous organelles; so, transcription occurs in the *cytosol*. Prokaryotic promoters are usually simple, allowing RNA polymerase to attach directly to them. For example, bacteria usually have *-10 and -35 elements*. These sequences of these elements are commonly found in many prokaryotic promoters. -10 and -35 represents how many base pairs upstream from the transcription starting site these elements exist. The rear part of RNA polymerase binds to the -35 element, while the leading part of the enzyme binds to the -10 element. This allows RNA polymerase to read the DNA template in the correct orientation.

Auxins

Promote the growth of stems by loosening cellulose fibers, increasing cell wall plasticity and causing *cell growth*. These plant hormones function with cytokinins to promote cell differentiation and division. Auxins are one of the main hormones responsible for plant *tropisms* - growth in a certain direction. The different types of tropisms are listed below. Auxin will concentrate on one side of the stem, and cause increased growth on this side. Stem growth will become asymmetric, and cause the stem to curve. *Phototropism* - the curving of a plant stem towards light. *Gravitropism* - the curving of a plant stem to oppose gravity. *Thigmotropism* - growth in response to contact (for example a vine growing up a wall).

Primase

Provides a 3' hydroxyl group for DNA polymerase to attach new nucleotides to.

Fibrous cartilage

Provides rigidity and resists tension, due to its *many* collagen protein fibers. ● Fibrous cartilage is found in the intervertebral discs and knee meniscus.

Hyaline cartilage

Provides support and cushions joints at the ends of long bones; additionally, it absorbs shock. It has a glassy appearance and its matrix is composed of *chondroitin sulfate*, collagen, and elastin. ● Hyaline cartilage can be found in between the ribs and sternum, in the nose, and the trachea. Therefore, hyaline cartilage is *slightly* flexible, but still has some rigidity.

transcription initiation

RNA polymerase binds to a specific section near the gene to be transcribed. This is called the promoter sequence. *Promoters* help attract RNA polymerases to bind to DNA in the correct location to transcribe a gene. Promoters can be upstream (or less frequently downstream) from a gene.

If the operator and operon are repressed

RNA polymerase cannot bind to the promoter site and the genes will not be transcribed.

transcription bubble

RNA polymerase opens DNA at the -10 element in prokaryotes, forming what is known as a *transcription bubble*. This is because there are many adenines doubly hydrogen bonded to thymines. Recall that the two H-bonds between these purines and pyrimidines are easier to break than triply hydrogen bonded cytosines and guanines.

If the operon is activated

RNA polymerase will bind to the promoter site and the genes under the operon's control are transcribed.

Completion of Meiosis II for oocyte

Recall from the reproductive section that the egg is *arrested* in *metaphase II* during of meiosis. After successful fertilization, the egg will go through the rest of meiosis II and produce a *second polar body* — to be expelled out of the body. This will result in a mature haploid oocyte which can fuse together with the haploid sperm to form a diploid zygote.

Natural speciation

Refers to a speciation event that occurs as a result of naturally-occurring evolution.

fundamental niche

Refers to the full range of environmental conditions where an organism *could survive*, in theory. In reality, competition between species usually restricts an organism to a specific, realized niche.

trophic level

Refers to the organism's position within a food chain or food web.

Digestion

Refers to the process of *breaking down* large food (e.g. fries) into smaller substances (e.g. fries —> glucose + fat) that can be absorbed and used by the body.

Hemocoel

Refers to the spaces inside an organism, where blood can freely flow around internal organs. Note that the hemocoel does not restrict blood into arteries and veins. Also, note that the hemocoel is a separate cavity to the coelom.

Topoisomerase (DNA gyrase)

Relaxes the DNA double helix from the tension the opening helix is creating .

Reflexes

Reliable behavioral responses following an environmental stimulus. Two different types of reflexes exist: simple and complex reflexes.

Stabilizing selection

Represented by a bell curve. It occurs when two extreme of a trait are selected against. The average trait or the most intermediate trait is favored. ● An example of this is height in the human population. The number of people with average height is greater than the number of individuals that are extremely tall or short.

Dolly the sheep

Reproductive cloning of a mammal by nuclear transplantation (somatic cell nuclear transfer) was first accomplished with Dolly the sheep using a mammary cell nucleus. Note that the embryo is identical to the animal that supplies the nucleus - not the (enucleated) egg donor. Cloning from nuclear transplantation can result in defects - potentially due to epigenetic changes in the chromatin that have occurred in the donor nucleus over its life.

Reproductive Isolation Mechanisms Overview

Reproductive isolation Prezygotic isolating mechanisms ● Habitat isolation ● Temporal isolation ● Behavioral isolation ● Mechanical isolation ● Gametic isolation Postzygotic isolating mechanisms ● Hybrid invariability ● Hybrid sterility ● Hybrid breakdown

Book lungs

Respiratory structures found in certain arthropods, like arachnids. They resemble an open book because they have 'sheets' of vascularized tissue on either side. These vascularized sheets are important because they create a big surface area for gas exchange.

Golgi apparatus

Responsible for TRANSPORT of various substances in vesicles (cis face is for incoming vesicles, trans face for secretory vesicles). Has flattened sacs known as CISTERNAE. Modifies the products of the ER, e.g. proteins: glycosylation/phosphorylation/sulfation.

parasympathetic nervous system

Responsible for stimulating the body's "feed and breed" and "rest and digest" responses. o *Preganglionic nerves* originate in the cervical and sacral portions of the spinal cord, and they synapse with *postsynaptic nerves* in ganglia on or near their effectors. Generally, preganglionic and postganglionic nerves release the neurotransmitter acetylcholine. o Effectors induce a decreased heartrate; increased salivary gland secretion, digestion, relaxation, and sexual arousal; and lung bronchi and pupil constriction.

sympathetic nervous system

Responsible for stimulating the body's "fight-or-flight" response.

sympathetic nervous system

Responsible for stimulating the body's "fight-or-flight" response. o *Preganglionic nerves* originate in the thoracic and lumbar portions of the spinal cord, and they synapse with *postsynaptic nerves* in ganglia just outside the spinal cord. The neurotransmitter released in this case is acetylcholine. o Postganglionic nerves then release the neurotransmitters norepinephrine and epinephrine to communicate with their effectors. o Effectors induce a higher blood pressure and heartrate, pupil dilation, relaxation of lung bronchi, as well as increased energy production through conversion of glycogen to glucose. "Housekeeping" tasks such as digestion, urination, and salivary gland secretion are inhibited.

Genetic Variation: Outbreeding

Results from mating with unrelated partners. This leads to mixing of different alleles which leads to new allele combinations.

Hybrid vigor (heterosis)

Results in a superior quality of offspring due to crosses between two different inbred strains of plants. The hybrid superior quality results from the reduction of loci with deletion of recessive homozygous conditions and increase in heterozygous advantage.

Sympatric speciation

Results in the formation of new species without presence of a geographic barrier. ● *Balanced polymorphism* ● *Polyploidy* ● *Hybridization*

Ribosome (Archaea vs Eubacteria)

Ribosomes are the cellular machinery for protein translation. Sometimes students have confusion about prokaryotes and ribosomes. Ribosomes are different from other organelles and are *not* covered by a membrane. Prokaryotes *lack* membrane bound organelles. Prokaryotes *do contain* ribosomes. Both archaea and eubacteria are prokaryotes; they have a *nucleoid* region (area where the genetic material of the prokaryote is located) where the ribosomes are assembled. *Differ*: Both Archaea and Eubacteria have *70S ribosomes*, but this is merely a reference to their size - the ribosome is very different in structure between bacteria and archaea.

rhodopsin

Rods express the protein rhodopsin (also known as visual purple), which is extremely light-sensitive. When it is excited by a photon of light, it leads to hyperpolarization of the photoreceptor cell. This stimulates depolarization of its associated bipolar cell and subsequently an action potential in the associated ganglion cell.

where are amino-acid derived hormones synthesized?

Rough ER and cytosol

Mnemonic: The pathway of sperm movement can be easily remembered by the acronym

SEVEn UP: *S*eminiferous tubules, *E*pididymis, *V*as deferens, (*n*othing), *E*jactulatory duct, *U*rethra, and *P*enis.

DAT Mnemonic: inflammatory response

SLIPR: Swelling Loss of function Increased heat Pain Redness

Steps of Aerobic Cellular Respiration

STEP 1: Glycolysis STEP 2: Pyruvate Decarboxylation STEP 3: Krebs Cycle (or Citric Acid Cycle or Tricarboxylic Acid Cycle) STEP 4: Electron Transport Chain (ETC)

Saliva

Saliva is secreted within the oral cavity by salivary glands. Saliva contains an enzyme, salivary amylase, which will begin chemical digestion of carbohydrates in the mouth. In addition, saliva functions to lubricate the partially digested food and forms it into a bolus (small round mass) so it can be passed down the pharynx and esophagus. =

Scanning Electron Microscopy (SEM)

Sample must first be dehydrated. Scans sample with a beam of electrons → electrons interact with surface atoms → produces a 3D image of a sample's surface. Advantages: High resolution Disadvantages: Costly, Extensive sample preparation (kills sample)

Sebaceous glands

Secrete *oily* and *waxy* products (*sebum*) into the hair follicle, which *lubricates* and *waterproofs* the hair and surrounding skin. They are located throughout the *entire body surface with the exception of the palms of the hands and soles of the feet*. Overactive sebaceous glands can contribute to *acne*.

Parathyroid Hormone (PTH)

Secreted by the *parathyroid gland*. PTH increases calcium when it is low in the blood by stimulating *osteoclasts* and depressing *osteoblasts*.

Calcitonin

Secreted by the *thyroid gland*. It opposes *PTH* because it acts to "tone down" calcium in the blood when it is too high. It does this by decreasing *osteoclast* activity; therefore, *osteoblasts* have less competition and can build more bone.

*Exo*crine

Secreting hormones into *ducts*. *Note: The pancreas carries out both endo- and exo-crine functions.

*Endo*crine

Secreting hormones into the *bloodstream*.

*Para*crine

Secreting hormones to *neighboring* cells (you can think of para as besides, hence neighboring). a. An example of paracrine signalling is when you cut yourself and blood clotting factors call out to neighboring platelets

Apocrine glands

Secretions are more oily and viscous than that of eccrine glands. And unlike eccrine glands, apocrine glands secrete their products into the *hair follicle* and are present in *specific locations* (armpit, nipple, ear canal, eyelid, nostril, and parts of the pubic area). Their function depends on their location and cell specialization. ■ *Ceruminous* glands are specialized apocrine glands. They produce *earwax (cerumen)*, which is secreted into the *external auditory canal*. ■ *Mammary* glands are also specialized apocrine glands. However, they are located on the *nipple areola*, and they produce *milk*.

Angiosperms

Seed-bearing tracheophytes that are also *flower*-bearing, and can produce fruit. Their seeds are protected, located in the fruit (considered the ovary of the plant). These are the most abundant type of plant living today. Angiosperms do not have flagellated sperm- all their sperm is wind or animal dispersed (often as pollen). Pollen is another example of evolutionary advancement- it is a highly efficient way of achieving fertilization. Many angiosperms package their sperm in these small, easily-movable pollen grains, which can easily be picked off one flower and deposited on another flower (fertilization) by the wind or by an animal (like a bee). They have more opportunities and ways to fertilize and get fertilized. Most angiosperms (and some gymnosperms) can exhibit *double fertilization*. Double fertilization is when a female gamete is fertilized by two male gametes or sperm. This will be further explained in the next section on Flower Structures. One of the notable characteristics of angiosperms is that they exhibit double fertilization. When the generative cell in the pollen travels down the pollen tube to the ovule, it divides to form two sperm cells. One sperm cell fertilizes the ovule to form the seed (embryo). The other combines with the polar nuclei of the ovule to form the endosperm (which we learned acts as the food/nutrient store for the embryo - see the section on The Seed for more details). In angiosperms, the ovary will turn into a fruit. Angiosperms don't produce fruit to provide us with yummy food- it is actually to help them reproduce. The fruit attracts and is eaten by an animal. The seeds in the fruit pass through the animal's digestive system, and are 'deposited' in a new location. This spreads the genes of the angiosperm to new locations (called *gene migration*).

There are three main types of neurons

Sensory (afferent) neurons Motor (efferent) neurons Association (interneuron) neurons

DNA helicase

Separates complementary strands at the replication fork.

Sesamoid bones

Sesamoid bones are embedded within *tendons* to increase the muscle's leverage on the bone it is attaching to; therefore, increasing the muscle's power. In this way, sesamoid bones act the same way a pulley does on one of the cable machines at your gym. ○ The most common example is the patella (kneecap).

plasmogamy

Sexual reproduction begins when two hyphae of a mycelium fuse their cytoplasm in a process known as plasmogamy.

Synapomorphies

Shared traits derived from an evolutionary ancestor common to all members of a group.

pituitary gland

Situated a level below the hypothalamus. In power terms, if the hypothalamus is the President, then the pituitary gland serves as the Vice President, controlling other part of government (other glands and organs) but must follow the President's direction. Technically, the pituitary gland is also known as the *hypophysis*. The pituitary gland has two separate lobes, the *posterior pituitary* and the *anterior pituitary*. We will look at both lobes separately since they each have their unique connection with the hypothalamus.

Chitinous exoskeletons

Skeletal system found outside the body (think exo = exit = outside). They are made of a polysaccharide (complex carbohydrate) called chitin, and are usually found covering insects.

Lacunae

Small spaces between lamellae that house bone cells. Lacunae connect to each other, as well as the central haversian canal, via a series of smaller canals called *canaliculi*. ● Note: canaliculi connect lacunae and haversian canals of a *single* osteon. *Volkmann's canals* connect *adjacent* haversian systems to the periosteum.

2. Cell surface receptors, which act as or activates another ligand-gated ion channels

So the first method we've now discussed in cell surface binding peptide hormones is activating second messengers. After the peptide hormones binds to a cell surface receptor, besides activating second messengers, the hormone can also bind to *cell surface receptors.* ○ A ligand-gated ion channel changes its shape once a ligand (substrate) binds. ○ It then allows certain *ions* to pass through the cell, which act as the postman that helps you deliver the message. ○ Remember: in this case, *no secondary messengers are involved*!

Intermediate protein

Soluble, fiber shaped, perform many functions. ex) fibrinogen

chance genetic mutations / variations,

Some organisms may develop unique phenotypic characteristics. If this characteristic allows for pursuit of different types of resources (as compared to similar species), then *niche overlap is minimized*, and potential competition is avoided. Because of this decreased competition, the unique individuals experience *greater reproductive success*, which results in higher prevalence of organisms with the advantageous, unique characteristic. This phenomenon is referred to as *character displacement*. An example of this demonstrated by the Galapagos finches' beak variations, which allow these birds to eat different types of seeds.

fever

Sometimes, *fever* can result from an *inflammatory response*. Fever is turned on and off by the brain. It is not a local response anymore — it becomes *systemic* (body-wide). When our body's temperature increases, it helps to *hinder* the growth of pathogens, and may sometimes *kill* the temperature-sensitive ones as well.

Mitochondrial Matrix

Space within the inner membrane Krebs cycle and Pyruvate Decarboxylation

Gause's law (competitive exclusion principle)

States that two species are not able to occupy the same niche while also maintaining their population levels. In the long run, the species that is more adapted to the niche will outcompete and dominate the other species.

Gause's law (competitive exclusion principle)

States that two species are not able to occupy the same niche while also maintaining their population levels. In the long run, the species that is more adapted to the niche will outcompete and dominate the other species. However, *resource partitioning* allows two species, that seem to compete for resources, to coexist. Resource partitioning occurs when these species use different means to obtain the same resource, or they seek out slightly different resources. Hence, these species occupy niches that are subtly different, and thus they are both able to survive in the long-run.

Steroid Hormones

Steroids are the 4-ring structures that belong in the same family as lipids. Ultimately, steroid hormones skip the requirements of a secondary messenger, and go directly into the nucleus to affect transcription and translation activities. Comparatively, *steroid* hormones have a *slower action time* than *peptide* hormones, because it triggers changes from a transcriptional level (changes gene expression) instead of directly affecting/releasing proteins that are already made in cells. This is why our body designed insulin to be a peptide hormone, whereas steroid hormones like estrogen and testosterone and can afford to work slowly - if your body consumes food, it needs insulin fast, but puberty... that definitely seemed to take its awkward time.

adrenal cortex

Stimulated by secretion of *ACTH* from the anterior pituitary. It secretes only *steroid* hormones. *Tip to remember: adrenal cortex produces *cortico*steroids: ● Corticosteroids, which includes: ○ *Glucocorticoids* (i.e. cortisol) ○ *Mineralocorticoids* (i.e. aldosterone) ● A small amount of *androgenic* steroid hormones (male sex hormones) ○ In males, the primary site of androgen production is the *testes* - the small amount produced by the adrenal cortex is not significant compared to that produced by the testes ○ Whereas in females, the production of androgen by the adrenal cortex may become significant in some cases.

Follicle Stimulating Hormone (FSH) in Females

Stimulates follicles in the ovary to develop. This in turn stimulates production of female sex hormones (progesterone and estrogen).

Follicle Stimulating Hormone (FSH) in males

Stimulates sperm to develop in the *seminiferous tubules*. Mnemonic: we know follicle stimulating hormone is abbreviated as FSH. The acronym *FSH* looks like the word *FiSH* and sperm look like swimming fish. So FSH helps development of sperm.

Luteinizing Hormone (LH) in males

Stimulates the *Leydig cells* of the testes produce *testosterone*. Leydig cells are interstitial cells next to the seminiferous tubules. Luteinizing hormone is abbreviated as *LH*. We can think about luteinizing hormone (LH) making men look *Large and Hairy* (L and H, just like LH) - testosterone makes men Large and Hairy, and luteinizing hormone (LH) stimulates testosterone production.

FRONTAL

Superior and anterior portion of the brain Involved in conscious thoughts, and it contains the *prefrontal cortex* for planning and decision-making, the *motor cortex* for voluntary muscle movement, and *Broca's area* for speech-formation.

the most important myofilaments are

THIN actin filaments and THICK myosin filaments.

Confocal Laser Scanning and Fluorescence

Tag certain structures with fluorescent marker, then use laser light to scan specimen. 2D image is displayed digitally. Advantages: Living samples ‐ can look at thin slices (keeping sample intact). Can look at specific parts of cell (e.g. view chromosomes during mitosis). Disadvantages: Fluorescence can cause artifacts

pituitary gland

Technically, the pituitary gland is also known as the hypophysis. The pituitary gland has two separate lobes, the posterior pituitary and the anterior pituitary.

the sarcomere

The *Z line* represents the periphery (ends) of each sarcomere. The sarcomere is defined as one Z line to the next Z line. The *M line* represents the midpoint of each sarcomere. Thin actin filaments branch from Z lines toward the center (M line). Thick myosin filaments branch from the M line, extending toward the Z lines. The sarcomere is further subdivided into bands and zones based on areas of overlap between the thick and thin myofilaments. The areas where only actin is present are called *I bands*, and these include the Z line itself. The areas where myosin and actin overlap are called *A bands*. Finally, the area where only myosin is present is called the *H zone*. *Mnemonic* to remember H zone, I band, and A band components of the sarcomere ○ H is a thick letter, so the *H zone* is the part of the sarcomere where we only have *thick* filaments (myosin). ○ I is a thin letter, the *I band* is the part of the sarcomere where we only have *thin* filaments (actin). ○ The *A band* is the entire length of the thick filament, including where the thick filament overlaps the thin filament. DAT Pro-Tip: Because the A band includes where the overlap of thick and thin filaments occur, the A band is the only zone/band that *doesn't shorten* during muscle contraction.

cardiac cycle

The *cardiac cycle* is regulated, in terms of rate, by the autorhythmic cells of the autonomic nervous system, but contractions are initiated independently of the autonomic nervous system. The heart contracts independently.

Cerebrum

The *cerebrum*, the largest part of the forebrain, consists of right and left hemispheres, which are connected by a thick bundle of nerves known as the *corpus callosum*. Components include the cerebral cortex and the underlying subcortical structures (olfactory bulb, hippocampus, and basal ganglia). ❖ The *cerebral cortex* processes sensory stimuli, and it is integral to perception, memory, voluntary movement, and learning. It is divided into the frontal, parietal, temporal, and occipital lobes.

Chemical digestion

The *chemical* breakdown of the mechanically digested particles into even smaller particles. This is usually accomplished with the help of key *enzymes* that we will explore coming up.

vascular tunic

The *choroid* contains the vasculature that supplies nutrients and oxygen to the retina. The *iris* is the pigmented (colored) component of the eye. It is thin and circular, and it controls the size of the pupil. Therefore, the iris controls how much light enters the eye. ● The *pupil* is a hole in the iris, and it allows light to enter the eye. The *ciliary body* contains the *ciliary muscle*, which controls the shape of the lens. It also contains the *ciliary epithelium*, which produces aqueous humor. ● The *lens* is a transparent, biconvex structure located behind the iris. Along with the cornea, it refracts light to focus it onto the retina. ● *Aqueous humor* is a watery fluid that fills the chamber between the lens and cornea (the anterior chamber). It functions to maintain the proper intraocular pressure, and it nourishes the avascular ocular tissues, such as the lens and posterior cornea.

Epidermis

The *epidermis* is the most *superficial* layer of the skin. The prefix epi- means above; hence, epidermis means "above the dermis". It is *thin* and *avascular*, meaning it does not contain blood vessels. Thus, it relies on diffusion of oxygen and nutrients from the neighboring dermis. The epidermis is composed of stratified squamous cells, which are flattened, disk-shaped cells arranged into multiple layers. There are four to five layers of cells in the epidermis, which are mostly *keratinocytes*. As the keratinocytes divide and differentiate, they migrate from the deeper to more superficial layers. Along the way they expel their nuclei and produce additional keratin. By the time they reach the most superficial layer, they are fully differentiated keratinocytes. Eventually, these keratinocytes are shed during epidermal turnover. The epidermis also contains additional, less abundant, cell types, such as melanocytes, Langerhans cells, and Merkel cells.

Sight

The *eye* is the organ devoted to the visual system. It allows organisms to receive and transduce visual stimuli. The eye consists of three main layers: The outermost layer is the fibrous tunic, the middle layer is the vascular tunic, and the innermost layer is the nervous tunic.

pistil

The *female* plant sex organ. It is composed of a *stigma* (top), *style* (tube down to the ovary), and *ovary* which contains the *ovule*. Ovules contain the plant's female gamete (egg). When they are fertilized by pollen, they develop into the seeds. Now let's talk about that process of fertilization.

Secondary growth

The *horizontal* growth of a plant at its *lateral* meristems, which include the *vascular cambium* and the *cork cambium*. Cambium is another word for lateral meristematic tissue. All plants undergo primary growth but *only woody plants* undergo secondary growth. Herbaceous (non-woody) plants do not exhibit significant secondary growth.

Limbic System

The *limbic system* is a collection of structures located beside the thalamus and just inferior to the cerebrum. It is associated with memory, emotions, and motivation. ❖ The *hippocampus* is essential to long-term memory consolidation and spatial navigation. It is located in the medial temporal lobe, beneath the cerebral cortex. ❖ The *amygdala* are two masses of nuclei associated with emotional memories. It is located deep within the brain, medial to the temporal lobes.

stamen

The *male* plant sex organ. It is composed of an *anther*, and a *filament* that supports the anther.

Olfaction (Smell)

The *olfactory receptor neurons* are located at the top of the nasal passage. There are about 10,000 different types of receptors which are capable of recognizing an equal number of olfactory stimuli, which enter the nasal cavity during breathing. Olfactory receptor neuron axons converge in the brain at the *olfactory bulb*, which continues within the brain as the *olfactory nerve* (a cranial nerve).

Chorion

The *outer layer* that surrounds the embryo.

Mechanical digestion

The *physical* breakdown of food. Examples of mechanical digestion include chewing food with the teeth in the mouth (teeth are important, future dentist!), and churning or mixing of food in the stomach.

Acrosomal reaction:

The *recognition* process between the sperm and the egg before they fuse together. Think of it as a process of mutual acknowledgement to ensure *same-species fertilization*.

nervous tunic

The *retina* is the innermost layer. It is light-sensitive and utilizes specialized photoreceptor cells, the rods and cones. ● *Cones* provide organisms with color-vision and are functional during times when there is high-intensity light. There are three different types of cone cells, each of which responds best to light within a certain range of wavelengths. ● The *fovea (macula)* is a small area of the retina located directly behind the pupil. It is more densely-packed with cones than any other portion of the retina, which allows for high visual acuity. ● *Rods* are responsible for black-and-white vision. They function in dimly-lit situations and are integral to effective night-vision. o Rods express the protein *rhodopsin* (also known as visual purple), which is extremely light-sensitive. When it is excited by a photon of light, it leads to hyperpolarization of the photoreceptor cell. This stimulates depolarization of its associated bipolar cell and subsequently an action potential in the associated ganglion cell. The axons of the ganglion cells form the optic nerve.

T-tubules

The *sarcolemma* has invaginations into the muscle cell that form tubes - these are the *T-tubules*. The T-tubules allow the action potential initiated on the muscle fiber to spread throughout the cell very quickly, ensuring a coordinated contraction.

voltage gated calcium channels

The *sarcoplasmic reticulum* is a specialized endoplasmic reticulum found in muscle fibers that stores *calcium* ions. A depolarization traveling the *T-tubules* triggers *voltage gated calcium channels* on the sarcoplasmic reticulum to open. This results in calcium being released from the sarcoplasmic reticulum and rushing into the *sarcoplasma*.

secondary phloem

The *secondary phloem* contributes to the *bark*. The bark is the collective term for the outermost layer of the plant that includes the phloem, cork cambium, and cork. Unlike secondary xylem which grows and adds onto older xylem, secondary phloem replaces older phloem. Old bark is constantly shed and replaced by newly formed bark.

secondary xylem

The *secondary xylem* along with the pith form the *wood*. The vascular cambium continuously divides to produce new, additional secondary xylem year after year. This constant production of secondary xylem is what forms the *growth rings* that you see in the cross section of a tree. Older rings are located closer to the center and newer rings are located closer to the outside.

Phloem and xylem are arranged to form

The *stele*, the central part of the root or stem. The stele is composed of xylem, phloem and supporting ground tissue (pith).

Sperm Tail Characteristics

The *tail* of the sperm is a long flagellum that moves around in a whip-like, beating motion that *propels* the sperm forward and gives it mobility. The tail (like all flagella of eukaryotes) is made of microtubules (which are made of tubulin, the building block of microtubules).

habitat

The *type of place* an organism lives in. It includes all *other* organisms present as well as the *physical and chemical aspects* of the environment. For example, the habitat of the bacteria of H. pylori is the digestive system of a human; the habitat of a pet lizard is its tank.

Primary growth

The *vertical* growth of a plant at its *apical* meristems (as explained in the previous section on Growth and Development).

binary fission (non-animal reproduction)

The DNA of a unicellular organism is replicated. These two identical DNA molecules migrate to opposite sides of the cell. A *septum* appears in the middle and forms a dividing wall to separate the two DNA. The septum then splits into two to create two separate cells, each with one copy of DNA. Binary fission occurs in *prokaryotes* and some organelles within eukaryotes (mitochondria and chloroplasts).

Mendel's Three Laws of Inheritance

The Law of Segregation The Law of Independent Assortment The Law of Dominance

RNA World Hypothesis

The RNA world hypothesis suggests that self-replicating RNA molecules were the precursor to current life (which now consists of DNA, RNA, and proteins). ❖ This hypothesis is supported by two main facts: RNA can store genetic information, like DNA. RNA can catalyze chemical reactions, similar to enzymes.

Alternation of Generations

The ability for an organism to regularly exist in and alternate between *both haploid and diploid* forms. *Fungi* exhibit this property. Fungi can spend part of their life as a multicellular haploid organism and part of their life as a multicellular diploid organism. Pro tip: This is a commonly tested topic on the DAT, so it is worth taking the time to memorize this diagram. This diagram may seem daunting but you really need to memorize two parts of it. The rest is common sense if you have a strong background on cell division. Let's start off with the *fusion of two gametes* (at the very right of the diagram). From mammalian reproduction, you might know that the fusion of two gametes (specifically a sperm and an egg, both of which are haploid) produces a *zygote* (which is diploid). It makes sense that the fusion of two gametes (one from each parent) results in the generation entering the diploid state. Now comes the first of the two things you need to memorize: a *zygote* becomes a *sporophyte* via mitosis. It makes sense that this happens through mitosis (and not meiosis) because we know in mitosis, the daughter cells retain the same number of chromosomes as the parent cells. In this case, the zygote (parent cell) is 2n and the sporophyte (collective daughter cells) is also 2n. A *sporophyte produces spores*. This happens via meiosis. It makes sense that the meiosis (the process that halves the number of chromosomes) of a sporophyte results in the generation entering the haploid state. Note: *sporangia* are the structures in which spores are formed. They are located on the ends of sporophytes. Think of sporangia as the specific structures that are part of the bigger sporophyte. Now comes the second of the two things you need to memorize: a *spore* becomes a *gametophyte* via mitosis. Again it makes sense that this happens through mitosis (and not meiosis) because we know in mitosis, the daughter cells retain the same number of chromosomes as the parent cells. In this case, the spore (parent cell) is n and the gametophyte (collective daughter cells) is also n. A *gametophyte produces gametes*. And we're back to the beginning. We're alternating states as we go from one generation to the next.

acid reflux

The acidic food mixture from the stomach *backflows* through the *cardiac sphincter* to the *esophagus*, which is not protected by mucous cells. This creates the burning sensation in the chest area (heartburn). Even though stomach acid can cause troubles at times, it is thanks to the acid that we are able to *kill bacteria* from food, *denature proteins* (recall extreme pH can denature proteins!), and create a *favorable environment for pepsin to function*.

Amnion

The amnion is the *inner layer* that is *closest* to the growing *embryo*. It forms a membrane around the embryo and secretes the *amniotic fluid* which gives a *water cushion* and *protect* the embryo from damage. Normally, the level of amniotic fluid can reach 0.8-1L at its peak — a floating baby! Mnemonic: When you hear of a pregnant woman having her 'water break' indicating that she's going into labor - this is in fact her amniotic membrane rupturing and the amniotic fluid being released.

Amnion

The amnion is the inner layer that is closest to the growing embryo. It forms a membrane around the embryo and secretes the amniotic fluid which gives a water cushion and protect the embryo from damage.

codon

The bases within a mRNA transcript are arranged in groups of three and each group is called a *codon*. For each position in a codon (position 1, 2, 3), one of the four different base options can be used. ● 4 options * 4 options * 4 options = 64 different combinations (codons) possible. ○ 61 combinations code for amino-acids ○ 3 combinations represent stop codons, which terminate translation. During translation, the ribosome will be clamped around three codons of the mRNA transcript. Ribosomes line-up codons with their anticodons; moreover, they catalyze the peptide bonds made between individual amino-acids, leading to the extension of the polypeptide protein chain.

Twitch Contractions

The brief contraction a muscle fiber experiences as the result of a *single* action potential stimulating an entire motor unit. For a given muscle fiber, a twitch will always be the same size and duration, as long as it was *depolarized* above a threshold voltage. This is known as the *all-or-none principle* of muscle contraction. Either the depolarization is above threshold in which all fibers twitch, or it is below threshold and none twitch. Each twitch has *three phases*: 1. *Latent phase* 2. *Contraction* 3. *Relaxation*

DNA polymerases

The class of enzymes that extends DNA in the 5' 3' direction. Several have proofreading capabilities that allow them to catch synthesis errors.

What would the coding strand look like if there is to be a stop codon in the mRNA?

The coding strand would be TAA, TAG, or TGA. The coding strand has the same sequence as the mRNA, with T in DNA replacing U in RNA.

What would the coding strand look like if there is to be a stop codon in the mRNA?

The coding strand would be TAA, TAG, or TGA. The coding strand has the same sequence as the mRNA, with T in DNA replacing U in RNA. It's important codons have three bases within them. If only two bases were in a codon, there would only be 4 x 4 = 16 combinations and there wouldn't be a unique code to represent each of the 20 amino acids.

Yeast

The common example of *nonfilamentous fungi*. They are unicellular eukaryotes that reproduces *asexually* by budding. Yeast are *facultatively anaerobic*, which means they can grow by aerobic respiration when oxygen is present; or, fermentation when oxygen is absent.

Growth at the Root Tips

The continual division of the apical meristem cells forms a *zone of division*. This, of course, is right above the apical meristem. These cells then absorb water and elongate, forming a *zone of elongation*. These cells eventually differentiate into specific plant tissues, becoming part of the *zone of maturation*. Keep in mind that the apical meristem is constantly dividing and producing more cells that join the zone of division. Therefore cells that were once in the zone of division will become part of the zone of elongation, and cells that were once in the zone of elongation will become part of the zone of maturation.

Egg Structure

The egg has several layers for the sperm to penetrate — it takes a lot of work for a sperm to be accepted! The outermost layer of the egg of a mammal is called the *corona radiata*. It is a *jelly coat* made up of follicular cells, which *nourished* the egg when it was a developing follicle inside the ovary. Within the corona radiata, there is a layer of *glycoproteins* called the *vitelline layer* that surrounds the plasma membrane of the egg. In *mammals*, this layer is called the *zona pellucida*. The zona pellucida is a VERY important structure for the acrosomal reaction, and it also appears on the DAT frequently, so make sure you remember it. Underneath the zona pellucida is the egg's *plasma membrane*.

Nephron Filtration

The excretory process begins when blood flows from the body and into the renal artery, which branches off into the *afferent arteriole*. The afferent arteriole then leads into the *glomerulus*, a ball/collection of blood vessels located in the renal cortex of the kidney. The glomerulus is strategically located adjacent to the *Bowman's capsule* of the nephron. Together, the glomerulus and Bowman's capsule are known as the *renal corpuscle*. This close proximity allows water and solutes (such as sugars and vitamins) from the blood and into the Bowman's capsule. These substances that filter from the blood and into the Bowman's capsule are collectively known as the *filtrate*. Larger substances like proteins and the blood cells themselves do not pass into the Bowman's capsule- they remain in the glomerulus. This process is called *filtration*. This is why it is said that the glomerulus *acts as a sieve*- it allows small substances (water and solutes) to pass into the Bowman's capsule while it keeps larger substances (proteins and blood cells) in the blood. Bowman's capsule has *podocytes* (long, foot-like processes) that wrap around the glomerulus in a way that they form *fenestrations* (means 'window' or 'opening'), or slits. These fenestrations are large enough for certain substances to pass through but small enough to prevent others. The glomerulus exits the Bowman's capsule via the *efferent arteriole*. The efferent arteriole goes on to form another set of capillaries called the peritubular capillaries. These *peritubular capillaries* surround the different tubules of the nephron and exchange water, salts, and other important molecules with them. This modifies the content of the filtrate through processes of reabsorption and secretion. Mnemonic: *A* comes before *E* in the alphabet, so the *A*fferent arteriole comes before the *E*fferent arteriole in the kidney (afferent enters and efferent leaves).

food web

The expanded version of a *food chain*; it depicts the interconnections between food chains within a community. Thus, it is a complete description of what eats what.

Incomplete Dominance

The expression of alleles is blended, producing a unique heterozygous phenotype. ex) Flower petals: R red x R' white = RR' comes out pink

Extraembryonic Development

The extraembryonic structures provide crucial *protection* and *nourishment* to the growing fetus. The extraembryonic structures are derived from the *trophoblast layer* of the blastocyst. Flashback: The cells of the blastula will divide and differentiate to form two structures: 1. Trophoblast ○ This is the outer ring of single-layer cells 2. Inner cell mass (ICM) ○ This is the inner bulk of cells surrounded by the trophoblast

Fast block

The fast block *happens first*. It occurs immediately after the sperm's membrane has fused with the egg's membrane. When the sperm penetrates into the egg, *sodium ions* diffuse into the egg and cause the egg membrane to *depolarize* (become *positively* charged). Depolarization *repels* additional sperms from binding for a few seconds. This is called the fast block because it happens right after fusion of sperm and egg, and because it lasts for only a short period of time.

Cotyledons

The first leaves to appear on a seedling. They contain nutrients from the seed to feed to the growing seedling.

pioneer species

The first species that inhabits a barren area and begins the process of ecological succession.

Divergent evolution

The formation of a two or more species that descend from a common ancestor and become increasingly different over time (results of speciation).

lamellae

The layers of an osteon

Liver Protein Metabolism

The liver plays a key role in protein metabolism and detoxification. This is why patients who suffer from liver problems (e.g. liver cirrhosis) cannot eat a protein-rich diet, otherwise conditions such as ammonia poisoning may arise. Here is how the liver metabolizes proteins: ● Synthesizing *plasma proteins* from absorbed amino acids ○*Albumin* is a major plasma protein that is made almost exclusively by the liver. ○ *Blood clotting factors* are also produced by the liver ● Synthesizing *non-essential amino acids* ○ It's important to note that non-essential amino acids *does not* mean that we don't need them. They are called non-essential because our *body can make them*, hence they are not essential from the diet. ● Converts dangerous *ammonia* to a safer *urea* for excretion ○ Protein metabolism tends to lead to a build-up of ammonia in the body. ○ A healthy liver will convert ammonia to urea (much less toxic) to be excreted from the kidneys.

Migration

The long distance and seasonal movements of animals from one region to another. The movement usually occurs in response to the availability of food and/or degradation of environmental conditions. This is observed in whales, birds, elks, insect, and bats migrating to warmer climates. Evidence suggests this is due to a genetic basis.

diaphysis

The long, hollow, shaft between the bumpy epiphyses. The outside is covered in a membrane called the *periosteum* (we will discuss this in a bit), which wraps itself around the cortical bone below. Note: the diaphysis isn't actually hollow. The "hollow" part is called the *medullary cavity*, which contains *yellow bone marrow*. ■ Yellow bone marrow is essentially just energy stored as fat. ■ The medullary cavity is lined by another membrane, called the *endosteum.*

Negative feedback loop

The loop *inhibits itself* and prevents overproduction of certain hormones. Example: During the menstrual cycle, *FSH and LH* cause an increase in progesterone and estrogen. The combination of increasing *progesterone and estrogen* tell the hypothalamus to stop producing GnRH, hence cutting off the secretion of LH and FSH from the anterior pituitary. Eventually, this causes the levels of FSH and LH to drop. *negative feedback* generally promotes *stability.*

pleurae

The lungs have a membranous cover

peripheral lymphoid tissues [TALAPS]

The lymph nodes, spleen, adenoids, appendix, Peyer's patches (in small intestine) and tonsils are peripheral lymphoid tissues [TALAPS]. These structures house immune system cells but cannot replenish them.

Eccrine glands

The main *sweat glands* of the body. While they are located throughout the *entire body surface*, they are the most abundant in the axilla (armpit), on the palms of the hands, and the soles of the feet. Eccrine glands are important for *thermoregulation* (regulation of body temperature).

testes

The male reproductive gland and are the site of *spermatogenesis* (the production of sperm). Specifically, spermatogenesis occurs in the *seminiferous tubules* located in the testes. The seminiferous tubules contain both 'nurse-like' *Sertoli cells* and spermatogenic cells that give rise to *spermatozoa*.

carrying capacity

The maximum population size (number of organisms of a given species) that an ecosystem can sustain.

Cladistics

The method of classification according to the proportion of measurable characteristics held in common between two organisms. The more characteristic they share, the more recently diverged from a common ancestor.

Territorial behavior

The methods that animals use to define a territory as their own and signal to other animals that they cannot trespass. It ensures adequate food/place to mate and rear young.

Sperm Midpiece Characteristics

The midpiece connects the head and the tail. Its most important characteristic is that it contains a lot of *mitochondria*. As you may recall, mitochondria are organelles that *produce ATP*. The sperm has to expend a lot of energy trying to move through the female reproductive system to reach and fertilize the egg. The mitochondria at the midpiece provide this necessary energy.

Active transport

The movement of molecules against their concentration gradients requiring energy. Usually solutes like small ions, amino acids, monosaccharides are transported.

neurulation

The nervous system development begin with *neurulation*, which includes the following steps: 1. The *notochord stimulates* the top portion of the *ectoderm* to thicken —> forms the *neural plate*. 2. The *neural plate* begins to fold onto itself —> forms the *neural fold/neural groove* ○ Note: it is named as the neural fold because of the creases created from the folding process. 3. The *neural fold* continues to fold until its edges touch —> forms a *complete hollow tube* called the *neural tube*. 4. *Neural tube* will differentiate into the *central nervous system* (brain+spinal cord) It is very important to remember here that the notochord does *NOT* develop into the neural tube, it simply *induces* the formation of neural tube from ectodermal cells. As the neural fold is folding into the neural tube, some cells from the *ectoderm roll off* and become the *neural crest cells*. These cells migrate to different locations of the body and go on to form *teeth, bones, skin pigmentation* etc... It is important to remember that *neural crest cells* are derived from the *ectoderm*.

Ecological succession

The process through which an ecological community develops and changes over time. This process is often predictable, and it either occurs in a new habitat or after a disturbance (such as a forest fire or mass extinction). The types of species present in the community change throughout this process, and it can occur over decades to millions of years. Ecological succession comes in two different varieties: primary succession and secondary succession.

Tetanus

The process where the muscle fibers of a motor unit are being *maximally stimulated* by a motor neuron and tension can *no longer increase*. This usually happens when we are sending action potentials down a motor neuron with such a *high frequency* that we don't experience any *relaxation*. In tetany, *twitches* blend together because the voltage gated calcium channels on the *sarcoplasmic reticulum* are constantly open, allowing for the maximal number of myosin binding sites to be available for *cross-bridge* formation. Simultaneously, *myosin ATPases* and the active calcium pumps of the *sarcoplasmic reticulum* are using a ton of ATP. Eventually, the prolonged tension and significant energy demands associated with *tetany* will cause *fatigue* and the contraction will cease completely

Changes in Allele Frequencies: Genetic drift

The random increase or decrease of allele by chance. The smaller the population, the larger the effect. ● *Founder effect* occurs when a small group of individuals become isolated from a larger population. This results in an allele frequency that is not the same as that of their population of origin. ● *Bottleneck* occurs when population undergoes a sharp reduction in size due to natural catastrophe etc. This is vulnerable to genetic drift.

Adaptive radiation

The rapid evolution of many species form a single ancestor. It occurs when the ancestral species is introduced to an area after a change in the environment makes new resources available for colonization. A common ancestor spawns many different species.

Dermis

The second layer of the integumentary system, the dermis, is located just deep to the epidermis. It is a network of dense irregular connective tissue that functions to cushion the body from injury and provide a home for functional structures of the skin, such as vessels, glands, nails, hair.

Seed Dormancy

The seed remains in a state of *dormancy* until environmental conditions (such as water, temperature, and light) are suitable for growth. When these conditions are met, the seed *breaks dormancy*.

seminiferous tubules

The seminiferous tubules do not fully mature the sperm (the sperm are not fully motile and cannot fertilize eggs at this point in their development). Therefore, they are transported by peristalsis (contraction of smooth muscle) to the epididymis for maturation.

epimysium

The sheath covering the muscle

The Nephron

The single, functional unit of a kidney. Kidneys are made up of thousands and thousands of individual nephrons.

anther

The site of *microspore formation*. In the anther, meiosis of precursor cells generates microspores. The microspore then undergoes mitosis to form two cells - a *generative cell* (which contains the male gamete, or sperm) and a *tube cell* (which eventually develop into the pollen tube- explained later on in this section). These two cells combined are the *pollen*.

