Biochemistry/Biology Kaplan Review

Watson Crick model

DNA is right handed, double helix with hydrogen bonds between nitrogenous bases.

3 common examples of epigenetics

DNA methylation, chromatin remodeling, and RNA interference.

biological agents that cause mutations

DNA polymerase may not repair incorrect base pair correctly. Viruses. Transposons.

Facultative parasitic bacteria

Damages a host cell. Can live and replicate inside or outside of a host cell.

Obligate parasitic bacteria

Damages a host cell. Must use host cell for replication

Lagging strand

Daughter strand in DNA replication that does not elongate continuously - it instead waits for replication fork to widen, placing RNA primers and polymerizing DNA in opposite direction or widening replication fork. This forms short Okazaki fragments.

Leading strand

Daughter strand that elongates continuously, widening the replication fork

Transverse tubules (T-tubules)

Deep invaginations in cell membrane of myofibers, which allow action potentials to travel into the interior of the thick cells. See light blue lines shown in image.

STratum basale

Deepest part of epidermis, which replenishes squamous epithelial cells of epidermis via mitosis.

Hemophilia

Defect in clotting proteins, such as thrombin, fibrinogen, accessory proteins. "loving to bleed".

Osmotic pressure

Defined as pressure it would take to stop osmosis from occurring. Given by van't Hoff equation (π= MiRT) M= molarity R= .0821 L-atm/K-mol T in Kelvin

How is CCR5 gene mutation beneficial?

Deletion of 32 base pairs in the gene - causes HIV resistance or delays AIDS onset.

How does delta G depend on the pathway of a reaction?

Delta G is totally dependent of the pathway of a reaction taken.

Tendons

Dense connective tissue that connects bones to muscles.

bacterial lawn

Dense growht of baceria seen in lab Petri dishes.

Colligative properties - definition and important examples.

Depend on the NUMBER of solute particles in the solution, regardless of what type of particle it is. Examples are boiling point elevation, freezing point depression, and vapor pressure depression, and osmotic pressure.

End plate potential

Depolarization of postsynaptic membrane in neuromuscular junction, which results when acetylcholine binds to its receptors, causing a sodium influx.

L-DOPA structure. What is this derived from?

Derived from phenylalanine and tyrosine.

Dopamine structure. What is this derived from?

Derived from phenylalanine and tyrosine. Essentially same as dopamine except without COOH group.

Noradrenaline structure. What is this derived from?

Derived from phenylalanine and tyrosine. Same as dopamine, but with added OH group as shown.

Adrenaline structure. What is this derived from?

Derived from phenylalanine and tyrosine. Same as noradrenaline, but with added methyl group.

What does monocistronic mean?

Describes most eukaryotic mRNA - the term means that one strand of mRNA only codes for one polypeptide (although it may make several copies of the same polypeptide). In other words, there is only one open reading frame.

Bipolar vs multipolar

Describes neurons with one dendrite (bipolar) vs neurons with many dendrites (multipolar)

Senescence

Describes process of aging at both cellular and organismal level. Apoptosis destroys and removes cells that need to be removed due to age.

What does polycistronic mean?

Describes prokaryotic mRNA. Term means that different open reading frames on the same mRNA allow for the mRNA to code for more than one polypeptide.

Pluripotent

Describes stem cell that gives rise to many different types of cells.

Unipotent

Describes stem cell that gives rise to one type of cell.

Population genetics

Describes the inheritance of traits in populations over time

Obligate intracellular parasite

Describes viruses - they are only able to reproduce within cells.

Autocrine activity

Describes when signalling molecules modify the activity of the cell which secreted them. For example, a T cell secretes interleukin 2, which binds to receptors on the same T cell to stimulate increased activity.

The Avery-Macleod-Mccarty experiment

Destroyed different elements of virulent bacteria used in Griffith experiment until it was determined that DNA was responsible for transfer of virulence from heat killed S strain to the live R strain.

Diaphysis vs. epiphysis

Diaphysis is the shaft of a long bone, epiphysis is the flared end of a long bone.

What is the diaphysis composed of? What is the epiphysis composed of?

Diaphysis is tube of compact bone only, containing yellow marrow (yellow marrow is filled with fat and is inactive). Epiphysis is shell of compact bone surrounding core of spongy bone.

What are the two periods of the cardiac cycle?

Diastole - ventricles are relaxed, blood is able to flow into them from the atria. In fact, atria contract during diastole. At the end of diastole, ventricles contract Systole - period of time in which ventricles contract, beginning at "lub" sound of AV valve slamming shut and ending at "dub" sound of semilunar valves slamming shut. Remember, this happens in both sides of the heart at the same time!

Pulse pressure

Difference between systolic and diastolic pressure.

Alleles

Different versions of a gene sequence. Two different alleles are on same gene locus, but have different DNA sequence and phenotype. each homologous chromosome contains an allele for a given gene.

Memory cells

Differentiated form of B-cell that forms after exposure to an antigen. Remain dormant for a while, waiting for the same antigen to appear. This is called clonal selection

Plasma cells

Differentiated form of B-cell. Actively produce and secrete antibody protein into the plasma.

Simple diffusion - definition and example?

Diffusion of a solute through a membrane without help from a protein. Example is cholesterol, which can move through plasma membranes due to hydrophobicity.

Facilitated diffusion - definition and example?

Diffusion of solute across a membrane, down a gradient, when the membrane itself is intrinsically impermeable to that solute. Often use integral membrane proteins. Example: glucose is shuttled into RBCs via a particular protein.

Dikaryon (fungus)

Dikaryon refers to a cell with two nuclei. Often occurs in fungi when two haploid gametes join together, but do not fuse yet.

Transmissible spongiform encephalopathyies (TSEs)

Diseases that cause degeneration in the nervous system, especially in the brain. The cause of this is prions (misfolded proteins) in nervous tissues that are resistant to degradation. Examples include mad cow disease (bovine spongiform encephalopathy) and kuru.

karyotype

Display of an organism's gemome. Created when cell is frozen in metaphase, stained, picture is taken, picture is cut so that homologs are paired, chromosomes are analyzed for abnormalities.

Excretion

Disposal of waste products

Denaturation

Disruption of a protein's shape without breaking peptide bonds.

Where is reabsorption of substances into blood most regulated in the nephron?

Distal convoluted tubule. Hormones regulate what is reabsorbed.

protein that finds ORI in prokaryote DNA (origin of replication)

DnaA.

endergonic reactions

Do not occur spontaneously, only occur if there is energy added.

Why do/don't eukaryotic transcription and translation happen simultaneously?

Don't, because the mRNA has be be capped, spliced, and moved from the nucleus to the cytoplasm. This is not the case in proks.

Provirus

Dormant form of viral genome in lysogenic cycle of animal cells (analagous to prophage). Herpes simplex 1 is an example.

Alveolar duct

Duct leading to alveoli. Walls are entirely made up of alveoli.

Brush border enzymes

Duodenal enzymes that hydrolyze smallest carbs and proteins (like disaccharides and dipeptides) into monosaccharides and amino acids. Located on surface of brush border epithelium.

Enterogastrone

Duodenal hormone which decreases stomach emptying.

Semiconservative replication

Duplicated dsDNA is made up of one strand of parental DNA and one strand of daughter DNA.

How does sympathetic system affect the heart?

During fight or flight situation, sympathetic postganglionic neurons directly innervate the heart, releasing norepinephrine. Second, epinephrine secreted by the adrenal medulla binds to the receptors on cardiac muscle cells.

How does a cell ensure it does not replicate DNA at inappropriate times in the cell cycle?

During the S (synthesis) phase, 2 of the 3 proteins that locate the ORI are destroyed immediately, preventing replication from occurring.

medial stack

Middle portion of golgi apparatus where protein modification occurs after the cis stack, but before reaching the trans stack.

LIpemia

Milky looking blood indicative of lipids flowing through the blood.

Prion

Misfolded version of a protein that already exists. These are self replicating, violating the central dogma. Prions act as replicating template for normal the normal proteins, worsening the infection.

What are the main differences between mitosis and meiosis?

Mitosis has one round of cell division, meiosis has two. Meiosis undergoes recombination.

Golgi apparatus functions and number of membranes

Modification and sorting of protein, some synthesis of macromolecules, such as polysaccharides. 1 membrane

Allosteric regulation

Modification of active site activity through interactions of molecules with other specific sites on the enzyme.

cap and tail

Modifications to hnRNA to produce stable mRNA prior to translation. The cap is located on the 5' end and consists of a methylated guanine nucleotide, and the poly-A tail is located on the 3' end and consists of a string of several hundred adenine nucleotides. Cap and tail revent digestion of mRNA by exonucleases that are free in the cell.

Evaporative water loss

Moisture of respiratory structures absorbs heat as it changes into water vapor, which is then exhaled during ventilation.

Pyrophosphate

Molecule composed of two phosphates (AKA orthophosphates) linked together by anhydride bond.

What is retinal? At what condition is retinal at rest? Describe its bonds during rest, and what effect this has. How does retinal change as it is activated?

Molecule derived from vitamin A that is present in rods and cones of retina. Binds opsin proteins, which change conformation when absorbing light. Retinal is at rest in the dark. During rest, it has several trans double bonds and one cis double bond. In this conformation, the sodium channels remain open. As it absorbs light, it becomes activated and converts to all-trans form. This triggers series of reactions that closes the sodium channel, causing hyperpolarization.

Hemoglobin

Molecules that populate RBCs in order to carry 4 oxygen molecules from the lungs to the tissues. Cooperative binding of oxygen.

Molality

Moles of solute/kg of solvent

Molarity

Moles of solute/liters of solution

Portion of brain that controls much of the endocrine system

Hypothalamus. Releases tropic hormones that regulate other tropic hormones. For example, it releases corticotropin releasing hormone, which causes secretion of ACTH, which causes increased secretion of cortisol.

Internal anal sphincter and external anal sphincter

INternal is smooth muscle, under autonomic control. External is skeletal muscle, under voluntary control.

Introns

INtervening sequences in DNA that code for noncoding RNA, which is eventually spliced out. Introns are often regulatory sequences, such as "enhancers".

Is it possible for independent assortment to not apply to certain genes? (independent assortment is mendelian law that states alleles of one gene are independent from alleles of another gene).

If the genes are right next to each other on a chromosome, they may be linked due to recombination of both genes occurring at the same time very frequently.

Synarthroses

Immovable joints, such as points in skull where bones are fused together.

Bilirubin

Important waste product, which is a breakdown product of heme.

What is the role of voltage-gated calcium channels in synaptic transmission?

In chemical synapses, when depolarization of the presynaptic membrane occurs, voltage gated calcium channels open. Calcium influx into presynaptic cell causes exocytosis of neurotransmitter stored in secretory vesicles. This binds to ligand gated ion channel receptor on postsynaptic membrane. Depolarization of postsynaptic cell may occur, often generating another action potential.

Where is proximal convoluted tubule located?

In cortex of kidney, along with bowman's capsule.

X chromosome inactivation

In female humans, one X chromosome is randomly inactivated in the blastocyst stage. Every cell that is produced from this inner cell mass is going to have the same X inactivation. However, certain cells and tissues in adults may have different X inactivation.

Where is there ribozyme activity in ribosomes? how does it work? (ribozyme activity is enzymatic activity of RNA).

In large subunit of both euk and prok ribosomes. The rRNA acts as an enzyme to contribute to peptide bond formation.

What happens to homologous chromosomes in mitosis? in meiosis?

In mitosis, they do not interact with each other at all. They simply line across the metaphase plate side by side. In meisosis, the homologous chromosomes pair up via synaptonemal complex and cross over genetic material before being split.

Where are actin and myosin located?

In myofibrils.

How does presence of glucose affect lac operon? (operon in bacteria)

Inhibits adenylyl cyclase, inhibiting production of cAMP. Presence of cAMP binds to CAP, and this complex binds to lac operon, allowing for transcription of Z, Y, and A genes. So glucose inhibits lac operon transcription.

penetration or eclipse (viruses)

Injection of viral genome into host cell. Called Eclipse because the capsid remains on the outer surface of the bacterium while the genome disappears into the cell. Follows the process of attachment (adsorption).

What is myelin? how does it work?

Insulating sheath around neurons. It works by not allowing ions to enter or exit where there is myelin, so it conducts action potentials at a greater rate. However, if the entire neuron were wrapped in myelin this would not work, as the ions would never be able to move across the membranes to create depolarization. That is why there are gaps between myelin sheaths (gaps are called nodes of Ranvier)

How does insulin affect glycolysis?

Insulin will convert fructose 6 phosphate to Fructose 2,6 bisphosphate by stimulating PFK-2. Presence of fructose 2,6 bisphosphate will stimulate PFK1 for glycolysis

Periplasmic space

Intermediate space in Gram-negative bacteria between the cell membrane and the outer lipopolysaccharide (sugars bound to lipids) layer. Often contains enzymes that degrade antibiotics.

Internal and external sphincter of bladder

Internal: made of smooth (involuntary) muscle contracts when bladder wall is stretched. External: Made of skeletal (voluntary) muscle, can be relaxed when person decides to.

Secretion (kidneys)

Involves addition of substances to filtrate of nephron, but NOT through typical method of filtration through bowman's capsule. Can increase rate at which substances are eliminated from the blood. Usually occurs via active transport.

Amoeboid movement

Involves changes in the cytoplasmic structure which cause cytoplasm and the rest of the cell to flow in one direction. Microfilaments are responsible for this.

Concentration and dilution (urine)

Involves selective reabsorption of water, where it is decided whether urine is concentrated or dilute.

Strong electrolyes

Ionic solutes that dissociate completely.

Weak electrolytes

Ionic solutes that remain ion-paired to some extent without dissociating completely.

What effect does irritant have on ventilation?

Irritant receptor triggers coughing and/or bronchoconstriction.

How is isocitrate dehydrogenase positively regulated? negatively regulated? (page 109)

Isocitrate dehydrogenase is an enzyme that drives the Kreb's cycle. positively regulated by ADP. Negatively regulated by ATP and NADH.