Slow block

The slow block is the longer-lasting solution to prevent polyspermy. It happens gradually after the sperm has fused with the egg. In addition to depolarization of the membrane, the fast block also triggers a release of calcium ions inside the egg's plasma membrane. The calcium ions will stimulate the egg to undergo the cortical reaction, the exocytosis (release) of cortical granules. The cortical granules play the key role in the slow block. They serve two functions: ● Changes the zona pellucida (vitelline layer) into an *impenetrable fertilization envelope*. ● Stimulate *proteases* (protein-cutting enzymes) to *sever the link* between the zona pellucida (vitelline layer) and the plasma membrane. ○ This prevents other sperm from reaching the egg's plasma membrane The slow block is much more effective than the fast block. However, due to its slow onset, the fast block is also crucial to prevent polyspermy before the slow block takes action. These two blocks work in conjunction to ensure a faithful marriage between a sperm and an egg, which in turn secure a viable embryo.

Large Intestine Structure

The small intestine connects into a pouch called the *cecum* — an important structure for water and mineral absorption. The cecum has a small finger-like projection called the *appendix*, which has negligible immune functions in human adults. The appendix likely used to have a function, though that is no longer the case. For most people, it is a silent *vestigial structure* (borrowing terms from our evolution chapter). But when it gets inflamed (*appendicitis*), it becomes a painful problem, and is removed surgically. After the cecum, digested food passes through the *colon* where water absorption is completed. This gradually hardens the feces until it is stored in the *rectum* and eventually expelled through the *anus*.

neuromuscular junction

The space between the *presynaptic* motor neuron and *postsynaptic* muscle fiber. When a motor neuron sends an action potential, it releases the neurotransmitter *acetylcholine* into the neuromuscular junction. Acetylcholine facilitates the opening of ligand gated sodium channels on the muscle fiber. This allows some sodium to enter the muscle fiber; therefore, creating a graded potential. This small depolarization opens nearby voltage gated sodium channels. When the voltage gated sodium channels open, we have successfully transferred an action potential from a neuron to a muscle!

Chloroplast Intermembrane space

The space between the outer and inner membranes.

neuromuscular junction

The space between the presynaptic motor neuron and postsynaptic muscle fiber. When a motor neuron sends an action potential, it releases the neurotransmitter acetylcholine into the neuromuscular junction.

Muscle Fiber Types

The speed at which a twitch contraction occurs is related to the *type* of muscle fiber, of which there are *three*: 1. *Slow oxidative fibers (type 1 fibers)* 2. *Fast oxidative-glycolytic fibers (type II-a fibers)* 3. *Fast glycolytic fibers (type II-b fibers)* DAT Pro-Tip: muscle fiber types vary in speed of contraction due to the type of ATPase on their myosin heads, which allows for the hydrolysis of ATP into ADP + Pi and ultimate cross-bridge cycling. *Type I* fibers have the slowest acting myosin ATPase, while *type IIb* fibers have the quickest acting myosin ATPase.

Sperm Structure

The sperm is composed of three major parts: the *head*, the *midpiece*, and the *tail*.

Germination

The sprouting of a seedling from a previously dormant seed.

Polyploidy (sympatric speciation)

The state of having more than two sets of homologous chromosomes. This results when an organism acquires an additional set of homologous chromosomes from one of its predecessors. This is often seen in plants and results in reproductive isolation of plants, and thus speciation.

Sperm Structure (Review)

The tip of the sperm's head is the *acrosome*, which contains *hydrolytic enzymes* that will digest through the outer coating of the egg in order to allow sperm penetration.

pith

The tissue found at the center of the root or stem. It is actually made of parenchyma tissue (which we just learned is a type of ground tissue). However it is functionally similar to vascular tissues in that it also *stores and transports materials* throughout the plant.

Biomass

The total mass of living organisms in an area or ecosystem.

Changes in Allele Frequencies: Gene Flow

The transfer of alleles from populations when individuals leave (emigration) or enter (immigration) populations.

transpiration

The transport of water in a plant is unidirectional- it only goes up. The main driving force behind this movement is *transpiration*. Transpiration is when water evaporates out through stomata in the leaves (and partially in the stem). Transpiration causes transpirational pull.

Genetic Variation: Geographic variation

The variation of a species dependent on climate or geographic conditions. A graded variation of a phenotype due to this is known as a *cline*; variation from north/south environments is a *north-south cline*.

if a cell has 46 chromosomes at the beginning at the beginning of mitosis

There would be a total of 92 chromosomes (92 chromatids)

Lymphocytes

These are a type of leukocytes which originate from the *bone marrow* but end up concentrating in lymphatic organs (e.g. lymph nodes, spleen, thymus)

Pathogens

These are all kind of harmful microscopic enemies (virus, bLymphocytesacteria etc...) that can cause diseases.

Irregular bones

These are exactly as you would expect - irregular. They do not fit into any of the above classes based on shape and they are composed of thin cortical layers surrounding abundant cancellous interiors. ○ Examples include bones of the pelvis and spine.

Cell walls

These are found in PLANTS, FUNGI, PROTISTS, and BACTERIA (cellulose in plants; chitin in fungi; peptidoglycans in bacteria, polysaccharides in archaea). Provides structural support.

Leukocytes

These are white blood cells (WBCs). (WBCS) are larger and phagocytize foreign matter and organisms. They do contain organelles but no hemoglobin. *Diapedesis* is the process by which WBCs become part of the interstitial fluid by slipping through the endothelial lining.

Short bones

These bones are *cuboidal*, meaning that they are as wide as they are long. Their main function is to provide support with very little movement. They are primarily cancellous bone, covered by a very thin layer of cortical bone. ○ A few examples include the carpals of the wrist or tarsals of the ankle.

Why do we need the extra step of activation? Why can't the active enzyme be secreted directly?

This extra little step is actually extremely crucial because pepsin is a digestive enzyme that digests *proteins*, and proteins are found everywhere inside a cell. It is important for the enzyme-producing cell *not to digest itself*. Therefore, It is important for enzymes which digest proteins (like pepsin, trypsin and chymotrypsin) to be inactive while in the cell that produces them. Hence, they are produced and stored in the cell as *zymogens*, and only activated when they enter the extracellular gastrointestinal lumen where they are meant to function, and begin digesting.

Chloroplast Stroma

This fluid material fills area inside inner membrane. The *Calvin cycle* occurs here (fixing CO2 → G3P).

Low [CO2] inside plant

This happens during daytime- light is available to carry out photosynthesis. Constant photosynthesis depletes [CO2] levels inside plant. Needs more [CO2] to carry out photosynthesis. Open stomata (to intake more [CO2]).

High [CO2] inside plant

This happens during nighttime- light is not available. Therefore, photosynthesis is halted. [CO2] levels inside plant build up. Does not need more [CO2] to carry out photosynthesis. Close stomata.

pressure flow hypothesis.

This hypothesis explains the movement of sugar in the phloem in relation to the movement of water. Source cells in the leaves produce sugar and load the sugar into the phloem at the leaves. This increases the sugar concentration inside phloem cells, creating a gradient that pulls water (from the xylem which is nearby) into these phloem cells. This, in turn, creates a turgor pressure in the phloem, which results in a bulk flow movement of the sugar (and water) from the source (leaves) down to the sink (roots).

Egg Cytoplasm Determinant

This is the *distant relative* (cytoplasm) who is not part of the core (nucleus) of the relationship, but who can still exert its influence. The egg's cytoplasm could be *unevenly* distributed, as we have seen in egg-laying animals with the vegetal and animal pole. This creates an axis and influences how the embryo can divide during cleavage. For example, let's make the animal pole North and the vegetal pole South. If the cell divides right down the *vertical* midline, we end up with two normal daughter cells each with some parts of animal and vegetal materials. However, if we divide across the *horizontal* midline, then we end up with two cells — one with no animal pole and the other one with no vegetal pole. These two daughter cells would later have abnormal development.

Embryonic Induction

This is the *influencer* of the marriage — the one who persuades others to do things. There are many "*organizers*" that exist in a growing fetus. These are the cells that secrete chemicals and influence what neighboring cells become in the future. The scientists who discovered the special property of the *gray crescent* in frog embryos also found a significant organizer. They found out that by transplanting the *dorsal lip of the blastopore* of embryo A onto embryo B, embryo B developed a second *central nervous system*. This is because the dorsal lip of the blastopore is *mesodermal* tissue that later becomes the *notochord*. And the notochord induces the formation of neural tube from ectodermal cells. Therefore, the dorsal lip of the blastopore is an example of an organizer.

Apoptosis

This is the *janitor* of the marriage — the one who cleans up and removes unnecessary things. Apoptosis is *programmed cell death* which is part of *normal* development. This process is equally important for adults and the developing fetus. In adults, our body is constantly cleaning up every day. Our body commands damaged and abnormal cells to die (otherwise cancer may result). In developing babies, it is the process that shapes and separates the fingers and toes by removes the *webbing* in between.

Homeotic genes

This is the *shotcaller* of the marriage — the bossy one who decides where things go. The homeotic genes act like the *master controller* which turn on and off different gene expressions across the organism. This will in turn decide which part of the embryo develops into what structures. These homeotic genes have been found across *many different organisms*, and they all contain the *same* short sequence of ~180 nucleotides (codes for ~60 AA, why? Because usually 3 nucleotides = 1 codon = 1 AA!). This common sequence is called a *homeobox*. The fact that this sequence is preserved in many organisms shows its crucial role to animal development. Another thing to note is that the sequence is *homologous* (inherited from the same ancestor). Let's look at an example of a drosophila fly, in which the homeobox was originally discovered. The homeobox is responsible for the head-to-tail development — it says "put the antenna at the front! Put the wings in the middle!" A fly with a mutant homeobox gene could have morphological mutations such as an extra pair of wings, or antenna where the legs should be.

RNA primer

This is why the enzyme *primase* first places a *RNA primer* at the origin of replication. The RNA primer gives DNA polymerase a 3' hydroxyl group to attach free *nucleoside triphosphates* to, creating a phosphodiester bond. The energy for creating these bonds comes from the hydrolysis of two phosphates from each new base.

stratum granulosum

This layer is mostly *keratinocytes* that have migrated from the stratum spinosum. They secrete *lamellar bodies*, which form a lipid-containing, hydrophobic membrane. This helps create the skin's *water barrier*.

Peptides Hormones Property: Water Soluble

This means that the peptide hormones can freely travel in the bloodstream. However, once the hormone reaches its target cell, it MUST bind to a *cell surface receptor* in the plasma membrane because it *CANNOT* pass through the membrane. Why is this the case? If we take a step back and revisit the structure of our cell's plasma membrane, we recall that it is a *phospholipid bilayer*, and they only allow *lipid-soluble* particles to pass through. Hence, peptide hormones *indirectly stimulate* receptor cells. It is considered indirect stimulation because the hormone binds to a cell surface receptor on the outside of the cell to then affect the inside of the cell.

Visceral structures

Those found inside an organism; such as; the mantle or an organ like the heart.

Isotonic contractions

Those where the muscle contracts against the same weight, which produces a *constant tension*. Curling a 25 lb dumbbell is an isotonic contraction because the weight is the same throughout; therefore, the *tension* on the muscle is the same. ● DAT Pro-Tip: Iso = same; tonic = tension Isotonic contractions can further be broken down into *concentric* and *eccentric* contractions. *Concentric contractions* occur when a muscle shortens as it pulls the bone it inserts onto, closer to the bone it originates from. *Eccentric contractions* occur when a muscle lengthens, despite tension being applied to the muscle fibers.

Isotonic contractions

Those where the muscle contracts against the same weight, which produces a constant tension. Curling a 25 lb dumbbell is an isotonic contraction because the weight is the same throughout; therefore, the tension on the muscle is the same.

Small motor units

Those which have *few* muscle fibers innervated by a single motor neuron. *Precision* movements are created by small muscles containing many motor units. ● Example: the rectus muscle of the eye has many, small motor units. They are not powerful muscles, but they are very precise.

Large motor units

Those which have *many* muscle fibers innervated by one motor neuron. *Powerful* movements are created by large muscles with few motor units. ● Example: the rectus femoris muscle of the thigh has a couple motor units, meaning each of these motor units are quite large. The rectus femoris is a powerful muscle used in standing, walking and running, squatting, and jumping.

Lung Volumes Overview

Tidal volume (VT) Inspiratory reserve volume (IRV) Expiratory reserve volume (ERV) Residual volume (RV) Vital capacity (VC) Inspiratory capacity (IC) Functional residual capacity (FRC) Total lung capacity (TLC)

palisade mesophyll

Tightly-packed cells that carry out *photosynthesis* and is found closer to the upper epidermis. You can remember this by thinking that both "*p*alisade" and "*p*hotosynthesis" start with the letter P.

Malpighian tubules

Tiny tubes found in an insect's abdomen. They act similarly to nephridia and kidneys because they osmoregulate the hemolymph. Similarly, they help insects to excrete uric acid. ○ DAT Pro-Tip: Mammals excrete urea, while birds, reptiles, and invertebrates tend to excrete uric acid.

in vitro mutagenesis

To determine the function of a gene, *in vitro mutagenesis* introduces specific mutations into a cloned gene, then that gene is returned to a cell and the mutant cell is observed for phenotype that may indicate the function of the missing normal protein (often an embryonic stem cell, so that it will develop into adult tissues with the disruption observed). A frequently used example of this technology in research are "knockout mice". ● In some cases RNAi can be used to achieve the same goal.

Phloem

Transports sugars. Sugars are created in the leaves via photosynthesis and are transported to other areas of the plant that need the sugar but cannot produce it. The primary target is the roots, where there is a high carbohydrate storage. *Source: leaves* *Sink: roots* Phloem is made up of *sieve cells* and *companion cells*. *Sieve cells* are long cells with pores that allow *substances to flow* through them. Sieve cells are connected together to form a sort of continuous tunnel through which substances flow. They lack organelles because they need to efficiently and quickly transport the sugars. Because they lack organelles, sieve cells are connected to *companion cells*, which have all the necessary organelles to carry out *metabolic functions* (such as load the sieve cells with the sugars they need to transport). Sieve cells and companion cells are connected via *plasmodesmata* (small channels that connect adjacent cells' cytoplasms), which allows for quick communication between the two.

troponin

Tropomyosin is held in place over the actin binding site of myosin by *troponin*.

Dinoflagellates, diatoms, and euglenoids

Unicellular, eukaryotic protists that generally reproduce asexually and can be found in aquatic environments. They are photosynthetic *autotrophs*, which means they produce organic matter from simple inorganic molecules. Dinoflagellates are also responsible for the algal bloom known as *red tide*, in which high concentrations of their presence can lead to a buildup of toxins and depletion of oxygen in the water. These organisms also have two flagella, which gives them the capability of moving around to find food when light is absent. They can parasitically infect certain animals, making them *heterotrophic* as well as autotrophic.

Radula

Unique to mollusks. They are essentially tongues covered in tiny teeth, which allows mollusks to 'sweep' food into their mouths and cut it into pieces.

Phase‐Contrast

Uses light phase changes and contrast to produce a 2D image of thin samples. Advantages: Detailed observation of living organisms (including internal structures). Good resolution and contrast. Disadvantages: Ineffective on thick samples. "Halo Effect" around sample edges.

petals

Usually the most noticeable and distinguishable part of the plant. They function to attract animals to achieve pollination.

Genetic Variation: Neutral Variation

Variation without selective value (e.g. fingerprints in humans).

Peripatric speciation

Very similar to allopatric speciation in that a population is isolated and prevented from exchanging genes from the "main" one (geographically), but one of the populations is much smaller than the other, so it is subject to accelerated genetic drift along with differing selection pressures.

Compound Microscope (Light)

Visible light is focused to produce a 2D image of a thin slice of sample. Advantages: Some living samples (single cell layer) Disadvantages: May require staining (kills samples)

Stereomicroscope (Light)

Visible light is focused to produce a 2D image of surface of sample Advantages: Living samples Disadvantages: Low resolution

Fish

Water enters mouth, passes over *gills* (evaginated structures, create large Sa, take O2 and deposit CO; can be external/unprotected or internal/protected), exists through *operculum* (gill cover). *Countercurrent exchange* between opposing movements of water and underlying blood maximizes diffusion of O2 into blood and CO2 into water. With countercurrent exchange, a gradient of O2 saturation exists over the full length of the exchange surface.

Water in Germination

Water is the most important environmental "cue" that kick starts germination. The absorption of water by the seed (called *imbibition*) causes it to swell up and *break the seed coat*. The water also activates certain enzymes that catalyze metabolic processes to produce energy for the growth process. The *radicle grows* into roots that anchor the seedling in place, and the *hypocotyl grows* into the young shoot.

capillary action in plants

Water's upward movement can also be attributed to *capillary action.* Capillary action is an *adhesive* force. Adhesion is when *dissimilar* particles of surfaces are attracted to each other. In plants, this adhesion happens between water molecules and the xylem vessels (two dissimilar surfaces). Water is attracted to the xylem, and this causes the water to climb upwards within the vessel.

Innate Immunity

We can think of the *innate immune system* as our body's frontline soldiers. These soldiers attack whenever there is enemy invasion. They are quick to act but lack specificity. Since they do not have a specific target, we describe the innate immunity as a *nonspecific immune response*. The first layer of innate immunity are *outer walls* — physical and physiological barriers that *prevent* infection from entering the body. This is also the body's very first line of defense. These physical/physiologic barriers serve as the first line of defense. However, if they are penetrated, the rest of the innate immune response kicks in. Innate Immunity — Inflammatory Responses2. Rally — recruitment of troops (aka. Immune cells) to the site of injury 3. Battle — immune cells attack pathogens. 4. Backup — activation of the complement system ● Innate immune response: *nonspecific, generalized protection* ● First line of defense: *barriers* to block pathogen entry ○ Skin, mucosa, oil gland, acid, antimicrobial enzymes (lysozymes), cilia, symbiotic bacteria

Organogenesis

We will focus on *organogenesis* (formation of new organs), namely those of the *nervous system*. The *notochord* plays a very important role. As is discussed in the diversity of life chapter, animals in the *chordata phylum* have a notochord. Recall that the *notochord* is derived from the *mesoderm* germ layer. It lies right underneath the ectoderm germ layer.

Parasitism

When *one organism benefits at the other organism's expense*. An example is a tapeworm in the gastrointestinal tract of a human. The parasitic tapeworm obtains shelter and food that passes through the GI tract, but the human is unable to absorb all of the nutrients from their food.

cohesion

When *similar* particles or surfaces cling to one another, for example water molecules clinging together within a column of water. *Transpirational pull* is a *cohesive* force. As water evaporates - because of cohesion - it pulls on the water column underneath it, and lifts the entire water column higher (bulk flow). This is known as the *cohesion-tension* theory, as tension (pulling) is causing via cohesion.

portal system

When a capillary bed is connected to another capillary bed through a portal vein. Now you may wonder why is this good? This is advantageous because it allows quick diffusion of hormones from the hypothalamus to the anterior pituitary without having to enter the systemic circulation, which would have been much slower. Portal systems exist not only between the hypothalamus and the anterior pituitary, but also in the *liver* and *kidney* as well.

Stimulus generalization

When a conditioned organism responds to stimuli but not identical to original conditioned stimulus.

Cladogenesis/branching evolution

When a new species branches out from a parent species.

frameshift mutations

When a ribosome attaches to the mRNA transcript, it begins scanning the for the *start codon* with the mRNA sequence *AUG*. Once the ribosome sees the AUG sequence, it will bring in a tRNA that is attached to the amino-acid *methionine*. The start codon sets the *reading frame* for the rest of the mRNA transcript. As codons are read in groups of three nucleotides at a time, the AUG sequence allows the ribosome to position itself properly. Each three nucleotide codon will now be read as intended. Example: If our transcript looks like this: ● CGTATAUGCGCTGA The ribosome will scan for AUG, and start transcribing from there. This means that the ribosome will start here: ● CGTAT |AUG| CGCTGA The ribosome will then read each group of three nucleotides (codon) in proper sequence from then on: ● CGTAT |AUG|CGC|TGA|.... Problems arise when you have an *insertion* or *deletion* of nucleotides, which can change how the transcript is read. There'll be a shift in the reading frame - i.e. *frameshift mutation*. *Frameshift mutations* affect how the ribosome will interpret the remaining codons. If we look at the transcript from the example above, let's imagine if we were to add two AA after the CG following the start codon: ● Example above: ○ CGTAT |AUG|CGC|TGA| ● Insertion of AA and frameshift: ○ CGTAT |AUG|CGA|ACT|GA Codons #2 and #3 have been affected, as well as any codons that appear after the insertion. The same is true for deletions, which would remove nucleotides and cause a frameshift mutation. The exception to a frameshift mutation being very destructive to protein function is the insertion or deletion of *three* nucleotides. This would either add or delete exactly one codon, and therefore the codons that come after this mutation would still be read within the same reading frame. A *duplication* is where a piece of DNA is copied and reinserted into the sequence. This too can cause a frameshift mutation.

Iteroparity

When an animal has multiple reproductive cycles over the course of its lifetime. Relatively few but large in size offspring are produced each time. Offspring are cared for and their survival rate is higher. This type of reproductive strategy is more favorable in dependable environments where adults are likely to survive and breed again. The competition for resources may be intense in this environment. An example is the human species.

Altruistic behavior

When an animal increases the fitness of another animal while decreasing its own. This can occur when an animal risks its safety in defense of another or in order to help another individual (of the same species) rear its young. ● This behavior increases *inclusive fitness* which is the fitness of the animal plus its relatives (animals who share some identical genes). ● *Kin selection* is the natural selection that increases inclusive fitness. An example of this is a squirrel warning the others when a predator comes. This action is risky to itself, as it could reveal its own presence. This behavior, however, saves its daughters, mothers, sisters, and aunts. ● The *haplodiploid* reproductive system of bees is an example. Males are haploid (born from unfertilized egg of queen) and female workers and queen are diploid (born from fertilized egg). The females are highly related to each other (same father whose genes all come from a queen mother and same queen). Inclusive fitness of female workers is greater if she promotes production of sisters by nurturing the queen than if she produced her own offspring. ● *Reciprocal altruism* is when unrelated members of the same species help each other. This tends to occur in species with stable social groups that are likely to meet again and will therefore allow for potential future benefit. ● *Hamilton's rule* is the principle that for natural selection to favor an altruistic act, the benefit to the recipient, devalued by the *coefficient of relatedness* (fraction of genes that are shared on average), must exceed the cost to the altruist. rB>C.

Insight

When an animal is exposed to a new situation and without prior experience performs a behavior that generates a positive outcome. ● An example of this is a chimpanzee stacking boxes to reach bananas that are previously out of reach.

Semelparity

When an animal only has a single reproductive episode before death. Many offspring are produced in this reproductive opportunity. The survival rate of the offspring if low but there is an increased number of them. This type of reproductive strategy is better for variable or unpredictable environments. An example is the salmon species.

Intramembranous ossification

When bone is created *directly* within a fibrous membrane. First, *osteoblasts* secrete *osteoid*, which hardens and encourages certain osteoblasts to mature into *osteocytes*. The osteocytes then form trabeculae, which gets wrapped by blood vessels, ultimately creating the *periosteum*. Finally, cortical bone begins to grow between the periosteum and trabeculae. ● Flat bones are primarily made through intramembranous ossification.

Endochondral ossification

When bones are created *indirectly*. First, a *cartilage model* is created at the eighth week of development. As development continues, the center of the cartilage model begins to *calcify*. At the twelfth week of development, capillaries and osteoblasts begin to invade the calcified center, *establishing the primary ossification center*. Finally, *secondary ossification centers* are established at the *epiphyses* and *osteoclasts* chew out the inside of the *diaphysis*, creating the *medullary cavity*. ● Long bones are made through endochondral ossification.

trp repressor protein

When environmental tryptophan levels are high, tryptophan binds to the trp repressor protein and activates it. The active trp repressor protein will then bind to the operator site, preventing tryptophan production. ● Note: the trp repressor protein is constitutively expressed; however, the When environmental tryptophan levels are low, no tryptophan is available to bind to the tryptophan repressor protein. This means that the trp repressor is inactive in the absence of environmental tryptophan. An inactive tryptophan repressor protein cannot bind to the operator; therefore, the five structural genes will be transcribed into mRNA. Then, the mRNA will be translated into the structural proteins that make up tryptophan synthetase.

Hybrid sterility

When hybrids become healthy, fit adults but cannot reproduce.

Hybrid breakdown

When hybrids mate and produce offspring that have reduced viability/fertility. Hybrid's children cannot reproduce!

Changes in Allele Frequencies: Nonrandom mating

When individuals choose mates based upon their particular traits (mates choose nearby individuals). ● *Inbreeding* is when individuals mate with close relatives. Note this changes genotype proportions but NOT allele frequency! ● *Sexual selection* is when females choose males based on superior traits.

Gametic isolation

When male gametes do not survive in environment of female gametes (gametes do not recognize others).

Mechanical isolation

When male/female genitalia are not compatible.

Hypertonicity

When muscles gain tone and thus feel *spastic and rigid*. Hypertonicity occurs at the result of damage to the *central nervous system*. ex) Damage to the central nervous system, as in the case of a stroke, can result in muscles feeling stiff.

Hypotonicity

When muscles lose tone and thus feel *flaccid*. Hypotonicity occurs at the result of damage to the *peripheral nervous system*, as well as *reduced electrolytes*. ex) Compression of a peripheral nerve, as in carpal tunnel syndrome, can leave your hand feeling weak.

Balanced polymorphism

When natural selection is due to polymorphism. An example of this is different colors in insects. One color can camouflage to a different substrate, and the insect that is another color that cannot camouflage will be eaten. Only insects with the same color can mate (isolated from other subpopulations).

Anagenesis/phyletic evolution

When one species replaces another, straight path evolution.

pollen tube

When pollen lands on the stigma of another plant (or rarely, on its own plant), the *tube cell* will elongate down the style towards the ovary, forming what is called a *pollen tube*. Now the *generative cell* (the male gamete or the sperm) travels down the pollen tube to meet the ovule (the female gamete or the egg) to form a seed (the embryo).

Temporal isolation

When species cannot mate/flower because they breed at different seasons/time.

Habitat isolation

When species do not encounter each other because they live in different areas.

Behavioral isolation

When species do not perform correct courtship rituals.

relaxation phase

When the *sarcoplasmic reticulum* actively pumps calcium back inside itself. *Troponin* returns to its resting shape and pulls *tropomyosin* back over actin's myosin binding sites, therefore preventing new cross-bridges from forming. This causes the tension in the muscle to decrease.

Gluconeogenesis

When the glycogen storage is depleted and our body requires even more energy: liver converts *glycerol and amino acids into glucose*.

heterozygote advantage

When the heterozygous condition has a higher relative fitness than either homozygous condition. ▪ An example of this is sickle cell anemia.

Heterozygote advantage

When the heterozygous condition has a higher relative fitness than either homozygous condition. ▪ An example of this is sickle cell anemia. Three different types of alleles exist for hemoglobin: AA, AS, SS. AA individuals have normal hemoglobin, whereas SS individuals suffer from sickle cell anemia. SS individuals normally die before puberty. Although SS individuals do not live to reproductive age, the AS phenotype is present at 14% in Africa because it has resistance against malaria.

Frequency-dependent selection (minority advantage)

When the least common phenotype has a selection advantage. Common phenotypes are selected against.

Frequency-dependent selection (minority advantage)

When the least common phenotype has a selection advantage. Common phenotypes are selected against. The rare phenotypes that are favored will soon increase in frequency and will be selected against after they become common. The rare phenotypes, therefore, cycle between low and high frequency. ▪ An example of this is predators that create a *"search image"* of their prey's most common phenotypes. Prey that have the rare phenotype escape the predator

Allopatric Speciation

When the population is divided by a geographic barrier. This prevents interbreeding between the two resulting populations. The gene frequencies in the two populations can diverge due to natural selection, mutation, and genetic drift. If the gene pools sufficiently diverge, the populations will not interbreed when the barrier is removed. A new species is formed. ● This form of speciation can be through *dispersal*. This occurs when the group is isolated by being physically removed from the original location of the larger group. ● This form of speciation can also occur through *vicariance*. This happens when the group is isolated by a geographic barrier but in the same overall location of the larger group.

aminoacyl-tRNA

When the tRNA binds to the amino acid, it is referred to as *aminoacyl-tRNA*. The enzyme creating this linkage is aminoacyl-tRNA synthetase. Codons in mRNA match up with the anticodon of an aminoacyl-tRNA. The aminoacyl-tRNA is what is actually carrying the amino-acid.

ventricular systole phase

When the ventricles contract (ventricular *systole* phase), the blood is forced through pulmonary arteries and aorta. The tricuspid and mitral valves snap shut (to prevent backflow). This causes the "lub" sound. ● Papillary muscles and chordae tendinae are attached to cardiac valves and force them closed during systole.

ventricular diastole phase

When the ventricles relax (ventricular *diastole* phase), the backflow into the ventricles causes semilunar (aortic and pulmonary) valves to close. This causes the "dub" sound.

Hybrid invariability

When the zygote fails to develop properly and dies before maturing into a healthy, fit adult of reproductive age.

Mullerian mimicry

When two or more harmful species that are not closely related, and share one or more common predators, have come to mimic each other's warning signals.

Parallel evolution

When two related species develop similar adaptations or traits after their divergence from a common ancestor.

Muscle Anatomy

When you look at a braided rope from afar, it looks like one big piece; but, as you get closer, you notice the smaller bundles. If you look even closer at each bundle, you would see many woven threads. Skeletal muscles are similar. They are bundles of fibers, much like a rope. Each bundle has a name; further, each bundle is encased in a protective sheath. The most obvious bundle is the muscle itself. The bundles inside a muscle are called *fascicles*, which contain even more bundles of individual muscle cells, called *muscle fibers*. Each muscle fiber contains many strands of contractile protein, called *myofibrils*. The sheath covering the muscle is called the *epimysium*, while the sheath covering the fascicles are called *perimysium* and the sheath covering muscle fibers are *endomysium*. The *sarcolemma* is the protective sheath encasing the muscle fiber (aka muscle cell). The sarcolemma is the muscle fiber's cell membrane. There is no sheath covering individual myofibrils. Instead, they lie in the muscle fiber's *sarcoplasma*. The sarcoplasm is the cytoplasm of the muscle fiber.

Tracheal tubes

Where gas exchange occurs in an insect; therefore, they function like lungs.

ejactulatory ducts

Where the vas deferens meets the seminal vesicles (discussed below). The ejaculatory ducts propel the sperm into the *urethra*, which leads to ejaculation of the sperm out of the *penis* as semen.

prokaryotic core RNA polymerase

While *prokaryotic core RNA polymerase* is able to bind directly to prokaryotic DNA, it lacks the ability to target promoter sites. To work around this, prokaryotic core RNA polymerase combines with *sigma factor* to form *RNA polymerase holoenzyme*. The sigma factor provides RNA polymerase holoenzyme the ability to target the promoter region of bacterial DNA.

There are *four* main zona pellucida proteins

ZP1, ZP2, ZP3, ZP4. *ZP3* is the zona pellucida protein that binds to sperm and stimulates the acrosome reaction. Good to keep this in mind!

5' capping

a 7-methylguanosine cap is added to the 5' end of the mRNA during elongation. This cap functions to protect the 5' end of the pre-mRNA transcript from degradation. The 5' cap also helps the ribosome bind to processed mRNA during translation.

myeloma

a cancerous plasma cell ▪ An antibody producing plasma cell can be fused with a myeloma to produce a *hybridoma* ● The benefit to a hybridoma is the combined longevity of a myeloma and the antibody producing ability of a plasma cell

plasmid

a circular piece of DNA independent form a bacterium's single circular chromosome.

genomic library

a collection of cloned DNA pieces from a genome. The library can then be screened to locate a gene of interest. The formation of a genomic library is a good opportunity to recap many of the techniques discussed above into a practical example: ● To create a genomic library, we first create multiple copies of the genes we are interested in cloning via PCR. Next, we must insert the gene(s) of interest into a plasmid: the plasmids (and the DNA copies containing the genes of interest) are cut with the same restriction enzymes. The sticky ends of the new DNA will then bind with the matching sticky ends of the plasmid, and the plasmid will be closed using DNA ligase - at this point the resulting plasmid is a recombinant DNA molecule. Note that the plasmid will also contain a gene for antibiotic resistance for screening purposes. Now that the plasmid is complete, we must add it to a bacteria to replicate it - in order for the bacteria to take up the plasmid, the bacteria must first be made competent via electroporation. Not all bacteria will take up the plasmids, so we use the plasmid's antibiotic resistance gene to determine which bacteria were "transformed" into recombinant bacteria that will survive treatment with the antibiotic.

Detritus

a combination of feces and decomposing organic matter.

With allolactose bound, lac repressor protein undergoes

a conformational shape change and cannot bind the operator region. This allows RNA polymerase to transcribe the operon genes. This regulation allows for the production of metabolic enzymes for lactose in the presence of lactose. But there is also a second level of regulation.

Blood

a connective tissue and 4-6 liters is contained in the human body. Heart pumps approximately 7000 L of blood a day! ❖ Blood is made up of 55% liquid (*plasma*) and 45% cellular components. Plasma is an aqueous mixture of nutrients, salts, gases, wastes, hormones, and blood proteins (immunoglobulins, albumin, fibrinogen, and clotting factors). ❖ Blood *serum* is the same as plasma minus any clotting factor proteins. ❖ The cellular components of blood are *erythrocytes*, *leukocytes*, and *platelets/thrombocytes*.

Nuclear lamina

a dense fibrillar network inside the nucleus of eukaryotic cells. It is composed of intermediate filaments and membrane-associated proteins. The nuclear lamina provides mechanical support. It also helps regulate DNA replication, cell division, and chromatin organization.

Autosomal dominant

a dominant allele on an autosome. If the allele is inherited from either parent, the offspring will be affected.

X-linked dominant

a dominant allele on the X chromosome. If the allele is inherited from either parent, the offspring will be affected. Cannot be passed from father to son.

anticodon

a group of three bases that codes for a specific amino-acid. tRNA (transfer RNA) is a type of RNA, that contains anticodons. *tRNA* molecules bind to amino-acids that will be added to a growing polypeptide.

villi

a hallmark of the small intestine. finger-like projections on the walls of the small intestine. Villi are important because they *increase the surface area* of the small intestine to *increase the efficiency of absorption*. To put it in perspectives, villi actually increase the surface area of the small intestine to about the size of a tennis court!

The blood flowing in from the capillaries has a

a high hydrostatic pressure. It is so high that it overcomes the blood colloid oncotic pressure working against it.

pupil

a hole in the iris, and it allows light to enter the eye.

food chain

a linear depiction of what eats what (Example: carrot - rabbit - fox - lion).

Nuclear envelope

a lipid bilayer that surrounds the nucleus. Nuclear pores cross the nuclear envelope for transport in/out (mRNA, ribosome subunits, nucleotides, proteins such as the RNA polymerase and histones, etc.).

A high concentration of CO2 results in

a low pH because the formation of bicarbonate (done in the presence of high concentration of CO2) results in H+ creation as well.

DNA mutation

a maintained, heritable change in the DNA nucleotide sequence. If a change in the DNA of a cell is maintained and heritable, it will pass the change onto its daughter cells. A mutation does not have to change a gene - for example, a mutation can be in 'junk DNA', aka DNA that serves no purpose.

nucleus

a membrane-enclosed organelle that contains most of its genetic material.

Size-exclusion chromatography

a method for protein separation on the basis of size. Larger proteins elute more quickly than smaller proteins.

Homologous chromosomes

a pair of chromosomes (one maternal and one paternal) that contain all the same genes in the same location (but not necessarily the same alleles, as each parent may contribute different alleles for a given gene). ● Humans have 22 pairs of autosomal chromosomes and a pair of sex chromosomes. In females (XX), the sex chromosomes are homologous but in males (XY) they are not.

Foreign DNA is typically introduced in the form of

a plasmid.

Glucose is stored in the body as

a polymer called *glycogen* in primarily the liver (2/3) and muscles (1/3). All cells are capable of producing and storing glycogen but only liver cells and muscle cells have large amounts.

RNA

a polymer of nucleotides that contain ribose sugar, not deoxyribose. ● The nucleotide thymine is not seen in RNA. It is replaced by uracil, which pairs together with adenine via 2 hydrogen bonds. ● Unlike DNA, RNA is usually single stranded. ● RNA is less stable than DNA (due to its extra hydroxyl group), making it more likely to participate in chemical reactions.

DNA probe

a radioactively labeled single strand of nucleic acid used to tag a specific DNA sequence.

Autosomal recessive

a recessive allele on an autosome. The offspring will only be affected if the recessive allele is inherited from both parents.

X-linked recessive:

a recessive allele on the X chromosome. If the allele is inherited from both parents, daughters would be affected. Inheriting a single copy of the allele will result in sons being affected (as men only have one copy of the X chromosome). Cannot be passed from father to son.

Attenuation of the trp operon involve

a regulatory segment of DNA between the operator region and five structural genes. This sequence is known as the leader sequence, which has four domains. Domain one contains codons for the amino acid tryptophan, while domain four is known as the attenuation sequence.

nucleotide

a ribose sugar attached to both a nitrogenous base and phosphate group.

nucleoside

a ribose sugar that is only attached to a nitrogenous base, no phosphate included.

operator region

a sequence of DNA that lies nearby or within the promoter site and is the key regulatory region of an operon. Either *activator* or *repressor proteins* (transcription factors) bind to the operator region to activate or repress the promoter. ● Hint: regulation of the operator region regulates the operon as a whole. This is because the operator region regulates the promoter site.

polysaccharides

a series of connected monosaccharides (an example of a polymer). bonded together via dehydration synthesis and broken via hydrolysis.

Western Blotting

a similar method but for proteins. Rather than a probe attaching via nucleic acid hybridization, a primary antibody specific to a protein is added. Then, a secondary antibody-enzyme conjugate will bind to the primary antibody to mark it for visualization.

point mutation

a single nucleotide change causing substitution (the change of one nucleotide to a different nucleotide), insertion (the addition of a nucleotide), or deletion (the removal of a nucleotide).

point mutation

a single nucleotide change causing substitution (the change of one nucleotide to a different nucleotide), insertion (the addition of a nucleotide), or deletion (the removal of a nucleotide). ● Both insertion and deletion of nucleotides can cause frameshift mutation. A *frameshift mutation* results in the 'reading frame' of an RNA transcript being shifted, causing different amino acids to be translated and resulting in impaired protein structure. ▪ Why does a frameshift mutation occur? Recall that *codons* are nucleotide triplets that specify an amino acid during translation (every three nucleotides in sequence corresponds to an amino acid in the protein). If nucleotides are added or removed, the nucleotide sequence will be offset, resulting in different triplets than the original sequence. ▪ If the number of nucleotides added or removed is a multiple of 3, then a frameshift is avoided (because the codons are still read correctly but an entire amino acid will have been added or removed).

fovea (macula)

a small area of the retina located directly behind the pupil. It is more densely-packed with cones than any other portion of the retina, which allows for high visual acuity.

lens

a transparent, biconvex structure located behind the iris. Along with the cornea, it refracts light to focus it onto the retina.

esophagus

a tubular structure that guides the food into the stomach.

Heparin

a type of anticoagulant which prevents blood from clotting too quickly.

inversion

a type of mutation where a sequence of DNA is excised, flipped, and reinserted back into the DNA sequence.

retrovirus

a virus that stores its genetic material as RNA; therefore, they infect host cells with RNA. retroviruses carry an enzyme called *reverse transcriptase*, which allows them to convert their RNA into *complementary DNA* (cDNA). cDNA is complementary to the RNA it was transcribed from. ex) *HIV (human immunodeficiency virus)*

Aqueous humor

a watery fluid that fills the chamber between the lens and cornea (the anterior chamber). It functions to maintain the proper intraocular pressure, and it nourishes the avascular ocular tissues, such as the lens and posterior cornea.

hydrogen bond

a weak intermolecular bond between molecules that results when a hydrogen attached to a highly electronegative atom is attracted to the negative charge on another molecule (with an F, O, or N atom). ex) between H2O molecules

Thromboplastin converts inactive plasma protein prothrombin to

active thrombin.

positive punishment

add something bad to decrease behavior ex) pushing a dog's nose when he jumps

positive reinforcement

add something good to increase the behavior ex) giving a dog a treat when he jumps

there are four different bases in RNA

adenine, uracil, guanine, and cytosine. The bases within a mRNA transcript are arranged in groups of three and each group is called a *codon*.

Fatty acids combine with

albumin in the blood which carries them

Gene pool

all the alleles for any given trait in the population.

ejection fraction

all the blood leaves the ventricles when the heart pumps. The percent that does is called the *ejection fraction*.

Growth occurs in

all three interphases, not just G's.

cooperativity

allows for an enzyme to become increasingly receptive to additional substrate molecules after a substrate molecule has attached to an active site ▪ Applicable to enzymes w/ multiple subunits that each have an active site ● E.g. hemoglobin binding additional oxygen (although hemoglobin is not an enzyme!)

resource partitioning

allows two species, that seem to compete for resources, to coexist. Resource partitioning occurs when these species use different means to obtain the same resource, or they seek out slightly different resources.

primary structure of a protein

amino acid sequence

The adrenal medulla secretes only

amino-acid derived hormones. Tip to remember: since adrenal medulla produce only amino-acid derived hormones, it produces catecholamines*.

When the tRNA binds to the amino acid, it is referred to as

aminoacyl-tRNA. The enzyme creating this linkage is aminoacyl-tRNA synthetase.

Hemophilia is

an X-linked recessive disease. A woman that is heterozygous for hemophilia (XHXh) is normally just a carrier for the disease, but if XH is inactivated, Xh can be expressed.

Positive Feedback

an action intensifies a condition so that it is driven further beyond normal limits (labor contraction, lactation, and sexual orgasm).

during mitosis and meiosis, chromatin exists in

an additional level of organization known as a chromosome.

Y-linked

an affected allele on the Y chromosome. Men only carry one copy of the Y chromosome, so if the allele is inherited from the father, any sons will be affected. Can only be passed from father to son.

allele

an alternative form of a gene. ● An example of an allele is eye color: blue, green, and brown eyes are different alleles of the eye color gene. ● A *wild type* allele is the 'normal' copy of an allele ● A *mutant* allele has an altered DNA sequence that can affect a gene's phenotype

While the ribosome is paused at domain one, domains two and three form

an alternative hairpin loop. The low tryptophan hairpin loop allows the ribosome to continue along the RNA transcript. Translation of the structural genes for tryptophan synthase occurs and more tryptophan is made. Hint: domains two and three cannot form a hairpin loop when tryptophan is high because the ribosome has no reason to pause at domain one.

An increase in CO2 pressure will result in

an increase in CO2 content in the blood. Deoxygenated blood carries an increasing amount of carbon dioxide.

the lac operon is an example of

an inducible operon.

Nucleoid

an irregular shaped region within the cell of prokaryotes that contains all/most genetic material (prokaryotes lack a nucleus).

Lymphatic system

an open secondary circulatory system which transports excess interstitial fluids (lymph) through the contraction of adjacent muscles. Some walls of larger lymph vessels have smooth muscle.

peptic ulcers

an open sore created on the stomach epithelium by acid corrosion.

lac operon

an operon seen in E. coli (a bacteria)

lac operon

an operon seen in E. coli (a bacteria). It is an example of an *inducible operon*. An inducible operon is one that is usually inactive, unless it is induced to become active. The lac operon will only be induced to become active if glucose is not present but lactose is. This further shows how the general purpose of an operon is to conserve cellular resources until they are required. In this case, E. coli do not want to wastefully produce lactose metabolic proteins if they are not needed.

fetus

an unborn baby of viviparous organisms. A human embryo becomes a human fetus after eight weeks of development.

tight junctions are present in

animal cells.

Histone *methylation*

another form of modification of histone proteins. Methylation adds non-polar methyl groups to the histone, and *reduces* DNA transcription.

Polyadenylation

another post-transcriptional modification of eukaryotic pre-mRNA. Both the 5' cap and the 3' poly A tail are signals to the cell that the mRNA has passed checkpoints and should be translated. The presence of these two signals prevents RNA degradation by *exonuclease*. ● Analogy: the 5' cap and 3' poly A tail are like the plastic aglet at the end of a shoe string, which protects the ends from fraying.

Attenuation

another way the trp operon can be regulated.

Attenuation

another way the trp operon can be regulated. Attenuation is based on the fact that, in bacteria, transcription of DNA into mRNA can occur at the same time mRNA is translated into protein. Translation cannot occur at the same time as transcription in eukaryotes. We will see more on why this is true in a little while. Attenuation of the trp operon involves a regulatory segment of DNA between the operator region and five structural genes. This sequence is known as the *leader sequence*, which has four domains. Domain one contains codons for the amino acid tryptophan, while domain four is known as the *attenuation sequence*. When tryptophan levels are high, domains three and four of the RNA transcript will attach, forming an attenuation hairpin loop. The attenuation loop will prevent ribosomes from translating the RNA transcript into protein. In this way, the structural proteins for tryptophan synthase are not made. If tryptophan levels are low, the ribosome will pause at domain one of the RNA transcript. This is because domain one contains codons for the amino acid tryptophan. If tryptophan is low, there are not many of these amino acids nearby; so, the ribosome needs to wait for a couple tryptophan amino acids to become available before it continue translating the RNA transcript into protein. While the ribosome is paused at domain one, domains two and three form an alternative hairpin loop. The low tryptophan hairpin loop allows the ribosome to continue along the RNA transcript. Translation of the structural genes for tryptophan synthase occurs and more tryptophan is made. Hint: domains two and three cannot form a hairpin loop when tryptophan is high because the ribosome has no reason to pause at domain one.

Later on, macrophages function as

antigen-presenting cells to activate adaptive immunity. You can think of an antigen as the unique ID of the enemy. Macrophages act as messengers that carry vital information about the enemies from the frontline soldiers (innate immunity) to the backup troops (adaptive immunity).

cells cannot recognize free floating antigens; they can ONLY bind to

antigens presented by antigen presenting cells (APCs).

protein denaturation

any secondary, tertiary, and quaternary structure is removed but the amino acid sequence (primary structure) remains intact. Protein denaturation usually occurs from excess temperature, chemical stress, pH variance, heavy metal salts, and radiation. A protein's 3D structure is critical to its function -loss of shape due to denaturation leads to loss of function.

The blood from the left ventricle goes to the aorta through the

aortic semilunar valve into the rest of the body via the following pathway: Aorta (largest vessel) → arteries → arterioles → capillaries → tissues → venules → veins → superior and inferior vena cava →cycle repeats.

Crypts

are like reverse villi - rather than projections, they are invaginations in the wall of the small intestine. The crypts contain cells that secrete enzymes and cells that produces epithelial cells.

Focal adhesions

are one way cells connect to the ECM. This type of connection uses actin filaments in the cell.

Ossicles

are three small bones named the malleus, incus, and stapes, which vibrate and transmit auditory information to the inner ear.

▪ 99% of neurons fall into this category.

association neurons

cAMP binds

atabolite activator protein (CAP). CAP bound to cAMP will bind upstream of the promoter region and help to attract RNA polymerase. This will increase the rate of transcription when glucose levels are low, leading to more mRNA transcripts. More mRNA transcripts mean more translation into functional lactose metabolic proteins.

Adhesion proteins

attach cells to neighboring cells and provide anchors for internal filaments and tubules (increasing stability).

the outer ear is composed of

auricle and the external auditory canal

Valves in the lymph vessels prevent

backflow. The fluid returns to the blood circulatory system through two ducts located in the shoulder region (thoracic duct and right lymphatic duct which empty into the left and right subclavian vein, respectively). It rejoins the blood as plasma.

binary fission

bacteria are asexual organisms, which means they do not reproduce by mating with another individual (rather, they divide by *binary fission*). Bacteria cannot increase genetic diversity via sexual reproduction or mating. However, bacteria are able to transfer genes *horizontally*, which contributes to increased genetic diversity. ● Note: horizontal gene transfer may also be called *lateral gene transfer*. It differs from vertical gene transfer because genes are not being passed from parents to offspring; rather, they are being passed within a generation.

Nucleosomes

basic units of DNA organization composed of 8 histones.

least numerous kind of leukocytes.

basophils They only make up less than 1% of all leukocytes.

transcription elongation

begins after RNA polymerase has aligned with the promoter correctly and the *transcription bubble* has been established. Elongation is when the RNA strand is extended. RNA Polymerase travels along the template strand (aka *noncoding* or *antisense strand*) in the 3' 5' direction; however, *it extends RNA in the 5' → 3' direction*. Therefore, the RNA transcript is complementary to the template strand; additionally, it is nearly identical to the *coding* (aka *sense*) strand. ● Remember: the only difference is that DNA will contain thymine, which is replaced by uracil in RNA. also, recall that DNA uses deoxyribose sugars, while RNA uses ribose sugars.

Interphase

begins after mitosis and cytokinesis are complete. It consists of a G1, S, and G2 phase. ❖ Interphase is a part of the *cell cycle*. ● The cell cycle consists of mitotic phases (mitosis, cytokinesis) + interphase (G1, S, G2 phases). ● 90% of the cell cycle is spent in interphase. Growth occurs in all three interphases, not just G's. ● Evidence suggests the cell cycle is regulated by molecular signals in the cytoplasm.

Cytokinesis

begins during the later stages of mitosis (most sources indicate it begins toward the end of anaphase). It is the division of cytoplasm to form 2 cells. ● Animal cells separate via creation of the *cleavage furrow*. ▪ Actin and myosin microfilaments shorten and the plasma membrane is pulled into the center. ● Plant cells separate via formation of a *cell plate.* ▪ Vesicles from Golgi bodies migrate and fuse to form a cell plate, out growth and merge with plasma membrane separating the two new cells. ▪ The cells don't actually separate from each other. The middle lamella cements adjacent cells together.

Watson & Crick

believed that semiconservative replication was the valid DNA model. *Meselson & Stahl's* experiment proved this was true.

Vertebrate skeletons

belong to organisms that do have a backbone and they are known as *endoskeletons* because they are found *within* the body.

↓Km

better substrate binding

Whenever there is an allergen, IgE will

bind and trigger the release of histamine from these two cells —> allergic reaction

Hemoglobin

binds to carbon monoxide with much greater affinity than myoglobin. ● It has 4 protein subunits compared to the one protein subunit of myoglobin. ● The hemoglobin curve is sigmoidal.

storage proteins

biological reserves of amino acids. ex) ovalbumin (egg whites), casein (milk), plant seeds

Each small cell resulting from cleavage is called a

blastomere

epiglottis

blocks the opening to the trachea, this is to ensure that solids and liquids can only enter the esophagus. However, sometimes the epiglottis doesn't close quick enough while we eat and talk at the same time, and this leads to choking as our body tries to expel the foreign material that just entered the trachea.

The lymph also monitors

blood for infection.

Evaporation

body heat is removed as liquid evaporates (endergonic)

Homologous structures

body parts that are similar in form and function and seem to be related in different species. This points to a common ancestor between the species.

Analogous structures

body parts that have the same function but have evolved independently as adaptations to their environments. This is also called a homoplasy.

Both the periosteum and endosteum are involved in

bone growth, repair, and remodeling, particularly in reference to the thickness of a bone

B-cells mature in the

bone marrow.

The anterior pituitary gland releases

both *tropic hormones* and *direct hormones*

glycogenolysis

break down glycogen.

Peroxisomes

break down various substances (H2O2 +RH2 => R + 2H2O), fatty acids, and amino acids.

Peroxisomes

break down various substances (H2O2 +RH2 => R + 2H2O), fatty acids, and amino acids. Common in liver and kidney where they breakdown toxic substances. In plant cell, peroxisomes modify the by-products of photorespiration. In germinating seeds, they are called GLYOXYSOMES. Peroxisomes break down stored fatty acids to help generate energy for growth. Peroxisomes produce H2O2 (HYDROGEN PEROXIDE) which is then used to oxidize substrates. They can also break down H2O2 if necessary via CATALASE (H2O2 => H2O + O2) since H2O2 is toxic to cells.

Chondroblasts are responsible for

building cartilage.

muscle fibers

bundles of individual muscle cells

the parathyroid hormone does the exact opposite of

calcitonin

endocrine

called the *islets of Langerhans*, and it secretes three key hormones: *insulin, glucagon and somatostatin* into the bloodstream.

Sex-influenced genes

can be influenced by sex of individual carrying trait (e.g. a Bb female not bald, Bb male is). ● *Genomic imprinting* is a similar phenomenon in which a specific allele is expressed (or not) depending on whether or not it is maternal or paternal. This is distinct from sex-influenced genes because in genomic imprinting the effect also occurs on autosomal chromosomes.

Laminin

can be seen as well acting similarly to fibronectin.

leading strand

can be synthesized *continuously* from a single RNA primer. This is because in the leading strand the replication fork is extending in the same direction that DNA polymerase is traveling,

Gel electrophoresis

can be used on DNA molecules to separate them on the basis of charge and size. In gel electrophoresis, different DNA molecules are added to an agarose gel that is under an electric field. The negatively charged DNA moves away from the negative end towards the positive end. Shorter DNA molecules moves further than larger DNA.

Gel electrophoresis

can be used on DNA molecules to separate them on the basis of charge and size. In gel electrophoresis, different DNA molecules are added to an agarose gel that is under an electric field. The negatively charged DNA moves away from the negative end towards the positive end. Shorter DNA molecules moves further than larger DNA. ● After electrophoresis, DNA can be sequenced or probed to identify the location of a specific DNA sequence. A *DNA probe* is a radioactively labeled single strand of nucleic acid used to tag a specific DNA sequence. ● Note that gel electrophoresis can also be applied to proteins. In the case of proteins, we must first add SDS (a compound that denatures, linearizes, and adds a negative charge to protein).

DNA microarray assay

can be used to monitor the expression of large groups of genes across the entire genome - this is useful for seeing which genes are transcribed in different tissues or at different stages of development.

DNA microarray assay

can be used to monitor the expression of large groups of genes across the entire genome - this is useful for seeing which genes are transcribed in different tissues or at different stages of development. In a DNA microarray assay, tiny amounts of a large number of single-stranded DNA fragments representing different genes are fixed to a glass slide in array on a grid in wells. Then, mRNAs are isolated from a cell and reverse transcriptase is used to make cDNA. In the microarray assay, the cDNAs are labeled fluorescently and then allowed to hybridize to a DNA microarray. So the wells that light up tell you which gene is expressed and color tells you where it is expressed (we usually differentiate samples/tissues with different color labels). Using this, expression of genes across the entire genome can be analyzed simultaneously.

pulse chase experiment

can be used to track the movement of proteins in a cell. ● In this experiment, radioactively labeled amino acids are added to cells which are then incorporated into proteins during synthesis - this is the "pulse". Next, non-radioactively labeled amino acids are added to the cells - the "chase". The purpose of the pulse is to allow for tracking of the radioactive proteins as they move through the cell, while the purpose of the chase is to prevent all subsequent proteins from being radioactive as well (which would make tracking impossible).

chromosomal breakage

can occur spontaneously or be induced as a result of mutagenic agents. The fragments of a chromosomal breakage can rejoin or may remain unrepaired. ● *Mutagenic agents* include cosmic rays, X-rays, UV rays, radioactivity, and chemical compounds ● E.g. colchicine which inhibits spindle formation and can induce polyploidy ● E.g. mustard gas

short bones are primarily

cancellous bone, covered by a very thin layer of cortical bone.

An inactive tryptophan repressor protein

cannot bind to the operator; therefore, the five structural genes will be transcribed into mRNA. Then, the mRNA will be translated into the structural proteins that make up tryptophan synthetase.

Obligate anaerobes

cannot survive in the presence of O2.

Sex-linked genetic disorders

carried on either the X or Y chromosome: ▪ X-linked dominant: a dominant allele on the X chromosome. If the allele is inherited from either parent, the offspring will be affected. Cannot be passed from father to son. ▪ X-linked recessive: a recessive allele on the X chromosome. If the allele is inherited from both parents, daughters would be affected. Inheriting a single copy of the allele will result in sons being affected (as men only have one copy of the X chromosome). Cannot be passed from father to son. ▪ Y-linked: an affected allele on the Y chromosome. Men only carry one copy of the Y chromosome, so if the allele is inherited from the father, any sons will be affected. Can only be passed from father to son.

heterozygous

carries a copy of the recessive allele on one of their homologous chromosomes and a copy of the dominant allele on their other homologous chromosome (e.g. Bb)

Erythrocytes

catalyze the conversion of CO2 and H2O to H2CO3.

Platelets aka thrombocytes

cell fragments that are involved in blood clotting.

Platelets aka thrombocytes

cell fragments that are involved in blood clotting. They lack nuclei. Platelets are small portions of membrane-bound cytoplasm torn from megakaryocytes. They stick to damaged epithelium and attract more platelets to the site of injury. They convert *fibrinogen* (inactive) to *fibrin* (active). They produce prostaglandins and other important enzymes.

G1 Phase

cell increases in size G1 checkpoint ensures everything is ready for DNA synthesis (cells produce protein, ribosomes, mitochondria) most variable in length

tight junctions are characteristic of

cells lining the digestive tract

beta glucose polymer carbohydrates

cellulose chitin

forward mutation

changes a wild type allele to a mutant allele

Some forms of lipoproteins found are

chylomicrons (large microproteins), low-density lipoproteins (LDL), and high-density lipoproteins (HDL).

ciliary body contains the

ciliary muscle and ciliary epithelium

Basal ganglia

clusters of neurons that specialize in processing and planning movements, especially well-practiced habitual actions.

Translocations

cocur when a chromosome segment is moved to another chromosome. This can be reciprocal (meaning two non-homologous chromosomes swap segments) or nonreciprocal (one chromosome segment is transferred to a different chromosome - this can also be referred to as an *insertion*). A Robertsonian translocation involves two different chromosomes breaking and rejoining near their centromeres.

the outer ear functions to

collect sound waves from the environment.

ionic bond

complete transfer of electrons from one atom to another. electronegativity of atoms are very different. ex) NaCl

Tight junctions

completely encircle each cell, producing a seal that prevents the passage of materials between cells.

Tight junctions

completely encircle each cell, producing a seal that prevents the passage of materials between cells. Prevent the passage of molecules and ions through the space between cells, so materials must actually enter the cells (by diffusion or active transport) in order to pass through the tissue. Present in animal cells. ● Characteristic of cells lining the digestive tract

eukaryotic ribosome

composed of 2 subunits: 60S + 40S = 80s unit. The two subunits are produced inside the nucleolus, then moved into the cytoplasm where they assembled into a single 80S ribosomes (larger S value indicates heavier molecule).

prokaryote ribosome

composed of 50S + 30S = 70S.

Brainstem

composed of the midbrain, the pons, and the medulla oblongata, and it connects the cerebrum to the spinal cord. ❖ The *reticular formation* is a network of cells within the brainstem that function to regulate sleep and arousal.

Isotonic contractions can further be broken down into

concentric and eccentric contractions.

Fibronectin

connect *integrins* to a network of *collagen* and *proteoglycans* in the ECM. This network also functions in transmitting mechanical and chemical signals between outside and inside of cell.

Ligaments

connect bones to other bones

Tendons

connect muscles to bone

The central nervous system (CNS)

consists of the brain, spinal cord, and interneurons

The peripheral nervous system (PNS)

consists of the nerves and ganglia outside of the central nervous system. Specifically, nerves that originates in the CNS but terminate outside of the brain and spinal cord are considered to be part of the PNS. Examples of this include the cranial and spinal nerves. o There are 12 pairs of *cranial nerves* and 31 pairs of *spinal nerves*. o A *ganglion* is a cluster of nerve cell bodies located in the PNS.

basophils

contain granules that can be released to nearby tissues.

Lymph nodes

contain phagocytic cells (leukocytes) that filter the lymph and serve immune response centers. When one is sick, lymph nodes fill with white blood cells and give the appearance of "swollen glands."

DNA nucleotide

contains a nitrogen base, five carbon sugar deoxyribose, and a phosphate group ● Nucleotides can be further categorized depending on their nitrogen base (purines and pyrimidines)

Myoglobin

contains a single chain/protein subunit that stores oxygen in muscles. Myoglobin has a higher affinity for oxygen than hemoglobin. The myoglobin curve is hyperbolic. Its curve is to the left of hemoglobin. It has no change in oxygen binding over a pH range.

Autonomic Nervous System

contains afferent sensory neurons, as well as efferent neurons, which are directly responsible for its effects. It innervates cardiac muscle and smooth muscle, and it is further broken down into the sympathetic nervous system and the parasympathetic nervous system. A balance between the *sympathetic* and *parasympathetic* systems must be kept to maintain homeostasis.

left ventricle

contains blood that enter through the left atrioventricular or *mitral* or *bicuspid* valve. ● The left AV valve prevents backflow into atrium. The aortic semilunar valve prevents it into the ventricle. The blood from the left ventricle goes to the aorta through the aortic semilunar valve into the rest of the body via the following pathway: Aorta (largest vessel) → arteries → arterioles → capillaries → tissues → venules → veins → superior and inferior vena cava →cycle repeats.

left ventricle

contains blood that enter through the left atrioventricular or mitral or bicuspid valve.

left atrium

contains blood that the lung has oxygenated. It enters via the pulmonary veins.

Pancreas

contains both *exocrine* and *endocrine* tissue

right atrium

contains deoxygenated blood which enters via the superior and inferior vena cava.

acrosome

contains digestive enzymes that help the sperm penetrate the egg for fertilization upon contact.

epidermis

contains keratinocytes and additional specialized cell types, and it has five layers: the stratum corneum, lucidum, granulosum, spinosum, and basale*. (The stratum lucidum is only present on the palms of the hands and the soles of the feet).

nucleoside

contains only a nitrogen base and five carbon sugar

right ventricle

contains the blood that is squeezed through the right atrioventricular (AV) or *tricuspid* valve and pumps blood into the *pulmonary artery* through the pulmonary semilunar valve. ● When the ventricle contracts, the AV valve closes to prevent backflow (lub sound). ● When the ventricle relaxes, semilunar valve prevents backflow from pulmonary artery back into ventricles by closing (dub sound of both semilunar valves).

inner ear

contains the cochlea and the semicircular canals. ▪ Vibrations of the stapes are transmitted to the cochlea via the *oval window*, which is a membrane-covered opening between the middle and inner ear. The *cochlea* is a spiral-shaped, hollow chamber of bone, which contains fluid. The ossicles exert pressure on this fluid, which influences the basilar membrane and the organ of Corti, which are present along the length of the spiral-shaped cochlea. ● The *basilar membrane* moves according to the "waves" of fluid inside the cochlea, which is determined by the original sound waves (frequencies) that were transmitted. ● The *organ of Corti* is a cellular layer atop the basilar membrane, and it is the sensory organ of hearing. As it moves with the basilar membrane, its *hair cells (stereocilia)*, which are actually closely related to microvilli, move, which induces action potentials in their associated neurons. Which part of the basilar membrane vibrates, and therefore which hair cells are activated, determines what the organism hears. ▪ The *semicircular canals* are fluid-filled, bony channels oriented in the three dimensions. Like the cochlea, they also contain *hair cells*. In this case, the hair cells are stimulated upon movement. This provides information about orientation and is important for proper balance.

diencephalon

contains the thalamus, hypothalamus, epithalamus, and subthalamus. ❖ The *thalamus* relays sensory information from the spinal cord to the cerebral cortex ❖ The *hypothalamus* is located below the thalamus and is a link between the nervous system and endocrine system. It controls water balance, blood pressure, temperature regulation, hunger, thirst, sleep, circadian rhythms, and sex.

choroid

contains the vasculature that supplies nutrients and oxygen to the retina.

When we inhale, the diaphragm (under lungs) and intercostal muscles (between ribs)

contract/flatten. The lung cavity opens up causing an increase in volume, which results in a decrease in pressure of the intrapleural space.

Accessory Glands

contribute certain secretions to the sperm to form semen. 1. seminal vesicles 2. prostate gland 3. bulbourethal glands

G1/S checkpoint

controls whether a cell will proceed from the *G1 phase* into the *S phase*. The G1 (GAP-1) phase is where cells grow after a recent division. The S (synthesis) phase is where DNA replication occurs in preparation for the next division. If the cell does not meet the criteria for entrance into the S phase, it will remain in *G0*. G0 is basically like a waiting room where the cell does not grow, nor will it replicate its DNA.

adenylyl cyclase

converts ATP cAMP, with cAMP acting as a secondary messenger that can then activate other proteins in the cell.

Each lamellar layer is made of

cortical bone and collagen fibers, which help bones resist torsion strain.

n metaphase, to keep track of the total number of chromosomes,

count the centromeres!

Integrins

couple the ECM outside of cell to cytoskeleton inside the cell and are involved in cell signaling. Their structure is a heterodimer of α and β subunits. Involved in wound repair

gluconeogenesis

create new glucose.

Polymerase Chain Reaction (PCR)

created by Kary Mullis, is an important technique for the amplification of DNA. The necessary ingredients of PCR are a heat resistant polyermase (e.g. Taq polymerase), nucleotides, primers, and buffer salts. The basic steps of a PCR are: 1. Denaturation: the double-stranded DNA molecule is heated to a high temperature (>90o C) to separate it into separate strands. 2. Annealing: As the temperature is cooled down (~55-65o C), the primers are able to attach to the separate strands. This will facilitate the next step... 3. Elongation: The temperature is raised (~70o C) and the heat resistant polymerase synthesizes complementary strands. ▪ The cycle then repeats to exponentially increase the number of DNA molecules. ▪ Reverse transcriptase can be combined with PCR to create large amounts of cDNA for various genes.

electronegativity

defines the ability of an atom to attract electrons.

Cancer cells

defy the five cell-specific regulations in place. Such cells are called transformed cells. ● Cancerous cells are a manifestation of defective cell differentiation. ● Cancer drugs that inhibit mitosis do so by disrupting the ability of microtubules to separate chromosomes during anaphase, thus stopping replication.

The epidermis protects us from

dehydration, UV radiation, and pathogens.

Avery-MacLeod-McCarty experiment

demonstrated that DNA was the 'heritable substance' causing bacterial transformation. ● At the time of Griffith's experiment, it was not known what component of the killed bacteria allowed for bacterial transformation. The Avery-MacLeod-McCarty experiment was similar to Griffith's experiment, but various digestive enzymes were separately added to the remnants of the heat-killed smooth bacteria: DNAse, proteinase, lipase, etc. Most of these mixtures had no effect, but when DNAse was added to the remnants of the heat-killed smooth bacteria, the mouse survived. Why did adding DNAse prevent the mouse from dying, but not the other enzymes? Remember that DNA is the genetic material containing the information for producing the protective capsule that the rough bacteria absorbed to become virulent. When an enzyme such as proteinase is added to the heat-killed smooth bacteria, proteins would be broken down, but the DNA would be unaffected, allowing the bacteria to still be transformed. DNAse digested the DNA remaining from the heat killed smooth bacteria, preventing bacterial transformation from taking place - as a result the rough bacteria never gained the ability to produce the protective capsule, and remained nonvirulent.

Cortical bone

dense and compact

Bulk flow

describes a collective movement of substances in the same direction in response to a force or pressure (e.g. blood flow).

Sympatric speciation

describes the formation of new species *without the presence of a geographic barrier*. Sympatric speciation can occur a number of ways: Balanced polymorphism Polyploidy Hybridization

Cardiac output

describes the volume of blood that is discharged from the ventricle each minute. ● Cardiac output (CO) = Stroke Volume (SV) X Heart Rate (HR)

DNA and RNA polymers

differ a bit in their structure. DNA is made of a polymer of nucleotides that have 3' (read '3 prime') hydroxyl groups on their ribose sugars. On the other hand, RNA is made of a polymer of nucleotides that have both 2' and 3' hydroxyl groups.

sexual dimorphism

differences in appearance of males and females

Alternative splicing

different mRNA molecules are produced from the same pre-mRNA primary transcript.

At the lungs, CO2

diffuses out of the plasma. The CO2 in the plasma is in bicarbonate form, so it has to re-enter the RBC where the carbonic anhydrase enzyme will catalyze the reverse reaction to turn it back into CO2. It will then diffuse out to the lungs.

Direct hormones

directly stimulate other organs

● Steroid hormones are lipid-soluble, hence they

directly stimulate receptor cells.

gene

distinct unit, or sequence, of genetic material that codes for a trait.

Antibodies are typically Y-shaped, consisting of a light chain and a heavy chain linked through

disulphide bonds.

S Phase

dna synthesis: second molecule of DNA replicated from the first, provides sister chromatids.

Stop codons

do not code for amino acids. Rather, they tell ribosomes to disassociate from mRNA and end protein translation. The stop codons in mRNA are UAA, UAG, and UGA.

passive transport

does not require the direct use of ATP Facilitated diffusion

When tryptophan levels are high

domains three and four of the RNA transcript will attach, forming an attenuation hairpin loop. The attenuation loop will prevent ribosomes from translating the RNA transcript into protein. In this way, the structural proteins for tryptophan synthase are not made.

Saturated fatty acid tails lack

double bonds and are straight chains that pack together closely In response to warm temperature, a cell would ↑ saturated fatty acids in the membrane to increase rigidity and avoid excess fluidity

Unsaturated

double bonds present Better for health: unsaturated = double bonds cause branching = stack less densely

In anaphase, the chromosome number

doubles

Avian Respiration

drastically different than human respiration. Due to the unique anatomy of birds, respiration is both continuous and unidirectional.

Blastopore

during gastrulation, the blastopore has the potential of developing into the mouth or the anus. The blastopore opens into the archenteron.

alveoli

each bronchiole branches ends in these small sacs, which are surrounded by blood-carrying capillaries. there are two types of epithelial cells in human alveoli:

alveoli

each bronchiole branches ends in these small sacs, which are surrounded by blood-carrying capillaries. there are two types of epithelial cells in human alveoli: *type 1*: structural support *type 2*: produces surfactant *surfactant* reduces the surface tension within the alveoli. it prevent water from collapsing alveoli.

At the end of anaphase,

each pole has a complete set of chromosomes, same as the original cell before replication.

Genetic Variation: Sexual reproduction

eads to genetic recombination via crossing over, independent assortment, and random joining of gametes.

Pyruvate commits to either

either aerobic cellular respiration or fermentation based on the presence of oxygen.

the nervous system uses what kind of signals?

electrical (action potentials)

The SA node spreads contraction to surrounding cardiac muscles via

electrical synapses made from gap junctions.

covalent bond

electrons are shared between atoms.

dipole

electrons spend more time around one atom, giving that atom slight negative charge and the other a slight positive charge.

For experimental purposes, bacteria can be made competent in a lab via

electroporation

Next, bacteria must then be "made competent" to take up the plasmid, accomplished via

electroporation (a brief electrical pulse applied to a solution with cells, creating temporary holes in plasma membrane through which DNA can enter) or a combination of heat shock + CaCl2.

Lipases

enzymes that break down fats into fatty acids and glycerol or other alcohols.

Lipases

enzymes that break down fats into fatty acids and glycerol or other alcohols. ● Lipases in adipose tissue are hormone sensitive (e.g. to glucagon). ● Fatty acids combine with albumin in the blood which carries them. ● Between meals, most lipids of plasma (mainly fatty acids) are in the form of lipoproteins. Some forms of lipoproteins found are chylomicrons (large microproteins), low-density lipoproteins (LDL), and high-density lipoproteins (HDL). Low density lipoproteins have a low density of proteins and a high fat density. They are considered unhealthy. High density lipoproteins have a high protein density and a low fat density. They are considered healthy.

Aminoacyl-tRNA synthetases

enzymes which couple tRNA to the amino acid it represents. Aminoacyl-tRNA synthetase binds to an amino acid as well as an ATP molecule. The enzyme hydrolyzes ATP to power the coupling reaction.

trachea

epiglottis covers the trachea during swallowing - ring cartilage (C-shaped) covered by *ciliated mucus cells.*

there are 4 types of tissues

epithelial (skin, internal covering), connective (bone, cartilage, blood), nervous, and muscle

nonpolar covalent bond

equal sharing of electrons between atoms. electronegativity of atoms are equal. ex) Cl2

If tissues do not receive enough oxygen, the kidneys can synthesize and secretes a hormone called

erythropoietin (EPO) to stimulate generation of more erythrocytes in bone marrow.

Yellow bone marrow

essentially just energy stored as fat.

Post-transcriptional modification

eukaryotic pre-mRNA is modified into processed mRNA. Processed mRNA is able to exit the nucleus (through a nuclear pore) and enter the cytoplasm, which is where translation occurs.

Protein denaturation usually occurs from

excess temperature, chemical stress, pH variance, heavy metal salts, and radiation. A protein's 3D structure is critical to its function -loss of shape due to denaturation leads to loss of function.

Hemorrhage

excessive bleeding results in a decrease in arterial pressure which is sensed by *arterial baroreceptors*. The body compensates for this reduced blood pressure by increasing the heart rate and systemic vascular resistance. ● Blood pressure has fallen so the body wants to raise it. Thus the body, wants to increase cardiac output via an increase in heart rate and an increase in systemic vascular resistance.

Hemorrhage

excessive bleeding results in a decrease in arterial pressure which is sensed by arterial baroreceptors. The body compensates for this reduced blood pressure by increasing the heart rate and systemic vascular resistance.

inside the lungs, as we inhale, the volume of the lungs

expands as the diaphragm drops. By doing so, we create a negative pressure relative to the atmosphere, causing air to rush in. The thoracic pressure decreases as the thoracic cavity size increases.

sliding filament model of muscle contraction

explains how myofilaments slide past one another to shorten the sarcomeres of a muscle cell, leading to contraction of the muscle as a whole.

To ensure efficient production of a gene that has been added to a plasmid,

expression vectors are often used - these vectors contain a highly active promoter upstream of the restriction site where new genes are added for maximum output.

The pace of the SA node

faster than the normal heartbeat but the parasympathetic vagus nerve innervates the SA node. This slows down the contractions.

Deoxygenated hemoglobin has a higher affinity for

for CO2 than does oxygenated hemoglobin. This is because hemoglobin without oxygen acts as a blood buffer by accepting H+. This reduced hemoglobin has a higher capacity to form carbaminohemoglobin rather than the oxygen carrying kind, explaining how the Haldane effect occurs.

Oparin and Haldane

formulated the organic "soup" theory. The theory states if there was O2 (very reactive) in the atmosphere, no organic molecules would have formed. Oparin's hypothesis was that the original Earth environment was reducing.

Enzymes can catalyze reactions in both

forward and reverse directions based on substrate concentration.

Dizygotic twins

fraternal twins. In this case, the mother ovulates two eggs and both eggs are individually fertilized by two different sperms. This leads to two different zygotes with slightly different genetic material (due to crossing over in meiosis).

Ribosomes

function in the synthesis of proteins. ● Ribosomes are made of rRNA and ribosomal proteins. ● Free ribosomes (those not attached to the endoplasmic reticulum) tend to make proteins that function within the cytosol of the cell.

chitin

functions as a structural molecule in fungal cell walls & arthropod exoskeletons. structurally similar to cellulose but with nitrogen-containing groups attached to each B-glucose ring.

glycogen

functions to store energy in animal cells. differs from starch in its polymer branching.

starch

functions to store energy in plant cells. consists primarily of amylose and amylopectin.

vector

functions to transfer foreign DNA into another cell. ● Examples of vectors include plasmids and bacteriophages

the most important decomposers

fungi some *bacteria* also play a role these cells/organisms *break down* the dead or decaying matter, which becomes a component of detritus

diffusion between alveolar chambers and blood

gas exchange across moist, sac membranes of alveoli via *simple diffusion.* O2 diffuses through alveolar wall, through pulmonary capillary wall, into blood, and into red blood cells. (CO2 is opposite). greater distance = lower efficacy

maternal effect gene

gene that when mutated in the mother results in a mutant phenotype in the offspring regardless of the offspring's own genotype. ▪ How does this happen? The mRNA or protein products of a maternal effect gene are placed in the egg while in the mother's ovary. If the mother has a mutated maternal effect gene → defective gene product → eggs end up defective. ● E.g. Egg-polarity genes (control the orientation of the egg) in flies. ▪ Maternal effect mutations are usually embryonic lethal.

Sex-linked genes

genes that reside on a sex chromosome. ● Example: the gene that causes color blindness is located on the X-chromosome, so it is said to be sex-linked. ● A consequence of women having two X chromosomes (XX) and men having just one (XY) is that men are more likely to have X-linked diseases; when a male inherits an affected X allele from his mother the affected gene will be expressed regardless of whether is dominant or recessive because there is no second copy of the gene on the Y chromosome to potentially mask its effect.

To introduce foreign DNA into a bacterium, we must first

get the foreign DNA into a plasmid. The plasmid is treated with the same restriction enzymes as the foreign DNA so the same sticky ends bind. DNA ligase stabilizes the attachments; then the plasmid is introduced into bacterium by transformation.

Viviparous organisms

give birth to live young.

glucose is not only broken down, but also can be produced via

gluconeogenesis

Photosynthesis produces

glucose

Two cycles of the Krebs cycle occur for

glucose because 2 pyruvates are made from 1 glucose in glycolysis.

The lac operon will only be induced to become active if

glucose is not present but lactose is. This further shows how the general purpose of an operon is to conserve cellular resources until they are required. In this case, E. coli do not want to wastefully produce lactose metabolic proteins if they are not needed.

Both fermentation and aerobic cellular respiration use

glycolysis and produce a pyruvate.

Erythrocytes get energy from

glycolysis since they lack organelles. This includes the mitochondria.

brain outer cortex is composed of

grey matter (neuronal cell bodies),

Tissue found in the root and stem of a plant can be broken up into three main categories:

ground tissue, vascular tissue, and dermal tissue

molecules

groups of 2 or more atoms joined via chemical bonds. chemical bonds are due to electron interactions.

Thigmotropism

growth in response to contact (for example a vine growing up a wall).

sarcolemma

has invaginations into the muscle cell that form tubes - these are the *T-tubules*. The T-tubules allow the action potential initiated on the muscle fiber to spread throughout the cell very quickly, ensuring a coordinated contraction.

Deuterostomes

have a blastopore that forms the anus. Embryonic cleavage of a deuterostome is radial and indeterminate.

Annelids

have a closed circulatory system. The blood is confined to vessels. The dorsal vessel functions as the main "heart" or pump; aortic arches link the dorsal and ventral vessels together which function in pumping blood. ● An example of an annelid is an earthworm. ● The same circulatory system is seen in certain mollusks (octopus and squid) and vertebrates. ● The path of the blood that moves away from the heart is aorta → arteries → arterioles → capillaries. ● The path of the blood back to the heard is capillaries → venules → veins. Mucus secreted by earthworm provides moist surface for gaseous exchange by diffusion. Circulatory system brings O2 to cells and waste products (CO2) back to skin for excretion.

Transgenic animals

have a gene introduced from the genome of another individual (often a different species).

Low density lipoproteins

have a low density of proteins and a high fat density. They are considered unhealthy. High density lipoproteins have a high protein density and a low fat density. They are considered healthy.

Prokaryotes

have a plasma membrane, DNA molecule, ribosomes, cytoplasm and cell wall (features also present in eukaryotic cells). Bacteria, Cyanobacteria, Archaebacteria Smaller (1‐10 um) Usually unicellular (some multicellular Cyanobacteria) Nucleus absent Single circular dsDNA Not wrapped around proteins (no chromatin). Present in a region of the cell called the *nucleoid* May also have plasmids No membrane bound cellular organelles Universally Present More complex cell wall structure formed from different molecules (*Peptidoglycan* in Bacteria; Polysaccharides in Archaebacteria). Many have sticky cell capsules surrounding the cell wall. Ribosomes: Smaller (*70S*) Subunits: 50S + 30S Smaller flagella Made from one protein filament *Flagellin* Powered by a proton pump in a rotatory movement Reproduction typically via *binary fission*

Cnidarians

have body walls 2 cells thick, and therefore all cells are in direct contact with either the internal or external environment. An example of this is the hydra.

Allosteric enzymes

have both an active site (for substrate binding) and an allosteric site (for binding of an allosteric effector - can be an activator or inhibitor)

Capillaries

have the smallest diameter and consist of a single layer of endothelial cells. Across this layer, gases, nutrients, enzymes, hormones, and waste diffuse.

Capillaries

have the smallest diameter and consist of a single layer of endothelial cells. Across this layer, gases, nutrients, enzymes, hormones, and waste diffuse. ● There are four methods for material to cross capillary wall: endocytosis and exocytosis (proteins), diffusion through capillary cell membrane (O2 and CO2), movement through pores in the cells (called fenestrations), movement through space between the cells (ions). ● Sometime pericytes (contractile cells) around the capillaries and venules throughout the body. ● Precapillary sphincters regulate the passage of blood into capillary beds. ● Capillaries exchange substances from the blood with the interstitial fluid that surrounds tissue cells. Two factors are important to consider: the blood hydrostatic pressure (pressure exerted from flow of blood pushing against the blood vessel) and the blood colloid osmotic pressure (osmotic pressure exerted by the blood proteins present in the plasma, notably albumin- want to pull water in, aka oncotic pressure). The tissue also has osmotic and hydrostatic pressure but they play minor roles. The blood flowing in from the capillaries has a high hydrostatic pressure. It is so high that it overcomes the blood colloid oncotic pressure working against it. Net filtration at the capillary end of the bed is therefore fluid moving outward. However, towards the end of the capillary bed, blood hydrostatic pressure has decreased enough that the blood colloid osmotic pressure overcomes it, and fluid flows back inward, resulting in net reabsorption at the venous end.

antibodies constant regions

have very similar amino acid coding sequence (antibody is a protein after all!) within a particular class of antibodies.

Sarcomeres

he functional unit of muscle fibers, which shorten to facilitate muscle contraction.

retina

he innermost layer. It is light-sensitive and utilizes specialized photoreceptor cells, the rods and cones.

Nucleolus

helps produce ribosomes inside the nucleus. rRNA is synthesized in the nucleolus. Ribosomal proteins are imported from cytoplasm and together with rRNA form ribosomal subunits. These subunits are exported to the cytoplasm for final assembly into complete ribosomes.

Bohr effect

hemoglobin O2 binding affinity decreases under conditions of low pH (high [CO2] and [H+]), causing oxygen loads to be released by hemoglobin because both O2 and H+ compete for binding at hemoglobin molecule.

In tissues, where CO2 concentration is high, O2 is released by

hemoglobin and CO2 is picked up.

Most seedless tracheophytes are

heterosporous (can produce both male and female spores).

Two important contents of the granules are

histamine and heparin.

DNA wraps around proteins called

histones

dsDNA wrapped around proteins called

histones form multiple chromosomes. Contained within the membrane‐bound nucleus Membrane bound cellular organelles present (Endoplasmic Reticulum, Golgi Apparatus, Mitochondria, Chloroplasts, etc.)

Sliding clamp proteins

hold DNA polymerase to the template strand.

The integumentary system is key to many

homeostatic functions such as heat and moisture regulation, and it is needed for production of vitamin D and protection from pathogens.

Meiosis I

homologous chromosomes pair at the plate, and migrate to opposite poles. There is no separation of sister chromatids. During Prophase I, the following critical structures and processes are observed: ● *Synapsis* is when the homologous chromosomes pair up. These pairs are referred to as *tetrads* (groups of 4 chromosomes) or bivalents. ● The *chiasmata* is the region when crossing over occurs of non-sister chromatids. ● The *synaptonemal complex* is a protein structure that temporarily forms between homologous chromosomes. This gives rise to the tetrad with chiasmata and crossing over.

metaphase I

homologous pairs are lined up across the metaphase plate. microtubules are attached to kinetochores of one member of each homologous pair.

anaphase I

homologous pairs within tetrads uncouple and are pulled to opposite sides (*disjunction*)

Lipases in adipose tissue are

hormone sensitive (e.g. to glucagon).

Tropic hormones

hormones which target and act on *other endocrine glands*, which will release their own hormones *Releasing hormones* (discussed above) from the hypothalamus are also considered tropic hormones, as they are hormones which target the anterior pituitary gland.

Heat capacity

how much a substance changes temperature in response to gain/loss of heat. A high amount of energy must be used to raise the temperature of water.

feedback systems

how our body manages and keeps all hormones under control.

The process by which chromatin is either tightly or loosely packed has to do with

how tightly DNA binds with histones.

dihybrid cross

identical to a monohybrid cross, except two different genes are studied concurrently. Gene loci must be on separate chromosomes for this experiment to be successful. To determine probabilities in a dihybrid cross, it is often easier to calculate the probability of each gene separately, then multiply the results together.

Monozygotic twins

identical twins. In this case, one fertilization gives rise to one zygote, which then divides to form two separate embryos. The two embryos have the exact same genetic material, that's why they become identical twins.

helper T cells (CD4 cells)

if an antigen is presented by *MHC II*: ● T cells activate and become *helper T cells*, also called *CD4 cells* They are called CD4 cells because they form a *co-receptor* CD4 in addition to its original TCR. ● Helper T cells are there to assist both innate and adaptive immunity. ○ They release *cytokines* to ramp up the immune response. ● Functions of cytokines: ○ Attract innate immunity cells e.g. macrophages, dendritic cells to where the identified antigen is present. ○ Stimulate clonal selection and proliferation of B cells and T cells

Antibodies are also known as

immunoglobulins

chemiosis

in Mitochondria the mechanism of ATP generation that occurs when energy is stored in the form of a proton (H+) concentration gradient across a membrane.

Attenuation is based on the fact that

in bacteria, transcription of DNA into mRNA can occur at the same time mRNA is translated into protein. Translation cannot occur at the same time as transcription in eukaryotes. We will see more on why this is true in a little while.

Extranuclear inheritance

in eukaryotes, genes also exist outside the nucleus, and can be found in mitochondria and chloroplasts. Defects in mitochondrial DNA can reduce cell's ATP production. Mitochondria passed to the zygote all come from the mother, so all mitochondrial related diseases are maternally inherited. ▪ DAT Tip: Mitochondria have their own 70S ribosomes that make mitochondrial proteins within the mitochondrial matrix!

Storage vacuoles

in plants store starch, pigments, and toxic substances (e.g. nicotine).

Contractile vacuoles

in single-celled organisms that collect and pump excess water out of the cells (prevent bursting). ● Utilizes ACTIVE TRANSPORT. ● Found in organisms that live in hypotonic environments in which it is necessary to pump out water to prevent lysing.

frameshift mutation results

in the 'reading frame' of an RNA transcript being shifted, causing different amino acids to be translated and resulting in impaired protein structure.

Cholesterol

in the plasma membrane of animals also influences fluidity ▪ In high temperatures, cholesterol molecules prevent phospholipids from Nucleic Acids excess movement, prevent excess fluidity ▪ In low temperatures, cholesterol molecules prevent phospholipids from packing together too closely, preventing excess rigidity ▪ Sterols provide similar function in plant cells. Prokaryotes use hopanoids instead of cholesterol in their plasma membranes.