Where does absorption begin in GI tract?

It begins in the duodenum and continues throughout the small intestine.

How does presence of lactose affect lac operon? (operon in bacteria)

It binds lac repressor protein, allowing for greater transcription of Z, Y, and A genes of lac operon.

How can UV light cause photochemical damage to DNA?

It can cause adjacent pyrimidines to covalently bond, resulting in pyrimidine dimers. This may distort DNA structure, causing mutations to occur.

Do viruses contain DNA or RNA? Is it linear, or circular? Is it double stranded or single stranded?

It can contain DNA OR RNA (but not both), it can be linear OR circular (but not both), and it can be single stranded OR double stranded (but not both). A virus can only contain one type of nucleic acid in its genome (example: linear, single stranded DNA).

What effect does uncompetitive inhibition have on a reaction's Vmax? on its Km?

It causes a decrease in Vmax and a decrease in Km (decreases Km because it increases the apparent affinity of the substrate for the enzyme, and it cannot readily dissociate).

What affect does hypoventilation have on blood pH?

It causes decrease in blood pH (more acidic), as CO2 is not exhaled from the lungs as frequently. This is referred to as respiratory acidosis.

How does cholesterol affect membrane fluidity at increased temperature?

It causes decreased fluidity. Seems counterintuitive. Cholesterol sometimes referred to as membrane antifreeze.

What affect does hyperventilation have on blood pH?

It causes increase in pH (more alkaline), as acidic CO2 is exhaled from the lungs. referred to as respiratory alkalosis.

What happens to the freezing point when a solute is added? why?

It decreases. The presence of solute particles interferes with the efficient arrangement of solvent molecules into a solid lattice.

How does the exterior protein shell of a virus change to accomodate a larger genome?

It does not. It cannot expand.

How does soap remove grease?

It forms micelles that surround the grease, allowing for the hydrophobic components of the soap to interact with the grease in order to remove it.

What happens to boiling point of a solvent when a dissolved solute is involved? Why?

It increases, as it requires more energy for the solvent to break apart from its bonds with solute particles.

How is SA node able to automatically excite the heart?

It induces action potentials by depolarizing the cardiac cells. It does so by sodium leak channels, which brings the cell potential to the threshold for voltage gated calcium channels. SA node is unique from other muscle cells because the inward flow of Ca2+ is really what drives it, not the influx of NA+.

How does the presence of tryptophan affect the Trp operon (in bacteria)?

It inhibits it. Tryptophan binds to trp repressor protein (which is synthesized by trpR gene) - this complex then binds to operator of Trp operon, blocking RNA pol.

what would arg- denote in regard to a bacteria?

It is an auxotroph - it will only form a colony when plated onto a minimal medium while in the presence of arginine.

what are ribosomes composed of?

It is an enzyme composed of many proteins and rRNA.

Where is most of water that is secreted into the GI tract reabsorbed?

It is mostly reabsorbed in the small intestine, with some being reabsorbed in the large intestine.

What is the coding strand in transcription? What else is this strand called?

It is the DNA strand in which transcription does NOT occur. It is called this, as it matches the RNA strand being synthesized exactly (other than T/U being switched). Also called the sense strand.

Why is phosphofructokinase so important?

It is the enzyme that initiates the committed step of glycolysis - there is not turning back once F6P is converted to F1,6bP because the reaction is so favorable and F1,6bP is not used for any other reactions than glycolysis.

How does a catalyst work?

It lowers the activation of a reaction by stabilizing the transition state, making it more favorable. Enzymes are catalysts.

What does it mean to be bloodtype B+?

It means you carry the dominant allele for the B antigen and the rhesus factor antigen. Produces antibodies for A antigen, and a recipient will not respond well to type A donation.

Which direction does replication fork move?

It moves in both directions from the ORI (origin of replication) and contains leading and lagging strands. IMPORTANT TO MEMORIZE

How does vasa recta participate in countercurrent exchange?

It moves in opposite direction of descending loop of henle, stealing its water and dumping it back to the renal vein eventually.

What is the rule about the direction of DNA polymerization?

It occurs in 5' to 3' direction without exception. IMPORTANT TO MEMORIZE.

What does DNA pol require in order to get started?

It requires a template and an RNA primer.

How does lysosome break down structures? What happens after that?

It uses acid hydrolases. After break down, it releases the molecular building blocks into the cytoplasm for reuse.

What pattern of expression will a recessive allele on the X chromosome display in males?

It will always be expressed, as there is only one X chromosome in males (therefore it is the only allele present).

What does it mean for an ion channel to be gated?

It will be opened in response to a specific stimuli.

What would lac+ denote in regard to bacteria?

It would mean the bacteria is capable of surviving on a minimal medium with only lactose as a carbon source (no glucose).

what happens to a cell in a hypotonic solution?

It would swell, as the water would move from low tonicity (the extracellular environment) to high tonicity (inside the cell). Due to semipermeability, solutes to not move.

Saltatory conduction

Jumping of action potentials from node of Ranvier to node of Ranvier (between myelin sheaths). This speeds up conduction process, as ions cannot enter or exit myelinated parts of the axon.

Synapse

Junction between axon terminus of a neuron and the dendrites, soma, or axon of a second neuron. Two types: electrical and chemical.

Functions of colonic bacteria

Keeps dangerous bacteria from proliferating, supply us with vitamin K which is essential for blood clotting.

Reproductive isolation

Keeps existing species separate. Include prezygotic and postzygotic barriers.

What protein helps make skin waterproof?

Keratin, which coats epidermis when squamous cells die.

Do enzymes play a kinetic role, or a thermodynamic role?

Kinetic (affect rate). In other words they do not affect favorability of a reaction.

What configuration are all aminio acids found in animals?

L (remember aLanine)

Hepatic portal system

LIver receives oxygenated blood from hepatic arteries. Receives venouse blood draining the stomach and intestines through hepatic portal vein. Extracts nutrients from blood coming from stomach and intestines. Also evaluates this blood and makes changes to body's physiology based on it (such as adjusting blood glucose level through glycogenolysis or gluconeogenesis.

How does respiratory system protect from disease?

LUngs provide a large moise surface where chemicals and pathogens can do harm. Mucociliary escalator and alveolar macrophages provide protection.

Megakaryocytes

Large bone marrow cells that are fragmented to form platelets.

Gallstone

Large crystal formed from bile made with ingredients in incorrect proportions.

Heme

Large multi-ring structure that has a single iron atom bound at its center. Binds to O2. There are 4 heme subunits in hemoglobin.

ATP synthase

Large protein embedded in mitochondrial membrane that contains proton channel. Uses proton gradient to synthesize ATP from ADP.

Renal pelvis

Large space where urine collects

Thallus

Large visible fungal structure visible to the naked eye. Vegetative portion funcgions in obtaining nutrients, fruiting body functions in reproduction.

Prometaphase

Last event in prophase in which the nuclear membrane disintegrates into vesicles. Allows for metaphase to begin.

Rectum

Last portion of colon.

Signal transduction

Ligand binds to a receptor, triggering a response from the cell.

Components of antibodies

Light chain and heavy chains, connected by disulfide bonds. Constant region and variable (antigen binding) region.

The Hayflick limit

Limit to the number of times a cell can replicate until telomeres become too small for replication to proceed.

Parietal pleura

Lines the inside of the chest cavity

Visceral pleura

Lines the surface of the lungs.

The Trp operon

Linked genes in bacteria that code for tryptophan.

Peptide bond

Linking together of amino acids between carboxyl group of one and alpha amino group of the other. Releases water (dehydration synthesis).

Steroid

Lipids that contain tetracyclic ring, based on the structure of cholesterol.

Plasma

Liquid portion of blood. Makes up 55% of blood. Consists of electrolytes, buffers, sugars, blood proteins, lipoproteins, CO2, O2, and metabolic waste products dissolved in water.

ketogenesis

Liver generates ketone bodies to generate ATP, as body is in starvation state and cannot undergo glycolysis (this may be because glycogen storage is depleted or because glucose cannot be taken into cells

Peripheral chemoreceptors

Located in aorta and carotid arteries and monitor P(CO2), pH, and P(O2) in blood.

Baroreceptors

Located in aortic arch and carotid arteries, which monitor pressure.

Epiglottis

Located in larynx Seals trachea during swallowing to prevent the entry of food.

Vocal cords

Located in larynx. folds of tissue positioned to partially block flow of air and vibrate, producing sound.

Respiratory control center

Located in medulla of brain stem. Controls involuntary process of breathing rate and depth.

Potassium leak channels

Located in plasma membrane of cells, allowing some potassium (but no other ions) to flow out of a cell down its concentration gradient. This causes more negative charge of interior of cell, increasing the resting membrane potential. (There is no way for sodium to reenter a cell like this once it is pumped out).

Voltage gated sodium channels

Located in plasma membranes of axon of neuron. Open in response to a change in membrane potential (at a threshold potential at approx -50 mV), allowing sodium ions to flow down their gradient into the cell and depolarize that section of membrane.

Microtubule organizing center

Location in which microtubules emerge. Contains a pair of centrioles (which are composed of a ring of 9 microtubule triplets). Essential in mitosis and in organization of euk flagella/cilia. General term for any structure that organizes microtubules in cells

RER functions and number of membranes

Location of synthesis/modification of secretory, membrane bound, and organelle proteins. 1 membrane.

Hypha

Long filament of fungal cells joined end-to-end.

Axons

Long slender projection that extends from the cell body of a neuron, in which action potential travels. Typically there is one axon.

What are the two layers of smooth muscle lining the gut

Longitudinal layer, which runs along the gut lengthwise, and circular layer which encircles it.

Lower esophageal sphincter (AKA cardiac sphincter)

Lower end of esophagus, entrance to stomach. Prevents reflux from stomach going back into esophagus.

Synovial fluid

Lubricates movable joints. Kept within synovial capsule within joints.

Brush border

Lumenal surface of small intestine is called this due to brush like appearance of microvilli.

Main difference between lytic cycle and lysogenic cycle (viruses)

Lytic cycle causes destruction of host cells by viruses, while lysogenic cycle allows virus to be incorporated into the host genome without destroying it.

MHC II (Major histocompatability complex II)

MHC II exist on special cells only, known as antigen presenting cells (APCs). These include macrophages and B cells. The cell chops up the antigen and displays them using MHC II. T helpers bind to this, recruiting T killer cells and immature B cells to be activated to the new antigen.

Asexual spore formation (fungus)

MItosis occurs in fungi to generate many spores from one cell.

What is more important for mitosis? microtubule organizing center (MTOC) or centrioles?

MTOC. Cetrioles are not even necessary for mitosis (they are not even present in plants).

WBCs that move by amoeboid motility (crawling)

Macrophages and neutrophils They are able to roam freely throughout tissues and hunt foreign particles and pathogens.

Erythropoietin

Made in kidney Stimulates RBC production in the bone marrow

Endoskeleton

Made of bone in vertebrates

Articular cartilage

Made up of hyaline cartilage. Line the surfaces of two bones that contact each other. Lacks blood vessels. Arthritis leads to destruction of articular cartilage.

Buffers in blood What is their function? What is the principle blood buffer?

Maintain constant pH of 7.4 - principle blood buffer is bicarbonate (HCO3-)

Z lines

Make up ends of sarcomeres. Remember, Z is at the end.

Isoprene

Make up terpenes. Comprised of (C5H8)n

Basolateral surface of epithelial cells in GI tract

Make up the sides and bottom of the cells.

Fruiting body of thallus (thallus is body of a fungus)

Makes spores. Mushrooms are fruiting bodies.

Extracellular matrix

Makes up extracellular material of connective tissue, which consists of fibers such as collagen and elastin, and ground substance.

Tonsils

Masses of lymphatic tissue in the back of the throat that help catch pathogens which enter the body through respiration or ingestion. Appendix is similar, found near beginning of large intestine.

Endocytosis

Materials taken into a cell to form a vesicle. Vesicle is called an endosome. These must form because cytoplasm is not allowed to mix with extracellular evironment.

Osteocyte

Mature bone cell within lacunae of compact bone. Contact other osteocytes through gap junctions, allowing exchange of nutrients.

Inspiratory capacity

Maximal volume of air which can be inhaled after a resting expiration.

Vital capacity

Maximum amount of air that can be forced out of th elungs after first taking deepest possible breath.

Carrying capacity

Maximum population at the stationary phase of growth for an environment.

Vmax (enzyme kinetics)

Maximum velocity of reaction rate (mol/sec). Occurs when enzymes are saturated with substrate.

Cephalad

Meaining "towards the head" or superior in humans.

Caudad

Meaning "toward the tail" or inferior in humans.

Spirometry

Measurement of volume of air entering or exiting the lungs at various stages of ventilation.

Splicing

Mechanism that occurs to eliminate stretches of non coding RNA (introns).

What part of the kidney is extremely salty, and why? what effect does this have?

Medullary interstitium. Ascending loop of Henle actively transports ions to this region. Due to its saltiness, it sucks water from collecting duct whenever the collecting duct's membrane becomes permeable to water (when ADH is present).

Difference between population and species

Members of same species CAN mate with each other, members of same population DO.

phosphoglyceride

Membrane lipids are derived from these. AKA diacylglycerol phosphate, or DGP.

PLeura

Membranes surrounding lungs, between the lungs and the wall of the chest cavity.

Law of segregation

Mendelian law that states that the two alleles of an individual are separated and passed on to the next generation singly. What stage does this separation occur? A: meiosis I, when homologous chromosomes separate.

Mycelium

Meshwork of hyphae (long filaments of fungal cells joined end-to-end).

Germination (bacteria)

Metabolic reactivation of an endospore.

Peroxisomes functions and number of membranes

Metabolize lipids and toxins using H2O2 that is formed as byproduct of peroxisome enzymes. 1 membrane.

N-terminal amino acid in eukaryotes

Methionine

Sulfur containing amino acid that is nonpolar.

Methionine

Transformation (bacteria)

Method in which bacteria increase genetic diversity by internalizing external DNA into its own genome.

Homologous recombination

Method of DSB repair (double strand break). DSB is identified and trimmed at 5' ends by nucleases (to break phospodiester bonds) and helicase (to unwind the DNA), creating SSDNA. Many proteins bind and search for complementary region of sister chromatid. This is then used as a template for DNA repair to occur. Requires a "joint molecule" where the chromatids cross over. Uses DNA polymerase and ligase to build corrected strand.

Clonal selection

Method of memory cells selecting B cells with specific antigen binding.

Nonhomologous end joining

Method of post replication DSB DNA repair that occurs in cells that are not actively growing or cycling through cell cycle. More common in eukaryotes. DNA ligase simply reconnects the broken chromosomes. This can cause base pairs being lost or chromosomes being connected in an abnormal way, and this is not the preferred method of DSB repair.

mRNA surveillance

Method of transcriptional control in euks. Degrades any mRNA molecules that are not high quality. These include defective transcripts (premature or missing stop codons for example) and stalled codons (ribosome is stalled in translation).

RNA interference (RNAi)

Method of transcriptional control in euks. silences gene expression after a transcript has been made. Mediated by miRNA and siRNA. siRNA typically bonds to complementary sequences on mRNAs, and this dsRNA is degraded.

RNA translocation

Method of transcriptional regulation by euks. Translation of mRNA transcripts will not occur until they are transported to the proper location to do so.

Exons

EXpressed region of RNA that is not spliced out. Ends up coding for protein.

Make up of hydrophilic hormones

Either peptides or amino acid derivatives. Differ from hydrophobic hormones, which are steroid hormones that bind to receptors in cellular interior

Resting membrane potential

Electric potential across the plasma membrane of approximately -70 mV, with interior of cell being negatively charged relative to exterior. After Na+/K+ ATPase pumps 2 K+ into cell and 3 Na+ out of cell, the interior of cell becomes somewhat negative and the extracellular environment becomes somewhat positive. Potassium also leaks out of cell through potassium leak channels, increasing the membrane potential.

What dictates equilibrium potential of an ion? What is the equation used to calculate this?

Electrochemical gradient (concentration of ions on either side of a membrane and electrical contribution of ions on each side of a membrane). Calculated by Nernst equation: E(ion) = (RT/zF)ln([X]outside/[X]inside) z is valence of an ion.

Action potentials

Electrochemical impulses that transmit and process information from one part of the body to the other. Localized area of depolarization of the plasma membrane that travels along axon. signal is transformed into a chemical signal by releasing a neurotransmitter at the synaptic cleft (synaptic transmission).

Role of bile

Emulsifies large fat particles in the duodenum, creating micelles. Micelles can then be broken down by pancreatic lipases.

Islets of Langerhans

Endocrine cells of pancreas, which are supplied with capillaries.

What composes the inner lining of all blood vessels?

Endothelial cells

Activation energy

Energy required to produce a transition state intermediate in a reaction (TS is an unstable, transient intermediate that must be reached before reactions can occur)

acid hydrolases - why are they called this?

Enzymes responsible for degradation in lysosomes. Called this because they will only degrade structures in an acidic environment - the lysosome is at a pH around 5, so this works. If lysosome ruptures, acid hydrolases will not be active because they will be in cytoplasm with a pH around 7.4 (this is a protective mechanism). Use hydrolysis.

Layers of skin

Epidermis, dermis, and subcutaneous tissue (AKA hypodermis).

Hominidae defining characteristics

Erect posture, intelligence, long period of parental care, cooperation

two tubes with openings in the pharynx

Esophagus and trachea

Domain, kingdom, phylum, subphylum, class, order, family, genus, and species of humans

Eukarya, animalia, cordata, vertebrata, mammalia, primates, hominidae, homo, sapiens.

How is asexual reproduction different in euks than proks?

Euks undergo mitosis, proks do not

Liver

Excretes many wastes by chemically modifying them and releasing them into bile. Deals wth hydrophobic or large waste products, which cannot be filtered out by the kidney.

Pancreatic acinar cells

Exocrine cells of the pancreas, which are organized into acini that drain into ducts

What is the difference between exocrine and endocrine secretions (in GI tract)

Exocrine glands secrete products into ducts that drain into GI lumen. Endocrine glands are ductless and secrete hormones that are picked up by capillaries and thus enter the bloodstream.

What is hyperopia? how is it corrected?

Farsightedness. Occurs when not enough curvature in lens or cornea causes light not to be bent sufficiently, focusing behind the retina. Can be corrected with a convex, converging lens which would cause light rays to converge slightly before reaching the cornea.

Chylomicrons

Fats absorbed from intestine are packaged into chylomicrons, which is a type of lipoprotein. They enter tiny lymphatic vessels in intestinal wall called lacteals, which empty into larger lymphatics, eventuallly drain into large vein near the neck.

Parasites

Feed off living organisms, doing harm to the host.

Why is glycolysis able to continue without the presence of oxygen, when a lack of oxygen implies a lack of NAD+ (because NAD+ is created in ETC, which requires oxygen), which is required for glycolysis to occur?

Fermentation, which involves transport of H from NADH to pyruvate in humans, forms lactate and NAD+.

Elastin

Fibrous extracellular protein, which gives tissue the ability to stretch and regain its shape. Secreted by fibroblasts.

Clathrin

Fibrous protein inside the cell that associates with cytoplasmic portions of the cell-surface receptors. Involved in receptor-mediated endocytosis.

Directional selection

Form of natural selection in which one extreme group of a population are removed, causing directionality to occur. For example - small giraffes are eliminated, pushing the selection process toward taller giraffes.

Stabilizing selection

Form of natural selection in which the extremes of a population are eliminated, leaving the more average groups of the population intact.

Kin selection

Form of natural selection. An animal may sacrifice itself to save its kin - for example a female lion may sacrifice herself to save her sister's children.

Hybrid breakdown

Form of postzygotic barrier in which individuals can produce offspring, but their offspring are unable to do so due to some biological defect. This prevents species from continuing.

Hybrid inviability

Form of postzygotic barrier in which individuals cannot produce a viable offspring. The offspring will not develop or mature normally, causing it to often die in embryonic stage.

Hybrid sterility

Form of postzygotic barrier in which individuals produce a sterile offspring. This does not allow for the offspring to pass on its genes, and the two species remain separate (horse and donkey).

Prezygotic barriers

Form of reproductive isolation that keeps individuals from mating from each other. May be due to ecological, temporal, behavioral, mechanical, of gametic reasons.

Postzygotic barrier

Form of reproductive isolation that prevents reproductive fitness of an offspring from occurring. Includes hybrid inviability or hybrid sterility.

Cladogenesis

Form of speciation in which branching occurs - species diverges into two species. Different from anagenesis, which is slow morphing of one species to another over time.

Microspheres

Formed spontaneously by proteinoids in water (proteinoids are proteins that are polymerized with the use of metal ions as catalysts. Do not use enzymes).

Bivalent (or tetrad)

Forms in prophase I of meiosis when two homologous chromosomes attached together during synapsis. Allows recombination to occur.

Chemical synapses. What happens to action potential? What does depolarization of presynaptic cell cause?

Found at the ends of axons where they meet their target cell. Action potential is converted to chemical signal. voltage gated calcium channels open, causing calcium influx into presynaptic cell and exocytosis of a neurotransmitter stored in secretory vesicles. This neurotransmitter then binds to ligand gated ion channel receptor on postsynaptic membrane. Depolarization of postsynaptic cell may occur, often generating another action potential.

Yellow marrow

Found in shafts of long bones, filled with fat and is inactive.

Red marrow

Found in spongy bone within flat bones, is the site of hematopoiesis. Its activity increases in response to erythropoietin, a hormone produced in the kidney.

Elastic cartilage

Found in structures (such as the outer ear and epiglottis) that require support and more flexibility than hyaline cartilage can provide; it contains elastin.

Carolus Linnaeus

Founded taxonomy.

Three roles of mouth in digestion of food

Fragmentation, lubrication, some enzymatic digestion

Electrolytes

Free ions in solution that enable the solution to conduct electricity.

Diarthroses.

Freely movable joints, such as hip, elbows, etc. Supported by ligaments.

Where does defecation occur>

From the rectum, through the anus.

Chromatin

Fully packed form of DNA, made of clusters of nucleosomes (which are made up of clusters of histones, which are wrapped by DNA).

Terpenoids

Functionalized-terpenes that incorporate other elements (example is Vitamin A (C20H30O))

Which plays a role in reproduction, a bacterial endospore or a fungal spore? why?

Fungal spore, because each fungus may produce a great number of spores, while a bacterium becomes a spore to "wait out the bad times" until becoming active again.

Saprophytes

Fungi that feed off dead animals

which base pairs have 3 H bonds between them? which have 2?

G-C have 3, A-T have 2

Gap phases

G1 and G2 - both occur between S phase and M phase. (order is M, G1, S, G2). Gap phases plus S phase form part of cell cycle between divisions, known as interphase.

What high energy phosphate bond is involved in the Kreb's cycle?

GTP

Nodes of Ranvier

Gaps between myelin sheath of a neuron, allowing depolarization to occur across a membrane. Concentrated with sodium and potassium channels.

What enzyme converts polypeptide into dipeptides and tripeptides?

Gastric acidity an dpepsin, pancreatic proteases (trypsin, chymotrypsin)

Exocrine glands within the gut

Gastric glands of stomach (which secrete acid and pepsinogen) and mucus secreting cells (called goblet cells).

Oncogene

Gene that can cause cancer when mutated or expressed at high levels.

Prophase

Genome becomes visible upon condensing into tightly packed chromosomes instead of diffuse chromatin. Nucleolus disappears, the spindle and kinetochore fibers appear, the centriole pairs move to opposite ends of the cell. Two MTOCs called asters form.

photoheterotrophs

Get energy from the sun, like plants, but require an organic molecule made by another organisms as their carbon source.

Phototrophs

Get their energy from light.

Chemotrophs

Get there energy from chemicals

Troponin

Globular protein bound to the tropomyosin on actin filaments that can bind Ca2+ needed for contraction to occur. Once Ca2+ is bound, tropomyosin is moved away, stopping obstruction of myosin binding sites.

What reactants go into glycolysis?

Glucose, 2 ATP, 2 NAD+, 2 Pi, and 2 ADP (2 more ADP are involved, but they are just the converted form of the 2 ATP).

Glyogenolysis

Glycogen breakdown. Occurs in response to hormone glucagon when blood sugars are low.

two enzymes involved with glycogen that are reciprocally controlled.

Glycogen synthase (the principle enzyme responsible for glycogen generation from glucose-1-phosphate) and glycogen phosphorylase (which serves to catabolize glycogen)

Pentose phosphate pathway

Glycolysis "shunt". Converts G6P into ribose 5 phosphate, which can be used to synthesize nucleotides. Generates NADPH and additional sugar precursors.

INtrinsic factor

Glycoprotein secreted by parietal cells of stomach, which complexes to vitamin B12 to allow for absorption in the ileum.

Examples of post translational modification in rough ER?

Glycosylation (addition of saccharides to proteins) or disulfide bond formation.

gray matter and white matter

Gray matter is composed of somas (bodies) and dendrites of neurons. White matter is composed of myelinated axons of neurons.

Bile

Green fluid containing bile acids, which are made from cholesterol in the liver and normally absorbed and recycled. Stored in the gallbladder until needed. Acts as vehicle for excretion of waste products by liver, and is essential for digestion of fats.

Complement system

Group of about 20 blood proteins that can nonspecifically bind to surface of foreign cells, leading to their destruction

taste buds are (blank) receptors

Gustatory. Gustatory receptors are a type of chemoreceptor.

Mammalia defining characteristics

Hair, 4 limbs, 4 chambered hear, diaphragm for respiration, mammary glands that produce mild, internal fertilization, some have placental development.

hemizygosity - define and give example

Haploid expression in a diploid organism (one allele of a gene may be lost to deletion or recombination. can lead to increased effect of a mutation on these chromosomes) An example is mitochondrial DNA - it is only passed on from the mother, so there is only one allele expressed - mothers will pass mitochondrial disease to all children. Another example is X chromosome DNA in men.

What is true of all somatic sensory neurons? What portion of CNS do they access? Where does it first synapse? Are they inside or outside meninges?

Have a long dendrite extending from a sensory receptor toward the soma, which is located just outside the CNS in a dorsal root ganglion. Axon extends from somatic sensory neuron's soma into the spinal cord. It first synapses in the CNS - sometimes travels all the way up to the brain stem before synapsing! They are outside meninges.

Catalytic receptors - definition and example?

Have enzymatic active site on cytoplasmic side of membrane, which is initiated by ligand binding at extracellular cell surface. Example - protein kinases

exothermic reactions

Have negative delta H, release heat.

endothermic reactions

Have positive delta H, require input of heat.

Integral membrane proteins

Have sections of hydrophobic AA sequences called transmembrane domains. Embedded in the plasma membrane, held there by hydrophobic interactions.

Gram negative bacteria

Haven thinner layer of peptidoglycan in the cell wall that gram positive bacteria, but also contain an additional outer layer containing lipopolysaccharide. Often show increased resistance to antibiotics and weaker gram staining due to extra protection.

Thermophiles

Heat loving bacteria, which can survive at temperatures up to 100°C in boiling hot springs or near geothermal vents in the ocean floor.

Effects of cortisol

Helps body deal with stress. Mobilizes glycogen and fat stores to provide energy during stress and also increases the consumption of proteins for energy.

How does glucose level affect lac operon in bacteria?

High glucose inactivates adenylyl cylase (an enzyme used to turn ATP into cAMP). With low cAMP, CAP is not able to activate lac operon. In low glucose, adenylyl cyclase is activated and CAP forms complex with cAMP that binds to promoter of lac operon. This helps activate RNA polymerase at the lac operon.

Where int he body does hemoglobin have a higher affinity for oxygen?

Higher affinity in the lungs, lower affinity in the tissues This allows it to pick up oxygen in the lungs and drop it off in the tissues.

only AA that can act as an acid or a base at physiological pH, making it prevalent in protein active sites.