Anchoring junctions

include *desmosomes* (keratin filaments within the cell attached to adhesion plaques which bind adjacent cells together via connecting adhesion proteins), *hemidesmosomes*, and *adherens junctions*. Provide mechanical stability and hold cellular structures together. These are present in animal cells in tissues with mechanical stress such as skin epithelium, cervix and uterus.

Microtubule organizing centers (MTOCs)

include CENTRIOLES and BASAL BODIES (found at the base of each flagellum and cilium and organize their development). Organized in a 9x3 array. Note: Plant cells lack centrioles and its division is by cell plate instead of cleavage furrow, but plants do have MTOC's.

Purines

include adenine and guanine, and have 2 rings.

Eukaryotes

include all organisms except for bacteria, cyanobacteria, and archaebacteria. Plants, Animals, Protists, Fungi Larger (10‐100 um) Usually Multicellular Nucleus present dsDNA wrapped around proteins called *histones* form multiple *chromosomes*. Contained within the membrane‐bound nucleus Membrane bound cellular organelles present (Endoplasmic Reticulum, Golgi Apparatus, Mitochondria, Chloroplasts, etc.) Cell wall present only in Plants (cellulose) and Fungi (chitin) Ribosomes Larger (*80S*) Subunits: 60S + 40S Flagella larger Made from *Tubulin* Microtubules arranged as *9 doublets surrounding 2 singlets*. Powered by ATP in a bending movement Typically via *mitosis*

Appendicular skeletons

include the bones found in the appendages, as well as the pectoral and pelvic girdle

Pyrimidines

include thymine and cytosine, and have 1 ring. ● An easy way to remember the pyrimidines: CUT the PYE (Cytosine, Uracil, Thymine).

Cytoskeleton

includes microtubules, microfilaments, and intermediate filaments. In eukaryotic cells, it aids in cell division, cell crawling, and the movement of cytoplasm and organelles. The cytoskeleton is found in both prokaryotes and eukaryotes.

Aquaporins

increase the rate of H2O passing (kidney and plant root cells).

● Peptide hormones are water-soluble, hence they

indirectly stimulate receptor cells.

Enzymes bind at the active site via

induced fit - enzyme binding is specific to structure.

Southern Blotting

initially begins with the process of *gel electrophoresis*. After electrophoresis is performed, the DNA fragments are separated into single strands and then transferred to a nitrocellulose membrane. A probe is then added that will hybridize and mark the target DNA fragment.

genes

instructions for making things our cells need to function, grow, and divide. Proteins are a major structural and functional component of cells, and many of our genes code for proteins. In order for cells to convert these genetic instructions into functional proteins, they must first be *transcribed* into RNA and then *translated*.

Midbrain

integral to control of motor movement and processing of auditory and visual stimuli.

Fast oxidative glycolytic fibers

intermediate in diameter and have *strong* contractions. These fibers also appear *dark red* because they have many blood capillaries, a high amount of myoglobin, and many mitochondria. They use oxygen to generate ATP via *aerobic respiration*; however, these types of fibers also *store glycogen*, which allows them to generate ATP via *anaerobic respiration*. Their twitch occurs about two times as fast as a type I fiber and they are reasonably *efficient*; although, they are *susceptible to fatigue*.

90% of the cell cycle is spent in

interphase

Before mitosis, chromatin condenses

into chromosomes.

Genetic Variation: Mutation

introduces a new allele.

Chromosomal aberrations

involve changes to segments of DNA - Duplications - Inversions - Translocations

Rho-dependent termination

involves a protein called Rho, which binds to the Rho binding site of the RNA transcript. ● Note: the information for the Rho binding site is encoded by the DNA, which is why it is ultimately expressed by the RNA transcript.

intramolecular bonds

ionic and covalent bonds

In the presence of high [CO2] and [H+], the hemoglobin structure

is altered to the reduced form that will release its oxygen.

Competency is useful because

it increases a bacteria's genetic diversity.

When an (F+) bacteria conjugates with an (F-) bacteria,

it transfers the F plasmid to that cell. This makes the (F-) bacteria (F+). This bacteria now contains the F factor and can conjugate with other bacteria. Other genetic information can be contained on the F plasmid and be laterally transferred during conjugation. ● Example: antibiotic resistance genes can be passed with the F plasmid, which is one way resistance can spread.

glycosidic linkage

joined by dehydration

Northern Blotting

just like Southern Blotting, but for RNA molecules.

DAT Pro-Tip: prokaryotes

lack a nuclear membrane; both transcription and translation can occur in the cytosol at the same time. The prokaryotic ribosome can translate an mRNA transcript as RNA polymerase is continuing to transcribe it.

Central vacuoles

large, and occupy most of plant cell interior. They exert TURGOR when fully filled to maintain rigidity. ● Central vacuoles also store nutrients and carry out functions performed by lysosomes in animal cells. ● Have a specialized membrane called the TONOPLAST.

Large arteries have

less smooth muscle (per volume) than medium sized ones. The larger ones are less affected by the sympathetic nervous system, but the medium sized arteries can constrict enough to reroute blood.

cAMP (cyclic adenosine monophosphate)

levels are inversely related to glucose levels. If glucose is high, cAMP levels are low. Alternatively, if glucose is low, then cAMP levels will be high. cAMP binds to *catabolite activator protein (CAP)*. CAP bound to cAMP will bind upstream of the promoter region and help to attract RNA polymerase. This will increase the rate of transcription when glucose levels are low, leading to more mRNA transcripts. More mRNA transcripts mean more translation into functional lactose metabolic proteins. Let's take a look at some scenarios: *Lactose present, glucose absent*: the lac repressor is not bound because allolactose is present. cAMP is high because glucose is absent. CAP is bound near the promoter because the levels of cAMP are high. The lac operon has been induced ● High transcription and high utilization of lactose occurs because the lac repressor protein is not bound; although, CAP is bound. CAP binding means that there is increased RNA polymerase attraction to the operon. *Lactose absent, glucose present*: the lac repressor protein is bound because allolactose is absent. Levels of cAMP are low because glucose is abundant. CAP is not bound near the promoter because of the low cAMP levels. The operon is turned off because of the lac repressor protein and the fact that CAP is not bound. *Lactose absent, glucose absent*: the lac repressor protein is bound to the operator region because allolactose is absent. Levels of cAMP are high because glucose is absent. CAP is bound upstream of the promoter because of the high cAMP levels. The operon is turned off because of the lac repressor protein. *Lactose present, glucose present*: the lac repressor protein is not bound because allolactose is present. cAMP is low because glucose is abundant. CAP is not bound because levels of cAMP are low. The operon has been induced. ● Only moderate transcription and low utilization of lactose occurs because the lac repressor protein is not bound; however, CAP is not bound either. No CAP binding means that there is reduced RNA polymerase attraction to the operon.

Photosynthesis begins with

light-absorbing pigments in plant cells that are able to absorb energy from light: chlorophyll a, b, and carotenoids (red, orange, yellow). Light is incorporated into electrons and excited electrons are unstable and re-emit absorbed energy. The energy is then reabsorbed by electrons of nearby pigment molecules.

Tube feet

like little suction cups that echinoderms 'walk' around on. They also use their tube feet to obtain food.

endosteum

lines the medullary cavity

lipoproteins

lipid core surrounded by phospholipids and apolipoproteins). Lipids are insoluble are must be transported in the blood via lipoproteins.

Between meals, most lipids of plasma (mainly fatty acids) are in the form of

lipoproteins

peroxisomes are common in

liver and kidney where they breakdown toxic substances.

Association (interneuron) neurons

located in the brain and spinal cord. They receive information (impulses) from sensory neurons and send information (impulses) to motor neurons. They are considered *integrators* because they evaluate sensory stimuli and form an appropriate response to it. ▪ 99% of neurons fall into this category. ▪ They are not required for some reflex arcs.

AV node

located in the lower wall of the right atrium/interatrial septa. It sends impulses through the *bundle of His* which passes between both ventricles. It branches into the ventricles via the *purkinje fibers* which results in the contraction of both ventricles simultaneously.

SA (sinoatrial) node or pacemaker

located in the upper wall of the right atrium. It is a group of specialized cardiac muscle cells that initiate by contracting both atria and sending impulses to stimulate the *AV (atrioventricular) node*. ● The SA node spreads contraction to surrounding cardiac muscles via electrical synapses made from gap junctions. ● The pace of the SA node is faster than the normal heartbeat but the parasympathetic *vagus nerve* innervates the SA node. This slows down the contractions.

SA (sinoatrial) node or pacemaker

located in the upper wall of the right atrium. It is a group of specialized cardiac muscle cells that initiate by contracting both atria and sending impulses to stimulate the AV (atrioventricular) node.

Euchromatin

loosely packed DNA it is easy for RNA polymerases to access the DNA code and transcribe our genes.

Proteins and large particles that cannot be taken up by capillaries are removed to

lymph

After they cross into the infected tissue through diapedesis, monocytes mature into

macrophages

The most common APCs that serve T cells are

macrophages, dendritic cells, and B cells

Microfilaments

made up of ACTIN and are involved in cell motility. Structures that are made up of microfilaments include skeletal muscle, amoeba pseudopod and cleavage furrow (a structure associated with cytokinesis).

atom

made up of neutrons, protons, and electrons

Microtubules

made up of the protein tubulin and provide support and motility for cellular activities E.g. spindle apparatus which guides chromosomes during division; E.g. FLAGELLA and CILIA (9+2 array; 9 pairs + 2 singlets in center) in all animal cells and lower plants (mosses, ferns). COLCHICINE is an alkaloid that will inhibit polymerization of microtubules.

Homeothermic animals

maintain a stable internal temperature in response to various external temperatures.

Phosphate buffer system

maintains the pH of internal fluids of all cells. ● H2PO4- and HPO42- act as acid and base (amphoteric). Bicarbonate is an extracellular buffer.

Mitochondria

make ATP and participate in fatty acid CATABOLISM (β-OXIDATON) (fatty acids are made in cytosol but broken down in the mitochondria). ● Have their own CIRCULAR DNA and ribosomes (evidence supporting the ENDOSYMBIOTIC THEORY). ● Have a DOUBLE LAYERED MEMBRANE. ● Cells with high energy requirements have a lot of mitochondria relative to other cells - e.g. heart and kidney cells.

Deacetylation

makes histones more positively charged, making them more tightly bound to negatively charged DNA. Since the DNA is more tightly bound, there is a *decrease* in transcription levels.

Monotremes

mammals that *lay eggs* e.g. platypus

Marsupials

mammals that carry their babies in a *pouch* e.g. kangaroo, koala

myofibrils

many strands of contractile protein in muscle fiber

Indeterminate cleavage

means cell fate isn't set early, and then if a cell was split off—this cell has complete potential and can go on to form a separate organism; when this happens in humans we get identical twins!

Determinate cleavage

means that the fate of the cell (ie. what that cell can develop into) is set or determined early on.

specificity constant

measures how efficiently an enzyme converts a substrate into product ▪ ↑ specificity constant = ↑ enzyme efficiency and substrate affinity ● ↑ substrate concentration = ↑ rate of reaction (until a point - when all enzyme molecules become fully saturated by substrate)

Receptor proteins

membrane proteins that bind ions and signaling molecules, causing changes on a cellular level. ex) insulin receptors, ligand‐gated ion channels

Platelets are small portions of

membrane-bound cytoplasm torn from megakaryocytes.

A third type of T cells that form after clonal selection is

memory T cells.

anaphase

microtubules shorten. each chromosome is pulled apart into two chromatids (once separated, each chromatid is considered a chromosome). chromosomes pulled to opposite directions (*disjunction*). at the end of this phase, each pole has a complete set of chromosomes. shortest step of mitosis.

Mammary glands

milk producing glands of female mammals.

Interphase begins after

mitosis and cytokinesis are complete. It consists of a G1, S, and G2 phase.

The cell cycle consists of

mitotic phases (mitosis, cytokinesis) + interphase (G1, S, G2 phases).

In plant cell, peroxisomes

modify the by-products of photorespiration. In germinating seeds, they are called GLYOXYSOMES.

Ribosomes

molecular machines composed of ribosomal RNA (rRNA) and protein. They are made of one *small* and one *large subunit*, which clamp around mRNA to form a complete ribosome. Ribosomes can be found *freely floating* in the cytosol or bound to the *rough endoplasmic reticulum* (eukaryotes only!). Their primary goal is to assist complementary base pairing between codons and anticodons, which is how polypeptide proteins are made during translation.

anaerobic respiration takes place in simple plants when

molecular oxygen is lacking

Evidence suggests the cell cycle is regulated by

molecular signals in the cytoplasm.

summary of cells involved in the innate immune response

monocytes --> macrophages neutrophils dendritic cells natural killer cells mast cells eosinophils basophils

Disaccharides are hydrolyzed into

monosaccharides, most of which can be converted to glucose or glycolytic intermediates.

cancellous bone

more spongy.

Molluscs

mostly have an open circulatory system except for cephalophods (closed, large O2 demands, gill hearts).

Transport vacuoles

move materials between organelles or organelles and the plasma membrane.

Transport proteins

move substances across a membrane.

motion proteins

movement generated at a cellular or at the level of the entire organism. ex) tubulin (flagella ‐cell movement), actin and myosin (skeletal muscles - organism movement)

transport proteins

movement of substances within and between cells. ex) hemoglobin (transport oxygen), cytochromes (carry electrons)

the middle ear functions to

mplify sounds and transmit auditory information to the inner ear, and it consists of the tympanic membrane and the ossicles.

Metabolism

muscle contraction and other metabolic activities generate heat.

Agonists

muscles involved in performing a desired motion

synergists

muscles that help *primary movers* and provide support to the joints

Sarcomeres contain an array of long, filament proteins, called

myofilaments

Desmotubules

narrow tubes of endoplasmic reticulum within *plasmodesmata*. Plant cells exchange material through cytoplasm surrounding the desmotubule.

Plasmodesmata

narrow tunnels between *plant cells*.

Gap junctions

narrow tunnels between animal cells (formed from *connexin* proteins) Prevent cytoplasms of adjacent cells from mixing, but allow passage of ions and small molecules Essentially channel proteins of two adjacent cells that are closely aligned These are present in *animal cells*. ● Tissues like the heart have these to pass electrical impulses.

Endomembrane system

network of organelles and structures, either directly or indirectly connected, that function in THE TRANSPORT OF PROTEINS and other macromolecules into or out of the cell

Endomembrane system

network of organelles and structures, either directly or indirectly connected, that function in THE TRANSPORT OF PROTEINS and other macromolecules into or out of the cell. Includes plasma membrane, endoplasmic reticulum, Golgi apparatus, nuclear envelope, lysosomes, vacuoles, vesicles, and endosomes but NOT the mitochondria or chloroplasts.

the most numerous and common type of leukocytes.

neutrophils about 40-70% of leukocytes are neutrophils!

Saturated

no double bonds Bad for health: saturated = straight chains = stack densely and form fat plaques

When environmental tryptophan levels are low,

no tryptophan is available to bind to the tryptophan repressor protein. This means that the trp repressor is inactive in the absence of environmental tryptophan

Glial cells

non-neuronal cells that provide neurons with support and protection. *Central Nervous System*: Oligodendrocytes Astrocytes Microglia Ependymal Cells *Peripheral Nervous System:* Satellite Cells Schwann Cells

Cofactors

non-protein molecules that assist enzymes (usually by donating or accepting some component of a reaction like electrons)

Since they do not have a specific target, we describe the innate immunity as a

nonspecific immune response.

Gas Exchange in Humans Overview

nose pharynx larynx trachea bronchi --> bronchioles alveoli diffusion between alveolar chambers and blood bulk flow of O2 diffusion between blood cells bulk from of CO2

The X chromosome that is inactivated can differ from cell to cell - as a result,

not all cells in a female mammal are necessarily functionally identical.

viruses

not considered to be living from a biological perspective

During the third step of glycolysis,

nother phosphate is added to an isomer of glucose-6-phosphate to form fructose 1,6-bisphosphate via the enzyme phosphofructokinase. This is irreversible and commits the glucose to glycolysis. This is a major regulatory point!

telophase

nuclear division. nuclear envelope develops. chromosomes --> chromatin nucleoli reappear

telophase I

nuclear envelop develop.s each pole forms a new nucleus that now has half the number of chromosomes - chromosome reduction phase to haploid.

prophase II

nuclear envelop disappears, spindle develops. no chiasmata. no crossing over.

telophase II

nuclear envelope develops and cytokinesis occurs. at completion of meiosis II, there are now 4 haploid cells.

platelets lack

nuclei

Prophase

nucleolus disassembles. chromatin condenses into chromosomes, nuclear envelope breaks down. mitotic spindle forms and microtubules (composed of tubulin) begin connecting to kinetichores).

Genetic Building Blocks

nucleotides and nucleosides

prophase I

nucleus disassembles, nucleolus disappears, chromatin condenses, spindle formation. synapsis occurs as homologous chromosomes pair up to form *tetrads.* crossing over occurs at the chiasmata - this allows for genetic recombination that results in changes to nucleotide sequence.

Double capillary beds or portal systems

occur in the hepatic portal system and the hypophyseal portal system between the hypothalamus and the anterior pituitary gland. ● The stomach, intestines, spleen drain via the hepatic portal vein to the capillaries of the liver. ❖ In a portal system a capillary bed pools into another capillary bed without first going to the heart. ● Capillary bed 1 drains into the portal vein which then drains into capillary bed 2 which in turn drains into a vein that returns the blood to heart. ● This allows the body to transport products in high concentrations from one part to another part of the body without having to distribute it throughout the rest of the body. ● In the liver, the portal system allows it to screen for toxic substances that are absorbed from the digestive tract before the heart pumps it throughout the body. ❖ Non-mammals also have a renal portal system.

Inversions

occur when a chromosome segment is rearranged in the reverse of its original orientation

Duplications

occur when a chromosome segment is repeated on the same chromosome, and can occur from unequal crossing over

Eccentric contractions

occur when a muscle lengthens, despite tension being applied to the muscle fibers.

Concentric contractions

occur when a muscle shortens as it pulls the bone it inserts onto, closer to the bone it originates from.

Point mutations

occur when one nucleotide is replaced by a different nucleotide. For example, instead of a codon containing an adenine, it is replaced by a guanine. DAT Pro-Tip: cystic fibrosis, sickle cell anemia, and Tay-Sachs disease all result from point mutations.

Lactic Acid Fermentation

occurs in human muscle cells and other microorganisms. ❖ The chemical equation is Pyruvate → Lactate (and NADH → NAD+) ❖ Once an excess amount of ATP is available, lactate is transported back to the liver to be converted back to glucose via the *Cori cycle*. ❖ Muscles that are actively contracting have higher lactate levels compared to resting muscles.

Alcohol Fermentation

occurs in plants, fungi (e.g. yeasts), and bacteria (e.g. botulinum) ❖ The chemical equation can be broken down into two steps. 1. Pyruvate → Acetaldehyde +CO2 2. Acetaldehyde → Ethanol (and NADH → NAD+)

Alcohol Fermentation

occurs in plants, fungi (e.g. yeasts), and bacteria (e.g. botulinum) ❖ The chemical equation can be broken down into two steps. 1. Pyruvate → Acetaldehyde +CO2 2. Acetaldehyde → Ethanol (and NADH → NAD+) ❖ Acetaldehyde is the final electron acceptor! Acetaldehyde accepts the electrons to form the final product of ethanol. This is similar to O2 being the final electron acceptor of cellular respiration, thus forming the final product of H2O.

Aerobic respiration

occurs in the presence of O2 and is divided into four metabolic processes: glycolysis, pyruvate decarboxylation, Krebs cycle, and the electron transport chain. Water is the final product.

Anaerobic Respiration

occurs in the presence of no O2 in the cytosol. It includes glycolysis and fermentation. ❖ Aerobic Respiration regenerates NAD+ via O2 which is required for the continuation of glycolysis. ● Without O2 there would be no replenishing, resulting in the accumulation of NADH. This would result in cell death with no new ATP. Therefore, fermentation occurs.

transcription termination

occurs when RNA polymerase transcribes a sequence that says the gene is finished. These sequences are called *terminators*.

Transformation

occurs when a bacterial cell takes up extracellular DNA from it's environment and incorporates it into their chromosome. If a bacterial cell is able to take up extracellular DNA through this manner, it is referred to as *competent*. Competency is useful because it increases a bacteria's genetic diversity. For experimental purposes, bacteria can be made competent in a lab via electroporation. *Electroporation* is when brief electrical impulses are applied to a cell membrane, in order to create temporary holes through which foreign DNA can pass. Foreign DNA is typically introduced in the form of a plasmid. Introducing foreign DNA into a bacteria experimentally allows for the testing of gene products (proteins), based on the *central dogma of genetics*. The central dogma of genetics says that DNA makes mRNA, which ultimately makes protein that can be used by the cell.

Transformation

occurs when a bacterial cell takes up extracellular DNA from it's environment and incorporates it into their chromosome. If a bacterial cell is able to take up extracellular DNA through this manner, it is referred to as competent.

Founder effect

occurs when a small group of individuals become isolated from a larger population. This results in an allele frequency that is not the same as that of their population of origin.

Noncompetitive inhibition

occurs when a substance inhibits an enzyme by binding at a location other than the active site - the substrate still binds, but the reaction is prevented from completing ▪ Km remains the same but Vmax is lowered

Competitive inhibition

occurs when a substance that mimics the substrate binds at the active site. ▪ Competitive inhibition can be overcome by increasing substrate concentration ▪ Km is raised but Vmax remains the same

Electrical neurotransmission

occurs when an action potential travels directly from neuron to neuron through gap junctions, which electrically couple the cells. o Less common than chemical neurotransmission o Bidirectional - either of the neurons can be the pre- or post- synaptic neuron o Occurs throughout the brain, but much less is known about these types of synapses.

Internal fertilization

occurs when an animal's male gamete (sperm) penetrates another animal's (must be the same species) female gamete (ovum).

Bottleneck

occurs when population undergoes a sharp reduction in size due to natural catastrophe etc. This is vulnerable to genetic drift.

missense mutation

occurs when the change in the DNA code results in the codon now coding for a different amino-acid. In terms of effect, one changed amino-acid in a large protein may not be that detrimental to folding (and therefore function). *Conservative missense mutations* occur when the mutated amino-acid has the same properties as the unmutated amino-acid. Example: UUU codes for phenylalanine. If this codon is mutated to UUG it would code for leucine. Both are hydrophobic amino acids and would likely not change the overall protein function. *non-conservative missense mutation*: occurs when the mutated amino-acid does not share the same properties as the unmutated amino-acid. This could result in the protein folding incorrectly, and function being changed.

nonsense mutation

occurs when the codon is mutated to a stop codon. This causes the ribosome to disassociate from the mRNA transcript and no more protein is translated. A premature stop codon makes the protein shorter and can be detrimental to protein function. ● Example: UAC (which codes for tyrosine) undergoes a mutation to UAG (which is a stop codon). Translation stops prematurely and the protein is shorter. The severity of a nonsense mutation depends on where the mutation occurs. If it occurs near the end of the protein, the damage may be minimal because most of the protein has already been translated. The slight shortening may not be enough to change how the protein folds and functions. However, if the nonsense mutation does not occur near the end of the protein, the protein can be significantly shortened. The resultant protein may be non-functional if this occurs.

Termination

occurs when the replication fork can no longer progress forward. This may occur when two replication forks meet. Termination of replication can also occur at a specific point in the DNA. For example, some sequences of DNA encourage protein binding, which physically stops the replication fork.

Transduction

occurs when virus particles transfer bacterial DNA between different bacterial hosts. The process of transduction occurs when a bacteriophage infects a bacterium and enters the lysogenic cycle. ● DAT Pro-Tip: a *bacteriophage* is a virus that infects bacteria. When the bacteriophage enters the lytic cycle and assembles new phage particles, pieces of bacterial DNA can also be packaged within the particles. When these bacteriophage infect the next bacterial cell, the foreign bacterial DNA they are carrying can incorporate into the new host's genome and transfer new genes.

Larger veins

often have valves to aid in the transport of deoxygenated blood back to the heart due to fighting gravity.

hen the cell is not dividing, the DNA is packaged into

one of two types of chromatin. This packaged DNA (chromatin), reduces the volume of the DNA allowing it to fit inside the nucleus, and helps control which genes are transcribed and translated.

DNA is antiparallel

one strand's *5' end* is attached to the other strand's *3' end*. Each strand's bases face inward, creating complementary base pairs with the other strand through hydrogen bonding. If the template strand is 5'-GTAT-3', the antiparallel complementary strand will be 3'-CATA-5'. The *5' end* of DNA is the end that has a terminal phosphate group. The *3' end* has a terminal hydroxyl group.

an inducible operon is

one that is usually inactive, unless it is induced to become active.

Negative Feedback

original condition is canceled so that conditions are returned to normal

Preganglionic nerves

originate in the thoracic and lumbar portions of the spinal cord, and they synapse with postsynaptic nerves in ganglia just outside the spinal cord. The neurotransmitter released in this case is acetylcholine.

The first layer of innate immunity are

outer walls — physical and physiological barriers that prevent infection from entering the body. This is also the body's very first line of defense.

in eukaryotes, genes also exist

outside the nucleus, and can be found in mitochondria and chloroplasts. Defects in mitochondrial DNA can reduce cell's ATP production. Mitochondria passed to the zygote all come from the mother, so all mitochondrial related diseases are maternally inherited.

Female Anatomy Overview

ovary uterus cervix vagina

Cellular Respiration

overall an oxidative, exergonic process (∆G = -686 kcal/mole). ● During respiration, high energy H atoms are removed from organic molecules (dehydrogenation). o The chemical formula describing cellular respiration is C6H12o6 + 6O2 → 6 CO2 + 6 H2O + energy

The acetyl CoA from pyruvate decarboxylation merges with

oxaloacetate to form citrate. The cycle has 7 intermediates.

bulk flow of O2

oxygen diffuses out of RBC's, across blood capillary walls, into interstitial fluids, and across cell membrane. (CO2 is opposite).

*read* chromosome and chromosome numbers during mitosis and meiosis

page 54

Polymers of amino acids joined by

peptide bonds

Human Heart overview

pericardium pulmonary circuit systemic circuit right atrium right ventricle pulmonary artery pulmonary semilunar valve left atrium left ventricle

the esophagus pushes the bolus of food via

peristalsis

Flower Structures Overview

petals stamen anther pistil seed

Neutrophils are

phagocytes — they eat (phagocytosis) and destroy pathogens. They are part of the innate response because they are not picky eaters — they engulf all kinds of pathogens.

goiter

physical enlargement of the thyroid gland

B cells can differentiate into two types of cells with the assistance from helper T cells:

plasma cells and memory B cells

Endomembrane system includes

plasma membrane, endoplasmic reticulum, Golgi apparatus, nuclear envelope, lysosomes, vacuoles, vesicles, and endosomes

Acetylation

positively charged amino acids removes the positive charge, relaxing the electrostatic attraction between the histones and the DNA. This relaxation means DNA is more loosely packed and *increases* transcription levels.

hypothalamic-inhibiting hormones

preventing the anterior pituitary from releasing its hormones

left AV valve

prevents backflow into atrium.

aortic semilunar valve

prevents backflow into the ventricle

blood-brain barrier

prevents or slows the passage of drugs, ions, and pathogens into the CNS. It is permeable to oxygen, carbon dioxide, glucose, and general anesthetics.

lethal gene

prevents survival of an organism. ▪ Lethal alleles can be dominant, recessive, or conditional ▪ In a standard Aa x Aa cross, we would expect to see a 1:2:1 genotype ratio of AA:Aa:aa. If a recessive allele were lethal, we would see a characteristic 1:2 ratio of AA:Aa (since the aa condition would not survive).

ciliary epithelium

produces aqueous humor.

type 2 alveoli

produces surfactant

Operons are common in

prokaryotes as a way to regulate genes as a group; however, they are sometimes found in eukaryotes as well

Allolactose levels are

proportionally and directly related to lactose levels.

platelets produce

prostaglandins and other important enzymes.

examples of unicellular movement

protozoans move via cilia and flagella amoeba move via pseudopodia

Pasteur's swan neck flask experiment

proved that spontaneous generation was invalid - life cannot be created from non-life. ● Pasteur's experiment: a broth was kept in a flask with a curved neck (to prevent microorganisms in the air from entering the solution). The solution was then boiled to destroy all microorganisms. When the curved neck remained on, the broth remained free of microorganisms. If the curved neck was removed, microorganisms began to grow in the broth. This established that microorganisms did not arise spontaneously, but came from existing microorganisms (contamination in the air). 117 of 422

Cones

provide organisms with color-vision and are functional during times when there is high-intensity light. There are three different types of cone cells, each of which responds best to light within a certain range of wavelengths.

Intermediate filaments

provide support for maintaining cell shape. e.g. keratin.

Extracellular matrix (ECM)

provides *MECHANICAL SUPPORT* and helps bind adjacent cells. Found *IN ANIMALS*, in areas between adjacent cells (beyond the plasma membrane and glycocalyx). It is often occupied by fibrous structural proteins, adhesion proteins, and polysaccharides secreted by cells. Collagen is most common here, we also see *integrin and fibronectin*.

nitrogenous bases

purines and pyrimidines

G2 Phase

rapid cell growth. preparation of genetic material for cellular division. cell replicates its organelles.

Sensory (afferent) neurons

receive a stimulus from the environment and transmit that information to the brain. There are 5 types of sensory receptors.

Sensory (afferent) neurons

receive a stimulus from the environment and transmit that information to the brain. There are 5 types of sensory receptors. ▪ *Mechanoreceptors* sense touch. ▪ *Thermoreceptors* sense temperature. ▪ *Nociceptors* sense pain. ▪ *Electromagnetic* receptors sense light. ▪ *Chemoreceptors* sense taste, smell, and changes in blood chemistry (such as a change in oxygen saturation).

olfactory bulbs

receive and transmit information about smells.

It is possible for yellow bone marrow to convert to

red bone marrow if the blood cell supply is low.

When hemoglobin is saturated by oxygen, its capacity to hold CO2 is

reduced

surfactant

reduces the surface tension within the alveoli. it prevent water from collapsing alveoli.

Genotype

refers to the actual DNA sequence of a gene, while *phenotype* refers the observable characteristics of that gene's expression. ● E.g. the genotype for blue eyes could be ACGGT, while the phenotype would be the blue color ● For the purpose of Punnett Squares, genotypes are often simplified to dominant and recessive genotype forms as single letters rather than the entire nucleotide sequence An example genotype for eye color (Bb): B represents the dominant allele for brown eyes, and b represents the recessive allele for blue eyes.

Hemizygous

refers to the condition of having a single copy of a gene instead of two. ● E.g. men have two different sex chromosomes (XY), and are therefore hemizygous for the genes present on each chromosome.

Chloride Shift

refers to the exchange of bicarbonate and chloride across the membrane of RBC's. ● Carbonic anhydrase is contained in RBC's. ● Remember when CO2 enters the RBC, carbonic anhydrase converts it to carbonic acid, which will break down into the bicarbonate ion. The bicarbonate ion diffuses out to plasma. As the bicarbonate leaves at tissues, Cl- enters. The opposite happens at the lungs. ❖ CO2 is carried in the blood in three forms: in physical solution, as bicarbonate ion, and in carbamino compounds (combined with hemoglobin and other proteins). ● Critical note: The majority is carried in the bicarbonate ion form. The least amount of CO2 is found in the plasma (CO2 is significantly more soluble in blood than O2).

Antiparallel strands

refers to the phosphodiester backbone of each strand running in opposite directions, from 5' to 3' at either end.

Wave summation

refers to the process of depolarizing muscle fibers in a motor unit again, during their *relaxation period*. This causes another twitch contraction to occur before completion of the previous twitch; therefore, subsequent twitches stack on top of the first twitch contraction, and the overall contraction is larger (summation of waves of contraction). ● DAT Pro-Tip: action potentials will *not* increase the force of a twitch during the *latent* or *contraction* phases because the muscle fiber is *refractory* at those times. Remember, we actively pump calcium into the *sarcoplasmic reticulum* during the *relaxation period*. If another action potential stimulates the voltage gated calcium channels on the *sarcoplasmic reticulum* to open as relaxation is occurring, we will experience a stronger contraction because there is leftover calcium in the *sarcoplasma* from the previous twitch. This means more myosin binding sites will be exposed on the actin, leading to more *cross-bridges* (more tension).

Mimicry

refers to when one species evolves to resemble another species.

locus

refers to where the gene is located within the genome. ● For humans, this would indicate on which of the 23 chromosomes a gene is located, and its physical location on that gene.

Benthic layers

regions at the very bottom of a body of water. These regions may also include some portions of the floor

Precapillary sphincters

regulate the passage of blood into capillary beds.

cAMP (cyclic adenosine monophosphate) levels

related to glucose levels. If glucose is high, cAMP levels are low. Alternatively, if glucose is low, then cAMP levels will be high.

At the lungs, where O2 concentration is high, hemoglobin

releases the CO2 it picked up from the tissue and grabs oxygen again.

Rho-independent termination

relies on a terminator sequence of DNA that causes the RNA transcript to fold into a *hairpin loop* (aka *stem and loop*). Hairpin loops can cause RNA polymerase to pause after a certain amount of time. Before the hairpin loop causes RNA polymerase to pause, transcription of a sequence of adenine DNA nucleotides into uracil RNA nucleotides will often occur. The combination of the weak bonds between adenine and uracil, as well as the pause caused by the hairpin loop, causes just enough instability for the RNA polymerase to fall off the DNA template and for the RNA transcript to be released.

Oxidative deamination

removes ammonia molecules directly from amino acids. ● Ammonia is toxic to vertebrates. Most aquatic species (and invertebrates) excrete ammonia directly. Insects/birds/reptiles convert ammonia to uric acid and then excrete it. Mammals/sharks/most amphibians convert ammonia to urea for excretion.

AUG

represents the start codon, which corresponds to the amino-acid methionine. The ribosome will assemble around an mRNA transcript and begin scanning for the start codon. The start codon tells the ribosome where protein translation should initiate translation.

Microaerobes

require O2 but are harmed by increasing amounts of it (e.g. H. pylori).

Rods

responsible for black-and-white vision. They function in dimly-lit situations and are integral to effective night-vision.

Radial cleavage

results in cells aligned on the vertical axis, with the top cells directly overlap the bottom cells.

Spiral cleavage

results in misaligned cells that deviate away from the axis, meaning that if you look at it from a top-down view, you can see that the bottom cells are shifted compared to the top cells.

Substrate level phosphorylation

results in the direct enzymatic transfer of a high energy phosphate to ADP and does not require any extraneous carriers.

backwards mutation

reverts a mutant allele to a wild type allele

modern atmosphere composition

roughly 78% nitrogen (N2), 21% oxygen, 1% argon, then less important gases.

Chemoreceptors

sense taste, smell, and changes in blood chemistry (such as a change in oxygen saturation).

Thermoreceptors

sense temperature.

Mechanoreceptors

sense touch.

association (interneuron) neurons receive information from

sensory neurons and send information (impulses) to motor neurons. They are considered integrators because they evaluate sensory stimuli and form an appropriate response to it.

Telomeres

sequences of repeated nucleotides at the end of a chromosome that don't code anything, they're basically a 'buffer' for the real genetic code we actually use. This way, as replication occurs and that small segment of DNA at the end is not replicated, we don't lose crucial pieces of genetic information. The telomere portion may not be replicated, but the telomere doesn't code for anything so this is OK. In body cells, telomeres shorten each time DNA is replicated until any further shortening would mean the loss of important information. At this point, these cells will be prevented from replicating their DNA and dividing. Telomeres are only necessary in eukaryotic organisms because they have linear chromosomes which have an 'end point'. Prokaryotes do not produce telomeres. There is no risk of losing parts of the chromosome during DNA replication because prokaryotic circular chromosomes contain no ends.

polymers

series of repeating monomers

Histones

serve to organize DNA which coil around it into a bundle.

Hershey & Chase

showed that DNA, not proteins, was the genetic material of Phage T2 (a virus). ● Phage T2 is a bacteriophage (a virus that infects bacteria). In order to determine what the genetic material of a virus was, Hershey and Chase ran two separate trials: one in which they placed a radioactive label on phosphorus in DNA of the virus, and one in which they placed a radioactive label on sulfur in protein of the virus. They then observed which radioactively labeled substance appeared within the bacteria. Result: only the radioactively labeled DNA appeared inside the bacteria, confirming DNA was the genetic material of the virus. Why did this confirm DNA was the genetic material? Recall that bacteriophages infect bacteria by attaching and injecting their genetic material into the bacteria, where it is then replicated and assembled into new viruses. When only the radioactively labeled DNA (and not protein) appeared within the cell, DNA was confirmed as the genetic material.

Gurdon's nuclear transfer experiment

showed that when the nucleus from a differentiated frog cell was placed into an enucleated egg cell, it gave rise to a new frog (although this ability decreased as the donor cell became more differentiated). ● What is this significance of Gurdon's experiment? It showed that fully differentiated cells don't lose their genetic information - they retain the full genome. No DNA is lost when a cell becomes differentiated - only its expression is altered.

Hormone proteins

signaling molecules circulated throughout the body to regulate organs. ex) growth hormone, prolactin, glucagon Covered in more detail in the endocrine section

Radial cleavage

simply indicates how the axis of embryonic cell cleavage is oriented.

monosaccharides

single sugar molecules. ex) glucose, fructose, galactose alpha vs beta carbon is based on the position of H and OH on the 1st (anomeric) carbon (OH down = alpha, OH up = beta)

monomers

single units polymers

Venules

small blood vessels that lead back to the vein. They are very thin and porous. They drain blood from capillary bed, after which they combine to form veins.

The left lung is

smaller (2 lobes) vs. right lung (3 lobes) to accommodate left-sided heart.

Arteries are wrapped in

smooth muscle and typically innervated by the sympathetic nervous system.

the esophagus is made up of

smooth muscles, hence we cannot control its contraction.

spontaneous recovery.

sometimes a behavior that was thought to be extinct can be recovered in a phenomenon

Viruses

sometimes called *phages*, are *not living cells*. A virus is a parasite which infects other cells. It relies on the cell it infects in order to 'survive'. Viral coats are made up of a series of protein subunits called *capsomeres*. Capsomeres come together to form a protective protein coat called the *capsid*. A virus has no cell wall, no plasma membrane, nor any organelles. It only has its nucleic acid and the protein coat covering it. ● Note: A virus can pick up a phospholipid *envelope* from a host cell's membrane; however, this is not a true plasma membrane belonging to the virus.

sarcoplasmic reticulum

specialized endoplasmic reticulum found in muscle fibers that stores calcium ions.

Adipocytes

specialized fat cells ● White fat cells contain a large lipid droplet composed primarily of triglycerides, with a small layer of cytoplasm around it. ● Brown fat cells have considerable cytoplasm, with smaller lipid droplets scattered throughout the cell and lots of mitochondria.

functional groups

specific cluster of atoms that give molecules unique properties. these are often referred to as R groups.

Kupffer cells

specific type of cells in the liver that destroy old or useless RBCs. phagocytes that also eat up bacteria.

Carrier proteins

specific type of transport protein. Unlike channels (which are simultaneously exposed to the extracellular and intracellular environment), carrier proteins are only exposed to one side at a time. Bind to a specific molecule → protein changes shape → molecule (e.g. glucose) passes across into or out of cell.

Erythrocyte resist strong shearing forces because they contain the protein

spectrin

Enzymes cannot change the

spontaneity of a reaction

alpha-glucose polymer carbohydrates

starch glycogen

endosymbiotic theory

states that eukaryotic cells originated mutually among prokaryotes (mitochondria, chloroplasts establish resident inside another prokaryotes).

Fats

store more energy than carbohydrates per carbon as their carbons are in a more reduced state. ● Hence why fats are 9 cals/g, whereas carbohydrates and protein are 4 cals/g.

structure proteins

strengthen and support tissues. ex) collagen (connective tissue), keratin (nails)

type 1 alveoli

structural support

Prokaryotic promoters are

sually simple, allowing RNA polymerase to attach directly to them. For example, bacteria usually have -10 and -35 elements. These sequences of these elements are commonly found in many prokaryotic promoters. -10 and -35 represents how many base pairs upstream from the transcription starting site these elements exist.

The ATP produced during glycolysis is via

substrate level phosphorylation.

Electron Transport Chain

takes place in the inner membrane/crista of the mitochondria. The *cristae* are the folds of the mitochondria and provide greater surface area for ETC to occur. ● In prokaryotes (which lack mitochondria), the ETC takes place across the cell membrane ● ETC couples exergonic flow of electrons with endergonic pumping of protons across the cristae membrane of the mitochondria. ❖ *Oxidative Phosphorylation* is the process in which ADP forms ATP from NADH and FADH2 via passing of electrons through various carrier proteins. ● Unlike substrate level phosphorylation, the energy of the phosphate group is not transferred to the ADP. The energy comes from the electron in the ETC establishing an H+ gradient that supplies energy to ATP synthase. ❖ Carrier proteins that form the ETC extract energy from NADH and FADH2 while pumping protons (H+) into the intermembrane space of the mitochondria. ATP synthase uses this gradient (an electrical and pH gradient) to make ATP as H+ shuttles back into the inner matrix. ❖ NADH pumps more H+ across the matrix, and produces more energy than FADH2. NADH produces 3 ATP and FADH2 produces 2 ATP. ❖ The final electron acceptor of the chain is *oxygen*. It combines with native H+ to form water (H2O). ❖ *Coenzyme Q (CoQ)/Ubiquinone* is a soluble carrier that is dissolved in the membrane that can be fully reduced/oxidized. It passes electrons as seen in the diagram above. ● Note: an oxidizing agent causes something else to get oxidized; the oxidizing agent itself is reduced; vice versa for the reducing agent. ❖ *Cytochrome c* is a protein carrier in the ETC, and is common in so many living organisms that is used to test for genetic relations. ● Cytochromes have non-protein parts such as iron which donate or accept electrons for redox.

Gibbs Free Energy (G)

tells us whether a chemical reaction can occur spontaneously: ΔG = ΔH - TΔS (H is enthalpy, T is temperature, and S is entropy). ● If ΔG is negative, the reaction can occur spontaneously. The reaction is *exergonic*. Formation of the products releases energy. ● If ΔG is positive, the reaction is nonspontaneous. The reaction is *endergonic*. Formation of the products requires energy. ❖ A system with a high G is considered less stable. ● Less stable systems will spontaneously change to more stable systems. ● In a spontaneous change, the ΔG of the system decreases (becomes more negative). This releases free energy that can be used to do work. ❖ A system with a low G is considered more stable. ● More stable systems have less work capacity. ● Chemical reactions can be "coupled" together if they share intermediates. ● The overall Gibbs Free Energy change is the sum of the ΔG values for each reaction. An unfavorable reaction (positive ΔG1) can be driven by a second, highly favorable reaction (negative ΔG2 where the magnitude of ΔG2 > ΔG magnitude of ΔG1). ● The principle of coupling reactions to alter the change in Gibbs Free Energy is the basic principle behind all enzymatic action in biological organisms, and is how ATP drives chemical work.

Enzyme efficiency is determined by

temperature and pH

Food vacuoles

temporary receptacles of nutrients; merge with lysosomes which break down food.

Stanley Miller

tested the above theory and produced organic molecules. Miller & Urey used ammonia, methane, water, and hydrogen sealed in flask and stimulated lightning. They saw the formation of several organic molecules, amino acids, and starting materials but no nucleic acids!