Histidine

Desmosomes - define and give example

Hold cells together, but do not form a seal. Anchored to plasma membrane via plaque formed by the protein keratin. Are concise points, are not bands around the cell. Example - human skin held together tightly, but do not form a complete seal.

Central (or Haversian) canal

Hole in the center of the osteon, which contains blood, lymph vessels, and nerves.

Peptide YY

Hormone produced by jejunum when colon is full, in order to reduce appetite.

Ghrelin

Hormone produced when stomach is empty to stimulate appetite.

Secretin

Hormone released by duodenum in response to acid in duodenum. Causes pancreas to release large amounts of high pH aqueous buffer (HCO3-)

Cholecystokinin

Hormone secreted by epithelial cells in the wall of the duodenum, which stimulates bile relesase, decreases gastric motility. Stimulates secretion of pancreatic enzymes.

Tropic hormones

Hormones that regulate hormones

Endochondral ossification

Hyaline cartilage is produced and then replaced by bone. Stimulated by growth hormone

Three types of caritlage

Hyaline, elastic, and fibrous

Pancreatic amylase

Hydrolizes polysaccharides to disaccharides

proteolysis, or proteolytic cleavage

Hydrolysis of a protein by another protein

Salivary amylase (ptyalin)

Hydrolyzes starch, breaking it into fragments. Yields disaccharides.

Pancreatic lipase

Hydrolyzes triglycerides at the surface of a micelle.

Steroid hormones - where do they bind receptors? Where do they bind to receptors and what are there effects? How long do the effects last? How do they travel through the bloodstream?

Hydrophobic molecules synthesized in smooth ER. Diffuse through plasma membrane into cytoplasm, finding receptor. Receptor steroid complex then enters nucleus, where it acts as a sequence specific regulator of transcription. Effects are exerted slowly, lasting for days or weeks. Travel through the blood stream by attaching to albumin proteins via hydrophobic interactions.

Septate hyphae

Hyphae (long filament of fungal cells joined end-to-end) are separated by walls called septae.

Aseptate (AKA coenocytic) hyphae

Hyphae (long filament of fungal cells joined end-to-end) joined together in long tube, with cytoplasmic contents and nuclei are shared among the many cells making up the hypha.

Haustoria

Hyphae (long filament of fungal cells joined end-to-end) specialised to digest and absorb nutrients in a parasitic fashion.

Km (enzyme kinetics)

Michaelis constant. Substrate concentration at which reaction rate is half of Vmax.

Aster

Microtubules that radiate out from the centrioles during mitosis. Called aster due to start shape.

Can a T helper cell become activated after encountering a foreign particle floating in blood? why or why not?

No. It only activates with antigen presented on MHC II. (in other words, antigen presenting cell must phagocytize and chop up antigen first and present it on cell surface.

Will a transmembrane protein inserted into the apical surface of an intestinal epithelial cell diffuse in the plane of the plasma membrane to reach the basolateral surface of the cell?

No. it is free to move around on the apical surface, but the tight junctions prevent it from diffusing to the basolateral surface.

Bone marrow

Non bony material found in shafts of spongy bones. Site of synthesis of all cells of the blood from a common progenitor.

Unbalanced translocation

Nonhomologous chromosomes undergo recombination, and genetic information is lost.

Balanced translocation

Nonhomologous chromosomes undergo recomination, but no genetic information is lost.

What are endotoxins? where are they found?

Normal components of the outer membrane of Gram-negative bacteria that are not inherently poisonous but cause a dramatic reaction in our immune systems. When gram negative bacteria die within our body, endotoxins are released and the immune system cells release chemicals that can cause someone to go into septic shock.

Protooncogenes

Normal versions of the genes that allow for regular growth patterns, but can be converted to oncogenes under the right circumstances (mutation or exposure to mutagen).

Pathway of conduction zone

Nose -> nasal cavity -> pharynx -> larynx-> trachea-> bronchi-> terminal bronchioles

pathway of inhaled air

Nose -> nasal cavity -> pharynx -> larynx-> trachea-> bronchi-> terminal bronchioles -> respiratory bronchioles -> alveolar ducts -> alveoli.

SER functions and number of membranes

Not actively involved in protein processing. Detoxification and glycogen breakdown in liver; steroid synthesis in gonads. 1 membrane

peripheral membrane proteins

Not embedded in a membrane, but are stuck to integral membrane proteins, held together by hydrogen bonding and electrostatic interactions.

Telophase

Nuclear membrane forms around the bunches of chromosomes at each end of the cell. Chromosomes decondense, nucleolus becomes visible in each daughter nucleus.

The default for repressible enzymes is (blank) and the default for inducible enzymes is (blank)

ON, OFF

Famous Christian Anfinsen experiment

Observed protein structure of ribonuclease (which has four disulfide bonds) when 1) exposing to reducing environment, 2) denature by adding urea, 3) remove reducing agent, allowing disulfide bridges to form, 4) removing the denaturing agent. This caused abnormal structure to result. Also performed same experiment in 1,2,4,3 order, which showed normal folding structure.

Liposomes

Occur when lipids are added to microspheres (microspheres are formed spontaneously by interaction of proteinoids with water). The lipids form a layer on the surface of the proteins).

Meiosis II

Occurs after meiosis I, in which homologous chromosomes were crossed over and split into separate cells. This process is nearly identical to mitosis, but has haploid number of chromosomes as opposed to diploid.

phosphodiester bond

Occurs in DNA between 3' OH group of one deoxyribose and the 5' phosphate group of the other deoxyribose.

Productive cycle (viruses)

Occurs in animal viruses. Enveloped viruses exit the host cell by budding through the host's cell membrane, becoming coated with this membrane in the process. Does not destroy the cell.

Lag phase

Occurs in bacteria prior to achieving exponential growth - bacterial cells do not divide yet even if cell conditions are ideal. The cells are busy producing components necessary for cell division to occur, such as dNTPs.

Hemolytic disease of the newborn (erythroblastosis fetalis)

Occurs when Rh- mother (negative for rhesus factor in blood) becomes exposed to Rh+ baby. This sensitizes the mother to Rh+, creating antibodies for future Rh+ exposure. If she were to have another child who was Rh+, she could kill the baby.

Inversion mutation

Occurs when a chunk of a chromosome breaks off, spins around, and reconnects in reverse orientation.

Termination (translation step in proks)

Occurs when a stop codon appears in the A site. This causes a release factor to enter the A site, which causes a peptidyl transferase to hydrolyze the bond between the tRNA and the polypeptide. Proks have 3 release factors. Ribosome then splits into subunits and releases polypeptide and mRNA.

Reciprocal inhibition

Occurs when an action potential causes an excitatory response and an inhibitory response at the same time. Example is concurrent relaxation of the hamstring and contraction of the quads in response to stimulation of patellar tendon by a reflex hammer.

Depolarization

Occurs when an action potential disturbs the resting membrane potential of -70 mV, making it less negative (and even positive). Caused by movement of ions into and out of neuron through ion channels during action potential. Repolarization then returns it to normal.

Nondisjunction

Occurs when chromosomes fail to separate correctly in meiosis I. This could cause a gamete to have 2 copies of one chromosome, or 0.

How is sickle cell anemia a beneficial mutation

Occurs when deoxygenated hemoglobin dimerizes, forming long chains and resulting in a sickle shape. These cells are often destroyed, leading to anemia. However, this condition is beneficial in resisting malaria, so it is more common in places where malaria is more common.

Gluconeogenesis

Occurs when dietary glucose is unavailable and glycogen/glucose is depleted. primarily occurs in liver. In simple terms, this is glycolysis in reverse.

Frequency summation

Occurs when more than one contraction occurs before Ca2+ ions are allowed to sequester on the sarcoplasmic reticulum. This increases the force of contraction.

Loss of heterzygosity

Occurs when one allele of a certain gene is lost, either through deletion or recombination event. This will cause that respective gene product to be lost, causing the remaining gene to be passed on.

Genomic imprinting

Occurs when only one allele of a gene is expressed. Genes can be unimprinted in subsequent generations, proving that it is an epigenetic process.

Threshold potential

Occurs when the potential of a cell reaches -50 mV. Once this threshold is reached, the voltage-gated sodium channels are opened and the Na+ moves down its concentration gradient into the cell, causing much greater depolarization (until it reaches about +35 mV membrane potential, when it inactivates). Channels are closed before threshold is reached.

Synaptic transmission

Ocurs when an action potential reaches the end of an axon at a synapse, releasing a neurotransmitter.

Double stranded DNA viruses

Often encode enzymes required for dNTP synthesis and DNA replication (although it doesn't technically need to). This allows it to undergo replication without having to wait for the host cell to initiate this.

Negative feedback, or feedback inhibitions (in reference to enzymes)

Often, presence of end product will inhibit enzyme activity earlier in a pathway.

How does depolarization continue along an axon?

Once the threshold is reached at a section of the axon, voltage gated sodium channels open and Na+ enters the cell at that point. Some of the Na+ then moves along the axon, depolarizing the adjacent portion of the neuron until it reaches its threshold point. This then causes voltage gated sodium channels to open at this portion of the cell as well. This continually occurs down the axon.

Reaction coupling

One favorable reaction is used to generate a thermodynamically unfavorable reaction.

Budding (fungus)

One form of asexual reproduction in fungus. A new smaller hypha (long filament of fungal cells joined end-to-end) or single cell grows outward from an existing one.

Fragmentation (fungus)

One form of asexual reproduction in fungus. Mycelium can be broken down into small pieces, each of which develops itself into a separate mycelium (meshwork of hyphae)

Spatial summation

One form of summation in which all synapses on post synaptic membrane are summed at a given moment in time. Differs from temporal summation, in which presynaptic neuron fires action potentials so rapidly that EPSPs or IPSPs pile up on top of each other.

Temporal summation

One form of summation in which presynaptic neuron fires action potentials so rapidly that EPSPs or IPSPs pile up on top of each other. Differ from spatial summation, in which all synapses on post synaptic membrane are summed at a given moment in time.

Major histocompatability complex (MHC)

One important group of cell surface proteins that are presented on the surface of cells. MHCs are constantly being monitored by T cells. MHC I proteins are found on the surface of every nucleated cell in the body. Their role is to randomly pick up peptides from inside the cell and display them on the cell surface, exposing any possible infection within the cell to T cells that are monitoring it. Killer T cells are recruited to destroy it. MHC II exist on special cells only, known as antigen presenting cells (APCs). These include macrophages and B cells. The cell chops up the antigen and displays them using MHC II. T helpers bind to this, recruiting T killer cells and immature B cells to be activated to the new antigen.

Hydroxyapatite

One of main ingredients in bone. Solid material consisting of calcium phosphate crystals. Form around collagen framework, giving bone is characteristic strength and flexibility.

Archaea

One of the domains of life. Prokaryotic. Can live in the world's most extreme environments, although they can also be found in less extreme environments. Cell wall lacks peptidoglycan. Share traits with eukaryotes, including presence of introns and the use of many similar mRNA sequences. Reproduce by fission or budding.

Lymphatic system

One way flow system which begins with tiny lymphatic capillaries in all the tissues of the body that merge to form larger lymphatic vessels, which merge to form lymphatic ducts. Acts like a suction pump to retrieve water, proteins, and white blood cells from the tissues.

If a molecule goes through a transition state with a negative charge, what amino acids might be expected on the active site of the corresponding enzyme?

One with a positive charge (his, arg, or lys) because this would stabilize the transition state (stabilizing the TS is the main function of enzymes, lowering the activation energy to get there!!!! Be careful though, enzymes do not ACT ON the TS.)

monosaccharide

Only contain a single carbohydrate molecule. AKA a simple sugar.

Flagella (bacteria)

Only exist in some bacteria, improves bacterial motility. Only means of bacterial locomotion.

heterogenous nuclear RNA (hnRNA)

Only found in eukaryotes. precursor to mRNA - has not undergone addition of cap and tail, and splicing yet, which is required for it to become mRNA.

Cells that undergo meiosis in females

Oogonia

Ligand gated ion channels - definition and example?

Open an ion channel in plasma membrane upon binding a particular neurotransmitter. sodium channel on surface of muscle cell at neuromuscular junction. Opens Na+ channel when bound to acetylcholine.

Sphincter of Oddi

Orefice that empties both the bile duct and pancreatic duct into the duodenum.

Endosymbiotic theory

Organelles such as mitochondria and chloroplasts were once an independent bacterial species, and they were engulfed by primitive euk cells. Inner membrane likely represents the bacteria's plasma membrane, outer membrane likely represents membrane of vesicle that engulfed it. Also, mitochondria can fuse together and produce polycistronic transcripts, displaying evolutionary relationship to proks.

Chemoheterotrophs

Organism that gets its energy and carbon source from chemicals (like glucose) produced by other organisms

Mutualists

Organism that lives in a symbiotic relationship where both organisms benefit.

Acini

Organized sacs of specialized epithelial cells that are present on exocrine glands. They secrete products which pass into ducts and into the GI lumen.

sapiens defining characteristics

Originated in Africa 200,000 years ago; highly developed brain capable of abstract reasoning, language, introspection, problem solving, self-awareness and rationality; unique in abilities to communicate and share ideas, ability to organize, advance and complex social structures.

Oncotic pressure

Osmotic pressure provided by plasma proteins (such as albumin) Therefore increased albumin in capillaries will lead to decrease in water flowing out of the capillaries. Albumin is more effective than salt at maintaining high osmolarity in the blood because it is too big to flow out of intercellular clefts of capillary (unlike NaCl).

Protoplast

Osmotically fragile structure of a bacterial cell that results from destruction of peptidoglycan cell wall (either by antibiotic, lysozyme from lytic cell of phages, etc.)

Oxidative phosphorylation

Oxidation of high energy electron carriers NADH and FADH2 coupled to phosphorylation of ADP to make ATP.

Does oxygen dissolve in blood? Does carbon dioxide?