Male Anatomy Overview

testes epididymis vas deferens ejactulatory ducts

Nucleoplasm

the "cytoplasm" of the nucleus.

DNA replication is regulated by

the *cell cycle* in eukaryotes

The small intestine is divided into

the *duodenum* (first part), *jejunum* (second part) and *ileum* (last part). Mnemonic: I think of a music *DJ* named *Eye (I)* to remember the order of duodenum, jejunum, ileum. *Duodenum* is mostly responsible for *digestion* (alliteration, *d*uodenum main area of *d*igestion), whereas the *jejunum* and *ileum* are responsible for *absorption*. *Note: no absorption of nutrients has occurred up until the small intestine. The mouth, pharynx, esophagus, and stomach were all used for digestion and movement of food - no absorption occurs here.

secondary structure of a protein

the 3D shape that results from its hydrogen bonding between amino and carboxyl groups of adjacent amino acids. Secondary structures include the alpha helix and beta sheet.

quaternary structure of a protein

the 3D structure from the grouping of two or more separate peptide chains.

the co2 produced during the krebs cycle is

the CO2 that the animal exhales when they breathe.

Km

the Michaelis constant. It represents the substrate concentration at which the rate if reaction is half of Vmax. It indirectly represents binding affinity.

Km

the Michaelis constant. It represents the substrate concentration at which the rate if reaction is half of Vmax. It indirectly represents binding affinity. ▪ A small Km indicates the enzyme requires only a small amount of substrate to become saturated (high affinity, maximum velocity is reached at low substrate concentrations). A large Km indicates the enzyme requires high amounts of substrate to achieve Vmax. ▪ ↑ Km = worse substrate binding, ↓Km = better substrate binding

Tonicity

the ability of an extracellular solution to cause water to move into or out of a cell

capillary action

the ability of water to flow without external forces, such as against gravity

Enterocytes

the absorptive cells that make up the villi, and are lined with microvilli.

The first step of glycolysis involves

the addition of a phosphate group to glucose via the enzyme hexokinase to produce glucose-6-phosphate. This is important because phosphorylated glucose cannot diffuse outside of the cell and traps the glucose in the cell.

Residual volume (RV)

the amount of air remaining in the lungs after maximum exhalation; air that cannot be exhaled.

Adhesion

the attraction between unlike substances. Water has strong adhesion. ● E.g. Wetting a finger to flip a page

Mean Arterial Pressure

the average pressure in the arteries during one complete cardiac cycle. ● Mean arterial pressure (MAP) = Cardiac Output (CO) X Systemic Vascular Resistance (SVR) ● Resistance is controlled by vasoconstriction and vasodilation. The larger the diameter, the less the resistance.

DNA forms two antiparallel strands of a double helix.

the bases of separate strands are connected via hydrogen bonds

thyroid gland

the biggest endocrine organ of our body. They thyroid gland is located in front of the trachea (the trachea is a part of our respiratory/breathing system). The thyroid gland manufactures and releases 3 main hormones into the blood, the first two are secreted in response to TSH coming from the anterior pituitary: 1. *T3 - triiodothyronine* (mnemonic: T3 corresponds with tri) 2. *T4 - thyroxine* 3. *Calcitonin*

Antibodies circulate in

the blood and lymph.

pulmonary circuit

the blood pathway from the right side of the heart to the lungs to the left side of the heart. ● Blood flows from right and left pulmonary arteries → arterioles → capillaries of the lungs → collects in venules → veins → pulmonary veins → left atrium.

Capillaries exchange substances from

the blood with the interstitial fluid that surrounds tissue cells. Two factors are importan

Association (interneuron) neurons are located in

the brain and spinal cord.

In the microarray assay,

the cDNAs are labeled fluorescently and then allowed to hybridize to a DNA microarray. So the wells that light up tell you which gene is expressed and color tells you where it is expressed (we usually differentiate samples/tissues with different color labels). Using this, expression of genes across the entire genome can be analyzed simultaneously.

The major components of the neuron

the cell body (soma), dendrites, and axon o The *cell body*, or *soma*, contains the nucleus and organelles. Most of the protein synthesis occurs here. ▪ The *axon hillock* is a specialized portion of the cell body that connects to the axon. This is the most easily excited portion of the neuron. The axon is a projection from the cell body, which carries impulses away. ▪ *Myelin* is a sheath that insulates many axons in vertebrates, increasing impulse conduction speed. *Nodes of Ranvier* are intermittent non-myelinated areas. In myelinated axons, the action potential "jumps" rapidly from node to node, which is termed *saltatory conduction*. Additionally, axons with larger diameters propagate impulses more quickly because there is less resistance to ion movements. o The *dendrites* receive information and relay it to the cell body.

Interphase is a part of

the cell cycle.

Fibroblasts

the cells which produce collagen and other connective tissue elements.

Central disks

the central portion of echinodermata where the arms radiate from. It contains the mouth and anus, as well as an opening for water to enter the water vascular system.

Macroevolution

the change in groups of related species over a long period of time.

silent mutation

the change in the DNA code results in no change in what amino-acid the codon codes for. This is due to the degeneracy of the genetic code.

silent mutation

the change in the DNA code results in no change in what amino-acid the codon codes for. This is due to the degeneracy of the genetic code. ● Silent mutations can also occur because there is less strict base pairing between the third base of a codon and anticodon. This is referred to as *'third base wobble'*. You can have a mutation in the DNA, but because the third base of the eventual codon binds less strictly to the anticodon, you can still end up with the right amino acid being delivered via the tRNA.

Microevolution

the changes in allele frequencies that occur over time within a population due to mutation, selection, gene flow, gene drift, and nonrandom mating.

chromosomal genetic disorders

the chromosome is damaged, duplicated, or missing in some way leading to disorders)

systemic circuit

the circulation pathway through the body between left and right sides of the heart.

Aneuploidy

the condition of a genome having extra or missing chromosomes, often caused by nondisjunction. ● E.g. Down Syndrome (Trisomy 21) - characterized by intellectual disability ● E.g. Turner Syndrome (XO, missing sex chromosome) - results in sterility and physical abnormalities. This is a monosomy. ● E.g. Klinefelter Syndrome (XXY) - results in sterility ● E.g. Edwards Syndrome (Trisomy 18) - characterized by heart defects

Thermoregulation

the control of exchange of heat with environment. ● *Ectotherms* obtain body heat from environment (aka poikilotherms/cold blooded). ▪ Examples include invertebrates, amphibians, reptiles, and fish. ● *Endotherms* generate their own body heat (aka hemeotherms/warm blooded). ▪ Endotherms have a much higher basal metabolic rate than ectotherms.

Pyruvate Decarboxylation

the conversion of pyruvate to acetyl CoA via the pyruvate dehydrogenase complex (PDC) enzyme. ❖ This metabolic process occurs in the mitochondrial matrix. ● In prokaryotes (which lack mitochondria), pyruvate decarboxylation takes place in the cytoplasm ❖ The product of the reaction is 1 NADH and 1 CO2. ● The two pyruvate molecules from glycolysis therefore produce a net of 2 NADH and 2 CO2.

Gravitropism

the curving of a plant stem to oppose gravity.

Phototropism

the curving of a plant stem towards light.

In prokaryotes (which lack mitochondria), the Krebs cycle takes place in

the cytoplasm

Prokaryotes do not have membranous organelles; so, transcription occurs in

the cytosol

photosynthesis only takes place during

the day

Glycolysis

the decomposition of glucose into pyruvate in the cytosol. ❖ In these series of reactions *2 ATP* molecules are added to the glucose, *2 NADH* produced, *4 ATP* are produced, and *2 pyruvates* are formed. ● The NET production is 2 ATP (made 4 ATP but used 2 ATP), 2 NADH, 2 pyruvate (+ 2 H2O + 2 H+) ❖ The ATP produced during glycolysis is via *substrate level phosphorylation*. ● Substrate level phosphorylation results in the direct enzymatic transfer of a high energy phosphate to ADP and does not require any extraneous carriers. ❖ The first step of glycolysis involves the addition of a phosphate group to glucose via the enzyme *hexokinase* to produce glucose-6-phosphate. This is important because phosphorylated glucose cannot diffuse outside of the cell and traps the glucose in the cell. ❖ During the third step of glycolysis, another phosphate is added to an isomer of glucose-6-phosphate to form fructose 1,6-bisphosphate via the enzyme *phosphofructokinase*. This is irreversible and commits the glucose to glycolysis. This is a major regulatory point!

Glycolysis

the decomposition of glucose into pyruvate in the cytosol. ❖ In these series of reactions 2 ATP molecules are added to the glucose, 2 NADH produced, *4 ATP are produced, and 2 pyruvates* are formed. ● The NET production is 2 ATP (made 4 ATP but used 2 ATP), 2 NADH, 2 pyruvate (+ 2 H2O + 2 H+)

hypodermis

the deepest layer of the integumentary system.

When we exhale,

the diaphragm rises, which decrease the volume of the lungs, and causes an increase in pressure relative to the atmosphere, and air rushes out. The diaphragm relaxes and expands. Exhalation is a passive process.

A small Km indicates

the enzyme requires only a small amount of substrate to become saturated (high affinity, maximum velocity is reached at low substrate concentrations). A large Km indicates the enzyme requires high amounts of substrate to achieve Vmax.

Helicase

the enzyme that 'unzips' the wound DNA double helix by breaking the hydrogen bonds between complementary purines and pyrimidines. In order to stop both strands from snapping back together, *single-strand binding proteins* attach to each strand of uncoiled DNA to keep them separated. As helicase unwinds the DNA, it actually creates tension ahead of the *replication fork* (where the strands separate). To relieve this tension, *topoisomerase* creates small nicks within the DNA double helix. ● Note: You may also hear about the enzyme *DNA gyrase* performing this action as well. DNA gyrase is a subtype of DNA topoisomerase found in bacteria and plants.

Telomerase

the enzyme that extends telomeres to prevent DNA from losing information, and is particularly active throughout the rapid growth and division that occurs after fertilization. High telomerase activity in body cells is often associated with cancer because the cell is effectively made to be immortal.

Listed from superficial to deep, the layers of the integumentary system are

the epidermis, dermis, and hypodermis.

Phylogeny

the evolutionary history and relationships among groups of organisms that is determined through macroevolution. It can be used to establish a phylogenetic tree.

auricle (pinna)

the external portion of the ear. It is what one thinks of when they hear the word, "ear."

Nondisjunction

the failure of chromosome pairs or chromatids to separate during mitosis (failure of two chromatids of a single chromosome during anaphase) or meiosis (homologous chromosomes can fail to separate during meiosis I, or sister chromatids can fail to separate during meiosis II). ● Meiotic nondisjunction can result in gametes with missing or extra chromosomes, creating conditions such as *trisomy* (three copies of a chromosome) or *monosomy* (only one copy of a chromosome). ● *Mosaicism* occurs in cells that undergo mitotic nondisjunction during embryonic development; as a result a fraction of body cells have extra or missing chromosomes

Krebs Cycle

the fate of the pyruvate that is produced in glycolysis. It takes place in the mitochondrial matrix.

Krebs Cycle

the fate of the pyruvate that is produced in glycolysis. It takes place in the mitochondrial matrix. ● In prokaryotes (which lack mitochondria), the Krebs cycle takes place in the cytoplasm ❖ The acetyl CoA from pyruvate decarboxylation merges with oxaloacetate to form citrate. The cycle has 7 intermediates. ❖ Two cycles of the Krebs cycle occur for glucose because 2 pyruvates are made from 1 glucose in glycolysis. ❖ The final products of the cycle are *3 NADH, 1 FADH2, 1 ATP* (via substrate level phosphorylation), 2 CO2. ● A net production of 6 NADH, 2 FADH2, 2 ATP (technically GTP), 4 CO2. ❖ The CO2 produced during the cycle is the CO2 that the animal exhales when they breathe.

Transcription

the first step of gene expression, and its main goal is to convert a sequence of DNA into a single strand of *messenger RNA* (mRNA). Like DNA replication, transcription has three stages: 1. Initiation 2. Elongation 3. Termination

Chromatin

the general packaging of DNA around histone proteins - this arrangement of DNA helps to condense DNA to fit within the nucleus of the cell. Throughout most of the cell cycle, DNA is packaged in the form of chromatin. However, during mitosis and meiosis, chromatin exists in an additional level of organization known as a *chromosome*.

Chromatin

the general packaging structure of DNA around proteins in eukaryotes. The tightness of the packaging varies depending on cell stage.

As testosterone levels rise, the high testosterone levels will create a negative feedback loop on

the hypothalamus and the pituitary. The hypothalamus will produce less gonadotropin releasing hormone (GnRH), and the pituitary gland will produce less LH and FSH. This results in less testosterone.

Cytosol

the intracellular fluid inside a cell. It is a part of the cytoplasm but does not include the components of the cell suspended within it (such as organelles). If the cytoplasm were a stew, the cytosol would be the liquid.

Gene therapy

the introduction of genes into an afflicted individual for therapy (e.g. via a retroviral vector to insert genome material into chromosomal DNA).

If lactose is present,

the lac operon can be transcribed. However, in the presence of glucose and lactose, lactose is not the ideal energy source.

Lactose present, glucose absent

the lac repressor is not bound because allolactose is present. cAMP is high because glucose is absent. CAP is bound near the promoter because the levels of cAMP are high. The lac operon has been induced ● High transcription and high utilization of lactose occurs because the lac repressor protein is not bound; although, CAP is bound. CAP binding means that there is increased RNA polymerase attraction to the operon.

Lactose absent, glucose present:

the lac repressor protein is bound because allolactose is absent. Levels of cAMP are low because glucose is abundant. CAP is not bound near the promoter because of the low cAMP levels. The operon is turned off because of the lac repressor protein and the fact that CAP is not bound.

Lactose absent, glucose absent

the lac repressor protein is bound to the operator region because allolactose is absent. Levels of cAMP are high because glucose is absent. CAP is bound upstream of the promoter because of the high cAMP levels. The operon is turned off because of the lac repressor protein.

Lactose present, glucose present

the lac repressor protein is not bound because allolactose is present. cAMP is low because glucose is abundant. CAP is not bound because levels of cAMP are low. The operon has been induced. ● Only moderate transcription and low utilization of lactose occurs because the lac repressor protein is not bound; however, CAP is not bound either. No CAP binding means that there is reduced RNA polymerase attraction to the operon.

During the menstrual cycle, follicle stimulating hormone (FSH) and luteinizing hormone (LH) cause an increase in progesterone and estrogen. The combination of increasing progesterone and estrogen causes

the levels of FSH and LH to drop. This is negative feedback.

Gluconeogenesis occurs in

the liver and kidney. The liver is responsible for maintaining the glucose concentration in the blood.

Most amino acids are deaminated in

the liver, and then converted to pyruvate or acetyl CoA or other Krebs cycle intermediates. These metabolic products enter cellular respiration at various points (varies by amino acid).

Viruses have two life cycles that they can rotate between

the lysogenic cycle and the lytic cycle. Both begin with a virus particle injecting its nucleic acid into the host cell's cytosol. In the *lysogenic cycle*, the viral nucleic acid will insert itself into the host's genome. This is beneficial to the virus because it's nucleic acid will be replicated whenever the host's DNA is replicated. The virus is considered dormant and does not harm the host while in the lysogenic stage. In the *lytic cycle*, a virus takes over the host cell's machinery and does end up harming the host. The lytic cycle includes breaking apart the host genome and replicating many copies of viral nucleic acid. Also, many rounds of transcription and translation occur, which allows the viral genome to make many viral proteins. Once made, the copies of viral nucleic acid can be packaged into the viral proteins to make new virus particles. These particles can then *lyse* (break apart) the host cell and go on to infect other cells. An important thing to note is that a virus has the capability of *switching* between the lysogenic and lytic cycles. For example, a virus can infect a cell and enter the lysogenic cycle. Here, it will remain dormant and replicate within the host genome. Eventually, the virus will be stimulated by favorable environmental conditions. This causes the host genome to break apart and the lytic cycle will begin. Here, it will take over the host cell machinery and destroy the cell. Then, the viral copies will spread to other cells and infect them through either of the two cycles.

Total lung capacity (TLC)

the maximum amount of air that the lungs can accommodate; expressed as IC + FRC.

Expiratory reserve volume (ERV)

the maximum volume of air that can be exhaled after a normal tidal volume exhalation.

Vital capacity (VC)

the maximum volume of air that can be exhaled after maximum inspiration; expressed as IRV + VT + ERV.

Inspiratory reserve volume (IRV)

the maximum volume of air that can be inhaled after a normal tidal volume inhalation.

notochord is derived from

the mesoderm germ layer.

Endomembrane system does NOT include

the mitochondria or chloroplasts.

forebrain

the most anterior component, and it is also the largest. It contains the cerebrum and diencephalon, which are further subdivided.

Small motor units with small fibers are innervated by

the most excitable neurons.

Hindbrain

the most posterior portion of the brain. It contains the cerebellum, pons, and medulla oblongata. ❖ The *cerebellum* coordinates, but does not initiate, movements. It is important for maintenance of balance, hand-eye coordination, proper timing of rapid movements, and fine motor skills. ❖ The *pons* relays information between the cerebral cortex and the cerebellum. ❖ The *medulla oblongata* is the center for involuntary functions such as breathing, sneezing, swallowing, vomiting, and control of heart rate.

Humans have a digestive tract with two openings:

the mouth and the anus

Respiration

the movement of gases in and out; also means cellular respiration producing ATP within mitochondria.

antagonists

the muscles involved in the opposite motion

Cohesion

the mutual attraction between like substances. Due to its ability to form many hydrogen bonds, water has strong cohesion which produces a high surface tension.

Acetylcholine Facilitates

the opening of ligand gated sodium channels on the muscle fiber. This allows some sodium to enter the muscle fiber; therefore, creating a graded potential. This small depolarization opens nearby voltage gated sodium channels. When the voltage gated sodium channels open, we have successfully transferred an action potential from a neuron to a muscle!

The axons of the ganglion cells form

the optic nerve.

The dermis has two layers:

the papillary dermis and reticular dermis. supports the epidermis and is home to many functional elements of the skin, such as glands and hair.

Tight junctions Prevent

the passage of molecules and ions through the space between cells, so materials must actually enter the cells (by diffusion or active transport) in order to pass through the tissue.

monohybrid cross

the phenotypically-dominant organism in question is bred, or "crossed," with another organism that is homozygous-recessive for the given trait. ● If the offspring display a dominant phenotype, then the parent organism is homozygous-dominant. ● If the offspring display a combination of dominant and recessive phenotypes, then the parent organism is heterozygous-dominant.

iris

the pigmented (colored) component of the eye. It is thin and circular, and it controls the size of the pupil. Therefore, the iris controls how much light enters the eye.

In between the pleura layers

the pleural space. This space has negative pressure relative to the atmosphere. Therefore, if one is stabbed, air rushes in and collapses the lung.

For cells capable of both aerobic cellular respiration or fermentation (facultative anaerobes and muscle cells), the pathway is selected based on

the presence of oxygen.

The end of metaphase is denoted by

the presence of centrosomes at opposite ends of the cell.

Genetic Variation: Diploidy

the presence of two copies of each gene. In heterozygous conditions recessive allele is stored for later generations. This allows for more variations to be maintained in the gene pool.

Archenteron

the primitive gut formed during gastrulation.

Penetrance

the probability that an organism with a specific genotype will express the corresponding phenotype. ● E.g. In a fully penetrant gene, 100% of individuals that carry the allele for blindness would be blind. In a gene that is not fully penetrant, not all individuals that carry the allele for blindness will be blind.

Pinocytosis

the process in which a cell *engulfs* dissolved material (liquid). Plasma membrane invaginates. Known as "cell drinking".

Phagocytosis

the process in which a cell *engulfs* undissolved materials (solid). The plasma membrane wraps outward around the material. Known as "cell eating". E.g. White blood cell engulfing antigens.

Translation

the process of converting mRNA (made during transcription) into a protein that can actually serve a purpose within the cell. Translation is accomplished by several pieces of cellular machinery. Two of the most important include: 1. *Ribosomes* 2. *tRNA molecules*

Initiation

the process of creating the *origin of replication*. Origins of replication tend to occur at *AT rich* segments because it is easier for initiator proteins to break two hydrogen bonds (A(2-)T) than three hydrogen bonds (G(3-)C).

Countercurrent exchange

the process of exchanging substances (such as ions) or heat between to fluids flowing in opposite directions. Example - flamingo standing in cold water: warm blood traveling away from the heart (through leg arteries) could transfer heat to blood returning to the heart (through leg veins).

Elongation

the process where new strands are created. There are several enzymes that aid in this process. DNA polymerase is one class of enzyme that is highly involved in new strand synthesis.

Conjugation

the process whereby bacteria transfer DNA between each other via a cytoplasmic bridge, called a *pili*. Bacteria that can produce this pili contain a special plasmid. A *plasmid* is a circular piece of DNA independent form a bacterium's single circular chromosome. The *F plasmid* is the special plasmid that contains the necessary DNA for producing a pilus. If a bacteria contains the F plasmid, it is referred to as (*F+*). Bacteria lacking the F plasmid are referred the as (*F-*). ● Mnemonic: F stands for Fertility - the F plasmid is the *fertility factor*, allowing bacteria to undertake conjugation. When an (F+) bacteria conjugates with an (F-) bacteria, it transfers the F plasmid to that cell. This makes the (F-) bacteria (F+). This bacteria now contains the F factor and can conjugate with other bacteria. Other genetic information can be contained on the F plasmid and be laterally transferred during conjugation. ● Example: antibiotic resistance genes can be passed with the F plasmid, which is one way resistance can spread.

Conjugation

the process whereby bacteria transfer DNA between each other via a cytoplasmic bridge, called a pili. Bacteria that can produce this pili contain a special plasmid.

sarcolemma

the protective sheath encasing the muscle fiber (aka muscle cell). The sarcolemma is the muscle fiber's cell membrane. There is no sheath covering individual myofibrils. Instead, they lie in the muscle fiber's sarcoplasma. The sarcoplasm is the cytoplasm of the muscle fiber.

nucleoid

the region within prokaryotic cells that contains most of the cell's genetic material. It is analogous to a eukaryotic nucleolus.

If tryptophan levels are low,

the ribosome will pause at domain one of the RNA transcript. This is because domain one contains codons for the amino acid tryptophan. If tryptophan is low, there are not many of these amino acids nearby; so, the ribosome needs to wait for a couple tryptophan amino acids to become available before it continue translating the RNA transcript into protein.

Taxonomy

the science of classifying organisms

endomysium

the sheath covering muscle fibers

perimysium

the sheath covering the fascicles

Cytoplasm

the site of metabolic activity and transport. It doesn't include nucleus, but does include cytosol, organelles, and everything suspended within the cytosol. ● The cytoplasm is an area, not a structure!

F plasmid

the special plasmid that contains the necessary DNA for producing a pilus. If a bacteria contains the F plasmid, it is referred to as (F+). Bacteria lacking the F plasmid are referred the as (F-). ● Mnemonic: F stands for Fertility - the F plasmid is the fertility factor, allowing bacteria to undertake conjugation.

Most of RBC destruction is done in

the spleen*

Genomics

the study of whole sets of genes and their interactions. Bioinformatics is the application of computational methods to the storage and analysis of biological data. ● The whole-genome shotgun approach is a sequencing strategy for the entire genome. In this approach, DNA from a chromosome is cut up into many pieces, which are then cloned and sequenced. A computer than analyzes the sequences and places them into an order.

Expressivity

the term that describes the variation of a phenotype for a specific genotype. ● E.g. Assume Bb is the genotype for body hair, and two individuals are both Bb but differ in their expressivity. In the individual with high expressivity, there would be a significant amount of body hair while the individual with low expressivity would have less body hair.

chromatids

the term used to describe the chromosome in its duplicated state.

Introducing foreign DNA into a bacteria experimentally allows for

the testing of gene products (proteins), based on the central dogma of genetics. The central dogma of genetics says that DNA makes mRNA, which ultimately makes protein that can be used by the cell.

There are two pleura layers:

the visceral layer lines the surface of the lungs and the parietal layer lines the inside of the chest cavity.

Functional residual capacity (FRC)

the volume of air remaining in the lungs after normal exhalation; expressed as ERV + RV.

Inspiratory capacity (IC)

the volume of air that can be inhaled after a normal exhalation; expressed as VT +IRV.

Tidal volume (VT)

the volume of air that is normally inhaled (or exhaled) in one quiet breath.

Stroke volume

the volume of blood discharge from the ventricles with each contraction. ● Stroke volume = end diastolic volume - end systolic volume

End systolic volume

the volume of blood in the ventricle at the end of contraction/systole.

End diastolic volume

the volume of blood in the ventricle just before contraction.

If steroid hormones bind to receptors located in the nucleus

then the molecule-receptor complex can directly bind with DNA.

Silent mutations can also occur because

there is less strict base pairing between the third base of a codon and anticodon. This is referred to as 'third base wobble'. You can have a mutation in the DNA, but because the third base of the eventual codon binds less strictly to the anticodon, you can still end up with the right amino acid being delivered via the tRNA.

Lysosomes

these are vesicles produced from Golgi that contain digestive enzymes (low pH for function). They are used to break down nutrients/bacteria/cell debris. Lysosomes function in APOPTOSIS when they release their contents into cell and AUTOPHAGY (intracellular breakdown of unneeded/defective cellular components).

If steroid hormones bind to receptors in the cytoplasm

they form a *molecule-receptor complex* that subsequently enters the nucleus.

Arteries

thick walled, muscular and contain elastic fibers. They carry oxygenated blood away from the heart. The exception to this rule is the pulmonary arteries which carries deoxygenated blood to the lungs from the heart

Arteries

thick walled, muscular and contain elastic fibers. They carry oxygenated blood away from the heart. The exception to this rule is the pulmonary arteries which carries deoxygenated blood to the lungs from the heart. ● Arteries are wrapped in smooth muscle and typically innervated by the sympathetic nervous system. ● Large arteries have less smooth muscle (per volume) than medium sized ones. The larger ones are less affected by the sympathetic nervous system, but the medium sized arteries can constrict enough to reroute blood. ● There are three layers or tunics: endothelial lining, middle layer of smooth muscle and elastic tissue, and other layer of connective tissues.

Veins

thin walled, and contain less muscle and elastic fibers than veins. They carry deoxygenated blood from the rest of the body towards the heart. The exception to this rule are pulmonary veins and umbilical veins that carry oxygenated blood back to the heart.

Veins

thin walled, and contain less muscle and elastic fibers than veins. They carry deoxygenated blood from the rest of the body towards the heart. The exception to this rule are pulmonary veins and umbilical veins that carry oxygenated blood back to the heart. ● Larger veins often have valves to aid in the transport of deoxygenated blood back to the heart due to fighting gravity.

DNA polymerase proofreading

this allows DNA polymerase to re-check it's work during DNA replication, correcting any errors it encounters.

Descent with modification:

this is a concept coined by Darwin to describe that over time and generations, traits providing reproductive advantage become more common within the population vis natural selection.

Nucleotide excision repair

this is a repair mechanism for DNA that has been damaged. The damaged strand is cut out and replaced with the correct sequence based on complementary base pairing.

Closed circulatory systems

those where blood is pumped through vessels by a heart. Blood doesn't fill empty body cavities in a closed circulatory system.

Cytosine bonds with Guanine through

three (3) hydrogen bonds in both DNA and RNA. 3 hydrogen bonds are stronger than 2 hydrogen bonds, so if a piece of DNA had more G-C nucleotides, it'd need a higher temperature to break the G-C bonds and to separate the strands. Mnemonic: CG3. Both C and G rhyme with three.

It's important codons have

three bases within them. If only two bases were in a codon, there would only be 4 x 4 = 16 combinations and there wouldn't be a unique code to represent each of the 20 amino acids.

Triglycerides

three fatty acid chains attached to a glycerol backbone

pharynx

throat - passageway for food and air; dust/mucus swept back here by cilia for disposal via spitting or swallowing

Both the platelets and damaged tissue release tissue clotting factor:

thromboplastin

T-cells mature in the

thymus The thymus technically does not make new T-cells, but the T-cells mature there so it houses fresh ones.

the biggest endocrine organ of our body.

thyroid gland

Heterochromatin

tightly packed DNA these areas of DNA tend to be inactive in transcription

In a DNA microarray assay,

tiny amounts of a large number of single-stranded DNA fragments representing different genes are fixed to a glass slide in array on a grid in wells. Then, mRNAs are isolated from a cell and reverse transcriptase is used to make cDNA.

The function of an operon is

to make sure the cell conserves its resources unless those resources are required. an operon is a group of genes under the control of one promoter sequence and one operator sequence. This means they function as a unit. If the conditions are right, the group of genes will be transcribed as one mRNA transcript.

3 types of stem cells

totipotent, pluripotent, and multipotent

external auditory canal (external acoustic meatus)

transmits sounds from the pinna to the tympanic membrane.

Movement of Water Overview

transpiration transpirational pull cohesion-tension capillary action root pressure osmotic gradient desiccation

Endocytosis

transports molecules into the cell (via active transport).

Exocytosis

transports molecules out of the cell (via active transport).

Counter Exchange System

traps heat in the center of the body, reducing heat loss from the extremities. ▪ Heat in the arterial blood emerging from the core of the body is transferred directly to the returning venous blood instead of being lost to the environment.

When environmental tryptophan levels are high,

tryptophan binds to the trp repressor protein and activates it. The active trp repressor protein will then bind to the operator site, preventing tryptophan production.

disaccharides

two sugar molecules joined together by a glycosidic linkage. e.g. sucrose (glucose + fructose), lactose (glucose + galactose), maltose (glucose + glucose)

Facultative anaerobes

undergo anaerobic respiration/fermentation when no O2 is available but they can use O2 when it is present (more efficient).

Facultative anaerobes

undergo anaerobic respiration/fermentation when no O2 is available but they can use O2 when it is present (more efficient). ❖ Both fermentation and aerobic cellular respiration use glycolysis and produce a pyruvate. ● Pyruvate commits to either aerobic cellular respiration or fermentation based on the presence of oxygen. ● For cells capable of both aerobic cellular respiration or fermentation (facultative anaerobes and muscle cells), the pathway is selected based on the presence of oxygen.

polar covalent bond

unequal sharing of electrons between atoms. forms a dipole. electronegativity of atoms are slightly different. ex) HCl

Steroids

used 4 ring structure (three 6-membered rings & one 5-membered ring). They are used as hormones (sex hormones, corticosteroids) and are a structural component of membranes (cholesterol).

Rosalind Franklin

used X-ray diffraction to create the photo that allowed Watson & Crick to deduce DNA was a double helix structure.

FRAP (Fluorescence Recovery After Photobleaching)

used in the observation of cell membrane diffusion. In FRAP, the whole cell is fluorescently tagged, then a special light is shone on a specific spot to remove fluorescence (photobleaching), resulting in a dark spot. We can then determine (based on how long that black spot remains and how much of the brightness recovers) the mobility and the motion of molecules over time in the cell membrane. Two important pieces of information are acquired as the fluorescence returns to this photobleached area: 1. How much light returns relative to the amount of light that was there before the photobleaching? This is the 'percent recovery'. 2. How fast did the fluorescent molecules migrate back into the photobleached area? This is a measurement of the 'diffusional mobility'. ● Application: FRAP can determine if a protein is able to move within a membrane (high percent recovery with fast mobility), or whether it is tethered other structural components of the cell (low percent recovery with slow mobility).

Reverse transcriptase

used to synthesize DNA molecules off an RNA molecule template. ● A reverse transcriptase is naturally used by some viruses, such as HIV. ● Reverse transcriptase is used in lab procedures to create *complementary DNA* (cDNA) off of mRNA templates. Why make cDNA? Recall that eukaryotic RNA contains introns that are removed in RNA processing before the final mRNA molecule is translated to protein. Prokaryotic RNA does not contain *introns*, so they cannot process them out. If you wanted to create recombinant DNA in a bacteria produce a desired gene product, the foreign DNA introduced to the bacteria cannot contain introns. Therefore, cDNA is created off the final mRNA template of the desired gene so that it can be efficiently transcribed and translated after insertion. ● Critical Review: Reverse transcriptase is used to make cDNA which lacks the introns that suppress transcription in prokaryotes.

Enzymes

usually) globular proteins that act as catalysts, lowering the activation energy and accelerating the rate of reactions. ● Enzymes can catalyze reactions in both forward and reverse directions based on substrate concentration. ● Enzymes remain chemically unchanged throughout a reaction (but can undergo conformational changes). ● Enzyme efficiency is determined by temperature and pH ● Enzymes cannot change the spontaneity of a reaction ● Enzymes bind at the active site via induced fit - enzyme binding is specific to structure.

Surface Area

vasodilation or vasoconstriction of extremity vessels results in heat retention or removal.

Fast glycolytic fibers

very large in diameter, which gives them *extremely powerful contractions*. They appear *white* because they have few blood capillaries, little myoglobin, and few mitochondria. This is due to the fact that *type II-b* fibers rely on *anaerobic metabolism* of stored glycogen to generate ATP; therefore, they have little use for oxygen. Their twitch occurs about four times faster than a type 1 fiber; however, they are *somewhat inefficient* and *fatigue rapidly*.

Arterioles

very small and wrapped in smooth muscle. They constrict or dilate to regulate blood pressure and reroute blood. They are major determinants of pressure as they have the greatest resistance to flow.

microsomes

vesicle-like artifacts from reformed pieces of the ER if a cell is broken up in a lab.

lympanic membrane (eardrum)

vibrates at the same frequency as the sound waves and transmits these vibrations to the ossicles.

larynx

voice box - if non-gas enters, cough reflex activates - note that the larynx is actually after the epiglottis in terms of sequence below

size principle of motor unit recruitment

we recruit small motor units first, then we recruit larger and larger motor units until we have achieved the tension we were aiming for. This is known as the size principle of motor unit recruitment and it helps us to avoid fatigue because different motor units within the same muscle are being stimulated at different times, giving them a chance to relax.

operon

when a group of related genes are under the control of one promoter site. Operons are common in prokaryotes as a way to regulate genes as a group; however, they are sometimes found in eukaryotes as well. The function of an operon is to make sure the cell conserves its resources unless those resources are required. an operon is a group of genes under the control of one promoter sequence and one operator sequence. This means they function as a unit. If the conditions are right, the group of genes will be transcribed as one mRNA transcript. If the operon is *activated*, RNA polymerase will bind to the promoter site and the genes under the operon's control are transcribed. If the operator and operon are *repressed*, RNA polymerase cannot bind to the promoter site and the genes will not be transcribed.

transition mutation

when a purine nucleotide is converted to another purine, or a pyrimidine is converted to another pyrimidine.

Electroporation

when brief electrical impulses are applied to a cell membrane, in order to create temporary holes through which foreign DNA can pass.

Nucleic acid hybridization

when the nucleic acids of one strand of DNA (or RNA) form base pairs with the complementary nucleic acids of a different strand. This is used in many of the techniques discussed in this section (for example, DNA probes mentioned above hybridize with their specific DNA sequence target). ● The expression of a single gene can be tested using a nucleic acid probe via a fluorescently labeled single stranded complementary nucleic acid for an mRNA of interest. This can be used 'in place' on an intact organism, a technique known as *in situ hybridization* that lets us view gene expression in tissues and small embryos.

G2 (GAP-2) phase

where additional cellular growth occurs after DNA has been replicated. The *M phase* can be either mitosis or meiosis, which will be discussed in another chapter. The I phase corresponds to *interphase*, which is the majority of the cell cycle. Notice that interphase includes every phase other than the M phase.

translocation mutation

where one sequence of nucleotides is excised and reinserted into the DNA sequence somewhere else. This can also cause a frameshift mutation, depending on where the cut is made, and how many bases are translocated.

inner medulla of brain is composed of

white matter (neuronal axons).

Codons in mRNA match up

with the anticodon of an aminoacyl-tRNA. The aminoacyl-tRNA is what is actually carrying the amino-acid.

jaundice

yellowish skin appearance due to the high levels of bilirubin in the blood that is not properly metabolized. patients who have liver disorders usually have jaundice

↑ unsaturated fatty acids

↑ membrane fluidity

In response to cold temperature, a cell would

↑ unsaturated fatty acids in the membrane to maintain fluidity and avoid rigidity

↑ saturated fatty acids

↓ membrane fluidity

DAT Tip: Know the resulting gametes of nondisjunction during meiosis I vs meiosis II

▪ Meiosis I non-disjunction: n+1, n+1, n-1, n-1 ▪ Meiosis II non-disjunction: n, n, n+1, n-1

ADH (Anti-diuretic hormone) aka vasopressin

○ *Diuretic*: any substance that increases diuresis (production of urine). ○ Hence, we can understand that ADH (anti-diuretic hormone) functions to *decrease urination*. ○ Why is this helpful? i. Imagine you just pulled an all-nighter studying for an exam, and after the exam you crash for 12 hours straight. The next morning when you do your morning routine in the bathroom, you see that your urine is much yellower than normal. This is due to the effects from ADH. Since you haven't drank water for 12 hours, the cells from your body are dehydrated. To prevent the cells from dying, ADH is released to reabsorb as much water as possible back into the body. ○ Target: *Nephrons* ○ How does ADH work (discussed in more detail in the excretory chapter)? i. ADH functions by inserting small water channels called *aquaporins* in the *collecting duct* of our nephrons in our kidneys. ii. This facilitates the re-uptake of water from the urine back into our body

In females, LH

○ A *surge* of LH triggers *ovulation* during the menstrual cycle ○ Ovulation leaves behind a structure called *corpus luteum* in the ovary. ○ Corpus luteum produces female sex hormones (progesterone and estrogen).

In males, LH

○ Act on *Leydig cells* (*tip on remembering: alliteration! LH acts on Leydig) ○ Triggers production of *testosterone* from Leydig cells ■ *Tip: think of luteinizing hormone (LH) as making men look Large and Hairy (L and H, just like LH)

Functions of cytokines:

○ Attract innate immunity cells e.g. macrophages, dendritic cells to where the identified antigen is present. ○ Stimulate clonal selection and proliferation of B cells and T cells

stratum corneum

○ Composed of *dead, fully differentiated keratinocytes* known as corneocytes, which are essentially flattened cells of keratin. ○ This layer provides protection against infection, dehydration, and physical harm.

Trypsin and Chymotrypsin

○ Digests proteins —> amino acids ○ Remember how pepsin from the stomach is first secreted as a zymogen, pepsinogen, as a form of protection? The same concept applies to trypsin and chymotrypsin, which are also proteases.

Catecholamines

○ Epinephrine (aka. Adrenaline) ○ Norepinephrine (aka. Noradrenaline)

● Function of parathyroid hormone

○ Increases blood calcium level

● Both T3 and T4 are responsible for:

○ Increasing basal metabolic rate in the body. ○ Tissue development for children (including neuronal). ● Both provide a negative feedback force on TSH.

■ Bile emulsifies fat into small droplets (not an enzyme!) ● Key enzymes:

○ Pancreatic amylase: carbs digestion ○ Pancreatic lipase: fats digestion ○ Enteropeptidase

where is the parathyroid hormone (PTH) secreted

○ Parathyroid gland

● B cells can become:

○ Plasma cells: release antibody ○ Memory B cells: don't release antibody, retain memory of antigen for future preventions. Key to vaccinations

stratum spinosum

○ Provides skin with strength and flexibility because of its high prevalence of *desmosomes* holding together keratinocytes. Desmosomes, cell-to-cell adhesion proteins, give the keratinocytes in this layer a "spiny" appearance. When you see the word spinosum, think of spiny desmosomes and strength. ○ Contains the highest prevalence of *Langerhans cells*, which are the *dendritic cells* of the epidermis. Thus, they are integral to *communication between the innate and adaptive immune systems* (learn more about this in the immunology chapter). Langerhans cells are present in all layers of the epidermis, but they are most abundant in the stratum spinosum.

Activate intracellular secondary messengers

○ Scenario: Imagine you want to send a letter to your mother who lives across a river, but you are terrified of water and cannot cross the river. Now, you see a postman on a boat. You hand the letter to him and tells him the address, he will then deliver the letter for you. ○ Now substitute you as a peptide hormone, the river as the cell membrane, and the postman as a secondary messenger.

Goblet cells:

○ Secretes mucus to protect the epithelial lining.

pancreatic amylase

○ Similar to salivary amylase (see section 2), pancreatic amylase breaks starch —> maltose

stratum lucidum

○ Similarly to the stratum corneum, this layer contains *dead keratinocytes*. However, they are not yet fully differentiated into corneocytes. ○ *Remember, this layer is only present in the palms of the *hands* and the soles of the *feet*.

In females, FSH

○ Since FSH's full name is follicle stimulating hormone, we can sort of "guess" its function — stimulating the development of follicles in ovaries. ■ *Note: A follicle is actually a premature egg bundled in a fluid-filled sac. During the menstrual cycle of a woman, typically many follicles develop but only one successfully ovulate with a mature egg. ○ Developing follicles will in turn produce estrogen and progesterone.

In males, FSH

○ Stimulates *sperm maturation* ○ *Tip: The acronym FSH looks like the word FiSH and sperm swimming look like fish. So FSH helps development of sperm.

how does the parathyroid hormone work?

○ Stimulates osteoclasts to chew up more bone —> more calcium is released from bones to the blood ○ Increases calcium reabsorption from the kidney and intestines

Oxytocin

○ Target: *Uterus* and *mammary gland* ○ How does Oxytocin work? i. It has two main functions, one during child labor, another during breastfeeding. ii. Child labor: ● Oxytocin causes uterine contraction through a positive feedback loop i.e. the more the uterine contracts, the more oxytocin is released which triggers even more contraction. iii. Breastfeeding ● Oxytocin triggers milk letdown when the baby begins suckling on the mother's nipple

Neutralization

○ The small intestine produces secretin (a hormone) in response to the entry of chyme from stomach. ○ Secretin stimulates the pancreas to secrete bicarbonate ions (HCO3-) into the duodenum via the pancreatic duct. ○ Bicarbonate is basic, and it neutralizes the acidic gastric juice that just entered the small intestine.

In ribonucleic acid (RNA)

○ There are 2' and 3' hydroxyl groups on the ribose sugar ○ Usually single stranded ○ G(3-)C while A(2-)U

In deoxyribonucleic acid (DNA)

○ There is no 2' hydroxyl group on the ribose sugar - there is only a 3' hydroxyl. ○ Usually double stranded ○ G=C while A=T ○ If a piece of DNA had more G=C bonds, it'd have a stronger bond between the two strands and take more energy (higher temperatures) to separate the strands

Memory B cells

○ These cells live for a long time, sometimes even for decades in our body. ○ They do not release antibodies. ○ They *save* the information about the antigen, and if the same antigen intrudes again within their lifespan, they will rapidly differentiate and proliferate into plasma cells to secrete corresponding antibodies. Memory B cells are key to *vaccinations*. The goal of a vaccination is to introduce a small amount of weakened or dead pathogen to our body. Right after the injection, our B cells would produce memory B cells in response to that specific antigen. Later on in our life, if we happen to come across that same pathogen again, our immune system can rapidly produce antibodies to counterattack before the pathogen proliferates. In addition to these two cell types, B cells can also *act as antigen-presenting cells* like macrophages and dendritic cells.

stratum basale

○ This layer provides continuous renewal of epidermal *keratinocytes*, and it houses other specialized cell types, such as *Merkel cells* and *melanocytes*. i. *Keratinocyte stem cells* live in this layer, and they divide to create the *keratinocytes* of the more superficial epidermal layers. ii. *Melanocytes*: Melano- stands for *melanin*, the pigment generated by this cell type. Melanin is transported to keratinocytes, and it is responsible for the skin's *pigmentation* and *protection* from *UV radiation*. This is why individuals with a greater level skin pigmentation generally have lower levels of skin cancer. iii. *Merkel cells* are specialized *mechanoreceptor* cells. A mechanoreceptor is a cell that has the ability to respond to external stimuli. Merkel cells are specifically attuned to respond to *light touch* sensations, which explains why they are extremely abundant in the *fingertips*. Each Merkel cell synapses with a *somatosensory* (somato=body) afferent nerve fiber, which conveys the message to the central nervous system.

enteropeptidase

○ When food enters the duodenum, glands in the duodenum release enteropeptidase. ■ Enteropeptidase is enzyme that activates trypsin which in turn activates chymotrypsin

Steroid hormones include

● *All* hormones made by the *adrenal cortex*: ○ Glucocorticoids (i.e. cortisol) ○ Mineralocorticoids (i.e. aldosterone) ○ Androgenic steroids ● *All* hormones made by the *reproductive organs*: ○ Progesterone ○ Testosterone ○ Estrogen ● *Tip: the ones ending with -sterone is a giveaway that they are steroids!

amino-acid derived hormones include

● *All* hormones made by the *adrenal medulla*: ○ Epinephrine (aka. adrenaline) ○ Norepinephrine (aka. noradrenaline) ○ Note: these two hormones are *polar* and *water-soluble*. Hence, they act similar to peptide hormones through *secondary messengers*. ● T3 and T4 (secreted by the thyroid) ○ Note: These two hormones are *non-polar* and *lipid-soluble*. Hence, they act similar to steroid hormones and go directly into the cell.

Peptide hormones include

● *All* hormones made by the *hypothalamus*: ○ GnRH (gonadotropin releasing hormone) ○ ADH (antidiuretic hormone, aka vasopressin) ○ Oxytocin ● *All* hormones made by the *anterior pituitary*: ○ TSH (thyroid stimulating hormone) ○ ACTH (adrenocorticotropic hormone) ○ LH (luteinizing hormone) ○ FSH (follicle stimulating hormone) ○ Prolactin ○ GH (growth hormone) ● *Glucagon* and *insulin*; *calcitonin* and *parathyroid hormone*

Mutations can be caused by a number of factors, including:

● *DNA polymerase errors* during DNA replication. ● Loss of DNA during the *genetic recombination* (crossing over of chromosomes), which occurs during mitosis and meiosis. ● *Chemical damage* from drugs. ● *Radiation* from things like gamma rays or UV light... wear sunscreen!

Mammalia (Placental)

● *Examples*: Bat, whale, mouse, human ● *Subphylum*: Vertebrata ● *Circulatory system*: Four chambered heart ● *Respiratory system*: Lungs ● *General characteristics*: Warm blooded (homeothermic), fetus supported by placenta

Mammalia (Monotremes)

● *Examples*: Duckbill platypus, spiny anteater ● *Subphylum*: Vertebrata ● *Circulatory system*: Four chambered heart ● *Respiratory system*: Lungs ● *General characteristics*: Warm blooded (homeothermic), feed young with milk, leathery eggs, mammary glands with many openings (no nipples)

Birds

● *Examples*: Eagle, blue jay ● *Subphylum*: Vertebrata ● *Circulatory system*: Four chambered heart ● *Respiratory system*: Lungs ● *General characteristics*: Warm blooded (homeothermic), eggs in shells

Mammalia (Marsupials)

● *Examples*: Kangaroo, opossum ● *Subphylum*: Vertebrata ● *Circulatory system*: Four chambered heart ● *Respiratory system*: Lungs ● *General characteristics*: Warm blooded (homeothermic), feed young with milk

Fish (Bony)

● *Examples*: Salmon, halibut ● *Subphylum*: Vertebrata ● *Circulatory system*: Two chambered heart ● *Respiratory system*: Gills ● *General characteristics*: scales, bony skeleton

Fish (Cartilaginous)

● *Examples*: Shark ● *Subphylum*: Fish (Cartilaginous) ● *Circulatory system*: Two chambered heart ● *Respiratory system*: Gills ● *General characteristics*: Jaws and teeth, reduced notochord with cartilaginous vertebrae (from here on: notochord is present only in embryonic stage, replaced by vertebrae in adulthood).

Amphibia

● *Examples*: Tadpole, frog, toad, salamander, newt ● *Subphylum*: Vertebrata ● *Circulatory system*: Three chambered heart ● *Respiratory system*: Gills (juvenile), Lungs (adult) ● *General characteristics*: No scales. Undergo metamorphosis. Tadpoles live in aquatic habitats, have tails and no legs. Adults live in land habitats, have two pairs of legs and no tail.

Reptilia

● *Examples*: Turtle, snake, crocodile, alligator ● *Subphylum*: Vertebrata ● *Circulatory system*: Three chambered heart ● *Respiratory system*: Lungs ● *General characteristics*: Mainly live on land, leathery eggs, internal fertilization, cold blooded (poikilothermic)

Fish (Jawless)

● *Examples*: agnatha, lamprey, hagfish ● *Subphylum*: Vertebrata ● *Circulatory system*: Two chambered heart ● *Respiratory system*: Gills, countercurrent exchange ● *General characteristics*: Notochord found in larvae and adult, cartilaginous skeleton

Gastrulation Revew

● *Gastrulation*: formation of three germ layers — ectoderm, mesoderm, endoderm. ● Beginning of gastrulation: cells *invaginate* from the *primitive streak* ● *Blastopore*: *opening* created by invagination ○ Deuterostomes: Anus ○ Protostomes: Mouth ● *Archenteron: hollow center cavity* inside embryo —> digestive tube

Stomach Digestion Review

● *Mechanical* digestion: *churning* of stomach ● *Chemical* digestion: enzymatic breakdown of *proteins* and *fats* ● Key enzymes: ○ *Pepsin* (activated from pepsinogen under low pH) ○ *Gastric lipase* ● Key cells: ○ *G cells* —> releases *gastrin* (hormone) —> stimulates parietal and chief cells ○ *Parietal cells* —> gastric juice (*HCl*) ○ *Chief cells* —> pepsinogen and gastric lipase ○ *Mucous cells* —> protection of *mucus*

To test for the presence of a specific gene sequence in someone's DNA

● *Method 1* - Take a drop of their blood, cut up the DNA into smaller pieces, and use PCR with a primer specific for the region that gene sequence appears. If that gene is present, lots of copies will be made via PCR. If the gene is not present, no copies will be made. ● *Method 2* - Amplify the cDNA of the gene sequence, then use a DNA microarray assay to detect the presence of fluorescence, indicating whether or not the gene is there.

Phyletic groups are:

● *Monophyletic* are a group of organisms that consist of an ancestral species and all its descendants. ● *Paraphyletic* are a group of organisms that consist of an ancestral species and some but not all descendants. ● *Polyphyletic* are a group of organisms that descend from more than one common ancestor.

Hyperthyroidism

● *Over-secretion* of T3 and T4 ● This results in *increased metabolic rate*, some of the symptoms are: ○ Hyperactivity ○ Anxiousness ○ Weight loss For hyperthyroidism, goiter actually results from a *hyperactive* thyroid gland. For example, In *Graves' Disease*, it is our body's *autoimmune system* that mistakenly attacks the cells of the thyroid gland and thereby overstimulating it.

passive vs active immunity

● *Passive immunity*: antibodies are given to an organism, not acquired. ○ IgG — transfer through placenta ○ IgA — transfer through breastfeeding ● *Active immunity*: acquired immunity Vaccines: artificially stimulates active immunity

Liver Blood Maintenance

● *Stores* blood ● *Filters* and *detoxifies* blood coming from the digestive system ○ The small intestine is connected to the liver through a *hepatic portal system* ■ A portal system is when a capillary bed is connected to another capillary bed through a portal vein. ■ We will get into more depth about a portal system in the endocrine section of the notes. For now, just remember that a portal system is advantageous because it allow *fast diffusion of substances.* ○ The liver then *removes toxic substances* from the absorbed food. ● *Erythrocyte* destruction ○ Erythrocytes are red blood cells (*RBC*) ○ There is a specific type of cells: *Kupffer cells* in the liver that destroy old or useless RBCs. ■ *Note: Most of RBC destruction is done in the *spleen* ○ RBCs contain *hemoglobin* (red pigment), hemoglobin is broken down by Kupffer cells into *bilirubin (yellowish pigment). ○ Bilirubin is secreted into *bile* (that's why bile has a yellowish-green color!) ○ This is also why patients who have liver disorders usually have *jaundice* — yellowish skin appearance due to the high levels of bilirubin in the blood that is not properly metabolized. ● *Bacteria* destruction ○ *Kupffer cells* are *phagocytes* that also eat up bacteria.

Lancelets (also known as Amphioxus)

● *Subphylum*: Cephalochordata ● *Circulatory system*: Cephalochordates lack a heart. Blood travels through a closed circulatory system by contractile blood vessels. ● *Respiratory system*: Gill ○ Note: in Cephalochordata, this gill is also used for feeding and excretion. ● *General characteristics*: Have all of the developmental characteristics of other chordates, but lack vertebrae. They have been extensively studied to examine the origin of vertebrates. Lancelets keep the notochord through adulthood.

Tunicates (also known as Urochordata)

● *Subphylum*: Tunicata ● *Circulatory system*: Both closed (fully developed heart and blood vessels) as well as open systems. ● *Respiratory system*: Gills ● *General characteristics*: Sessile, filter feeders, hermaphroditic, both sexual and asexual (budding) reproduction. Tunicates live in benthic habitats and only have a notochord as larvae.

After antibodies are released into the humor, they can

● *Tag* the specific corresponding antigen for removal —> signal it should be phagocytosed ● *Coat* the antigen in antibodies, which neutralizes it ● Activate the *complement* system These functions all share a common goal — annihilate the pathogen containing the specific antigen.

Ribosomes contain three sites that are crucial to the process of translation

● *The A site* (A for aminoacyl-tRNA) ● *The P site* (P for peptidyl-tRNA) ● *The E site* (E for exit) Aminoacyl-tRNAs enter the *A site* of a ribosome during translation. Peptidyl-tRNA will be waiting for the incoming aminoacyl-tRNA at an adjacent site - the *P site*. *Peptidyl-tRNA* carries a polypeptide chain as opposed to just one amino acid. When the aminoacyl-tRNA arrives, the ribosome will catalyze a *peptide bond* between the last amino acid of the polypeptide on the peptidyl-tRNA and the single amino acid on the aminoacyl-tRNA. The polypeptide will then be passed to the aminoacyl-tRNA at the A site, converting it to a new peptidyl-tRNA. Once this conversion has been made, the entire ribosome will shift over one codon. This results in the tRNA the was at the P site moving to the *E site* and ultimately exiting from the ribosome. Similarly, the aminoacyl-tRNA (now peptidyl-tRNA) that was at the A site will be moved to the P site. This leaves the A site empty in preparation of the next aminoacyl-tRNA.

In placental mammals, the allantois

● *Transports waste* from fetus to the placenta to give to the mother ● Becomes the *umbilical cord* later in development. ● In adults, the allantois becomes the *urinary bladder* (another sac for waste storage!)

Hypothyroidism

● *Under-secretion* of T3 and T4 ● This results in *reduced metabolic rate*, hence leading to a spectrum of symptoms including: ○ Lethargy (lack of energy) ○ Weight gain ○ Low heart and respiratory rate For hypothyroidism, the thyroid produces a low level of T3 and T4. As a result, the hypothalamus secretes more TRH to tell the anterior pituitary to produce more TSH to stimulate the thyroid. As time passes, the *excessive stimulation* results in enlargement of the thyroid gland.

Factors Influencing Development Review

● 4 main factors that influence development: ○ Embryonic Induction ○ Homeotic genes ○ Cytoplasmic determinants ○ Apoptosis ● Embryonic Induction: ○ Organizers that influence the development of neighboring cells ○ e.g. dorsal lip of blastopore in frog embryos ● Homeotic Genes: ○ Master switch controller that turns gene expressions on and off ○ E.g. Homeobox gene (homologous in many organisms) ● Cytoplasmic determinants ○ Uneven distribution of materials in cytoplasm guides cell division ○ E.g. animal pole vs. vegetal pole ● Apoptosis ○ Cleans up and remove unnecessary/potentially harmful things ○ E.g. removing of webbing between digits

adrenal gland review

● Adrenal cortex only produces steroid hormones: *glucocorticoids, mineralocorticoids, androgenic steroids*. ○ Stimulated by *ACTH* from anterior pituitary ● Adrenal medulla only produces amino-acid derived hormones: *catecholamines* ○ Directly stimulated by the *sympathetic nervous system*

Pancreas Overview

● Alpha (α) cells —> glucagon ○ *Increases* blood glucose level ● Beta (β) cells —> insulin ○ *Decreases* blood glucose level ● Delta (δ) cells —> somatostatin ○ Inhibit both glucagon and insulin secretion

Frog and Chick Embryos Review

● Animal pole: ○ Very active cleavage, little yolk ● Vegetal pole: ○ Little activities, a lot of yolk ● Frog embryos ○ Go through uneven holoblastic cleavage. ○ Animal pole is dark, vegetal pole is pale ○ Gray crescent forms at the opposite end of sperm entry ■ Dorsal lip of blastopore forms @ gray crescent —> gastrulation begins here ■ Cell containing a bit of gray crescent can become a complete embryo ● Chick embryos ○ Egg-laying animals tend to have huge yolk for nourishment ○ Flat blastula —> blastodisc (analogous to ICM)

Photosynthesis Pigments

● Antenna pigments (chlorophyll b, carotenoids, phycobilins [red algae pigment], and xanthophylls) capture wavelengths that chlorophyll a does not. These pigments pass energy to chlorophyll a where direct light reaction occurs. Chlorophyll a has a porphyrin ring (alternating double and single bonds, double bonds critical for light reactions) complexed with a *magnesium* atom inside. ● Note: Red and blue light are most effective at promoting photosynthesis, while green light is the least effective.

Genetic disorders can follow a number of inheritance patterns:

● Autosomal recessive ● Sex-linked ▪ X-linked dominant ▪ X-linked recessive ▪ Y-linked

Adaptive Immunity - B Cells Summary

● B cells —> antibody-mediated immunity/humoral immunity ● BCR = antibodies = immunoglobulins ○ BCR is the bounded version ■ BCR can bind to free or presented antigens ■ Unique and uniform ○ Antibodies/immunoglobulins are freely secreted ● B cells can become: ○ *Plasma cells*: release antibody ○ *Memory B cells*: don't release antibody, retain memory of antigen for future preventions. Key to vaccinations ● Antibody: ○ Y-shaped, heavy + light chain, constant + variable region ○ 5 classes: IgM, IgA, IgE, IgD, IgG

Here is a more comprehensive list of the tissues mesoderm develops into:

● Bone and skeleton ● Muscles ● Cardiovascular system ● Gonads ● Adrenal cortex ● Spleen ● Notochord

What do T3 and T4 have in common?

● Both T3 and T4 are derived from the amino acid *tyrosine* (recall we covered them as the third type of hormones in section 1). ● Both T3 and T4 are released in response to *TSH* from the anterior pituitary. ● Both T3 and T4 are responsible for: ○ *Increasing basal metabolic rate* in the body. ○ *Tissue development for children (including neuronal)*. ■ Side note: If an infant is born with severe hypothyroidism (under-secretion of T3 and T4), mental retardation can result if no treatment is given within the first two months. ● Both provide a *negative feedback* force on TSH. ○ If our body detects a higher level of T3 and T4, it will shutdown the production of TSH from the anterior pituitary.

a more comprehensive list of the tissues ectoderm develops into

● CNS (brain and spinal cord) and PNS ● Sensory parts of the ear, eye, and nose ● Epidermis layer of skin, nails, and hair ● Mammary and sweat glands ● Pigmentation cells ● Jaws and teeth ● Adrenal medulla

Fertilization Review

● Capacitation *destabilizes* the sperm's membrane protein and lipids ○ Prepares for acrosome reaction ○ Hyperactivate the sperm ● *ZP3* of zona pellucida binds to sperm —> *acrosome* reaction ● Fast block: ○ Sodium ions *depolarizes* egg membrane —> prevents further sperm binding for a brief moment ● Slow block: ○ Calcium ions triggers exocytosis of *cortical granules* —> make zona pellucida impermeable + cut the link between z.p. and plasma membrane ● Monozygotic twins: identical, one zygote —> two embryos ● Dizygotic twins: fraternal, two zygotes —> two embryos

Cyclin‐dependent kinases (Cdk's)

● Cdk enzymes activate proteins that regulate cell cycle by phosphorylation. ● Cdk's are activated by the protein cyclin.

Embryogenesis in Mammals Review

● Cleavage: ○ Increase in # of cells ○ Total mass stays the same ○ Each cell becomes smaller in size. ● Radial cleavage ○ Deuterostome ○ Aligned cells ● Spiral cleavage ○ Protostome ○ Shifted cells ● Determinate cleavage ○ Cells have set fate ● Indeterminate cleavage ○ Cells have all the potential ● Holoblastic cleavage ○ Even cleavage throughout the embryo ● Meroblastic cleavage ○ Uneven cleavage ● Morula: solid ball of cells (~12-16 cell stage) ● Blastula: ball of cells with a hollow center (~128 cell stage) ○ Hollow center: blastocoel ● Zona hatching: Lysis of zona pellucida to allow implantation ● Blastocyst: ○ Trophoblast —> extraembryonic structures ○ Inner cell mass ■ Hypoblast ● Partially contribute to yolk sac, rest degenerate ■ Epiblast ● Core of the embryo

Growth Hormone

● Direct Hormone ● Aka Somatotropin (somato- means cells of the body, -tropin means hormone) ● Stimulates the cells of the body to grow, reproduce and divide.

Prolactin

● Direct Hormone ● Prolactin has two phases of effects: ○ During pregnancy: *stimulates mammary gland* development ○ After childbirth: *increases milk production* ■ Note: oxytocin stimulates milk letdown, but prolactin stimulates milk production ● Tip to remember: prolactin stimulates lactation (milk production)

In placental animals, the chorion

● Forms the *placenta* along with maternal tissue ○ The chorion is responsible for the fetal half of the placenta ○ The placenta is a platform of *exchange of gases, nutrients, and wastes* between the fetus and the mother.

Extraembryonic Structures Review

● Four extraembryonic structures: ○ Amnion ■ Amniotic fluid —> protection + shock absorption ■ Amphibians and fishes do NOT have an amnion! ○ Chorion ■ Placental mammals: forms the placenta ■ Egg-laying animals: gas exchange membrane ○ Allantois ■ Stores waste ■ Placental mammals: forms the umbilical cord ■ Egg-laying animals: fuses with chorion ○ Yolk sac ■ Provide nutrients ■ Placental mammals: only works until placenta takes over ■ Egg-laying animals: always working!

testes and ovaries review

● In females: ○ LH surge triggers ovulation and production of estrogen and progesterone ○ FSH promotes follicular development —> more estrogen and progesterone ● In males: ○ LH stimulates Leydig cells to produce testosterone ○ FSH helps sperm maturation

In egg-laying animals, the allantois

● Initially *stores uric acid* ● Later *fuses* with the *chorion* and joins in to help with gas exchange because it is rich in blood vessels

Liver Digestion Review

● Key liver functions: ○ Digestive ■ Production of bile —> stored in gallbladder —> secreted into duodenum ○ Blood ■ Blood storage ■ Blood filtration ■ Blood detoxification ■ Removal of old RBCs —> bilirubin from hemoglobin —> bile ○ Glucose Metabolism ■ Glycogenesis ■ Glycogenolysis ■ Gluconeogenesis ○ Protein Metabolism ■ Synthesizing plasma proteins e.g. albumin, clotting factors ■ Ammonia —> urea ■ Synthesizing non-essential amino acids

❖ Prophase I has 5 sub-steps.

● Leptotene (chromosomes start condensing) → zygotene (synapsis begins; synaptonemal complex forming) → pachytene (synapsis complete, crossing over) → diplotene (synaptonemal complex disappears, chiasma still present) → diakinesis (nuclear envelope fragments, chromosomes complete condensing, tetrads ready for metaphase).

IgD

● Monomer The function is not well understood, and only a small amount is produced ● *Tip: IgD stands for IgDon't, as we don't know much about it!

IgG

● Monomer ○ *Tip: IgG stands for IgGo, so it can go through the placenta! ● Also activates complement system

Organogenesis Review

● Neurulation process: ○ Notochord induces ectoderm cells to thicken —> neural plate —> neural plate folds onto itself —> neural fold/groove —> fold until a tube is formed —> neural tube —> CNS ● Notochord: mesoderm ● Neural tube: ectoderm ● Neural crest cells: ectoderm ● Somites: mesoderm ● *Totipotent* stem cells: can become any cell of the body ● *Pluripotent* stem cells: can become any one of the 3 germ layers ● *Multipotent* stem cells: can become any cell from a specific lineage

Photosynthesis Description

● Photosynthesis begins with light-absorbing pigments in plant cells that are able to absorb energy from light: *chlorophyll a, b, and carotenoids* (red, orange, yellow). Light is incorporated into electrons and excited electrons are unstable and re-emit absorbed energy. The energy is then reabsorbed by electrons of nearby pigment molecules. ● The process ends when energy is absorbed by one of two special chlorophyll a molecules (P680 & P700). P700 forms pigment cluster (PSI) and P680 forms pigment cluster (PSII).

feedback loops review

● Positive feedback loop: loop ramps up ○ E.g. oxytocin and prolactin ● Negative feedback loop: loop inhibits itself ○ E.g. progesterone and estrogen inhibit production of GnRH

Hypothalamus and Pituitary Review

● Posterior Pituitary —> *n*eurohypophysis ○ Consists of neuronal tissue ○ *Cannot* make its own hormones ○ Stores and releases *oxytocin* and *ADH* made from the hypothalamus ● Anterior Pituitary —> *adeno*hypophysis ○ Consists of glandular tissue ○ *CAN* make its own hormones —> (FLAT PiG) ○ Connected to the hypothalamus through *hypophyseal portal system* ● Pineal Gland —> *Melatonin*

Recap of the valves

● Right side: ▪ Between atrium and ventricle: Right atrioventricular valve aka Tricuspid valve ▪ Between ventricle and pulmonary artery: Pulmonary semilunar valve ● Left Side: ▪ Between atrium and ventricle: Left atrioventricular valve aka Bicuspid valve aka Mitral valve ▪ Between ventricle and aorta: Aortic semilunar valve

Alpha (α) cells

● Secrete hormone *glucagon* ● When secretion happens? ○ When there is a *low blood glucose level*, typically during fasting or in between meals ● Function of glucagon ○ *Increase* blood glucose level ● How does it achieve this? ○ It targets *2* out of the 3 glucose storages: ■ Stimulate the *liver* to convert glycogen back to glucose ■ Stimulate *adipose* tissue to convert triglycerides back to glucose ■ *Note: muscle cells are NOT the main target here!

Beta (β) cells

● Secrete hormone *insulin* ● When secretion happens? ○ When there is a *high blood glucose level*, typically right after eating ● Function of insulin: ○ *Decrease* blood glucose level ○ Just like how PTH has the opposite effect of calcitonin, insulin also acts in the *opposite* direction of glucagon. ● How does it achieve this? ○ It stimulates *all 3* glucose storages: ■ Liver: glucose —> glycogen ■ Muscle: glucose —> glycogen ■ Adipose: glucose —> triglycerides

Delta (δ) cells

● Secretes hormone *somatostatin*. Somatostain is aka growth hormone inhibiting hormone, and (you guessed it) - inhibits growth hormone secretion, ● Function of somatostatin: ○ Inhibits the secretion of both *glucagon* and *insulin*.

Large Intestine Digestion Review

● Structure of large intestine ○ Cecum —> Colon —> Rectum —> Anus ● Functions of large intestine ○ Water absorption ○ Salt absorption ○ Vitamin production and absorption

If an antigen is presented by MHC I:

● T cells activate and become cytotoxic T cells, also called CD8 cells

if an antigen is presented by MHC II:

● T cells activate and become helper T cells, also called CD4 cells

How are T3 and T4 different?

● T4 has *one more iodine* atom than T3, hence the name. ● T3 is the active form of the hormone, hence much more *potent*. ○ T3 is about 4x more potent than T4! ● T4 is the main circulating form of the hormone, because T4 is more stable and has a *longer half-life* than T3. ○ Therefore, in the blood, we would mostly find T4 circulating. ○ Our body tissue converts T4 into the more potent T3 upon uptake. ○ Hence, we can say that T4 is a *prohormone* (a precursor) to T3.

In egg-laying animals, the chorion

● The chorion lies right *underneath the egg shell* ● It functions as a membrane for *gas exchange* (remember eggshells have pores to allow gases to come and go!)

Genome‐to‐Volume ratio (G/V)

● The genome size remains constant throughout life. As the cell grows, only the volume increases. Genome/Volume will be small. ● As Genome/Volume decreases, the cell exceeds the ability of its genome to produce sufficient amounts of regulation for cellular acvities. Some large cells (paramecium, human skeletal muscle) are multinucleated to deal with this.

Small Intestine Digestion Review

● The hormone *secretin* is released when food enters the small intestine: ○ Signals pancreas to release bicarbonate ions —> neutralize acid chyme ● The hormone *cholecystokinin* is also released when food enters small intestine: ○ Slows down gastric emptying ○ Signals the pancreas to release digestive enzymes ○ Signals the gallbladder to release bile ■ Bile *emulsifies* fat into small droplets (not an enzyme!) ● Key enzymes: ○ Pancreatic amylase: carbs digestion ○ Pancreatic lipase: fats digestion ○ Enteropeptidase ■ Activates trypsinogen into trypsin ● Trypsin ○ Activates chymotrypsinogen into chymotrypsin ○ Trypsin + chymotrypsin: protein digestion ● Villi + microvilli increase surface area for absorption

cholecystokinin

● The hormone cholecystokinin is also released when food enters small intestine: ○ Slows down gastric emptying ○ Signals the pancreas to release digestive enzymes ○ Signals the gallbladder to release bile

secretin

● The hormone secretin is released when food enters the small intestine: ○ Signals pancreas to release bicarbonate ions —> neutralize acid chyme

Integumentary System Review

● The integumentary system has three layers: the *epidermis*, *dermis*, and *hypodermis.* ● The *epidermis* contains *keratinocytes* and additional specialized cell types, and it has five layers: the *stratum corneum, lucidum*, granulosum, spinosum, and basale*. (The stratum lucidum is only present on the palms of the hands and the soles of the feet). ● The *epidermis protects* us from dehydration, UV radiation, and pathogens. ● The *dermis* has two layers: The *papillary dermis* and *reticular dermis*. ● The dermis *supports the epidermis* and is *home to many functional elements* of the skin, such as glands and hair. ● The *hypodermis* is the deepest layer of the integumentary system.

Positive feedback loop

● The loop *ramps up* and reinforces a stimulus i.e. the rich gets richer. Example 1: An infant *nursing* (suckling) stimulates the mammary gland. This serves as a signal to the posterior pituitary to release *oxytocin* and the anterior pituitary to release prolactin. Prolactin increases milk production. Oxytocin triggers the milk *let down* reflex, which increases contractions of smooth muscle in the breast and release the milk. As the baby continues to suckle, more oxytocin and prolactin are produced, therefore more milk is produced and let down. Example 2: During labor, *oxytocin* causes contractions. The baby presses against the cervix of the *uterus*, and this stimulates a nerve. The nerve signals the hypothalamus and pituitary gland to release more oxytocin, which causes more contractions, which causes greater pressure on the cervix, which causes more oxytocin release, which causes more contractions...etc. This loop continues and amplifies until the baby is out. *positive feedback* generally promotes *exponential growth* (like uterine contraction)

In egg-laying animals, the yolk sac

● The yolk sac is the *sole player in providing nutrients* to the young fetus.

In placental animals, the yolk sac

● The yolk sac usually has a *transient* function — it nourishes the fetus until the placenta is mature and ready to take over this role. ● The yolk sac is the *first location of blood cell formation* for the fetus.

Pluripotent stem cells:

● These are less "do-it-all" than totipotent stem cells ● They are cells that can differentiate into *any of the 3 germ layers* (ecto, meso, and endoderm) ● Examples include: ○ Cells from inner cell mass (ICM) —> embryonic stem cells (ESCs)

Totipotent stem cells

● These can become *any cell* in the body ● Examples include: ○ Zygote ○ Blastomeres of the morula (identical stem cells resulting from cleavage)

Multipotent stem cells

● These have even less potential than the pluripotent stem cells ● They are cells that can only differentiate into a few cell types of a *specific tissue type* ● Examples include: ○ Hematopoietic stem cell —> can divide into many blood cells e.g. monocyte, lymphocyte

Cilia

● These little *hair-like* projectiles which are found in the respiratory tract. ● They are like small brooms that sweep away unwanted guests that come in.

skin

● Thick *epidermis, dermis, and hypodermis* ○ Pathogens unable to penetrate through intact skin ● Possesses *mucous membranes* ○ Trap pathogens that do enter (for example, through a laceration/cut) and secrete lysozyme ○ *Lysozymes* are antimicrobial proteins that are found in many types of body secretions, such as tears, saliva, Ciliaand mucous. It is a type of enzyme that nonspecifically breaks down bacterial cell walls ● *Sebaceous* glands ○ Oil (sebum) itself serves as an additional physical barrier ○ The fatty acids in sebum possess antimicrobial properties

Adrenocorticotropic Hormone (ACTH)

● Tropic Hormone ● It is released in response to stress ● It stimulates the *adrenal gland cortex* to release *glucocorticoids* to combat stress

Follicle Stimulating Hormone (FSH)

● Tropic Hormone ● It plays an important role in *follicle growth* in females and *maturation of sperms* in males (refer to section 6 for more details).

Leutinizing Hormone (LH)

● Tropic Hormone ● It stimulates *ovulation*, the formation of *corpus luteum* in females and production of *testosterone* in males (refer to section 6 for more details)

Thyroid Stimulating Hormone (TSH)

● Tropic Hormone ● It stimulates the *thyroid gland* to produce *T3* and *T4* which then ramps up metabolism in the body (refer to section 3 for more details)

certain ages related to the universe and its lifeforms

● Universe: 12-15 billion years old ● Solar System: 4.6 billion years old ● Earth: ~4.5 billion years old ● Microfossils of prokaryotes: 3.6 billion years old ● Photosynthetic bacteria: 2.3 billion years old ● Eukaryotes: ~2-2.5 billion years old

Other Lipid Derivatives

● Waxes Structure: esters of fatty acids and monohydroxylic alcohols Function: used as protective coating or exoskeleton (lanolin) ● Carotenoids Structure: fatty acid carbon chains with conjugated double bounds and 6-membered rings at each end. Function: Pigments which produce colors in plants and animals. Includes the carotenes and xanthophylls (subgroups) ● Porphyrins (tetrapyrroles) Structure: 4 joined pyrrole rings, often complexed w/ metal ion E.g. Heme (complexes with Fe in hemoglobin), Chlorophyll (complexes w/ Mg)

Surface‐to‐Volume ratio (S/V)

● When a cell grows the volume gets larger more rapidly ( 4/3 πr2 ) vs. surface area (4πr2 ). ● When Surface/Volume is large, cellular exchange becomes easier. ● When Surface/Volume is small, cellular exchange is hard, and leads to cell death or cell division to increase SA.

Calcitonin

● Where it is secreted ○ *Parafollicular cells* of the thyroid ● Function ○ *Decreases blood calcium level* (tip to remember: calcitonin tones down calcium!) ● How does calcitonin work? ○ *Stimulates osteoblasts* to build more bone (osteoblasts build bone) —> uses up more calcium from the blood ○ *Inhibits osteoclasts* from chewing up bones (osteoclasts chew bone down) —> less calcium is released from bones to the blood ○ *Decreases calcium reabsorption* from the kidney and intestines

parathyroid hormone (PTH)

● Where it is secreted ○ *Parathyroid gland* ● Function ○ *Increases blood calcium level* ● How does PTH work? ○ *Stimulates osteoclasts* to chew up more bone —> more calcium is released from bones to the blood ○ *Increases calcium reabsorption* from the kidney and intestines hormone that does the exact OPPOSITE of calcitonin, but it is secreted from the parathyroid gland located on the back of the thyroid gland.

Cell Division

❖ *Cell division* is nuclear division (karyokinesis) followed by cytokinesis. ❖ In diploid cells, there are two copies of every chromosome, forming a pair called *homologous chromosome*. ❖ Humans have 46 chromosomes, 23 homologous pairs, and a total of 92 chromatids (depending on stage of division). ❖ *MTOCs* are microtubule organizing centers - in animal cells these are the centrosomes. A pair of MTOCs are found outside the nucleus. ● In animal cells, each MTOC contains a pair of centrioles. ● Plants have MTOCs, but they are not centrosomes. ❖ Mitosis occurs in somatic cells and meiosis occurs in gametes (egg, sperm, pollen). ● Fusion of two haploid gametes = fertilization/syngamy = diploid zygote

DNA sequencing

❖ *DNA sequencing*, as the name implies, is used to determine the sequence of base pairs in a DNA or RNA molecule. ● Dideoxy chain termination was the early method of sequencing DNA - its specifics are unimportant for the DAT. ● Next generation sequencing is currently used, and records which nucleotide is added to a growing strand during its synthesis. ❖ Amino acid sequencing can be performed via *Edman degradation* (its specifics are also unimportant for the DAT).

Gas Exchange Mechanisms

❖ *External Respiration* is entry of air into lungs and gas exchange between alveoli and blood. ❖ *Internal Respiration* is an exchange of gas between blood and cells and intracellular respiration processes

Hardy-Weinberg Equation (Genetic Equilibrium)

❖ *Genetic equilibrium* occurs when allele frequencies remain constant from generation to generation. Therefore, there is no evolution. ❖ Genetic equilibrium requires the following conditions: no mutation, all traits are neutral (no natural selection), population must be isolated (no gene flow), large population (no genetic drift), mating is random, no net migration. ❖ To evaluate genetic equilibrium three values should be evaluated: ● Allele frequencies for each allele (p, q) ● Frequency of heterozygous (pq + pq = 2pq) ● Frequency of homozygous (p2, q2) ❖ Genetic variation of populations at equilibrium can be calculated using the following equations: ● All alleles sum to 100%: p + q = 1 ● All individuals sum to 100%: p2 + 2qp + q2 = 1 ● Bout must be true for Hardy Weinberg! ❖ Example: A plant population with 85% Red (R) and 15% white (r) -> q2 = 0.15 (rr) and p2 + 2qp = 0.84 (RR+Rr) ● We can find q and p by taking the square-root and plug in the two equations to find heterozygous frequency and homozygous dominant frequency.

Respiratory Acidosis and Alkalosis

❖ *Respiratory acidosis* comes from inadequate ventilation. ● Enough CO2 is not cleared out and is accumulates so more H+ is formed as described by the reactions above. This causes a drop in pH in tissues. ❖ *Respiratory alkalosis* comes from breathing too rapidly. ● CO2 is lost very quickly and H+ and HCO3- start to combine to form CO2 via the reactions above. This causes the pH to rise. ❖ In order to distinguish between respiratory acidosis/alkalosis and metabolic acidosis/alkalosis, determine the cause of the imbalance. Respiratory comes from breathing issues and metabolic comes from anything else. ● In metabolic acidosis and alkalosis, breathing may be altered to compensate, but the cause is not breathing related. ● An increase in H+ or CO2 will cause an increase in breathing rate (hyperventilation). High blood O2 partial pressure would cause a decrease in breathing rate (hypoventilation).

Chemistry of Gas Exchange

❖ 98% of blood oxygen binds rapidly and reversibly with protein hemoglobin inside RBCs, forming oxyhemoglobin. ❖ The hemoglobin structure is a 4 polypeptide subunit, each has a *heme cofactor* (organic molecule with iron atom center). ● Each iron atom can bind with one O2 molecule. ● Because of the cooperativity effect, when one O2 binds the rest bind easier (this is why hemoglobin has a sigmoidal shape). Likewise, when one O2 is released, the rest release easier. ❖ As the pressure of oxygen increase, the saturation of hemoglobin increases. This is ideal because in the lungs we are oxygen rich and want to hang on to it, but in the tissues we are oxygen poor (lower oxygen pressure) so the hemoglobin will release the oxygen to the tissues. ❖ *Carbon monoxide* (CO) has a 200x greater affinity for hemoglobin than oxygen does. It forms carboxyhemoglobin. In order to displace the bound CO, pure O2 needs to be administered.

The Law of Dominance

❖ A dominant allele masks the effect of a recessive allele. ❖ For example, an organism with a dominant eye color allele (brown) on one chromosome and a recessive eye color allele (blue) on the other chromosome will simply display the phenotype of the dominant allele (brown eyes).

EKG/ECG of Heart Contraction

❖ A normal EKG/ECG consists of waveforms that correspond to different parts of one heartbeat. ❖ *P wave* is the first deflection and indicates atrial depolarization. ❖ *QRS complex* follows the P wave and represent the ventricular depolarization and contraction. ❖ *T wave* follows the QRS complex and represents ventricular repolarization.

Adenosine Triphosphate (ATP)

❖ ATP is considered an RNA nucleotide due to its ribose sugar. ❖ ATP is an unstable molecule because the 3 phosphates in ATP are negatively charged and repel one another. ● When one phosphate group is removed via hydrolysis, a more stable molecule (ADP) results. ● The change from a less stable molecule to a more stable molecule always releases energy. ❖ ATP provides energy for all cells by transferring phosphate from ATP to another molecule.

final electron acceptor of alcohol fermentation

❖ Acetaldehyde is the final electron acceptor! Acetaldehyde accepts the electrons to form the final product of ethanol. This is similar to O2 being the final electron acceptor of cellular respiration, thus forming the final product of H2O.

Relationship of Basal Metabolic Rate (BMR) and Body Size

❖ As body size of mammals increases, their basal metabolic rate increases. ❖ Basal metabolic rate per kilogram of body mass decreases as body mass increases. ❖ An increase in body temperature leads to an increase in metabolism (↑ body temp = ↑ metabolism). ❖ Increasing age leads to a decrease in metabolism (↑ age = ↓ metabolism).

Meiosis I DAT Tips

❖ At the end of anaphase I, there is a total of 46 chromosomes if a cell has 46 chromosomes at the beginning because 23 chromosomes are pulled to each pole by independent assortment and no chromatids are separated at anaphase I. ❖ Prophase I has 5 sub-steps. ● *Leptotene* (chromosomes start condensing) → *zygotene* (synapsis begins; synaptonemal complex forming) → *pachytene* (synapsis complete, crossing over) → *diplotene* (synaptonemal complex disappears, chiasma still present) → *diakinesis* (nuclear envelope fragments, chromosomes complete condensing, tetrads ready for metaphase).

Avian Respiration

❖ Avian respiration is drastically different than human respiration. Due to the unique anatomy of birds, respiration is both continuous and unidirectional. ● Air sacs allow birds to exchange gas during both inhalation and exhalation. ● Oxygen rich incoming air is first stored in air sacs before entering lungs during exhalation, so it is not mixed with the deoxygenated exhaled air. ❖ In mammalian respiration, there is tidal breathing. We breathe in and out through the same tubing, inhibiting gas exchange during exhalation. ● Deoxygenated air is mixed with some fresh air during inhalation, some of it is re-breathed. This is much less efficient than birds.

DAT Tips on mitosis

❖ Before mitosis, chromatin condenses into chromosomes. Presence of chromosomes means mitosis is occurring. ❖ Each metaphase chromosome consists of 2 closely attached sister chromatids. ❖ The end of metaphase is denoted by the presence of centrosomes at opposite ends of the cell. ● Before moving on to anaphase, the cell checks that each chromosome is attached to microtubules with their kinetochore. This ensures that in anaphase the sister chromatids split evenly. ❖ In metaphase, to keep track of the total number of chromosomes, count the centromeres! ❖ In anaphase, the chromosome number doubles. ❖ At the end of anaphase, each pole has a complete set of chromosomes, same as the original cell before replication. ● There would be a total of 92 chromosomes (92 chromatids) if a cell has 46 chromosomes at the beginning. ❖ It is important to note that unlike meiosis, NO genetic variation occurs in mitosis.

Scientific Proof of Evolution: Biogeographists

❖ Biogeographists have shown that unrelated species look alike when found in similar environments of different regions of the world. They use geography to describe the distribution of species.

Heredity DAT Tips

❖ Codominance is typically represented with two capital letters, e.g. AB blood type ❖ Incomplete dominance is typically represented as capital letters, with one letter having an additional apostrophe, e.g. AA' for alleles A and A' ❖ Phenotype ratios and genotype ratios are not necessarily the same. ● Take the cross of Aa x Aa for example. The offspring genotype ratio would be 1 AA: 2 Aa: 1 aa, but the phenotype ratio would be 3:1 (AA and Aa produce the same dominant phenotype, while aa represents the recessive phenotype). ❖ A heterozygote cross resulting in a 1:2:1 phenotype ratio of offspring is characteristic of *incomplete dominance* ● E.g. using the earlier in complete dominance flower color example, RR' x RR' → 1 RR (red) : 2 RR' (pink) : 1 R'R' (white) phenotype ratio ❖ To determine the probability of two or more independent events occurring together multiply the probabilities of each separate event. ● Say you were asked to calculate the probability of a specific outcome (aaBb) in the cross of AaBB x aabb. Instead of doing a complex probability calculation, it is easier to do two separate crosses of Aa x aa and BB x Bb, then multiply the probability outcomes of each separate cross together to find the solution. The probability of aaBb is (probability of aa) * (probability of Bb) ● (1⁄2)*(1)=1⁄2 ❖ In a pedigree analysis, if a phenotype "skips" generations, be suspicious of an autosomal recessive disorder. If the phenotype does not skip a generation, it is more likely to be an autosomal dominant disorder. Be suspicious for X-linked recessive disorders as well - if a father doesn't have the phenotype, neither will any of his daughters.

visual communication

❖ Communication can occur *visually* during displays of aggression (agnostic behavior) or during courtship. Most animals precede mating with courtship behaviors. ● As a display of aggression, wolves will bare their teeth. To display submission, they lay on their backs. ● Male sage grouse assemble into groups (*leks*) to preform courtship dances. ● Multiple components in stickleback mating use visual communication. The female is attracted to the red belly of the male and adopts a head-up posture to initiate courtship. In response to this, the male makes zigzag motions and the female follows the male to nest. The female enters the nest and deposits her eggs in response to the male prodding her tail. The female leaves and the male enters and fertilizes the eggs. The red belly, head-up posture, zigzag motion, swimming to nest are all visual cues here.

Scientific Proof of Evolution: Comparative Anatomists

❖ Comparative anatomists describe two kinds of structures that provide evidence of evolutionary relationships. ● *Homologous structures* are body parts that are similar in form and function and seem to be related in different species. This points to a common ancestor between the species. ● *Analogous structures* are body parts that have the same function but have evolved independently as adaptations to their environments. This is also called a homoplasy. ▪ An example of this are cacti and euphorbia. Both plants have the characteristic thick stems that are needed for water storage to adapt to the climate of the desert regions. However, both plants species belong to different plants families. ● To distinguish between analogous and homologous, determine if the species are from the same class (e.g. both mammals?). If not, it is likely the structures are analogous and not homologous.