Oxygen does not because it is too hydrophobic. Carbon dioxide can dissolve in blood (about 7% of CO2 transported in blood is transported in this way).

High energy phosphate bond in pyrophosphate.

P-O-P

What components of cellular respiration require TPP (thiamine pyrophosphate) prosthetic group?

PDC (pyruvate dehydrogenase complex) and alpha-ketoglutarate dehydrogenase complex of the Kreb's cycle.

How is PFK positively regulated? negatively regulated? (page 109)

PFK is an enzyme that drives glycolysis. It is positively regulated by AMP and F-2,6-BP. Negatively regulated by ATP.

Key components of lac operon:

POZYA: 1) P region is promoter of transcription of Z, Y, and A genes. 2) O region is operator site to which Lac repressor binds 3) Z gene: codes for enzyme beta-glactosidase, which cleaves lactose into glucose and galactose 4) Y gene: codes for permease, a protein which transports lactose into the cell 5) A gene: codes for transacetylase, transfering an acetyl group from Acetyl-CoA to beta-galactosides (this function not required for lactose catabolism)

Hormones that maintain proper blood levels of calcium and phosphate

PTH (parathyroid hormone), calcitriol, and calcitonin. PTH and calcitriol stimulate osteoclast activity, increasing calcium concentration in blood and calcium reabsorption by kidneys and intestines. Calcitonin inhibits osteoclast activity, decreasing calcium conc in blood.

redox pair

Pair of molecules that participate in oxidation-reduction reaction. When an atom is reduced, another atom MUST be oxidized.

What two ducts empty into duodenum?

Pancreatic duct (delivers exocrine secretions of pancreas such as digestive enzymes and bicarbonate) and common bile duct (which delivers bile from gallbladder).

The intrinsic firing rate of the SA node is about 120 beats/min. Why is the average resting heart rate around 60-80?

Parasympathetic nervous system continually inhibits depolarization of SA node. In particular, vagus nerve contains preganglionic axons which synapse in ganglia near the SA node. The postganglionic neurons innervate the SA node, releasing ACh, which inhibits depolarization by binding to the receptors on the cells of the SA node. NOTE that ACh is typically stimulatory, but it is sometimes inhibitory such as in this case. It really depends on the receptor.

What cells secrete HCl in stomach?

Parietal cells, located in gastric mucosa

Juxtaglomerular cells (JG)

Part of JGA. Located in afferent arteriole. baroreceptors that secrete renin in response to low systemic blood pressure (which raises BP). JG cells are also stimulated by chemoreceptors in DCT called macula densa when the filtrate osmolarity decreases (indicating poor filtration rate and low BP).

Sheath (virus)

Part of capsid that contracts using the energy of stored ATP, injecting the genome into the host (this occurs in bacteriophages, but not in animal viruses due to the bacterial cell wall)

AV bundle (bundle of His)

Part of conduction pathway in the heart following the AV node. Separates into left bundle branch and right bundle branch, and then into Purkinje fibers.

Purkinje fibers

Part of conduction pathway in the heart, branching off left bundle branch and right bundle branch. Allows impulse to spread rapidly and evenly over both ventricles.

Microfilaments - what are they and what are they composed of?

Part of cytoskeleton. Rods formed in cytoplasm from polymerization of the globular protein actin. Responsible for gross movements of entire cell, including pinching cell into two cells for cell division and amoeboid movement (changes in cytoplasmic structure which cause cytoplasm and the rest of the cell to flow in one direction).

Intermediate filaments

Part of cytoskeleton. Thickness is between microfilaments and microtubules. Provide strong cell structure and resist mechanical stress. Made up of several polypeptides.

Conduction zone

Part of respiratory system that participate only in ventilation, not respiration.

Coacervate

Particle that includes polypeptides, nucelic acids, and polysaccharides. Coacervates made with preexisting enzymes are capable of catalyzing reactions.

Respiratory zone

Parts of respiratory system that participate in actual gas exchange (respiration).

Trachea

Passageway that must remain open to permit air flow. Closed off by epiglottis during swallowing. Rings of cartilage prevent its collapse.

Alveolar macrophages

Patrol alveoli, engulfing foreign particles so that gas exchange can occur at simple squamous epithelium.

Two common types of covalent bonds between AAs in proteins.

Peptide bonds and disulfide bridges between cysteine R groups

Regulation of release for peptide vs steroid hormones?

Peptide hormones are stored in vesicles until a signal for secretion is received. Steroids are synthesized only when needed and then used immediately, not stored.

Transport of peptide vs steroid hormones?

Peptide hormones are transported freely and steroids are bound to protein carriers

What is a main difference between the way peptide hormones and steroid hormones bind to receptors?

Peptide hormones bind to receptors on the outside of cells while steroid hormones bind to receptors within cells (because they are hydrophobic, and are able to pass through membranes independently).

Mechanism of effect of peptides vs steroid hormones

Peptide hormones bind to receptors that generate second messengers which result in modification of enzyme activity. Steroids bind to receptors that alter gene expression by regulating DNA transcription.

Comparison of the timing of effect of peptide vs steroid hormones

Peptides - rapid shortlived. Steroids - slow, long-lasting

Carrier proteins

Perform facilitated diffusion by binding the molecule to be transported across a membrane, causing a conformational change in the protein that allows for the molecule to be transported.

Testcross

Performed when one individual is crossed with another individual that has homozygous recessive genotype in order to determine the genotype of the first individual.

relative refractory period

Period between action potentials in which neuron can be induced to transmit an action potential, but higher depolarization than usual is required because membrane is hyperpolarized (the brief period at which membrane potential is more negative than membrane resting potential, and is at -90 mV).

Absolute refractory period

Period between action potentials where a neuron will not fire another action potential no matter how strong a membrane depolarization is induced. Voltage gated sodium channels are inactivated during this time.

Refractory period

Period in which neuron is nonresponsive to membrane depolarization and unable to transmit another action potential for a short period of time. Consists of absolute refractory period (where a neuron will not fire another action potential no matter how strong a membrane depolarization is induced) and relative refractory period (in which neuron can be induced to transmit an action potential, but higher depolarization than usual is required because membrane is hyperpolarized).

What effect does decreased pH in blood have on ventilation?

Peripheral chemoreceptors and medullary respiratory center detect decrease in pH, and increase respiratory rate.

What effect does increased CO2 in blood have on ventilation?

Peripheral chemoreceptors and medullary respiratory center detect decrease in pH, and increase respiratory rate.

What effect does decreased oxygen in blood have on ventilation?

Peripheral chemoreceptors detect decrease in pH, and increase respiratory rate. Medullary respiratory center is not involved in this.

Phases of membrane potential in cardiac muscle cell

Phase 0 - depolarization. Upstroke of action potential due to fast Na+ channels opening and Na+ influx. Phase 1 - initial repolarization. Na+ channels inactivate, K+ channels open, K+ efflux Phase 2 - plateau. Ca2+ channels open, Ca2+ influx, K+channels open, K+ efflux. Ca2+ and K+ ions balance each other out, causing plateau. Phase 3 - Repolarization. Ca2+ channels close, K+ channels still open, K+ efflux. Phase 4 - resting membrane potential. Inward and outward current are equal. K+ channels close.

Phases of action potential of SA node.

Phase 4 - slow inward Na+ current through leak channels Phase 0 - inward Ca2+ current through voltage gated channels. Phase 3 - outward K+ current through voltage-gated channels.

Metaphase I. Difference between metaphase in meiosis?

Phase in meiosis following prophase I. Alignment of tetrads along metaphase plate. Difference is that this is the alignment of tetrads, as opposed to alignment of sister chromatids.

Telophase I

Phase of meiosis in which cell divides, forming haploid cells from diploid cells. Each cell contains 1 of each homologous chromosome, which have undergone recombination already.

Anaphase I

Phase of meiosis that occurs after metaphase I. Homologous chromosomes separate and sister chromatids remain together.

Incomplete dominance

Phenotype of a heterozygote shows blended mix of both alleles (i.e. red and white alleles may cause pink phenotypic expression in flowers). Both alleles are denoted with capital letter in this case (R for red and W for white)

Homologous structures

Physical structure shared by two different species. For example, dog paws resemble distorted human hands. Due to common ancestor. Different from analogous structures, which do not occur as a result of common ancestry.

Opsin

Pigment proteins within rods and cones that change their tertiary structure upon absorbing light. Binds to retinal, which is derived from Vitamin A.

Vagus nerve

Most important example of a cranial nerve - decreases heart rate and increases GI activity. (part of parasympathetic division) of autonomic NS).

Is vesicle transport through a cell (through the rough ER, golgi apparatus, and plasma membane) unidirectional or bidirectional?

Mostly unidirectional, occasionally has to send proteins in reverse direction if a mistake is made.

Secondary immune response

Much swifter and stronger than primary immune response. Body remembers past antigen and reacts accordingly. Basis for vaccines.

What does mesoderm form?

Muscle tissue, bone, blood vessels, and nongland organs.

Antagonistic vs. synergistic muscles

Muscles that are responsible for movement in opposite directions vs. muscles that move a joint in same direction. biceps and triceps vs. brachialis vs brachioradialis

Recessive lethal alleles

Mutant alleles that can cause death an organism if expressed in homozygous manner.

Factors that affect Hardy Weinberg equilibrium (HW equilibrium states that allele frequency will not change given these assumptions)

Mutation, migration, natural selection, non-random mating, and random drift. What is random drift? In a small population, it cannot contain a great variety of alleles diue to random events that can alter allele frequencies significantly and have a large influence on future generations.

What structure makes muscle cells striated?

Myofibrils.

What is different between myoglobin and hemoglobin?

Myoglobin only contains one subunit with heme that has one binding site for oxygen. Therefore, no cooperativity. Hemoglobin has 4 oxygen binding subunits

Thick filaments of myofibrils?

Myosin

What enzyme uses ATP to create movement in muscle cells?

Myosin

Order of protein made in translation.

N-->C

Make up of backbone of polypeptide

N-C-C-N-C-C pattern

The oxidation of glucose is accompanied by the reduction of which two high energy electron carriers?

NAD+ and FAD (nicotinamide adenine dinucleotide and flavin adenine dinucleotide).

Acetylcholine. Where does it play a role? What is its effect? Is it excitatory or inhibitory? What degrades it?

Plays role in neuromuscular junction (between neurons and skeletal muscle). Secreted from presynaptic cell, binds to receptor on postsynaptic cell, causing sodium channels to open on postsynaptic cell. This depolarizes the cell, causing action potential to occur. Acetylcholine in the synaptic cleft is degraded by acetylcholinesterase (AChE).

Equilibrium potential

Point at which there is no longer a gradient driving ions across a plasma membrane. Based on combination of concentration gradent and electrical gradient. For Na+, it is around +50 mV. For K+, it is around -90 mV.

Epiphyseal line

Point of fusion between diaphysis and epiphysis in adults.

Optic disk

Point where ganglion cells converge to form optic nerve. AKA the blind spot (contains no photoreceptors).

Origin of skeletal muscle

Point where muscle attaches on the bone closer to the center of the body

Insertion of skeletal muscle

Point where muscle attaches on the bone more distant from the center of the body.

Obligate anaerobes

Poisoned by oxygen because they lack certain enzymes necessary for the detoxification of free radicals which form spontaneously in the presence of oxygen.

Polymerase

Polymerization (e.g., addition of nucleotides to the leading strand of DNA by DNA polymerase III).

Proteinoids

Polypeptides formed in primitive earth by the use of metal ions as catalysts. Occurred before existence of enzymes.

Preganglionic neuron. What neurotransmitter do these neurons release?

Portion of autonomic efferents. Has its cell body in the brainstem or spinal cord. Sends an axon to an autonomic ganglion, located outside spinal column. Within this ganglion, the axon synapses with a post-ganglionic neuron (which sends an axon to an effector, such as a smooth muscle or gland). All autonomic preganglionic nurons release acetylcholine as their neurotransmitter.

Chordata defining characteristics

Possess notochord, dorsal hollow nerve cord, and pharyngeal gill slits at some time in embryonic development.

Motor end plate

Post synaptic membrane at neuromuscular junction (the myofibril membrane).

Where is ADH produced? What is its target and effect?

Posterior pituitary. ADH secreted when blood volume is low or plasma osmolarity is too high. Causes epithelial cells of distal nephron to become permeable to water.

B cells

Precursors to antibodies. Derived from stem cells in bone marrow. Proliferate and differentiate into plasma cells and memory cells when immature B cells come into contact with an antigen for the first time.

Feedforward stimulation

Presence of one of reactants stimulates an enzyme further down the enzymatic pathway (for example if A->B->C->D, presence of A may stimulate activity of enzyme that converts C to D).

Envelope (viruses)

Present in many animal viruses - surrounds the capsid. Derived from host cell membrane. This envelope is acquired by budding through host cell membrane.

pyloric sphincter

Prevents passage of food from the stomach into the duodenum. Does not open when small intestine already has a large load of chyme or acidity.

two primary sequences of a promoter (area of DNA that recruits RNA pol) in bacteria

Pribnow box at -10 and -35 sequence (negative means number of nucleotides upstream from start site of transcription).

Main difference between the atmosphere of primitive earth and current earth

Primitive earth likely didn't contain oxygen in its atmosphere - the atmosphere was a reducing environment. As an electron acceptor, oxygen was able to break organic bonds, forming monomers.

Oxidative catabolism

Process by which energy is extracted from a molecule by oxidizing it. This is the manner by which we get energy from glucose.

Crinophagy

Process by which lysosome digests excess (unneeded) secretory products of the cell.

Photosynthesis

Process by which plants store energy in the form of bond energy of carbohydrates, using the sun

Local autoregulation

Process by which tissues in need of extra blood flow are able to requisition it themselves. Certain metabolic wastes have a direct effect on arteriolar smooth muscle causing it to relax. So when a tissue does not have enough blood flow, wastes build up causing vasodilation.

Translocation (translation in proks)

Process in translation in which empty tRNA moves to E site, tRNA with peptide attached moves to P site, and the next codon to be translated to the A site. Receives help from elongation factor EF-G (often called a translocase), which costs one GTP. EF-Tu then eventually helps remove empty tRNA from E site.