Scientific Proof of Evolution: Comparative Biochemists

❖ Comparative biochemists have shown that organisms with common ancestors have common biochemical pathways.

Calvin Cycle

❖ Description: Fixes CO2, repeats 6 times, uses 6CO2 to produce C6H12O6 (glucose). ● This is the "dark reaction", but it cannot occur without light because it is dependent on the high energy molecules produced from the light reaction (ATP and NADPH). ● The energy used to drive the light-independent (dark) reactions comes from light (photons). Light energy ultimately drives photosynthesis, and is the original source of energy stored in glucose chemical bonds. ● Plants do have mitochondria that make ATP. Plant mitochondria that produce ATP are used as energy for general cellular processes, while the ATP produced from photosynthesis in the chloroplast is used to drive photosynthesis further in the Calvin Cycle. The Calvin cycle then makes glucose for plant cells to break down and use as energy. ❖ Location: Stroma. *1. Carboxylation* 6CO2 + 6RuBP → 12PGA. *RuBisCo* (most common protein in the world) catalyzes this reaction. (Thus named because PGA is 3C). *2. Reduction* 12ATP + 12NADPH converts 12PGA → 12G3P or 12PGAL. Energy is incorporated; by‐products (NADP+ and ADP) go into noncyclic photophosphorylation. *3. Regeneration* 6ATP convert 10G3P → 6RuBP. This allows the cycle to repeat. *4. Carbohydrate synthesis* 6*CO2* + 18ATP + 12NADPH + H+ →18ADP + 18Pi + 12NADP+ + *1 glucose (2 G3P)*. In summary, 2 remaining *G3P* are used to build glucose.

Chemiosmosis in Chloroplasts

❖ Description: This process uses an H+ gradient to generate ATP. ❖ Location: Across the *thylakoid membrane*. *1. H+ ions accumulate inside thylakoids* H+ are released into lumen when H2O is split by PSII. H+ is also carried into lumen from stroma by cytochrome between PSII and PSI. *2. A pH and electrical gradient is created* The pH created is about 5. *3. ATP synthase generates ATP as H+ ions move across the thylakoid membrane* ADP is phosphorylated to create ATP. ADP + Pi → ATP. 3H+ ions are required for 1 ATP *4. Calvin cycle produces 2G3P using NADPH, CO2, and ATP* At the end of the e‐ transport chain following PSI, 2e‐ produces NADPH.

Cyclic Photophosphorylation

❖ Description: This replenishes ATP when the Calvin cycle consumes it. When the excited 2e- from PSI join with protein carriers in the first electron transport chain and generate 1 ATP as they pass through, these 2e- are recycled into PSI and can take either cyclic or noncyclic path. ❖ Location: *Stroma lamellae* (pieces connecting the thylakoids)

Other Carbohydrates

❖ Disaccharides are hydrolyzed into monosaccharides, most of which can be converted to glucose or glycolytic intermediates. ● Remember, glucose is not only broken down, but also can be produced via *gluconeogenesis*. Gluconeogenesis occurs in the liver and kidney. The liver is responsible for maintaining the glucose concentration in the blood. ● Glucose is stored in the body as a polymer called *glycogen* in primarily the liver (2/3) and muscles (1/3). All cells are capable of producing and storing glycogen but only liver cells and muscle cells have large amounts. ● After large meals, *insulin* stores glucose as glycogen. *Glucagon* has the opposite effect and turns on glycogen degradation. Insulin activates the PFK enzyme, while glucagon inhibits it. Think about it this way: insulin says "hey, we've got a lot of glucose around, so let's chew up," whereas glucagon says "uh oh, not enough glucose around, don't chew it up- we need it for the brain, other tissues can use other energy sources."

Patterns of Evolution Overview

❖ Divergent evolution ❖ Convergent evolution ❖ Parallel evolution ❖ Coevolution

The Law of Segregation

❖ During meiosis (anaphase 1), homologous chromosomes separate from one another. This results in haploid gametes that contain only one allele per gene. ● Thus, an offspring inherits only one of each type of allele per parent. ● What does this law really mean, in practical terms? The law of segregation basically says you'd only pass one set of your alleles down to your kid (you produce haploid gametes), not both. Using the gene for eye color as an example, say you specifically carry two different alleles: one for blue eyes and one for brown eyes. When you make your gametes, you can't pass both the blue allele and the brown allele down to your kid - only one or the other. Why? Because at Anaphase I, the homologous chromosomes pairs split up. One of those homologues in the pair has your blue allele on it and the other has the brown allele on it. Since they separate at Anaphase I, any gametes produced thereafter are guaranteed to only have one or the other.

The Law of Independent Assortment

❖ During meiosis (prophase 1), the lining up and subsequent separation of one pair of homologous chromosomes does not influence that of a different pair of homologous chromosomes. ● Thus, the separation of one pair of chromosomes is completely independent from the separation of another; therefore, alleles for different traits are passed on independently of one another. ● What does this law really mean, in practical terms? The law of independent assortment basically says your different chromosome pairs separate completely independently of one another. Let's go back to the above example: say your different eye color genes were on the first chromosome pair, and your hair color genes (blonde and brown) were on a completely different chromosome pair. Independent assortment says that during Anaphase I, the way that your first chromosome pair separates (e.g. whether your blue eye color separated to the left or to the right), has no impact whatsoever on where that completely different chromosome pair with hair color will separate (e.g. whether blonde hair will go to the left or to the right).

Scientific Proof of Evolution: Embryologists

❖ Embryologists have shown that similar stages of development (*ontogeny*) occur among species that related. This establishes the evolutionary relationships seen in phylogenetic trees. For example, gill slits and tails are found in fish, chicken, pig, and human embryos. ● Ontogeny recapitulates phylogeny is the theory of recapitulation that states that embryological stages represent our past evolutionary ancestors. This is theory is now considered defunct.

ontogeny

❖ Embryologists have shown that similar stages of development (ontogeny) occur among species that related. This establishes the evolutionary relationships seen in phylogenetic trees. For example, gill slits and tails are found in fish, chicken, pig, and human embryos.

beta oxidation

❖ Fatty Acids are broken down for energy via *beta oxidation*. ● Beta oxidation takes place in the mitochondrial matrix. ● Before the fatty acid enters beta-oxidation, it must be activated. Two ATP molecules are spent activating the entire chain. ● The fatty acid is converted into acetyl CoA, which enters the Krebs cycle. Animals cannot convert fatty acids to glucose. Acetyl CoA, specifically, enters the Krebs cycle. Plants and bacteria use a modified version of the Krebs cycle called *glyoxylate cycle* that produces sugar from acetyl CoA. ● Every 2 carbons from a fatty acid chain makes an acetyl CoA. ● Saturated fatty acids produce 1 NADH and 1 FADH2 for every cut into 2 pieces. Note this is NOT the same thing as for every 2 carbons- e.g. 18C chain is 9 2C pieces but cut only 8 times. Each cut is the beta oxidation step. ● Unsaturated fatty acids produce 1 less FADH2 for each double bond because it can't use the first step of beta oxidation: the double bond forming step. ● Beta oxidation results in a BIG yield of ATP. It yields more ATP per carbon that carbohydrates. There is more energy in fats than sugars.

Foraging Behavior

❖ Foraging behavior is not just eating but also includes the activities an animal uses to search for, recognize, and capture food. The goal is to increase the amount of food obtained while decreasing the energy spent and risks. ❖ Formation of *herds, flocks, schools* allow animals to use cooperation to carry out a behavior more successfully as a group. It provides the benefit of concealment, vigilance, and defense. In *concealment*, animals escape the notice of predators as most of the animals are hidden from view. In *vigilance*, the animals heighten their awareness of the predator by taking turns between foraging and watching for predators. In *defense*, the number of animals in the group can mob their predator or shield their young. ❖ *Packs* are made of a group of animals of the same species that live and hunt together. Animals living in packs can successfully attack large prey. ❖ *Search images* help animals find favored or plentiful foods based on specific and/or abbreviated target 'image.' An example of this humans finding a book on a bookshelf by only using the color and shape of the book (without reading the title) or identifying a police car by using a black and white search image.

Genetic Variation

❖ Genetic recombination during meiosis and sexual reproduction originates from three events: ● *Crossing over during prophase I* ● *Independent assortment of homologous chromosome during metaphase I* ▪ The random orientation of homologous chromosomes allows for the production of gametes with many different assortments. ● *Random joining of gametes aka germ cells (which sperm fertilizes which egg)* ▪ Joining of gametes is random, but some sperm cells have a genetic composition that gives them a competitive advantage - so not all sperm cells are "equally" competitive.

Noncyclic Photophosphorylation: Light-Dependent Reaction

❖ Goal of this reaction is to attach a phosphate on ADP to make ATP using light (ADP + Pi + light → ATP) ❖ Overall reaction of this step ● H2O + ADP + Pi + NADP+ + light→ATP + NADPH + O2 + H+ ❖ Location: *Thylakoid membranes*, but *photolysis* takes place inside the *thylakoid lumen* (passes electrons to the membrane for noncyclic photophosphorylation). *1. Photosystem II* Electrons trapped by P680 in PSII are energized by light. *2. Primary e‐ acceptor* Two excited e‐ are passed to primary e‐ acceptor; primary because it is the first in chain of acceptor. *3. E‐ transport chain* Consists of a plastoquinone complex (PSII) which contains proteins like *cytochrome* and cofactor Fe2+; analogous to oxidative phosphorylation. *4. Phosphorylation* 2e‐ move down chain → lose energy (energy used to phosphorylate about 1.5ATP). *5. Photosystem I* e‐ transport chain terminates with PSI (P700); they are again energized by sunlight and passed on to another primary e‐ acceptor. From this point forward it can go to the cyclic or noncyclic path. If noncyclic... *6. NADPH* 2e‐ then pass down a short electron transport chain (with proteins like *ferredoxin*) to combine NADP+ + H+ + 2e‐ → NADPH (coenzyme) (this step takes place only in the noncyclic pathway). *7. Splitting of water (photolysis)* The loss of 2e‐ from PSII (initially) is replaced when H2O splits into 2e‐, 2H+, and 1⁄2O2 (The H+ produced is used for NADPH formation and the 1⁄2 O2 contributes to release as oxygen gas). This occurs at PSII.

Number of heart chambers

❖ Human and bird hearts have 4 chambers. ❖ Reptiles and amphibians have 3 chambers. ● An exception to this is crocodiles and alligators. They have 4 chambers. ❖ Fish have 2 chambers.

Control of Respiration

❖ Human respiration is controlled by the *medulla oblongata* which signals the diaphragm to contract. ● When the partial pressure of CO2 increases, the medulla stimulates an increase in the rate of ventilation. ● The diaphragm is the only organ which only and all mammals have, and without which no mammal can live. It is a skeletal muscle that is innervated by the phrenic nerve. ❖ *Central chemoreceptors* in the medulla monitor [H+] in the cerebrospinal fluid (CSF). ● H+ ions do not cross the blood brain barrier but CO2 does. Carbon dioxide is converted to the H+ ion via carbonic anhydrase in the CSF. ❖ *Peripheral chemoreceptors* in the carotid arteries and aorta monitor arterial [CO2], [O2], and [H+]. ❖ In an active body, there is increased CO2 production. It enters the plasma to be converted to HCO3- and H+, causing the blood pH to drop and respiratory rate to increase. ❖ Oxygen and pH are mainly monitored by the peripheral chemoreceptors.

Transfer of CO2 and O2 via RBCs

❖ In the red blood cell, we see both the Haldane and Bohr effect at play. ● Remember: In tissues, there is a high concentration of CO2, and hemoglobin has a low affinity for O2. ● When CO2 from the tissue enters the RBC, it combines with the water in the RBC to produce *carbonic acid* (H2CO3). The carbonic acid will dissociate and release an H+ to produce a *bicarbonate ion* (HCO3-). CO2 + H2O H2CO3 H+ + HCO3- ● The proton (H+) that is released will bind with *oxyhemoglobin* (HbO2) to produce H+Hb + O2. This oxygen is released into the tissue. H+ + HbO2 H+Hb + O2 ● CO2 will also compete with the oxygen bound to the hemoglobin. Carbon dioxide that binds with HbO2 will produce HbCOO- and H+ and O2. The oxygen is released into the tissue. The proton (H+) that is formed can also participate in the reaction with oxyhemoglobin detailed above, and release another oxygen into the tissue. CO2 + HbO2 HbCOO- + H+ + O2 ● When the RBC goes back to the lung, the hemoglobin is either bound to CO2 or H+. In the lung, the presence of O2, will cause the reverse of all the reactions described above. This will lead to the release of both CO2 and H+ (in the form of bicarbonate) and production of oxyhemoglobin.

C2 Photosynthesis (Photorespiration)

❖ Involves fixation of oxygen by the *rubisco* enzyme but produces no ATP or sugar. Rubisco is not "efficient" or fast because it will fix both CO2 and oxygen at the same time if both are present. ❖ The byproducts of photorespiration are metabolized by *peroxisomes*

Lungs

❖ Lungs are invaginated structures. ❖ The left lung is smaller (2 lobes) vs. right lung (3 lobes) to accommodate left-sided heart. ❖ The lungs have a membranous cover known as the *pleurae*. ● There are two pleura layers: the *visceral layer* lines the surface of the lungs and the *parietal layer* lines the inside of the chest cavity. ● In between the pleura layers is the *pleural space*. This space has negative pressure relative to the atmosphere. Therefore, if one is stabbed, air rushes in and collapses the lung. ❖ Pressure of the *intrapleural* space decreases as we inhale. ● When we inhale, the *diaphragm* (under lungs) and *intercostal muscles* (between ribs) contract/flatten. The lung cavity opens up causing an increase in volume, which results in a decrease in pressure of the intrapleural space. ● Similarly, inside the lungs, as we inhale, the volume of the lungs expands as the diaphragm drops. By doing so, we create a negative pressure relative to the atmosphere, causing air to rush in. The thoracic pressure decreases as the thoracic cavity size increases. ● When we exhale, the diaphragm rises, which decrease the volume of the lungs, and causes an increase in pressure relative to the atmosphere, and air rushes out. The diaphragm relaxes and expands. Exhalation is a passive process.

Lymph Vessels

❖ Lymphatic system is an open secondary circulatory system which transports excess *interstitial fluids (lymph)* through the contraction of adjacent muscles. Some walls of larger lymph vessels have smooth muscle. ❖ Proteins and large particles that cannot be taken up by capillaries are removed to lymph. ❖ The lymph also monitors blood for infection. ❖ Valves in the lymph vessels prevent backflow. The fluid returns to the blood circulatory system through two ducts located in the shoulder region (thoracic duct and right lymphatic duct which empty into the left and right subclavian vein, respectively). It rejoins the blood as plasma. ❖ *Lymph nodes* contain phagocytic cells (leukocytes) that filter the lymph and serve immune response centers. When one is sick, lymph nodes fill with white blood cells and give the appearance of "swollen glands." ❖ Lymph also transports absorbed fat from small intestine to the blood. ❖ The thymus and bone marrow are the primary central lymphoid organs that can replenish immune cells. *T-cells* mature in the thymus and *B-cells* mature in the bone marrow. The thymus technically does not make new T-cells, but the T-cells mature there so it houses fresh ones. ❖ The lymph nodes, spleen, adenoids, appendix, Peyer's patches (in small intestine) and tonsils are *peripheral lymphoid tissues [TALAPS]*. These structures house immune system cells but cannot replenish them.

Oxygen Dissociation Curves

❖ Oxygen dissociation curve shows the percentage of hemoglobin bound with O2 at various partial pressures of O2. ● Oxygen saturation of hemoglobin depends on CO2 pressure, pH, temperature of blood. ❖ If the curve is shifted to the right this means oxygen is released easily, and hemoglobin has a low oxygen affinity. ● This happens by an increase in CO2 pressure, H+ concentration, or temperature. These are physiological states where tissues need more oxygen. ● At higher temperature, oxygen unloads more easily. ● 2,3-DPG concentration increase can also shift the curve to the right. It is produced in the presence of diminished peripheral tissue oxygen capacity from an intermediate compound in glycolysis. It decreases the affinity of hemoglobin for oxygen. At low oxygen levels an enzyme catalyzes the synthesis of 2,3- DPG. Hence, ↑ [2,3-DPG] = ↓ affinity of Hb for oxygen. This is helpful for unloading oxygen during anemia and at high altitudes. At high oxygen levels, oxyhemoglobin inhibits the enzyme that synthesizes 2,3-DPG, decreasing the overall concentration of 2,3-DPG. ● During exercise, muscles have a higher metabolic rate, produce more carbon dioxide and lactic acid, and the temperature rises. They consequently need more oxygen. The right shift means, O2 is released more easily. ● Remember: "CADET face Right!" - CO2, Acid, 2,3-DPG, Exercise, and Temperature. ❖ If the curve is shifted to the left this means that oxygen is not released easily, and hemoglobin has high oxygen affinity. ● This happen by a decrease in CO2 pressure, H+ concentration, or temperature. ● Fetal hemoglobin curve is shifted left of the adult. It has a higher binding affinity to grab O2 from maternal blood. ❖ Myoglobin of muscles has hyperbolic curve (structure doesn't do allosteric cooperative binding, single subunit). ● Myoglobin has a higher oxygen affinity than hemoglobin and saturates quickly. ● Oxygen is released from myoglobin in very low oxygen "emergency muscle" situations.

Fetal Circulation

❖ Oxygenated, nutrient rich blood from the placenta is carried to the fetus via an umbilical vein. From the umbilical vein, there are two paths that the blood can take. ● First path: Half of the blood enters the *ductus venosus* (which allows the blood to bypass the liver) → carried to inferior vena cava → right atrium→ right ventricle → *ductus arteriosus* (conducts some blood from pulmonary artery to the aorta [bypassing the lungs/fetal circulation]) → aorta. ● Second path: Half of the blood enters the liver/portal vein → right atrium → foramen ovale (allows blood to bypass pulmonary circulation by entering the left atria directly from the right atria since there is no gas exchange in fetal lung) → left atrium → left ventricle → aorta. ❖ Carbon dioxide acts a respiratory stimulant on the receptors in the baby's nose. It stimulates the baby's first breath. ❖ The temperature changes from leaving the mother's womb also stimulates the baby to breath. ❖ The first breath is difficult as the lungs are collapsed and the airways are small. This causes resistance to air movement and therefore *surfactant* is very important. Surfactant prevents the air sacs in the lung from collapsing and reduces the surface tension. ❖ Sometimes a mother may attack her child's RBC in a condition called *erythroblastosis fetalis* or Rh incompatibility/hemolytic disease of the newborn (HDN). ● The mom passes antibodies through the placenta that attach the *Rh+ factor* in the fetus. Rh factor is an antigen present in the blood. Remember that the mother is Rh-. These antibodies form after the mother gives birth to the first child that is Rh-positive. When she becomes pregnant again with a Rh-positive child, these antibodies will attack the blood cells of the second fetus.

Scientific Proof of Evolution: Paleontologists

❖ Paleontologists study fossils that reveal prehistoric existence of extinct species. Fossils are often found in sediment layer; the deeper the fossil, the older the species. ● Large, rapid changes observed in fossils show evidence of new species. ● Fossil types include actual remains, petrification, imprints, molds, and casts. ● *Continental drift* is the theory that the supercontinent Pangea slowly broke apart to 7 continents. Fossils of the same species are found on different continents, suggesting that the continents were once a single landmass.

Classification of Membrane Proteins

❖ Peripheral: Loosely attached to one surface of the phospholipid bilayer. ❖ Integral: Embed inside the lipid bilayer. ● Transmembrane: Spans the entire phospholipid bilayer, going through both sides. This is a subtype of integral membrane protein.

Plant Respiration

❖ Photosynthesis only takes place during the day. ● Photosynthesis produces glucose and gives off oxygen; while respiration requires oxygen to degrade glucose. ❖ Plants undergo aerobic respiration similar to animals. ● Glucose → 2 ATP +2 Pyruvic Acid ● Gases diffuse into air space by entering and leaving through *stomata* of leaves or *lenticels* in woody stems. ● Anaerobic respiration takes place in simple plants when molecular oxygen is lacking.

Proteins

❖ Proteins are the least desirable source of energy. It is used only when carbohydrates and fats are unavailable. ❖ Most amino acids are deaminated in the liver, and then converted to pyruvate or acetyl CoA or other Krebs cycle intermediates. These metabolic products enter cellular respiration at various points (varies by amino acid).

Natural Selection

❖ Responsible for producing *adaptations* (superior inherited traits) that increase individual's *fitness* (ability to survive and produce fertile offspring; if lots of offspring are produced but they die, this is not good fitness!). ❖ Darwin believed that evolution occurs through natural selection because: ● Populations possess an enormous reproductive potential if all offspring produced survive. ● Population size remains stable. Populations generally fluctuate around a constant size. ● Resources are limited. Resources do not increase as a population grows larger. ● Individuals compete for survival. A growing population will exceed the available resources and compete. ● There is variation among individuals in a population such as skin color (very pale to very dark). ● Much variation is heritable as DNA is passed down between generations. ● Only the most fit individuals survive. This is called "survival of the fittest." ● Evolution occurs as favorable traits accumulate in the population. The best adapted individuals have the best adapted offspring which in turn also have the most offspring. ❖ *Important*: individuals do NOT evolve, populations evolve.

Phospholipid membrane permeability

❖ Small, uncharged, nonpolar molecules (polar molecules can only pass through if small and uncharged) and hydrophobic molecules can freely pass across the membrane. ❖ All other molecules require a transporter (large, polar, charged molecules).

Auditory Perception

❖ The *ear* allows one to hear and maintain balance. It is composed of three main parts: the outer ear, the middle ear, and the inner ear.

Nerve Impulse Transmission

❖ The *resting membrane potential* of a neuron is -70 mV, meaning the neuronal cell is *negatively polarized*. Polarized is just a fancy word meaning "electrically different" on one side compared to the other. A negatively polarized membrane is more electrically negative intracellularly compared to extracellularly. If there were two extracellular positive charges and only one intracellular, the membrane would be negatively polarized. Similarly, if there were two intracellular negative charges and only one extracellular, the membrane would also be negatively polarized. The total sum of the intracellular charges (both positive and negative) compared to the extracellular charges determines the cell's membrane potential, and therefore polarization. Several ion pumps and channels maintain the resting membrane potential. o The *sodium-potassium pump* (*Na+/K+-ATPase*) moves three sodium ions out of the cell per every two potassium ions it pumps into the cell. ▪ Overall, this results in a net removal of one positive charge from the inside of the cell. ▪ ATP dependent process o *Potassium channels* allow potassium to flow down its concentration gradient, from inside to outside the cell. ▪ Decreases the number of intracellular positively-charged ions, leading to a negative polarization. o Negatively-charged proteins and nucleic acids residing inside the cell also contribute to the negative resting potential. The action potential 1. In the absence of stimuli, the cell maintains a *resting membrane potential* of -70 mV. If the combined effect of the IPSPs and EPSPs cause the membrane potential to reach -50 mV (the *threshold level*), an *action potential* is generated. The axon hillock is the site where IPSPs and EPSPs are summated. And if the threshold level is reached, an action potential will propagate through the adjacent axon. This is an all or nothing process. ▪ An *excitatory postsynaptic potential (EPSP)* is a stimulus that makes a postsynaptic neuron more likely to generate an action potential by causing positively-charged ions (often Na+) to flow into the neuron. ▪ An *inhibitory postsynaptic potential (IPSP)* is a stimulus that inhibits the postsynaptic neuron from generating an action potential by causing negatively-charged ions (often Cl-) to flow into the neuron or positively-charged ions (often K+) to flow out of the neuron. 2. Once the threshold level is reached, *voltage-gated sodium channels* open, and Na+ moves into the cell down its concentration gradient, which was previously established by the sodium-potassium pump. This results in *depolarization* to a membrane potential of +30 mV. 3. Voltage-gated sodium channels close, halting the movement of Na+ into the cell. At the same time, *voltage-gated potassium channels* open, allowing K+ to flow out of the cell. This is the basis of *repolarization*, which reestablishes the negative membrane potential. However, now there is a relatively high level of sodium inside the cell and potassium outside the cell. 4. K+ continues to flow out of the cell until the membrane potential reaches -80 mV. When this occurs, the neuron is in a state of *hyperpolarization*. This is the basis of the relative refractory period. 5. Following an action potential, the neuron enters a *refractory period*, a time when the neuron is unresponsive to stimuli. ▪ *Absolute refractory period*: During this time, voltage-gated sodium channels are locked shut for a set period of time. Because only channels further downstream can open, an action potential is inhibited from moving backwards. Additionally, this establishes the maximum frequency of action potentials. ▪ *Relative refractory period*: During this time, the cell is in a state of hyperpolarization, but an abnormally large stimulus may generate an action potential.

Gustatory Perception (Taste)

❖ The *taste buds* are located in small bumps termed *papillae*, which are throughout the oral cavity on the tongue, throat, cheeks, and roof of the mouth. Each taste bud contains 50-100 cells, each of which is specialized to sense either sweetness, sourness, saltiness, bitterness, or umami. When a substance stimulates the taste receptor cell, an action potential is generated and propagated to the brain for processing.

Central dogma of genetics

❖ The central dogma of genetics states that information flows from DNA → RNA → proteins ❖ Biological information cannot be transferred backwards from protein to protein or protein to nucleic acid

Blood flow

❖ The heart contracting causes blood to move through arteries because of the creation of *hydrostatic pressure*. This is the pressure of the blood enclosed within the blood vessels. ❖ Blood pressure drops as it reaches the capillaries, and reaches near zero in the venules. ❖ Despite the decrease in blood pressure, the blood continues to move through the veins back to the heart because of assistance via skeletal muscles that line the veins. Contraction of these muscles squeezes and constricts veins. Valves in the veins keep the blood flowing towards the heart and prevent backflow. ❖ Cross sectional area of veins is about 4x higher than that of arteries. ❖ Total cross sectional area of capillaries is far greater than that of arteries or veins. Capillaries are the narrowest vessels, BUT there are far more capillaries. Therefore, the total cross-sectional are of all them put together is higher than any other cross sectional area. ❖ Since blood flow rate is approximately constant, blood velocity is inversely proportional to total cross-sectional area. ❖ Blood pressure drops as we go from the aorta to the capillaries because of energy loss due to increased resistance as the vessel diameter decreases. ● This seems contradictory since BP = CO * SVR (BP is blood pressure, CO is cardiac output, and SVR is systemic vascular resistance). So if resistance increase, why does pressure decrease? The blood pressure formula above applies to mean arterial pressure (MAP), measured at arteries by a *sphygmomanometer*. When a blood vessel constricts, resistance increases, which in turn increases the blood pressure. This is true in the part of the tube before the constriction, which is the location where we measure BP. The pressure of the tube after the constriction is what is lowered, hence why the blood pressure effectively decreases as we go through smaller diameter vessels. By the time the blood travels to the venules/veins, the original source of blood pressure/flow (the beating of the hear) is virtually gone, which is why the pressure continues to decrease further still. ❖ Arterioles have the greatest resistance to flow (high ability to constrict). ❖ At any given them, most of the blood is the veins/venules/venous sinuses.

Heart Contraction

❖ The heart is a large muscle, but unlike skeletal, it is not anchored to bone. Its fibers form a net and the net contracts upon itself, which squeezes blood into arteries. ❖ Note that the ventricles have thicker walls than atria and generate higher blood pressures (ventricles must pump blood throughout the body and lungs; atria just need to generate enough pressure to fill the ventricles). ❖ Left ventricle is thicker than the right because it needs to pump blood to most of the body; the right ventricle just needs to pump to the lungs. ❖ Remember: systole occurs when the atrium or ventricles contract. Diastole occurs during relaxation of atrium or ventricles. ❖ Each time the heart beats, the atria expands. ❖ The pressure falls in the chest each time a person breathes.

testcross

❖ The objective of a testcross is to determine an organism's genotype for a given trait. ● A *monohybrid* cross is used to test a single gene. ● A *dihybrid* cross tests two different genes simultaneously. ❖ Testcross generations are labeled as follows ● *P*: parental ● *F1*: Filial 1 hybrid First generation of offspring The result of breeding the parental organisms ● *F2*: Filial 2 hybrid Second generation of offspring The result of breeding the F1 organisms

papillae

❖ The taste buds are located in small bumps termed papillae, which are throughout the oral cavity on the tongue, throat, cheeks, and roof of the mouth. Each taste bud contains 50-100 cells, each of which is specialized to sense either sweetness, sourness, saltiness, bitterness, or umami.

Pathology of Human Respiratory System

❖ The trachea and upper respiratory system contain *ciliated pseudostratified columnar epithelial cells*. ● The trachea, bronchi, and larger bronchioles in the respiratory tract contain *goblet cells* for mucus production. ❖ Smoking damages the cilia of respiratory cells, leading to retention of toxins in the lung. As a result, goblet cells increase the production of mucus. The lungs, however, can no longer efficiently move the mucus out. This leads to an unproductive cough. ● Disease that are associated with this pathology are *bronchitis*, *emphysema*, and *lung cancer*. ● *Emphysema* is a condition marked by destruction of the alveoli.

CAM Photosynthesis

❖ This is another add-on to C3, called crassulacean acid metabolism; almost identical to C4. 1. *PEP carboxylase* fixes CO2 + PEP → OAA; OAA → malic acid. 2. *Malic acid* is shuttled into vacuole of cell. 3. At *night*, stomata are open (opposite of normal), PEP carboxylase is active, malic acid accumulates in vacuole. 4. During the *day*, stomata are closed. Malic acid moves out of vacuole and is converted back to OAA (requires 1 ATP), releasing CO2 (moves into Calvin cycle with rubisco) and PEP. ❖ Overall advantage is that CAM photosynthesis can proceed during the day while stomata are closed (reducing H2O loss). Occurs in cacti, crassulacea, desert plants.

C4 Photosynthesis (Hatch-Slack Pathway)

❖ This process evolved from C3 photosynthesis. In C4 photosynthesis, when CO2 enters a leaf it gets absorbed by mesophyll cells (then moved to bundle sheath cells). Instead of being fixed by rubisco into PGA, CO2 combines with PEP to form OAA by PEP carboxylase (in mesophyll). ● OAA has 4C (hence C4 photosynthesis) ● OAA → Malate and is then transported through *plasmodesmata* into bundle sheath cells. ● Malate → pyruvate + CO2. CO2 can be used in the Calvin cycle. ● Pyruvate is moved back to the *mesophyll*, then pyruvate → PEP (this process requires 1 ATP → AMP). ❖ Overall, the purpose is to move CO2 from *mesophyll* to *bundle sheath cell* (this leaf structure = *Kranz* anatomy). Little O2 presence in bundle sheath cells reduces competition while rubisco is fixing. This minimizes photorespiration and H2O loss from the *stomata* (leaf pores). ❖ Found in hot, dry climates (faster fixation speed and more efficient). Requires one additional ATP (which becomes AMP). C3 typically occurs in mesophyll cells, but in C4 it occurs in bundle-sheath cells. Examples: corn, sugarcane

Energy Production from Cellular Respiration

❖ Total Energy from 1 glucose is about 36 ATP, but in prokaryotes it is 38 ATP (not actual yield as mitochondrial efficacy varies) ● A difference exists in the ATP yield between eukaryotes and prokaryotes because prokaryotes have no mitochondria so they do not need to transfer the two NADH molecules into the mitochondrial matrix. In eukaryotes, NADH is transported into the mitochondrial matrix via active transport, costing 1 ATP each. Prokaryotes use the cytoplasm and the cell membrane for cellular respiration. Pyruvate is also actively transported into the mitochondrial matrix (in eukaryotes) but its transport is secondary active transport (symport with protons). It doesn't directly use ATP.

Absorption of Fats

❖ Triglycerides in the lumen of the small intestine (the tube itself) are broken down via lipases into monoacylglycerides and fatty acids. ● Monoacylglycerides and fatty acids are absorbed into the *enterocytes* (cell lining of the small intestine). There, they are reassembled into triglycerides, and then (along with cholesterol, proteins, phospholipids) packaged into chylomicrons which move on to the lymph capillary for transport to the rest of the body where they are stored as adipose tissue. ❖ In absorption, nutrients enter the blood steam from the villi of the small intestine and then go to the liver for regulation of blood nutrient content. From the liver, they go to the heart and rest of the body.

Alternative Energy Sources

❖ When glucose supply is low, the body uses other energy source. ● From highest to lowest priority: carbohydrates > fats > proteins ❖ These alternative energy sources are first converted to glucose or glucose intermediates, then are degraded in either glycolysis or the Krebs cycle.

To introduce foreign DNA into a bacterium, we must first

❖ get the foreign DNA into a *plasmid*. The plasmid is treated with the same restriction enzymes as the foreign DNA so the same sticky ends bind. DNA ligase stabilizes the attachments; then the plasmid is introduced into bacterium by transformation. ● To ensure efficient production of a gene that has been added to a plasmid, *expression vectors* are often used - these vectors contain a highly active promoter upstream of the restriction site where new genes are added for maximum output. ❖ Next, bacteria must then be "made competent" to take up the plasmid, accomplished via *electroporation* (a brief electrical pulse applied to a solution with cells, creating temporary holes in plasma membrane through which DNA can enter) or a combination of heat shock + CaCl2. ❖ Once the plasmid has entered the bacteria, the bacteria can now can be grown to produce a product, form a clone library, etc. ● An antibiotic resistance screen is used to filter out bacteria that did not successfully uptake the plasmid. A gene for antibiotic resistance is included in the plasmid; bacteria that have taken up the plasmid (and by extension have the antibiotic resistance gene) will successfully survive antibiotic treatment, while those without the plasmid will perish.

There are three different types of hormones:

1) peptide hormones 2) steroid hormones 3) amino-acid derived hormones The first two types have distinct properties, while the last type is a little ambiguous. ● Hormones are *chemical* signals ● *Peptide* hormones are *water-soluble*, hence they *indirectly* stimulate receptor cells. ● *Steroid* hormones are *lipid-soluble*, hence they *directly* stimulate receptor cells. ● Peptide hormones have a *faster* onset than steroid hormones. ● Tyrosine-derived amino acids share properties common to both peptide and steroid hormones.

There are 4 main extraembryonic structures that are important for the DAT:

1. Amnion 2. Chorion 3. Allantois 4. Yolk Sac

Point mutations can be subdivided into:

1. Silent mutations 2. Nonsense mutations 3. Missense mutations

Each metaphase chromosome consists of

2 closely attached sister chromatids.

Adenine and Thymine pair together via

2 hydrogen bonds

Cytosine and Guanine pair together via

3 hydrogen bonds

tertiary structure of a protein

3D structure due to noncovalent interactions between the R-groups of amino acids. These interactions include hydrogen bonding, ionic bonding, hydrophobic effect (R-groups are pushed away from the water center), disulfide bonds (the covalent exception to tertiary structure), and Van der Waals forces.

At the end of anaphase I, there is a total of

46 chromosomes if a cell has 46 chromosomes at the beginning because 23 chromosomes are pulled to each pole by independent assortment and no chromatids are separated at anaphase I.

earth's crust atmosphere

47% oxygen, 28% silicon

The spliceosome scans the pre-mRNA for

5' and 3' splice signals within the mRNA code; these sites signal the spliceosome to start and stop its splicing—precisely removing the intron.

Krebs Cycle net production

6 NADH, 2 FADH2, 2 ATP (technically GTP), 4 CO2.

Photosynthesis overall reaction

6CO2 + 6H2O → C6H12O6 + 6O2 (Alternatively: 6CO2 + *12H2O* → C6H12O6 + 6O2 + *6H2O*)

Glycocalyx

A CARBOHYDRATE coat that covers outer face of cell wall of some bacteria and outer face of plasma membrane (in some ANIMAL CELLS). It consists of glycolipids (attached to plasma membrane) and glycoproteins (such as recognition proteins). It may provide adhesive capabilities, a barrier to infection, or markers for cell-cell recognition.

Habituation

A learned behavior that leads to a decrease in response to stimulus after being repeatedly exposed to it. It allows individuals to ignore repetitive events known to be inconsequential from experience. This allows individuals to be focused on other, more meaningful events. ● An example of this is sea anemones disregarding repeated "feeding" stimulation with a stick. ● If the stimulus no longer regularly applies, the response will recover over time. This is *spontaneous recovery*. ● The opposite of habituation is *sensitization*. It is an increased response to repeated stimulus.

uterus

A muscular organ that functions to provide an ideal environment for a fertilized egg to implant into, grow, and ultimately develop into an embryo. It is composed of three layers: *perimetrium* (outer layer), *myometrium* (smooth muscle, middle layer), and *endometrium* (inner epithelial layer, lined by mucous membranes). The uterus leads to the *cervix*, a narrow opening that leads to the *vagina*.

Batesian mimicry

A non-harmful animal mimics the coloring of a harmful animal. An example is a harmless fly that mimics the coloring of a stinging bee.

Sere

A particular stage of an ecosystem.

apex predator

A predator at the "top of the food chain." No other organisms prey on an apex predator. This could be the tertiary consumer, or something even higher in the chain.

Group translocation

A process seen in prokaryotes. The substances being transported across a membrane is chemically altered in the process (this prevents it from diffusing back out).

periosteum

A protective fibrous membrane that *covers* cortical bone; except, at the articular joints of long bones where articular cartilage covers and protects opposing epiphyses from grinding against each other. The periosteum has two sub-layers: 1. A highly innervated and vascularized *outer fibrous layer*. 2. An *inner/cambium layer*, which has collagen fibers that allow for attachment of the periosteum to the cortical bone beneath. ■ Extra info: the inner layer of the periosteum also contains osteoprogenitor cells.

artificial speciation

A result of artificial, intentional methods such as *selective breeding* (a method where only organisms with a given phenotypic trait are chosen for reproduction).

active transport

ATP is used in the movement of substances E.g. Na+-K+ pump to maintain gradients.

ecosystem

An *ecological community (biotic) plus the abiotic factors* with which they interact.

Simple reflex

An automatic 2 nerve (afferent/ efferent) response to a stimulus. It is controlled at the spinal cord (lower animals).

dendritic cells

Another type of cell that is crucial for the innate immune response. You can think of dendritic cells as surveillance guards roaming in tissues detecting potential threats. A dendritic cell can scan its local environments by taking a sip from its surroundings through a process called pinocytosis. *Pinocytosis* = cell *drinking* *Phagocytosis* = cell *eating* Once it detects a pathogen, it will phagocytose the pathogen like macrophages and neutrophils. Similar to macrophages, dendritic cells also play the role of *antigen-presenting cells* (discussed later on in more detail). Dendritic cells then migrate to *lymph nodes* along with macrophages to activate the adaptive immune response.

cnidaria general characteristics

Aquatic habitats, some have stinging cells (nematocysts), some have life cycles that switch from polyp to medusa forms, sexual or asexual reproduction, gastrovascular cavity acts as hydrostatic skeleton to aid in movement.

Huntington's Disease

Autosomal Dominant Degenerate nervous system disease

Achondroplasia

Autosomal Dominant Dwarfism

Blotting Techniques

Blotting techniques allow for the identification of target fragments of DNA, RNA, or protein. An easy way to remember the blotting techniques is SNOW DROP Southern - DNA Northern - RNA Western - Proteins

Recap of Fluid Movement in the Excretory System

Body - renal artery - glomerulus - Bowman's capsule - proximal convoluted tubule - descending limb of loop of Henle - ascending limb of loop of Henle - distal convoluted tubule - collecting duct - renal pelvis - ureter - bladder - urethra Filtration Secretion Reabsorption Excretion

bone remodeling

Bones undergo lifelong *bone remodeling*, which is the constant back and forth between *ossification* (bone growth) and *resorption* (bone loss). ● Analogy: imagine you and a friend arm-wrestled once a day... sometimes you would win and sometimes your friend would win - bone remodeling works the same way. The primary mechanisms that affect bone remodeling include: 1. Parathyroid hormone 2. Vitamin D 3. Calcitonin Bone remodeling is an important way to maintain homeostasis. Bones serve as reservoirs of organic and inorganic substances. When we are not getting enough of these substances, we must *resorb* them from bone to make sure our cells continue to function correctly. ● Extra info: Diets high in calcium, fruits, vegetables, and lean meats are a great way to avoid bone loss through resorption. Similarly, weight training stimulates the release of growth factors that encourage ossification :)

archaea vs eubacteria cell wall similarity

Both Eubacteria and Archaea possess a cell wall. The cell wall surrounds the cell membrane and offers protection and structural support to the cell.

Observational Learning vs Insight

Both observational learning and insight allow animals to learn new behaviors without receiving reinforcement. This reduces the amount of time required for a new behavior to be acquired. Daily cycles of behavior are circadian rhythms. Learning involves adaptive responses to the environment. In higher animals, capacity of learning is closely associated with degree of neurological development.

Bryophytes

Bryophytes are *nonvascular* plants. Examples of bryophytes are mosses, hornworts, and liverworts. As the word "nonvascular" suggests, most bryophytes do not have vascular tissue, which we know is how many plants transport materials throughout the plant. Bryophytes also do not have roots. This limitation forces bryophytes to be relatively simple. Bryophytes must remain *small and short*. This about it: if bryophytes were tall, they would have no effective way of getting water and nutrients up to the top. They *grow horizontally* so that everything can be near the water and nutrient source (think about a moss growing horizontally along a tree stump). With all this in mind, it makes a lot of sense that bryophytes are mostly found in *moist habitats*. Although bryophytes do not have roots, they do contain *rhizoids* (hair-like projections) which aid in water absorption and provide minor anchorage. Bryophytes spend most of their life cycle in the *gametophyte* stage. They possess flagellated sperm and use spores as their dispersal unit. They have a reduced sporophyte, which consists of a seta, foot, and sporangia. The sporophyte is usually dependent on and attached to the gametophyte for survival.

Klinefelter Syndrome

Chromosomal XXY; sterility; causes mental retardation

membrane fluidity

Cells are capable of changing membrane fatty acid composition.

Chemiosmosis in Mitochondria

Chemiosmosis is the mechanism of ATP generation that occurs when energy is stored in the form of a proton (H+) concentration gradient across a membrane. ● The Krebs Cycle produces NADH and FADH2. ● NADH and FADH2 are oxidized (lose electrons) resulting in the transportation of H+ from matrix to intermembrane space. This results in the formation of a pH and electric charge gradient (an *electrochemical gradient*). ● ATP synthase uses the kinetic energy from the flow established by this gradient (proton motive force) to create ATP by letting the protons flow from the intramembrane space back to the matrix.

Eumetazoans

Cnidaria Animals with true tissues (tissues, organs, and a digestive cavity).

Nerve nets

Cnidaria Found in organisms without a central nervous system and cephalization (head and brain). Nerve nets contain neurons that are quite spread apart and are typically found in organisms with radial symmetry.

Medusa

Cnidaria Motile Cnidarians, such as a jellyfish. Medusa only reproduce sexually.

Polyps

Cnidaria Non-motile Cnidarians, such as a coral. Polyps can reproduce asexually by budding or sexually as a hermaphrodite or as individual sexes.

Diploblasts

Cnidaria Organisms having two cellular layers: endoderm and ectoderm. There is no mesoderm in a diploblastic organism.

Radial symmetry

Cnidaria Refers to a symmetry around the central axis. Think of cutting a pie into eight symmetrical slices - this is radial symmetry.

Stability

Continued production of hybrid individuals.

Fungus-like protists

Different from fungi because they do not have a cell wall made of chitin. Additionally, fungus-like protists, such as *slime molds*, are different from actual fungi because they can move with flagella or cilia - although they usually do not. Fungus-like protists are *saprophytic*, which means they feed on decaying matter. For this reason, many of these types of protist are found living in moist soil with a lot of organic matter. They ingest their food similarly to an amoeba, whereby the cell takes in entire bits of food through *phagocytosis*. Fungus-like protists tend to reproduce via asexual reproduction and sporulation. The spores they send out are resistant to environmental conditions because the cell wall of the spore is very thick and strong.

Countercurrent exchange

Diffusion by bulk low in opposite directions (e.g. blood and water in fish gills).

Simple diffusion, osmosis, dialysis

Diffusion of different solutes across a selectively permeable membrane.

cholecystokinin

Digestion in the small intestine not only involves enzymes from the small intestine itself, but also other accessory organs like the *pancreas, liver, and gallbladder*. As the small intestine detects proteins and fats coming in, cells in the lining of the duodenum release a hormone *cholecystokinin* (CCK), the signal calling out for help. This hormone lets the accessory glands know it's time to act. Some effects of CCK includes: ● *Slows down gastric emptying* (inhibits the transfer of stomach contents to the small intestine) ○ It tells the stomach: "hey stomach, give me a sec!" ○ This gives the small intestine more time to digest and absorb what has entered. ● *Stimulates the pancreas* to release its digestive enzymes into the duodenum. ● *Stimulates the gallbladder* to release *bile* into the duodenum.

Regulatory mechanisms Overview

Evaporation Metabolism Surface Area Counter Exchange System

Acetylcholine

Excitatory NT of the neuromuscular junction in vertebrates. Pre-synaptic NT of the sympathetic and parasympathetic nervous systems. Post-synaptic NT of the parasympathetic nervous system.

absorbed into *lacteal*

Fatty acid + glycerol

Fertilization

Fertilization is the *joining* of a *haploid sperm* and a *haploid egg* to form a *diploid zygote*. However, the process is much more complicated than it sounds. There are many steps involved in this fusion, it's almost as complex as going from dating someone to marrying that person. For the DAT purpose, we will talk about several main events that take place during fertilization: 1. Capacitation 2. Acrosomal Reaction 3. Polyspermy Block 4. Completion of Meiosis II for oocyte 5. Zygote formation

Fungi Reproduction

Filamentous fungi may reproduce asexually when environmental conditions are good. If environmental conditions are not as good, chances are that the fungus will reproduce sexually. Asexual reproduction begins when a haploid mycelium grows a spore producing structure. The spores produced from this structure are also haploid; so, they can grow by *mitosis* and form a new mycelium that is genetically identical to the parent mycelium. It is important that both the parent and offspring are genetically identical because conditions were good for the parent; so, it wants to produce offspring that will be able to thrive in the environment as well. Sexual reproduction begins when two hyphae of a mycelium fuse their cytoplasm in a process known as *plasmogamy*. Because each hyphae contains a haploid nucleus, the single fused cell now contains two haploid nuclei aka *pronuclei*. Eventually, the pronuclei fuse in a process known as *karyogamy*, leading to the production of a single diploid cell. This diploid cell will then produce a spore forming structure that sends out haploid spores through *meiosis*. Eventually, the spores will grow into a new haploid mycelium that is genetically different from the mycelium it originated from. It is important that the new mycelium is genetically different because conditions were bad for the parent mycelium. The parent wanted to produce offspring that would be different from itself, so the offspring may have a better chance at survival in the unfavorable environment.

aphotic zone

From the bottom of the disphotic zone to the ocean's floor. Almost no light penetrates this layer. Because there is so little sunlight, *photosynthetic plants cannot survive here*. Like the disphotic zone, there are some *bioluminescent species* present in this zone. While they are few, select fish species are able to survive here by living off of dead matter that has sunk to the ocean's floor.

Embryonic yolk

Functions to *provide nutrients* to the growing embryo.

stomata / lenticels

Gases diffuse into air space by entering and leaving through stomata of leaves or lenticels in woody stems.

Stomach Acid

Gastric acid kills many microbes with its *low pH*Symbiotic bacteria

*Mnemonic on differentiating α and β cells

Gluc*α*gon is secreted by *α cells*! There is no a in the word insulin, hence it is secreted by β cells.

absorbed into *capillaries*

Glucose + amino acid

DNA ligase

Glues together separate pieces of DNA.

amoeba digestion

Grabs the entire chunk of food inside itself through its *pseudopods* (extension/protrusion of the amoeba used for in moving and feeding). Afterwards, the digestion process begins within its cells.

Griffith's experiment

Griffith showed that genetic traits could be transferred between different bacterial strains (bacterial transformation) via an 'unknown heritable substance'. ● *Griffith's experiment* used two strains of pneumonia: a smooth (S) strain (which had a protective capsule shielding it from the immune system, allowing it to be virulent) and a rough (R) strain (which lacked the protective capsule, and was therefore nonvirulent). Smooth strain injection would kill a mouse, while a rough strain injection would not. If a smooth strain was heat-killed and injected, it would also not kill the bacteria. But when the smooth strain was heat-killed and added to a solution with living rough strain bacteria, and the solution was then injected into a mouse, the mouse would be killed. ▪ What killed the mouse? Recall that *bacterial transformation* allows bacteria to absorb DNA from its surrounding and incorporate it into its genome. When the smooth strain was heat-killed and its remains were added to the rough strain bacteria, the rough strain bacteria were transformed when they absorbed the smooth strain's DNA. This new genetic information allowed the rough strain to produce the protective capsule that shielded it from the immune system and allowed it to be virulent, resulting in the death of the mouse.

Peroxisomes produce

H2O2 (HYDROGEN PEROXIDE) which is then used to oxidize substrates. They can also break down H2O2 if necessary via CATALASE (H2O2 => H2O + O2) since H2O2 is toxic to cells.

CO2 mainly transported as

HCO3- ions in plasma, liquid portion of blood.

allolactose

However, in the presence of lactose, an isomer of lactose (*allolactose*) will bind to the lac repressor protein. Allolactose levels are proportionally and directly related to lactose levels. With allolactose bound, lac repressor protein undergoes a conformational shape change and cannot bind the operator region. This allows RNA polymerase to transcribe the operon genes. This regulation allows for the production of metabolic enzymes for lactose in the presence of lactose. But there is also a second level of regulation. As mentioned before, lactose is not the preferred energy source, glucose is. If lactose is present, the lac operon can be transcribed. However, in the presence of glucose and lactose, lactose is not the ideal energy source.

Human Reproduction

Humans engage in *sexual reproduction*, meaning offspring are created by the joining of two distinct gametes (in the case of humans, a male sperm and a female egg). Human reproduction is a well tested area of the DAT, so we'll get into the details.

Reinforcement

Hybrids are less fit than the purebred species. The species continues to diverge until the hybrids can no longer occur.

cnidaria examples

Hydra, jellyfish, sea anemone, coral

cytotoxic T cell (CD8 cells)

If an antigen is presented by *MHC I*: T cells activate and become *cytotoxic T cells*, also called *CD8 cells* ○ They are called CD8 cells because they form a *co-receptor* CD8 in addition to its original TCR. ● CD8 cells will recognize every cell containing the presented antigen, and kill it. To see how CD8 cells kill pathogens, we need to go back a bit to innate immunity and compare CD8 cells and their close relative, natural killer cells. Similarities: ● Both release: ○ *Perforin*: perforates (poke holes in) pathogenic cell membranes, causing cell lysis (cell breakdown). ○ *Granzymes*: a protease which stimulates a target cell to undergo apoptosis (programmed cell death)—useful for killing cancerous cells. Differences: ● NK cells react *faster* than CD8 cells because they do not require antigen-presentation and activation ● CD 8 cells are more *specific* than NK cells because they target a specific antigen on a pathogen.

plumule

In between the hypocotyl and the epicotyl. The plumule eventually develops into the *young leaves*.

mesophyll

In between the upper epidermis and the lower epidermis is the mesophyll, the middle part of the leaf. There are two types of mesophyll: *palisade mesophyll* and *spongy mesophyll*.

saltwater biome vs freshwater biome

In contrast to a *saltwater biome*, an aquatic biome is considered a *freshwater biome* if it has a salt content of less than 0.1%. However, these account for just *3-4%* of all aquatic biomes. Between saltwater and freshwater biomes you may find an *estuary*-- where freshwater from a coast (via a river or stream) meets a saltwater ocean. Additionally, where the ocean meets land, you find an *intertidal zone* - this zone is above water at low tide and below water at high tide.

Complete digestive systems

Include a basic alimentary canal, as well as the accessory digestive structures that go into breaking down food into smaller and smaller pieces. Examples of a few mollusk digestive structures include salivary and mucous glands.

Cyclosis/streaming

Intracellular circulation Circular motion of cytoplasm around cell transport molecules.

Endoplasmic reticulum

Intracellular circulation Provides channel through cytoplasm and direct continuous passageway from plasma membrane to nuclear membrane.

Brownian motion

Intracellular circulation Random particle movement due to kinetic energy, spreading small suspended particles throughout the cytoplasm.

Stimulus discrimination

Involves the ability of the learning organism to differentially respond to slightly different stimuli (e.g. only respond to 990 to 1010 Hz range).

At the tissues, a high concentration of carbon dioxide is present.

It diffuses into the blood, and into the RBC. In the RBC: the carbonic anhydrase turns the CO2 into H2CO3, which then becomes bicarbonate and H+.

melatonin

It is secreted by a pea-sized gland called the *pineal gland*. Melatonin functions to regulate our *circadian rhythm*, which can be fine-tuned by light. When there is light, our body knows it's day time and time to work. When it's dark, our body knows it's time to sleep and call it a day.

Proteins are the least desirable source of energy

It is used only when carbohydrates and fats are unavailable.

memory T cells

Just like memory B cells, these long-lived cells are crucial to protecting our body from future invasion of the same antigen. If there is another encounter with the same antigen, the memory T cells will help the adaptive immune response to 'turn on' more quickly.

PARIETAL

Just posterior to the frontal lobe Contains the *somatosensory cortex*, which is responsible for feelings of temperature, touch, pressure, and pain, as well as proprioception (where your body parts are located in space).

Speciation

Leads to the formation of new species. It begins when gene flow ceases between two sections of a population. The first thing that happens in speciation is interruption of gene flow between populations. ❖ *Species* are a group of individuals capable of interbreeding.

prostate gland

Make the semen *more alkaline* (basic) so that the sperm can survive the acidity of the female reproductive tract.

Meselson & Stahl's experiment

Meselson and Stahl grew E. coli in medium containing nucleotides with 15N (an isotope of nitrogen). These bacteria were then transferred to medium with 14N nucleotides. In both cases, bacteria will incorporate the nucleotides of the medium they are in when replication. When the 15N bacterial DNA was replicated in the new medium, it was observed that the resulting DNA was not as dense as the original 15N DNA, but not as light as 14N DNA - instead it was a density between the two (implying that semiconservative replication took place: one strand of DNA contained the original 15N nucleotides, while the newly synthesized strand contained the new 14N nucleotides). When replication continued for another round in the new media, the results were further consistent with semiconservative replication.

somites

Mesoderm cells contribute to *two masses* of cells on each side of the notochord. These cells are called *somites*. And they eventually become the *vertebrae and skeletal muscles* associated with the axial skeleton.

Erythrocytes lack

a nucleus or organelles to maximize hemoglobin content and do not undergo mitosis.

The Neuron

Neurons are the functional units of the nervous system. They are highly specialized cells, which no longer have the capacity to divide. They are also highly dependent on glucose for survival, and, unlike most cells, they do not require insulin for facilitated transport of glucose into the cell.

Neutrophils

Neutrophils are your infantry units, the most numerous and common type of leukocytes. About 40-70% of leukocytes are neutrophils! Neutrophils are phagocytes — they eat (phagocytosis) and destroy pathogens. They are part of the innate response because they are not picky eaters — they engulf all kinds of pathogens.

five main types of leukocytes

Never Let Monkeys Eat Bananas Never = Neutrophils Let = Lymphocytes Monkeys = Monocytes/Macrophages Eat = Eosinophils Bananas = Basophils

amphibia general characteristics

No scales. Undergo metamorphosis. Tadpoles live in aquatic habitats, have tails and no legs. Adults live in land habitats, have two pairs of legs and no tail.

Non-Animal reproduction

Non-animal reproduction is much simpler than animal reproduction. All non-animals reproduce *asexually* meaning only one organism is needed to reproduce and create offspring (asexual means no sex is involved). Therefore all offspring are genetically identical to the parent. All the following processes are examples of asexual reproduction. binary fission budding regeneration parthenogenesis

Electron Tomography

Not a form of microscopy, but the 3D model build up using TEM data (multiple slices are integrated into a 3D model). Advantages: Can look at objects and their relative positions in 3D. Disadvantages: Costly, Extensive sample preparation (kills sample)

Law of parsimony

Occam's Razor. This is the simplest explanation that is most likely correct. In relation to phylogenetic trees, the fewest number of changes with respect to synapomorphies is likely the most correct representation of reality.

Parapatric speciation

Occurs in a continuous population that doesn't mate randomly; individuals are more likely to mate with geographic neighbors. Divergence may happen due to reduced gene flow since selection pressures vary across the population's habitat (different niches that are adjacent but not isolated by a geographical barrier). This occurs across sharp environmental gradients.

Green glands

Osmoregulatory and excretory structures for nitrogenous wastes. They are found in aquatic crustaceans.

Coxal glands

Osmoregulatory and excretory structures of nitrogenous waste in arachnids.

hypothalamus

Our body's master controller, it serves to regulate our internal environment and maintain *homeostasis*.

Satellite Cells

PERIPHERAL NERVOUS SYSTEM Support ganglia

Schwann Cells

PERIPHERAL NERVOUS SYSTEM wrap around axons to produce myelin sheaths. One Schwann cell can only myelinate a single neuron.

Peptide Hormones

Peptides are short spans of *amino acids* chained together by *peptide bonds*. Therefore, we can understand peptide hormones as small protein chains.

There are two different types of feedback loops:

Positive feedback loop and Negative feedback loop

Auxins

Promote the growth of stems by loosening cellulose fibers, increasing cell wall plasticity and causing cell growth.

Single strand binding proteins

Proteins that prevent the two strands from coming back together after they separate.

Cnidaria

Protozoa and Hydra Direct with the environment: large surface areas and every cell is either exposed to environment or close to it → simple diffusion of gases directly with outside environment (e.g. flatworms). Small animals only.

Circulation in Invertebrates Overview

Protozoans Cnidarians Arthropods Molluscs Annelids

Ground tissue

Provide *structural support* to the plant and therefore, make up the most of a plant's mass. There are three types of ground tissue: *Parenchyma* tissue cells act as *filler* tissue and make up the *bulk* of the entire plant. They have the thinnest cell walls of the three. *Collenchyma* tissue cells provide extra support to the plant, especially in areas where the plant is actively growing. They have irregular cell walls. *Sclerenchyma* tissue cells provide the *main structural support* of the plant. They have the thickest cell walls of the three.

Channel proteins:

Provide passageway through membrane for hydrophilic (water-soluble) substances (polar, and charged).

Hybridization

Results in two different forms of a species (or closely related species) after mating and are produced along a geographic boundary called *hybrid zone* (more genetic variations, means that the hybrid can live beyond range of either parents). There are multiple outcomes for hybrids. *Reinforcement* *Fusion* *Stability*

Where are peptides synthesized?

Rough ER

Gymnosperms

Seed-bearing tracheophytes whose seeds are not protected. The most common example are *conifers* (*cone*-bearing plants). Other examples are fir, spruce, aspen, redwood, and pine. Gymnosperms were the first seed plant on earth (meaning they appeared before angiosperms). Most do not have flagellated sperm - the sperms are dispersed by wind. Their dispersal unit is (obviously) seeds. Gymnosperms disperse spores, and their dominant generation is sporophyte.

annelida General Characteristics

Segmented bodies, coelom is divided by septa, sexual (hermaphrodites) and asexual (regeneration) reproduction, longitudinal and circular muscles

Special Senses

Senses that have specialized organs devoted to their function. Examples include vision, hearing, taste, and smell.

Analogous trait

Similar characteristics resulting from convergent evolution, therefore these are not derived from a common ancestor.

Metaphyses

Similar in structure to the epiphyses and are found immediately between the *medullary cavity* and the *epiphyseal plate*.

T cell receptors (TCR)

Similar to B cells, T cells have T cell receptors (TCR) on their surfaces. Every T cell has a unique and uniform TCR that binds to only one kind of antigen. Hence, T cells also go through clonal selection.

Spiral cleavage

Simply indicates how the axis of embryonic cell cleavage is oriented.

Pleiotropy

Single gene has more than one phenotypic expression. ex) - Gene in pea plants that expresses seed texture also influences phenotype of starch metabolism and water uptake. - Gene causing sickle cell anemia leads to multiple health conditions.

Globular protein

Soluble, folded tightly, perform many functions. ex) albumin

Slow oxidative fibers

Small in diameter; therefore, they have *weak* contractions. This muscle types appear *dark red* because they contain a rich network of blood capillaries for providing oxygen, myoglobin for storing oxygen, and mitochondria. They rely upon high amounts of *oxygen* because they generate ATP by *aerobic respiration* only. Their twitch lasts the longest of the three types of muscle fibers; however, their contractions are extremely *efficient* and *resistant to fatigue*.

Spiracles

Small openings on the exoskeleton that allow air to enter - think of them like nostrils all over your body. They branch into the tracheal tubes.

Mitochondria Intermembrane Space

Space between the outer membrane and the inner membrane H+ released during ETC are found here

Facilitated diffusion

Spontaneous passive transport of molecules across a membrane using transport proteins.

Types of Natural Selection

Stabilizing selection Directional selection Disruptive selection Sexual selection Artificial selection

Salivary amylase:

Starch —> Maltose

Game theory

States that the fitness of a particular behavioral phenotype is influenced by other behavioral phenotypes in population. The outcome depends on strategies of all the individuals involved.

Menstrual Cycle

Start by looking at the end of the cycle, on day 28. Note that estrogen (also known as estradiol) and progesterone levels are dropping. Estrogen and progesterone are hormones that have negative feedback on (or inhibit the function of) the *hypothalamus and pituitary gland*. As *estrogen and progesterone drop*, the hypothalamus and pituitary lose the inhibition these two hormones exerted, meaning the hypothalamus and pituitary gland can *start producing hormones again*. Now, let's go to the beginning of the cycle (day 1). The hormones of the hypothalamus and pituitary gland are not shown in the figure, but this is what begins the menstrual cycle. As mentioned above, dropping estrogen and progesterone means that the hypothalamus is no longer inhibited, and can start to produce its hormones. The *hypothalamus* gland produces *gonadotropin releasing hormone (GnRH)*, a tropic hormone that causes the release of *luteinizing hormone (LH)* and *follicle stimulating hormone (FSH)* from the *anterior pituitary gland*. *Tropic hormones* are hormones that are *released from one endocrine gland* and *stimulate another* endocrine gland to release hormones. *FSH* will bind to the *ovaries* and cause ovarian *follicles* to develop. One follicle on the ovary will develop the most, and become the dominant *Graafian follicle* (aka tertiary follicle)—this is where the egg to be ovulated will release from. The developing follicles (particularly the Graafian follicle) will start to produce increasing amounts of *estrogen*. *Estrogen* causes the *endometrium* (the inner lining of the uterus) to *thicken* its tissue, and becomes engorged with blood. This is to prepare the uterus in case fertilization of an egg occurs, and the developing embryo wants to implant into the endometrium. Notice in the image that as estrogen (estradiol—in blue) increases, the endometrium (bottom of the image) thickness increases proportionally. This *increase in estrogen* levels stimulates a rapid *spike in LH*. This spike in LH causes *ovulation*—the release of the egg from the follicle. In order for a fertilized egg to be implanted to the uterus, the egg must first be transported from the ovary to the uterus through the *oviduct* (fallopian tube). The ovaries do not directly connect to the oviducts. The oviducts have *fimbriae* (fingerlike projections), and an ovulated egg is swept into the oviduct by the cilia of the fimbriae. *Microtubules* form a key structural and functional component of cilia. The egg leaves the ovary, and begins to travel down the fallopian tube, where it could meet a sperm gamete, if sexual intercourse has occurred between the female and a male. After ovulation, the remnants of the *follicle* (which has released the egg) develops into the *corpus luteum*. The corpus luteum begins to produce *progesterone* (and some estrogen). Progesterone joins estrogen in making the uterine lining receptive to embryo implantation by stimulating thickening the endometrial tissue and engorging it with blood. The corpus luteum is maintained by FSH and LH levels. However, the combination of *increasing progesterone and estrogen* causes the levels of *FSH and LH to drop* (remember the negative feedback we talked about before). If implantation does NOT occur: With lower FSH and LH, the corpus luteum can no longer be maintained. Therefore, progesterone levels drop (remember, the corpus luteum was the source of progesterone), and the progesterone stimulation of estrogen production stops. With decreasing progesterone and estrogen, the endometrium can no longer be maintained, and the uterine line will slough off, causing menstruation (the female period). If implantation does occur: Menstruation is prevented if implantation occurs. If an embryo implants into the endometrium, the outer layer of the placenta begins to secrete *human chorionic gonadotropin (HCG)*. Human chorionic gonadotropin *maintains the corpus luteum*, preventing the corpus luteum from degenerating. The corpus luteum is therefore able to continue to produce high levels of progesterone and estrogen, and the endometrium is not shed.

Vestigial structures

Structures that appear to be useless but had ancestral function; eg: humans (appendix and tail), horse (splits), python (legs reduced to bones), insects (pair of wings under fused wing cover).

sunlight's influence on aquatic ecosystems

Sunlight greatly influences aquatic ecosystems. *Deeper* parts of the ocean receive *less light*, and this has an effect on which plants and animals can survive there. In fact, the layers of the ocean are categorized based on the amount of sunlight they receive. From superficial to deep, these layers are: the euphotic zone, the disphotic zone, and the aphotic zone.

Bundle sheath cells

Surround and *protect* the vascular bundles in the leaves from air exposure. As a refresher, vascular bundles is the system that transports materials such as water and sugars. These are only found in C4 plants.

Sertoli cells

Surround and nourish the developing sperm cells within the testes. They are activated by Follicle-Stimulating Hormone (FSH). Sertoli cells also secrete the peptide hormone *inhibin*, which acts on the anterior pituitary to *inhibit further FSH release*.

Most Common Joints

Synovial joints, typically contain hyaline articular cartilage.

amphibia examples

Tadpole, frog, toad, salamander, newt

hypocotyl

The bottom region of the *young shoot* (above the roots but below the cotyledons).

Epiphyses

The bumpy parts at the ends of long bones. Looking at the outside of an epiphysis, you would notice *articular cartilage* covering compact bone. This is because epiphyses form *synovial joints* with other bones. If you could peak inside an epiphyses, you would see spongy bone containing red bone marrow. ○ DAT Pro-Tip: red bone marrow is where a process called *hematopoiesis* occurs. Hematopoiesis is the process where stem cells create new blood cells.

appendix

The cecum has a small finger-like projection called the appendix, which has negligible immune functions in human adults. The appendix likely used to have a function, though that is no longer the case. For most people, it is a silent vestigial structure (borrowing terms from our evolution chapter).

archaea vs eubacteria cell wall difference

The cell wall of Eubacteria contains peptidoglycan whereas in Archaea it does not. The lipids in the cell wall of Eubacteria is linked via esters, whereas the lipids in the cell wall of Archaea is linked via ethers.

Evolution

The change in allele (traits) frequencies in populations over time. It gives rise to biodiversity at the level of populations, species, or groups of species.

Chick embryo

The chick embryo serves as a model embryo for all egg-laying animals, such as birds, reptiles, fishes, and monotremes. The key thing here to understand is that if an embryo develops within an egg, it *does not have a direct connection* with the mother i.e. through the placenta. When there is no mommy to provide nutrients, these embryos need a huge yolk to nourish themselves. As we discussed earlier, the yolk has very little cleavage activities. In a chick embryo, the blastula actually has a very *flattened* shape (pushed by the yolk!). Hence, it is also called the *blastodisc*. The blastodisc is analogous to the *inner cell mass* in mammalian cells. Similar to mammals, chicks do have a primitive streak. Due to the flattened shape of the blastodisc, after gastrulation happens at the primitive streak, we get a very *elongated blastopore*.

Hemolymph

The equivalent to blood in an arthropod.

snRNA

The functional part of the spliceosome is made up of *snRNA* (small nuclear RNA) and proteins. Collectively, snRNA and proteins are referred to as *snRNP's* (small nuclear RiboNucleic Protein; pronounced 'snurps'). The spliceosome scans the pre-mRNA for 5' and 3' splice signals within the mRNA code; these sites signal the spliceosome to start and stop its splicing—precisely removing the intron.

snRNA

The functional part of the spliceosome is made up of snRNA (small nuclear RNA) and proteins. Collectively, snRNA and proteins are referred to as snRNP's (small nuclear RiboNucleic Protein; pronounced 'snurps').

Stimulus generalization gradient

The further from original conditioned stimulus, and results in a lesser magnitude of response.

single nucleotide polymorphisms (SNPs)

The genome of humans differs roughly one every 1000 nucleotides. These differences are called *single nucleotide polymorphisms* (SNPs). SNP's can be used as genetic markers for disease-causing alleles (the SNP's don't cause disease, but are physically close enough be linked to their presence).

Development

The growth of a seedling into a more mature plant.

seed coat

The hard outer layer that covers and protects the seed from various external forces (such as mechanical stress, too much water, fluctuations in temperature...).

Sperm Head Characteristics

The head is the part of the sperm that contains the *nucleus*, meaning the head contains all the *genetic information*. The head also has an organelle called the acrosome at the very tip. The *acrosome* contains digestive enzymes that help the sperm *penetrate* the egg for fertilization upon contact.

pericardium

The human heart is surrounded by a *pericardium*, a fluid filled sac that surrounds the heart. It protects and lubricates the heart for proper function.

Cancellous bone

The inner network of bones. Unlike cortical bone, it does not contain osteons; rather, it contains a web of *trabeculae* soak up bone marrow like a sponge. Since it behaves like a sponge, it is softer and more flexible than cortical bone. ● Analogy: imagine putting a dry sponge in a small bowl of water. It is safe to say that sponge would quickly absorb the water and become waterlogged - this is how spongy cancellous bone in an epiphysis behaves! It acts as a sponge that soaks up red bone marrow.

Chloroplast Inner membrane

The inner plasma membrane composed of a phospholipid bilayer.

hydroxyapatite

The inorganic component of bone matrix. Gives bones density and strength. Hydroxyapatite is crystallized *calcium, phosphate, and water*.

Integumentary System

The integumentary system contains the skin, as well as associated hair, nails, glands, and nerves, and it is organized into three distinct layers.

Integumentary System

The integumentary system contains the skin, as well as associated hair, nails, glands, and nerves, and it is organized into three distinct layers. Listed from superficial to deep, the layers are the epidermis, dermis, and hypodermis. However, the "skin" is only composed of the epidermis and dermis. The integumentary system is key to many homeostatic functions such as heat and moisture regulation, and it is needed for production of vitamin D and protection from pathogens.

Polygenic inheritance

The interaction of many genes to shape a single phenotype with continuous variation. ex) Height, skin color

lac repressor protein

The lac repressor is coded by the gene *lacI*, which is not part of the lac operon. ● DAT Pro-Tip: the lacl gene is *constitutively expressed*; constitutive expression means that the gene is always being transcribed and translated. As such, the lac repressor protein is always being created. The lac repressor protein binds to the operator. If the repressor is bound on the operator, RNA polymerase will not be able to bind effectively to the DNA and the lac genes will only be transcribed and translated at very low levels.

Role of the gallbladder

The liver produces *bile* and sends it to the gallbladder for storage and concentration. ○ Bile is secreted from the gallbladder into the small intestine to *emulsify fats.* — breaking down fats into smaller fat droplets that are easier to digest. ○ Remember: bile is *NOT* an enzyme, emulsification is a type of *mechanical* digestion - *not* enzymatic breakdown.

Kinesis

The non-directional movement of an animal in response to a stimulus. It slows down in favorable conditions and speeds up in an unfavorable condition. This is observed when animals scurry when a rock is lifted up.

Abiotic factors

The nonliving elements in an ecosystem, like temperature, sunlight, and water levels.

RNA polymerase binding

The rear part of RNA polymerase binds to the -35 element, while the leading part of the enzyme binds to the -10 element. This allows RNA polymerase to read the DNA template in the correct orientation.

Predation

The relationship between the *predator* (hunter) and the *prey* (hunted). The prey can be either a plant or an animal. For example, the tiger hunting the elk, or the rabbit hunting the carrot.

convergent evolution

The opposite of divergent evolution. If two species of *differing ancestry* become *more similar*, they have undergone convergent evolution. This often occurs because they *share a similar selection pressure or environment*. An example of this is between fish and whales, which have both independently evolved to swim. In the case of convergent evolution, *more competition develops* for the same resources.

sensitization

The opposite of habituation is sensitization. It is an increased response to repeated stimulus.

osteoid

The organic component of *bone matrix*. Contains various *proteins* and *type 1 collagen fibers* that give bones slight flexibility and *tensile strength*.

cortical bone

The outer layer of bone. The density of cortical bone is what allows bones to support our weight. Analogy: cortical sounds like court (i.e. a tennis court). Tennis courts are usually hard and outside.

Chloroplast Outer membrane

The outer plasma membrane composed of a phospholipid bilayer.

fibrous tunic

The outermost layer, the fibrous tunic, consists of the sclera and cornea. ▪ The *sclera* is the opaque "white of the eye." It is made of collagen and elastic fibers, and it functions to maintain the shape of the eyeball and protect the underlying structures. ▪ The *cornea* is the transparent, anterior portion of the eye. It covers the iris and pupil, and it focuses light onto the retina.

radicle

The part of the embryo that develops into the young *root*. It is the first to emerge from the seed coat and anchors the plant into the soil. Easy way to remember: both radicle and root start with the letter R. The rest of the parts of the embryo (hypocotyl, plumule, and epicotyl) make up the young shoot (anything above the soil).

ovary

The part of the female reproductive system responsible for the production of *ovums* (eggs). Females have two ovaries. When eggs are released from the ovary, they travel through the *oviduct* (also known as the *fallopian tube*) to the uterus.

pharynx

The pharynx is a special region common to the respiratory system and digestive system merge, which then separate into the trachea and esophagus. This is why we can breathe through our mouth, as well as eat! When we inhale air into our oral cavity, air travels through the pharynx into the trachea.

Growth Factors

The plasma membrane has receptors for growth factors that stimulate cells for division (such as damaged cell).

potency

The potential of the stem cell.

Primary active transport

The process in which energy (ATP) is directly used to move against a concentration gradient.

Secondary active transport

The process in which energy is indirectly used to move against a concentration gradient (usually by coupling with a 'counter ion' moving down its concentration gradient). Considered secondary active transport because the other substance's gradient was usually established with ATP. Can use *antiporters* (one molecule moves in while another moves out) or *symporters* (both molecules travel in the same direction).

chemotaxis

The process of moving to a location in response to a chemical signal is called chemotaxis. Chemo = chemicals, and taxis = movement. In the inflammatory response, many white blood cells are drawn to the site of injury via chemical signals to arrive.

Osmoregulation

The process of moving water across a semipermeable membrane due to the solute concentrations on either side of that same membrane.

Convergent evolution

The process of two unrelated species, independently evolving similar traits as a result of having to adapt to similar environments (analogous traits).

Symbiosis

The relationship between two species. Can be: *mutualism* (beneficial/beneficial), *commensalism* (beneficial/neutral), *parasitism* (beneficial/detrimental) "Living together." It refers to a *close, long-term interaction* between two organisms (symbionts) in their environment. This interaction is sometimes necessary for the survival of the symbiont. Mutualism, commensalism, and parasitism are types of symbiosis.

Dermis

The second layer of the integumentary system, the *dermis*, is located just *deep to the epidermis*. It is a network of *dense irregular connective tissue* that functions to cushion the body from injury and provide a home for functional structures of the skin, such as vessels, glands, nails, hair. The dermis has *two layers*. The more superficial, thinner layer is the *papillary dermis*. The deeper and thicker layer is the *reticular dermis*.

cecum

The small intestine connects into a pouch called the cecum — an important structure for water and mineral absorption.

small intestine

The small intestine is where the digestive party is taken to a climax — *90% of digestion and nutrient absorption* occur here!

Appeasement behavior

The social behavior that is displayed to mitigate aggression or avoid attacking by showing an inferior social stance (e.g. moving/turning away).

Behavioral ecology

The study of behavior that explains how specific behaviors increase fitness.

Testes and Ovaries

The testes in males and ovaries in females are both influenced by *LH* and *FSH* secreted from the anterior pituitary. Testes and ovaries each produce their own set of hormones: testes produce *androgens* (i.e. *testosterone*) and ovaries produce *progesterone* and *estrogen*.

Hypodermis

The third and final layer of the integumentary system. The prefix hypo- means "below"; thus, the hypodermis is located *beneath the dermis*. Another name for the hypodermis is the *subcutaneous tissue*. This layer contains larger *nerves* and *blood vessels* than those in the dermis, and its main components are *loose connective tissue* and *adipose (fat) tissue*. In fact, it's main function is *fat storage*.

primary central lymphoid organs that can replenish immune cells.

The thymus and bone marrow

Recognition proteins

These include the major-histocompatibility complex (MHC) on macrophages used to distinguish between self and foreign; they are glycoproteins due to oligosaccharides attached.

Cystic fibrosis

Thick mucus buildup in respiratory tracts

Determinate vs. Indeterminate cleavage

This category is based on the *fate of each cell* after cleavage. *Determinate* cleavage refers to blastomeres that have a *decided fate* after it is made from cleavage. For example, a cell could be born and destined to become one of the cardiovascular organs. *Indeterminate* cleavage refers to cells which *do not have a pre-set fate*. After the blastomere is made, it can be split off from the rest of the cells and can go on to form a separate organism. When this happens in humans we get identical twins!

Amino-Acid Derived Hormones

This third category can be ambiguous because some hormones have characteristics of peptide hormones while some have properties of steroid hormones, there is no clear cut line. When we say they are derived from amino acids, they are actually derived mostly from the amino acid *tyrosine*.

Passive immunity

This type of immunity is temporarily provided to an organism by the *transfer* of active immunity components from one animal to another - that is, antibodies are *given* to the animal, rather than generated by that animal. Recall our lesson on B cells and antibodies, we talked about 5 classes of antibodies. Out of the 5, only *IgG* can cross the placenta, and *IgA* is found in body secretions such as milk. A fetus/newborn baby is *immuno-naive*, which means that they have not been exposed to the world with pathogenic microbes. Therefore, the fetus has not generated its own active immunity. This is where the mother steps in and protects the baby by *passing down* her own antibodies to the fetus through placenta (IgG) or breastfeeding (IgA). These antibodies will safeguard the baby until the infant generates their own active immune response.

3 types of differentiated T cells

cytotoxic T cell (CD8 cells) helper T cell (cd4 cells) memory T cell

Xylem

Transports *water*. Water is taken in from the soil by the plant at the roots and transported to other areas of the plant that need the water but do not have direct access to it. The primary target is the leaves. *Source: roots* *Sink: leaves* Xylem is made up of two types of cells: *tracheids* and *vessel elements*. Tracheids are long, thin, and are organized so that they are in contact with other tracheid cells by overlapping their tapered ends. Water flows from tracheid to tracheid through *pits* found at these ends. Vessel elements are shorter and stouter, and are in contact with other vessel elements. Water flows from vessel element to vessel element through *perforations* along their cell walls. Along with water conduction, both also provide structural support.

competition

Two organisms compete for the same resources. For example, a tiger hunting the same type of prey that a lion hunts.

Muscles

Turn chemical energy into mechanical energy by contracting across a joint. In doing so, they *pull* the bone they *insert* upon closer toward the bone they *originate* from. It's important to note that because of this, muscular contraction is always a pull (a contraction). The opposing force to a given movement is generated by an opposing muscle group contracting. For example, forearm lifting is generated by contracting biceps, whereas forearm extension is generated by contracting triceps.

Hemophilia

X-Linked Recessive Abnormal blood clotting

Color blindness

X-Linked Recessive Inability to distinguish between different colors

Duchenne

X-Linked Recessive Muscular dystrophy

Fragile X Syndrome

X-linked Dominant Intellectual disability

Transpirational pull

a cohesive force

Proteinoids

abiotically produced polypeptides. These can be formed in the lab by dehydrating amino acids on hot, dry substrates.

Hemidesmosomes

are another way the cell connects to the ECM. This type of connection uses *intermediate filaments* e.g. *keratin*.

Before moving on to anaphase, the cell

checks that each chromosome is attached to microtubules with their kinetochore. This ensures that in anaphase the sister chromatids split evenly.

the endocrine uses what kind of signals?

chemical signals

Enzymes remain

chemically unchanged throughout a reaction (but can undergo conformational changes).

chondroblasts mature into

chondrocytes when they become trapped by the matrix they secrete. Chondrocytes are found in cartilaginous lacunae and are responsible for maintaining cartilage.

Throughout most of the cell cycle, DNA is packaged in the form of

chromatin

During cell replication, the DNA is tightly packed into

chromosomes

metaphase II

chromosomes align on metaphase plate like in mitosis, but there are now half the number of chromosomes.

metaphase

chromosomes line up in a single file in the center. each chromatid is complete with a centromere and attacked kinetochore. centrosomes are at opposite ends of the cell. karyotyping is performed here.

Meiosis II

chromosomes spread across the metaphase plate and sister chromatids separate and migrate to opposite poles. It is similar to mitosis. ❖ Interphase may occur in between Meiosis I and Meiosis II. It depends on the species.

Chymotrypsin is secreted as

chymotrypsinogen

Seedless tracheophytes examples

club moss, quillworts, fern, and horsetail.

glycogenesis

create glycogen.

platelets stick to

damaged epithelium and attract more platelets to the site of injury.

Batesian mimicry

deceptive; harmless species have evolved to imitate the warning signals of a harmful species directed at a common predator.

Pressure of the intrapleural space

decreases as we inhale.

There are four methods for material to cross capillary wall:

endocytosis and exocytosis (proteins), diffusion through capillary cell membrane (O2 and CO2), movement through pores in the cells (called fenestrations), movement through space between the cells (ions).

In monocots, nutrients are stored in the form of

endosperm (a tissue)

There are three layers or tunics

endothelial lining, middle layer of smooth muscle and elastic tissue, and other layer of connective tissues.

the photosynthesis process ends when

energy is absorbed by one of two special chlorophyll a molecules (P680 & P700). P700 forms pigment cluster (PSI) and P680 forms pigment cluster (PSII).

Holoenzyme

enzyme + cofactor

induced fit

enzyme binding is specific to structure.

Apoenzyme

enzyme w/out its cofactor

platelets convert

fibrinogen (inactive) to fibrin (active).

Thrombin converts

fibrinogen into fibrin. Fibrin threads coat the site of injury and trap blood cells to form a clot.

An antibiotic resistance screen is used to

filter out bacteria that did not successfully uptake the plasmid. A gene for antibiotic resistance is included in the plasmid; bacteria that have taken up the plasmid (and by extension have the antibiotic resistance gene) will successfully survive antibiotic treatment, while those without the plasmid will perish.

nose

filters, moistens, warms incoming air-mucus secreted by *goblet cells* traps large dust particles here

Seedless tracheophytes have

flagellated sperm, meaning it can move on its own (does not travel via wind or animal).

The brain can be divided into the

forebrain, midbrain, and hindbrain.

cellulose

functions as a structural molecule for the walls of plant cells and wood.

Poikilothermic animals

have internal temperatures that vary in response to the external environment.

Axial skeletons

include the bones at the core of an endoskeleton

the immune system can be divided into 2 categories:

innate and adaptive

Glycolipids

like phospholipids but with a carbohydrate group rather than a phosphate group.

ciliary muscle

ontrols the shape of the lens

Coenzymes

organic cofactors (e.g. vitamins)

NADH and FADH2 are

oxidized (lose electrons) resulting in the transportation of H+ from matrix to intermembrane space. This results in the formation of a pH and electric charge gradient (an electrochemical gradient). ● ATP synthase uses the kinetic energy from the flow established by this gradient (proton motive force) to create ATP by letting the protons flow from the intramembrane space back to the matrix.

photosynthesis gives off

oxygen

the optimal pH for pepsin to demonstrate maximum activity

pH ~= 2

immune defense proteins

prevent and protect against pathogen attack. ex) antibodies

motor (efferent) neurons

stimulate *effectors*, which are target cells that elicit a response. Examples include stimulation of muscle movement and secretion of sweat glands.

Peroxisomes break down

stored fatty acids to help generate energy for growth.

lagging strand

synthesized *discontinuously*. This is because in the lagging strand the replication fork is opening in the opposite direction to the how DNA polymerase is traveling. In the lagging strand, small *Okazaki fragments* build up a discontinuous DNA strand, meaning several RNA primers are required.

negative reinforcement

take away something bad to increase a behavior ex) not pushing a dog's nose when he jumps

negative punishment

take away something good to decrease behavior ex) no longer paying attention to the dog when he jumps

large motor units with large fibers are innervated by

the least excitable neurons.

They are called monocytes when

they are in their immature state in the blood vessels.

amphipathic

they have both hydrophobic and hydrophilic properties

Adenine bonds with thymine/uracil in DNA through

two (2) hydrogen bonds. However, thymine does not exist in RNA; it is instead replaced with uracil. Adenine bonds with uracil in RNA through two (2) hydrogen bonds.

bronchi --> bronchioles

two bronchi, which enter the lungs and branch into narrower bronchioles

In dicots, nutrients are stored in the form of

two cotyledons (leaf-like structures)

Phospholipids

two fatty acids and a phosphate group (+R) attached to a glycerol backbone ● These molecules are amphipathic

Linked genes

two or more genes that reside close together on a chromosome, and are therefore less likely to be separated by recombination during meiosis, and are more likely to be inherited together. ● A *linkage map* uses recombination frequency to show the positions of genes rather than physical distance units. The closer together the genes are, the less likely separation by recombination is.

Inorganic cofactors

usually metal ions (e.g. Fe2+and Mg2+)

Enzymes

usually) globular proteins that act as catalysts, lowering the activation energy and accelerating the rate of reactions.

Placenta

vascular organs found in the uterus of a pregnant mother (viviparous mammal). These organs provide nourishment to the fetus through a tube known as the umbilical cord.

histamine

vasodilation and making capillaries more permeable.

transversion mutation

when a purine nucleotide is converted to a pyrimidine nucleotide or vice versa.

↑ Km

worse substrate binding

pancreatic lipase

○ Works together with bile to breakdown and digest fats ○ It digests the emulsified fats —> glycerol and fatty acids

IgA

● Dimer ○ *Tip: when you think of IgA, think of IgAnd, when there is this and that —> dimer

Scientific Proof of Evolution: Molecular Biologists

❖ Molecular biologists investigate nucleotide and amino acid sequences of DNA and proteins from different species. If the species are closely related, a higher percentage of sequences are shared. ● More than 98% of the nucleotide sequence in humans and chimpanzees is similar. ● The amino acids in cytochrome c are often compared.

Brain

❖ The outer *cortex* is composed of grey matter (neuronal cell bodies), and the inner *medulla* is composed of white matter (neuronal axons). ❖ The *brain* can be divided into the forebrain, midbrain, and hindbrain. o The *forebrain* is the most anterior component, and it is also the largest. It contains the cerebrum and diencephalon, which are further subdivided.