Fermentation (in humans)

Process of proton transfer from NADH to pyruvate in the absence of O2 to form NAD+ and lactate, allowing glycolysis to continue.

Grastrulation

Process that produces GI tract during embryogenesis.

Integrative function

Processing sensory information by the CNS

Mitochondria functions and number of membranes

Produce ATP via Krebs cycle and oxidative phosphorylation. 2 membranes.

Tumor suppressor genes

Produce proteins that are the inherent defense system to prevent conversion of cells into cancer cells.

Leptin

Produced by fat in order to suppress appetite in order to maintain stable lipid content in adipose tissue. Secreted in response to increased triglyceride levels.

Endospores

Produced by some types of gram-positive bacteria under unfavorable growth conditions. Dormant form of bacteria. Endospores have tough, thick external shells comprised of peptidoglycan. Contain genome, ribosomes, and RNA required for spore to become metabolically active when conditions become favorable.

Where is calcitonin produced? What is its target and effect?

Produced in C cells of the thyroid. Secreted when Ca2+ is too high. Removes Ca2+ from the blood by deposition into bone, reduced absorption in the gut, and excretion in the urine.

Where is aldosterone produced? What is its target and effect?

Produced in the adrenal cortex. Causes sodium reabsorption and potassium secretion by synthesis of basolateral Na+/K+ ATPase in distal nephron.

Meiosis

Produces haploid cells such as gametes from a diploid cell. Occurs in testes to create haploid spermatozoa, occurs in ovaries of females to produce ova.

cystine

Product of two cysteine residues bonding together via disulfide linkage. Play an important role in stabilizing tertiary protein structure.

F1 generation

Progeny of a test cross (test cross is when an individual is bred with a homozygous recessive individual)

Apoptosis - describe the process.

Programmed cell death. Begins with shrinking of cell and disassembly of cytoskeleton. Nuclear envelope breaks down and genome is broken into pieces. Cell surface proteins emerge, signalling for phagocytic cells to deconstruct and clear the dead cell.

Pili

Projections on the bacterial surface that allow it to attach to different surfaces.

Main distinction between prokaryotes and eukaryotes

Prokaryotes do not contain membrane bound organelles (they do contain ribosomes however)

What kind of organism uses Shine-Dalgarno sequence?

Prokaryotes. This sequence is upstream of open reading frame, and initiates tranlsation.

Which AA will never be found in an alpha helix and why?

Proline, because its structure causes a polypeptide chain to kink.

Muscle spindles are an important example of what type of nerve receptor?

Proprioceptor. It is a mechanoreceptor that detects muscle stretch.

Joint capsule receptors

Proprioceptors that detect pressure, tension, and movement in the joints.

Golgi tendon organs

Proprioceptors that monitor tension in tendons.

Difference between prosthetic group and cofactor

Prosthetic groups as covalently bound to an active site of an enzyme. While cofactors are crucial for enzymatic activity, they are not directly in contact.

Caspases

Proteases responsible for carrying out events of apoptosis. Contain a Cysteine in active site, and cleave proteins at aspartate acid site (hence the name c-asp-ases). Grouped into initiator and effector caspases.

Hypodermis

Protective, insulating layer of fat

Capsid

Protein coat that surrounds the viral nucleic acid genome. Provides external morphology used to classify viruses.

sigma factor

Protein needed for the initiation of transcription in bacteria. Is released after open complex is formed.

T cell receptor

Protein on the surface of T-cell that can bind antigen.

Proteolytic enzyme, or protease

Protein responsible for performing hydrolysis reaction of polypeptide (cutting the polypeptide).

Synaptonemal complex. What is it? What is the protein structure of this? when does it form?

Protein structure that mediates synapsis, the process of meiosis in which homologous chromosomes are joined to form tetrads. It works like a zipper, providing connection of chromosomes. Lateral parts of zipper are composed of SYCP2 and SYCP3, and track of zipper is made up of SYCP1. Forms in early meiotic prophase I. It is interdependent with recombination.

Effector caspases

Protein that aids in apoptosis. In response to cell death signals, initiator caspases are first activated. Effector caspases are then activated, which cleave variety of cellular proteins to trigger apoptosis.

Initiator caspases

Protein that aids in triggering apoptosis. Respond to extra or intracellular death signals by clustering together and activating each other. This activation leads to activation of effector caspases (which cleave a variety of cellular proteins to trigger apoptosis) in a cascade of activation.

Thrombin

Protein that converts fibrinogen into fibrin. Fibrin is able to hold platelet plugs in place and dries to form scabs.

Mnemonic for remembering which proteins must contain signal sequence (go through rough ER)

Proteins that end up in ER, golgi apparatus, and lysosomes must go through ER. ER GAL

Hershey and Chase experiment

Proved that DNA was hereditary material, not protein. Did so by radiolabeling viral DNA with phosphorous isotope (because phosphorous is in DNA) and labeling viral protein capsid with sulfur isotope (because sulfur is in proteins with cysteine or methionine). Upon injecting both types of viruses into bacterial cells, radiolabeled phosphorous was present in bacteria, not radiolabeled sulfur.

Myoglobin

Provides oxygen reserve by taking O2 from hemoglobin and releasing it as needed.

Cytoskeleton

Provides structural support supplied by the cell wall in bacteria, plants, and fungi. It also allows movement of the cell and its appendages and transport of substances within the cell. In animal cells, composed of microtubules, intermediate filaments, and microfilaments (proteins).

Where does most reabsorption of substances into blood occur in nephron?

Proximal convoluted tubule

Transversion (point mutation)

Purine is replaced by pyrimidine (or the opposite).

What has more stored energy: orthophosphate (AKA phosphate) or pyrophosphate?

Pyrophosphate, by far. (details for why are not that important, but negative charges repel each other strongly, less resonance structures, less favorable interaction with water).

How does glycolysis connect to fatty acid synthesis?

Pyruvate from glycolysis is used to create acetyl CoA, which is used in krebs cycle. Acetyl CoA also attaches to citrate and shuttles out from the mito matrix to the cytoplasm, where acetyl CoA is then used for fatty acid synthesis.

Erythrocytes

RBCs

Primase

RNA polymerase that synthesizes RNA primers for each template strand during DNA replication - typically 8-12 nucleotides long, later replaced by DNA.

Are there more Na+ leak channels or K+ leak channels in a cell?

Ratio of K+ leak channels to Na+ leak channels is about 100:1, making a cell nearly impermeable to Na+

Large intestine

Reabsorbs water and ions from feces. Doesn't really excrete anything, but processes wastes already destined for excretion. Also excretes ions into feces using active transport.

ADH function

Reabsorbs water from distal nephron back into bloodstream when person is dehydrated. Does so by making walls of distal nephron (primarily collecting duct) permeable to water. Raises BP.

If an allele does not produce a functional protein, is this typically a dominant or a recessive trait?

Recessive because the other copy of the gene can typically make up for this if it is a copy that produces the protein (this would be dominant).

Is recombination more or less likely to occur if two genes on the same chromosome are far apart?

Recombination is more likely. They would be more likely to assort independently. They also would be less likely to be linked (obviously).

GI motility

Refers to rhythmic contraction of GI smooth muscle.

Open complex

Refers to separated strands of DNA just prior to replication

Humoral immunity

Refers to specific protection by proteins in plasma called antibodies/immunoglobulins.

Dense connective tissues

Refers to tissues that contain large amounts of fibers (especially collagen), such as tendons, ligaments, cartilage, and bone.

Monosynaptic reflex arc

Reflex that only involves two neurons and one synapse. Example is muscle stretch reflex when patellar tendon is tapped with reflex hammer. Involves sensory neuron and motor neuron as shown in image.

What has longer refractory period, cardiac or neuronal cells?

Refractory period refers to period of time in which a new action potential will not be induced. Longer in cardiac cells because action potential in cardiac cells lasts much longer (due to slow calcum channels).

Gametangia (fungus)

Region of fungal hyphae that specialize in reproduction. Either produce and release gametes, serve as a site of gamete fusion, or fuse with gametangia from other fungi of the same species.

H zone

Region of sarcomere composed of only thick filaments

I bands

Region of sarcomere composed of thin actin filaments Remember I is a thin letter.

Vasoconstriction and vasodilation

Regulated by substances such as nitric oxide and enothelin. Important in maintaining blood pressure, tissue oxygenation, and thermoregulation.

Kinase

Regulatory enzyme that adds a phosphate group to a molecule from a high energy carrier, such as ATP (e.g. PFK)

what role to endothelial cells play in inflammation?

Release of inflammatory chemicals to injured tissue stimulates endothelial cells to express adhesion molecules, which allow WBCs to adhere to endothelial cells and ultimately enter injured tissue.

G-protein linked receptor

Relies on G-protein. Does not directly transduce a signal - does so with the help of a second messenger. What is the most important second messenger? A: cAMP

Excision repair

Removal and replacement of defective bases in DNA prior to DNA replication.

When does repolarization occur? How does it occur?

Repolarization occurs after a neuron becomes sufficiently depolarized (at +35 mV). Once this is reached, voltage gated sodium ion channels inactivate and potassium channels open. Slowly, as K+ leaks out of the cell, the cell's membrane potential becomes very negative. The K+ channels do not close until resting membrane potential (-70 mV) is surpassed (when it reaches around -90 mV).

Targeting signals

Required for proteins in secretory path to end up in a location other than the plasma membrane (ER, golgi, lysosome)

Localization signals

Required in proteins made from cytoplasmic ribosomes in order to determine whether they end up in nucleus, mitochondria, or peroxisome.

Anaerobic respiration

Respiration that occurs using an alternate final electron acceptor from oxygen. For example, instead of reducing O2 to H2O, some bacteria reduce SO4 2- to H2S, or CO2 to CH4.

Function of DNA pol III (in prokaryotes)

Responsible for super-fast, super-accurate (high processivity) elongation of leading strand. Also has 3' to 5' exonuclease activity (it moves backwards to eliminate an incorrect nucleotide that may have been added). It does not repair mistakes, just eliminates them.

Divergent evolution

Results in cladogenesis (branching of one species into two separate species. May be by allopatric or sympatric speciation).

Examples of symbiotic bacteria

Rhizobia fixes nitrogen in nodules that exist on the roots of legumes Cyanobacteria fix nitrogen in marine environments. Some bacteria in human gut help defend against other pathogenic strains, synthesize Vitamin K for blood clotting, and digest undigested materials.

Nucleolus

Ribosome factory. No membrane separating it from the rest of the nucleus. Contain DNA, RNA polymerases, rRNA, and protein components of ribosome.

Where is loop of henle located?

Right after PCT, it dips down into the renal medulla via the thick descending limb and then back toward the cortex via the thin/thick ascending limb.

What are fungi cell walls composed of?

Rigid cell walls are composed of chitin, a structure found in exoskeletons of insects.

Cleavage furrow

Ring of microfilaments encircles an elongating cell, initiating cytokinesis.

Two components of nephron

Rounded region surrounding capillaries where filtration takes place, known as capsule. Coiled tube known as renal tubule, which receives filtrate from capillaries in the capsule at one end empties into collecting duct at the other end.

what phase of the cell does DNA replication occur?

S (synthesis) phase

Examples of flat bones. What are the main functions of flat bones?

Scapula, ribs, bones of skull. They are the location of hematopoiesis and are important for protection of organs.

Two types of glial cells that form myelin. What is the main difference between them?

Schwann cells (in peripheral nervous system) and Oligodendrocytes (in CNS).

How does a hydrophilic (peptide or AA derivative) hormone communicate with the interior of a target cell?

Second messenger cascade

Renin

Secreted by baroreceptors called JG cells of afferent arteriole in order to increase BP. Converts angiotensinogen (protein made in liver) to angiotensin I, which is converted to angiotensin II by ACE in the lungs. Causes vasoconstriction and stimulates release of aldosterone.

Histamine

Secreted in response to gastrin or stomach stretching, which binds to parietal cells and stimulates acid release.

G cells

Secretes gastrin, which stimulates acid and pepsin secretion and gastric motility. Gastrin secretion is stimulated by food in the stomach and parasympathetic stimulation

Regulated secretory pathway

Secretory proteins are stored in secretory vesicles and are only released at certain times, usually in response to a signal or change in extracellular environment (example is pancreatic cells or B-cells of the immune system).

Structure of virus

See image. Base plate is blue cube

Summary of hormones of the endocrine system

See page 385.

Comparison of skeletal, cardiac and smooth muscle

See page 491!!! have this memorized. One other thing that is not in that table is that smooth muscle cells do not have T tubules, because cells are narrow and short. So T tubules are not needed to spread action potential throughout cell.

Factors that regulate ventilation rate

See page 521!!!

Epiphyseal plate

Seen between diaphysis and epiphysis of bones in childhood. Disk of hyaline carilage that is actively being produced by chondrocytes. As chondrocytes divide, diaphysis and epiphysis are forced apart. Then cartilage is replaced by bone (ossified).

How would you describe the permeability of the plasma membrane?

Semipermeable. It is permeable to water, but not most polar solutes.

Referred pain

Sensation when autonomic pain receptors create the illusion of pain on the skin when their nerve paths cross somatic afferents from the skin.

Muscle stretch reflex

Sensory neuron detects stretching of a muscle. This sends an action potential to a motor neuron cell body in the spinal cord. The motor neuron's long axon synapses with the muscle that was stretched, causing it to contract. This occurs when patellar tendon is stretched by reflex hammer and quad contracts.

Ileocecal valve

Separates ileum from cecum

Enhancer sequences

Sequence of DNA located far away from promoter, but regulate transcription in eukaryotes (likely by DNA looping after being bound by activator proteins).

Nuclear localization sequence

Sequence of basic amino acids located on some large proteins, allowing them to be transported into the nucleus by specific transport mechanisms.

Lac operon

Sequence of linked genes responsible for metabolism and transport of lactose in bacteria.

Promoter

Sequence of nucleotides on a chromosomes that activates RNA pol to begin transcription.

Which AAs are often modified by the attachment of a phosphate group via a kinase, making the AA much more hydrophilic?

Serine, threonine, and tyrosine (AAs with OH groups)

Inhibitory interneuron

Short neuron which forms an inhibitory synapse with a motor neuron, innervating a target muscle. Interneurons connect afferent and efferent signals.

truncated

Shortened, by cutting off the top or end.

How do some prokaryotes use methylation to identify mismatched bases in DNA not corrected by DNA pol during replication?

Shortly after DNA synthesis, parental strand will be marked with methylated bases and daughter strands will not. This will allow for the cell to know which base needs to replaced in a mismatch (for example, if there is an A-C mismatch, this is how they would know which one of the bases was incorrect).

Frederick Griffith experiment

Showed that cell extracts can transform bacteria, indicating biological macromolecules carry genetic information.

alternative splicing

Shuffling of exons included in transcribed mRNA due to several factors, leading to many alternatives and increasing the complexity of gene expression.

Basolateral surface

Sides/bottom of epithelial cell; faces opposite side of lumen

Postganglionic neuron. What do parasympathetic postganglionic neurons release? What do sympathetic postganglionic neurons release?

Signal from preganglionic neuron in autonomic nervous system is synapsed to autonomic ganglion, which is synapsed to postganglionic neuron. These neurons send axon to an effector (smooth muscle or gland). All parasympathetic postg neurons release acetylcholine. Most sympathetic postg neurons release norepinephrine.

Blood serum

Similar to plasma, although it lacks all proteins involved in clotting.

Ventilation

Simple movement of air into and out of lungs.

IS element (transposons)

Simplest type of transposon. Contains a transposase gene (which creates transposase that cuts and pastes the gene), flanked by inverted repeats.

SA node

Sinoatrial node. Cells of SA node act as the pacemaker of the heart. initiates each action potential that starts each cardiac cycle.

Thymus

Site of t cell maturation

Multinucleate syncytia

Skeletal muscle cells are multinucleate syncytia, formed by fusion of individual cells during development.

What does the ectoderm form?

Skin, hair, fingernails, as well as all nervous system structures.

Dendrites

Slender projections that extend from soma of neuron. Receive signals.

Amphiarthroses

Slightly movable joints, which provide movability and support. Vertebral joints for example.

Okazaki fragments

Small fragments of daughter DNA created in lagging strand during replication.

Synaptic cleft

Small gap between synaptic knob of a neuron and the dendrites of the target neuron.

Cilia - definition and example

Small hairs on a cell surface which move fluids past the cell surface. Example: mucociliary excalator, which lines human respiratory tract and sweeps mucus toward the mouth.

Epitope

Small site that an antibody recognizes within a larger molecule.

Venules

Small veins where blood collects after passing through capillaries. Blood flows from capillaires, to venules, to veins, to the heart.

Arterioles

Smaller arteries, more distant from the heart and with less pressure than arteries.

Fimbriae

Smaller structures of bacteria that are not involved in locomotion or conjugation but are involved in adhering to surfaces.

Myofibrils

Smaller units composed within myofibers. LIke a specialized organelle, responsible for striated appearance in skeletal muscle and generates contractile force of skeletal muscle.

Terminal bronchioles

Smallest and final branches of conduction zone. Smooth muscle of walls of terminal bronchioles is too thick to allow adequate diffusion of gases, so no gas exchange occurs here.

Miniature end point potential

Smallest measurable EPP (depolarization of post synaptic membrane in neuromuscular junction upon binding of acetylcholine and sodium influx). Occurs when one ACh vesicle is exocytosed.

What type of muscle is GI muscle?

Smooth muscle.

what is more thermodynamically favorable, polymerization of nucleoside monophosphates or nucleoside triphosphates and why?

NTPs, because doing so releases a pyrophosphate group, which releases enough energy for the polymerization reaction to occur when hydrolyzed.

Concentrations of ions inside and outside of cell (Na+, K+, Cl-, and Ca2+) Don't need to know exact numbers, just trends.

Na+ higher concentration outside cell. K+ lower concentration outside cell. Cl- higher concentration outside cell. Ca2+ higher concentration outside cell.

Electrolytes in plasma of blood.

Na+, K+, Cl-, Ca+2, Mg2+

Upper esophageal sphincter

Near top of esophagus, regulates movement of food through esophagus

Is the pleural pressure positive or negative?

Negative, meaning the two pleural membranes are drawn tightly together by a vacuum, keeping the surface of the lungs drawn up against the inside of the chest wall.

Which is larger - the cardiac output of the left ventricle or right ventricle?

Neither. They are equal. The same amount of blood must pass through both sides of the heart or blood would back up in either the pulmonary or systemic circulatory system.

futile cycling

Net loss of energy due to activation of two opposing processes (such as glycolysis and gluconeogenesis)

Ganglia

Neuronal bodies found in bunches outside the CNS. Inside the CNS, these bunches are called nuclei.

Neuroendocrine cells

Neurons that secrete hormones into the bloodstream.

Role of glutamate in vision

Neurotransmitter released by rods and cones in retina onto bipolar cells in the dark, inhibiting them from firing. Photoreceptors stop releasing glutamate upon exposure to light. Remember, "gloomy glutamate" is released in the dark.

Excitatory neurotransmitter

Neurotransmitter that causes depolarization of postsynaptic membrane upon binding. Opposite of inhibitory neurotransmittors, which hyperpolarize the cell.

Granulocytes

Neutrophils - phagocytose bacteria resulting in pus, amoeboid motility, chemotaxis Eosinophils - destory parasites; allergic reactions basophils - store and release histamine, allergic reactions.

Can ion channels move ions against an electrochemical gradient?

No they can only participate in facilitated diffusion.

Are neurons the only cells with a resting membrane potential?

No, all cells have it. Neurons and muscle cells are unique in using the resting membrane potential to generate action potentials.

if a mutation in a euk fat cell reduces the level of several proteins related to fat metabolism, does this mean these proteins were all encoded by the same mRNA?

No, because euk mRNA is monocistronic. A more likely explanation is that the number of different genes throughout the genome have related regulatory sequences that bind the same sequence-specific transcription factors. This is a means used by euks to achieve coordinated expression of genes.

Does transcription require a primer?

No, because the primer in DNA synthesis is an RNA strand.

Are viruses able to synthesize ATP?

No, but they are able to acquire ATP from their previous hosts and store it in their capsids. This often powers penetration into cells.

Do ligand gated ion channels propagate action potentials in cardiac muscle?

No, ligand gated ion channels may help to create threshold depolarization required to trigger an action potential, but do not play a role in propagating it. Propagation requires voltage gated ion channels.

Does DNA replication occur between meiosis I and II?

No.

Surfactant

Soapy substance that coats alveoli, reducing surface tension and preventing alveoli from collapsing due to surface tension. Mixture of phospholipids, proteins, and ions.

Two types of T cells

T helpers (CD4 cells) and T killers (cytotoxic T cells or CD8 cells).

Why are T cells named as such?

T stands for thymus, which is gland they are developed in during childhood.

What parts of the capsid attach to the surface of the host cell?

Tail fibers and base plate

Binomial classification

Taxonomical classification system in which each organism is given two names: genus and species.

Boiling point definition

Temperature at which atmospheric pressure is equal to vapor pressure.

Examples of steroid hormones

Testosterone and estrogen

stop codons

The 3 codons that do not code for an amino acid. They signal that the protein is complete.

What is the template strand in transcription? what are other names for it?

The DNA strand in which transcription occurs on. Other names are non-coding, transcribed, and antisense strand, as the strand itself is comlementary to the RNA strand being put to use in translation.

Cardiac conduction system

The action potential in the heart is trasmitted from the atrial syncytium to the ventricles by the cardiac conduction system.

Stroke volume

The amount of blood pumped with each systole is known as the stroke volume (SV)

Copy number variation

The amount of copies of a gene that are present can cause variation of the amount of proteins that are produced.

Peripheral resistance (in terms of hemodynamics AKA blood flow)

The amount of friction stopping blood flow. Follows Ohm's law, the same way current does (except with slightly different terms). ΔP = QR Similar to V = IR ΔP = pressure gradient between arterial system and venous system. Q = blood flow R = resistance

Henry's law

The amount of gas that will dissolve into liquid is dependent on partial pressure of that gas as well as the solubility of that gas in the liquid. For oxygen: [O2] dissolved = P(O2) x S(O2)

Blastopore

The anus is derived from the blastopore during embryogenesis.

What are the semilunar valves?

The aortic valve and the pulmonary valve - the valves between the large arteries and the ventricles of the heart.

How do tRNA anticodon bases become more "flexible" with their binding to bases of the mRNA codon?

The base at the 5' end of the anticodon does not always have to be an exact match - it can "wobble". This often occurs when a base of tRNA is covalently modified, such as adenine to inosine. (Inosine can bind to A, U, or C).

What can happen in a chromosome with two transposons facing the same direction?

The chromosome can loop around, causing the transposons to be in parallel orientation. Recombination occurs between them, and DNA between transposons is deleted. This deletion take a transposon with it, which may be incorporated elsewhere.

Fibroblast

The derivation of all connective tissue. Has ability to secrete fibrous material, such as collagen.

Downstream (transcription)

The direction in which transcription occurs. This is the 3' to 5' direction of the template strand (the strand in which transcription is occurring) because RNA synthesis occurs in 5' to 3' direction. So it moves in the 3' end of the transcript and coding strand. This is the positive direction. For example, 5 nucleotides downstream of start site would be labeled +5 on coding strand (which is the strand that transcription is NOT occurring on. DO NOT GET CONFUSED BY THIS).

Log phase

The exponential phase of bacterial growth

Bohr effect

The fact that decreased pH, increased CO2, and increased temperature stabilize tense hemoglobin, lowering its affinity for oxygen These are the conditions of active tissues! so oxygen is not going to be stolen from active tissues by hemoglobin (which makes sense)

Perfusion

The flow of blood through a tissue.

How do fatty acid, amino acid, and glycogen synthesis differ from protein or nucleic acid synthesis?

The former are not template driven. In other words, they are not "read" by the enzymes based on their structure.

A bands

The full length of the thick myosin filaments in sarcomeres. Includes both overlapping regions of thick and thin filaments, as well as region composed of only thick filaments.

Countercurrent exchange

Some animals perform this, allowing them to exchange both water and heat. Nasal passages warm and humidify the air entering the respiratory system, exiting air is cooled and de humidified. WOrks to thermoregulate during ventilation.

Transduction (viruses)

Sometimes occurs during the lysogenic cycle (where viral genome is incorporated into host cell's genome, replicated, and then activated, excising and lysing the cell) when the viral genome takes some of the host genome with it. This often causes the genome to code for things it previously was unable to code for. Increases bacterial genetic diversity

Intercellular clefts

Spaces between endothelial cells which make up the capillary wall. Nutrients, wastes, and WBCs can pass through these spaces.

Osmosis

Special type of diffusion in which solvent diffuses rather than solute. Describes net movement of water across semipermeable membrane from region of low solute concentration to high solute concentration in an effort to dilute the higher concentration solution.

Juxtaglomerular apparatus (JGA)

Specialized contact point between the afferent ateriole and the distal tubule, which control glomerular filtration rate (and blood pressure) by releasing renin. Composed of juxtaglomerular cells (JG) at afferent arteriole and macula densa at distal tubule.

Sarcoplasmic reticulum

Specialized smooth endoplasmic reticulum located in myofiber, which enfolds each myofibril in the cell. Is specialized to sequester and release Ca2+. Contains active transporters which rapidly remove calcium from sarcoplasm, becomes depolarized by action potentials of T-tubule network, causing Ca2+ ions to rush out of SR. This causes change in conformation of tropomyosin, allowing myosin to bind actin, which causes muscle contraction.

Glial cells

Specialized, non-neuronal cells that typically provide structural and metabolic support to neurons. Maintain a resting membrane potential but do not generate action potentials.

Diploid

Species with two copies of each chromosome.

Receptor mediated endocytosis - definition and name an important example.

Specific form of endocytosis, where site is marked by pits coated with clathrin (inside the cell) and receptors that bind to a specific molecule (outside the cell). Example: Uptake of lipoproteins that contain cholesterol by cells. This receptor-lipoprotein complex is then taken into a vesicle (endosome) that is transported to a lysosome, where lipoprotein is degraded. Lipoprotein receptor is then transported back to the cell surface.

Cells that undergo meiosis in males

Spermatogonia

micelle

Spherical structure that forms as a result of fatty acids in an aqueous solution. Hydrophilic heads (carboxylic acid components) surround the structure to interact with water and hydrophobic carbon chains lie within the sphere (or solvation shell) to avoid contact with water.

Spicules (AKA trabeculae)

Spikes of bone in spongy bone.

Anaphase

Spindle fibers shorten, centromeres of each sister chromatic pair are pulled apart. Cell elongates and cytokinesis begins with the formation of a cleavage furrow, which is accomplished by a ring of microfilaments encircling the cell and contracting.

Abiotic synthesis

Spontaneous polymerization of monomers that occurred in primitive earth, before enzymes were present. Metal ions in clay and other rocks likely acted as the catalysts. Polypeptides created in this way were called proteinoids.

Storage unit for glucose in plants. Alpha glycosidic linkages.

Starch

Name of the site where transcription starts

Start site

Where does digestion start and end?

Starts in mouth, completed in duodenum and jejunum.

Hardy Weinberg equilibrium

State in which allele frequencies no longer change. Occurs after one generation. Does not apply to the first generation

Hardy Weinberg law

States the frequencies of alleles in the gene pool of a population will not change over time provided a number of assumptions (the assumptions are not actually realistic).

Example of electromagnetic receptors

Stimulated by electromagnetic waves. In humans, this includes photoreceptors.

Glucagon

Stimulates liver to hydrolyze glycogen and release glucose into blood stream, and stimulates adipocytes to release fats into blood stream

4 properties that need to be communicated to the CNS by sensory information.

Stimulus modality, stimulus location, stimulus intensity, and stimulus duration.

What effect does stretching of the lung have?

Stretch receptor in the lung inhibits inspiration.

Hyaline caritlage

Strong and somewhat flexible. Present in larynx and trachea. Joints are also lined by hyaline cartilage known as articular cartilage.

Cartilage

Strong but very flexible extracellular tissue secreted by cells called chondrocytes

Collagen

Strong fibrous protein, which is secreted from fibroblasts.

tetanusq

Strongest possible contraction from repeating series of stimulations.

Alveoli

Structure across which gases diffuse. tiny sacs with very thins walls.

Nuclei (not related to nucleus)

Structure of neuronal cell bodies within CNS that are bunched together. When outside of CNS, these bunches are called ganglia.

Analogous structures

Structures that share the same function in 2 different species, but not due to common ancestry. Example is flagella in sperm and bacteria. Different from homologous structures, which are due to common ancestry.

Enzyme kinetics

Study of rate of formation of products that undergo enzymatic reactions.

chemical kinetics

Study of reaction rates

Detergents

Substances that solubilize oils, while simultaneously remaining water soluble. Phospholipids are examples of these. Like soaps, but stronger.

Gene pool

Sum of all genetic information in a population

Hypoxia

Supply of oxygen is reduced even though there is adequate circulation. Due to adequate circulation, wastes are adequately removed. Different from ischemia because ischemia implies inadequate blood flow. Wastes are not adequately removed with ischemia.

Apical surface of epithelial cells in GI tract

Surface of cells facing into the lumen.

Peritubular capillaries

Surround renal tubule of nephron, extracting and secreting certain substances from and to the renal tubule. Drain into venules that lead to renal vein.

Crossing over or recombination

Swapping of genetic information at gene loci of homologous chromosomes that occurs in prophase I of meiosis. Longest step in meiosis due to complexity. Provides variation during sexual reproduction. Precision is very important in this step, as genes on homologous chromosomes have to align perfectly for it to occur.

two mechanisms of dissipating excess heat

Sweating dilatation of blood vessels in the dermis (cutaneous vasodilation) results in heat loss by conduction or convection, when air blows past the skin.

Neuromuscular junction

Synapse between an axon terminus (synaptic knob) and a myofiber. Is a long invagination of the cell membrane. Ach is the neurotransmitter.

Intramembranous ossification

Synthesis of bone from an embryonic tissue called mesenchyme. Results in flat bones.

S phase

Synthesis phase in cell cycle. Cell actively replicates its genome.

Ribosomes functions and number of membranes

Synthesize proteins. 0 membranes.

Urea

Synthesized by the liver and releases into the blood stream. Carries excess nitrogen resulting from protein breakdown.

Portal systems

Systems that allow blood to pass through specific parts of the body without passing through the entire body. Blood passes through two sets of capillaries in this case. Examples are hepatic portal system (intestine to liver) and hypothalamic-hypophysial portal system.

Fibrin

Threadlike protein which forms mesh that holds platelet plug together. When it dries, it becomes a scab, sealing and protecting the wound. Formed by fibrinogen protein being converted into fibrin by a protein called thrombin when bleeding occurs.

Two AA derivative tyrosine hormones

Thyroid hormone and catecholamines

Lacteals

Tiny lymphatic vessles in the intestinal wall that chylomicrons travel through.

Papilla (kidneys)

Tips of medullary pyramids. Each papilla empties into calyx, which converge to form renal pelvis.

Functional syncytium

Tissue in which cytoplasm of different cells can communicate via gap junctions. Present in cardiac muscles but not in neurons.

Purpose of RBC

To transport O2 to the tissues from the lungs and CO2 from the tissues to the lungs. Carries oxygen using hemoglobin.

Cardiac output - definition and equation

Total amount of blood pumped per minute (CO) CO (L/min) = stroke volume (L/beat) x heart rate (beats/min)

Enthalpy

Total heat content of a thermodynamic system. Correlates with bond energy. Denoted by H.

Upstream (transcription)

Towards the 5' end of the coding strand anywhere beyond the 5' end of the transcript. Upstream nucleotides are labeled with negative sign. REMEMBER: THE TRANSCRIPT IS THE NEW RNA BEING CODED AND THE CODING STRAND IS THE DNA STRAND OPPOSITE TO WHERE TRANSCRIPTION IS OCCURRING. CODING STRAND IS ESSENTIALLY IDENTICAL TO TRANSCRIPT OTHER THAN U/T SWITCHES.

RNA polymerase III

Transcribes tRNA, long ncTNA., siRNA, some miRNA, and a subset of rRNA.

What is a main difference in the timing of transcription and translation in prokaryotes vs eukaryotes? why this difference?

Transcription and translation can occur simultaneously in proks, but not in euks. This is because in euks, the RNA must be packaged and transported across the nuclear membrane to the cytoplasm before it can be translated. Prokaryotes do not have a nucleus, so this is not an issue

Cap independent translation

Translation in eukaryotes that beings in the middle of the mRNA molecule, not relying on the 5' cap. Relies on internal ribosome entry site (IRES). Cap independent translation often occurs when cells are under stress because cap dependent translation is often inhibited. This is less common than cap dependent translation.

cap dependent translation

Translation of eukaryotes requires recognition of the 5' cap on mRNA. This is more common in euks, but there is also cap independent translation.

Na+/K+ ATPase

Transmembrane protein in plasma membrane of all cells in the body. Pumps 3 Na+ out of cell and 2 K+ into cell against their gradients using energy from ATP hydrolysis (primary active transport). The creation of this gradient often allows for secondary active transport of other molecules to be pumped across the membrane.

Passive transport

Transport across a membrane that does not require cellular energy.

Active transport

Transport across a membrane that requires cellular energy. Against the concentration or electrochemical gradient. Always involves a protein.

Secondary active transport

Transport of a molecule across membrane against gradient, without directly using ATP hydrolysis. Instead, ATP hydrolysis will create a gradient for another molecule, and the gradient of this molecule will power the transport of another molecule.

Primary active transport

Transport of molecule across membrane against gradient is powered by ATP hydrolysis.

What happens to ammonia in the blood stream?

Transported to the liver, whee it is converted to urea. Then absorbed into the blood stream and excreted as urine.

Transposons

Transposable elements. Sections of genetic material that are mobile, able to "jump around the genome". These often cause mutations and chromosome changes.

Kreb's cycle is also known as the....

Tricarboxylic acid cycle (TCA cycle) or citric acid cycle.

Pore

Tube through a membrane which is so large that it is not selective for any particular molecule. Formed by polypeptides called porins. Not present in euk plasma membrane.

Teratomas

Tumors with formed tissues from multiple germ layers. Occurs when oncogenes cause a cell to dedifferentiate, then redifferentiate to become something different.

Primary bronchi

Two branches of trachea, which each supply one lung. Collapse prevented by small plates of cartilage.

Homologous chromosomes

Two nonidentical copies of a chromosome. Contain the same genes, but differ in DNA sequence (alleles).

Parallel evolution

Two species go through similar evolutionary changes due to similar selective pressures - for example: After the ice age, all organisms would be selected for their abilities to tolerate cold.

Convergent evolution

Two species possess many analogous structures due to similar selective pressures - birds and bats are a good example.

Allopatric speciation

Type of cladogenesis. Geographical isolation leads to reproductive isolation, causing split of two species.

Pinocytosis

Type of endocytosis. Cell drinking. Non specific uptake of small molecules and extracellular fluid via invagination.

Triglycerides

Type of lipid. fats. located in adipose cells, store energy.

Silent mutation

Type of point mutation in which a codon is altered, but the same AA is produced (this is possible because codons are degenerate).

Nonsense mutation

Type of point mutation in which a regular codon is replaced by a stop codon, stopping protein construction prematurely.

4 agents that denature proteins.

Urea (which disrupts hydrogen bonding), extremes of pH, extremes of temperature, and changes in salt concentration (tonicity).

Principle metabolic waste product

Urea, a breakdown product of amino acids

Facultative anaerobes

Use oxygen when its available, but don't need it.

Selective reabsorption

Useful items, such as glucose, water, and AAs are reabsorbed while wastes and some water are left in the renal tubule.

acyl-CoA synthetase

Using 2 ATP, this enzyme activates free fatty acids into fatty acyl-CoA, which can then be transported to mitochondrion.

Autotrophs

Utilize CO2 as their carbon source.

Slow calcium channels

Voltage gated calcium channel that is involved in the cardiac muscle action potential. These are not involved in neurons. These channels stay open longer than the fast sodium channels do, causing membrane depolarization to last longer in cardiac muscle than in neurons, producing a plateau phase.

Fast sodium channels

Voltage gated sodium channels that play an important role in cardiac muscle; they also play an important role in neurons.

Expiratory reserve volume

Volume of air that can be expired after passive resting expiration.

INspiratory reserve volume

Volume of air that can be inspired after a relaxed inspiration.

Hematocrit

Volume of blood occupied by the red blood cells. Normal HCT is 40-45% of blood in males, 35-40% in females.

Leukocytes

WBCs

fluid mosaic model

Way of describing the cell membrane - it is a mosaic of lipids and proteins that are free to move back and forth fluidly. Proteins and lipids are able to diffuse laterally, but are not able to flip-flop.

Primates defining characteristics

Well developed cerebral cortex, opposable thumbs, omnivorous, foreward facing eyes

What does the endoderm form?

The inner linings of the digestive system, urinary system, and respiratory system, as well as glandular organs such as the liver and pancreas.

What is more negatively charged, the interior of a cell or the exterior?

The interior - it has a resting membrane potential of -70 mV due to sodium ions being pumped out more than potassium ions being pumped in (and leaking potassium through potassium leak channels).

Penetrance - define and example

The likelihood of a genotype being expressed as the expected phenotype. Level of expression in certain genes depends on many factors. Example: mutation in gene that could cause breast cancer could depend on if the person smokes, has children, diet, etc.

Gestalt

The whole exceeds the sum of its parts. In other words, when a human perceives an object, rather than seeing lines, angles, colors, etc, they perceive the whole - a face or a table or a dog.

Cranial nerves

There are 12 pairs. They convey sensory and motor information to and from the brainstem.

Spinal nerves

There are 31 pairs. Convey sensory and motor information to and from the spinal cord.

How many inheritance patterns should you be familiar with, what are they?

There are 6. They are autosomal recessive, autosomal dominant, mitochondrial, Y-linked, X-linked recessive, X-linked dominant.

How is the attachment of the appropriate amino acid to tRNA possible? (considering the amino acid acceptor site on tRNA is always CCA?)

There are specific aminoacyl-tRNA synthetase enzymes for each AA that recognize specific AA and specific tRNA based on their 3 dimensional structures.

Number of RNA polymerases in prokaryotes? in eukaryotes?

There is 1 RNA polymerase complex in prokaryotes (alpha2betabeta'sigma). Don't mix this up with the many DNA polymerases in prokaryotes!! There are many RNA polymerases in eukaryotes - the 3 important ones are RNA polymerase I, II, and III.

Vascular functions of endothelial cells?

These cells line the inner wall of all blood vessels. Vascular functions include: 1) vasodilation and vasoconstriction 2) inflammation 3) angiogenesis 4) thrombosis (blood clotting) control

antigen presenting cells (APCs)

These include macrophages and B cells. The cell chops up the antigen and displays them using MHC II. T helpers bind to this, recruiting T killer cells and immature B cells to be activated to the new antigen.

What can happen in a chromosome with two transposons facing opposite directions?

They align themselves in parallel orientation. Recombination occurs, and DNA between the transposons becomes inverted.

What is true of all somatic motor neurons?

They all innervate skeletal muscle cells, use ACh as their neurotransmitter, and have their cell bodies in the brain stem of ventral (front) portion of spinal cord.

How do viruses encode multiple proteins within the same gene length?

They are able to produce multiple proteins with multiple open reading frames within the same piece of DNA - there is overlap.

Where are B cells and T cells produced?

They are both produced in the bone marrow. B cells are matured in the Bone marrow, while T cells are matured in the Thymus. However, they are both produced in the bone marrow.

Function of tight junctions in epithelial cells of GI tract?

They are bvands that run all the way around the sides of the epithelial cells, creating a barrier that separates body fluids from extracellular environment.

How are peptide bonds formed and maintained if they are less thermodynamically favorable than individual AAs?

They are formed by stored energy. Once formed, they do not revert back to individual AAs because the activation of the hydrolysis reaction is too great.

Why do cartilage injuries take a long time to repair?

They are not directly supplied by blood because they are avascular.

Most important sites of regulation in a enzymatic pathway have what in common?

They are typically very exergonic (irreversible).

What happens to RNA primers that are placed on DNA strands during DNA replication?

They become replaced by DNA fragments, which are joined together by an enzyme called ligase. IMPORTANT TO MEMORIZE

How competitive inhibitors affect Vmax and Km? (enzyme kinetics)

They do not affect Vmax, they just cause the reaction to take longer to reach Vmax. It causes an increase in Km.

How are archaea structurally different from bacteria?

They do not contain peptidoglycan cell wall. Presence of introns.

How do enzymes (catalysts) affect delta G of a reaction?

They don't.

How do villi and microvilli contribute to small intestine function?

They increase surface area, which allows for greater absorption.

When do potassium channels open during an action potential? when do they close?

They open when the membrane potential reaches +35 mV, allowing the membrane potential to become more negative again (this works along with Na+/K+ ATPase, speeding up this process significantly). They close when the membrane potential becomes -90 mV.

Meselson and Stahl proved what about the nature of DNA replication?

They proved that it was semiconservative (the new dsDNA was made up of one strand of parental DNA and one strand of daughter DNA).

How do eukaryotes identify mismatched bases in DNA that were not corrected by DNA pol during replication?

They recognize the free 3' terminus of the leading strand or spaces between Okazaki fragments on lagging strand.

How do endothelial cells affect thrombosis (blood clotting)

They secrete substances that inhibit coagulation cascade (inhibit clotting).

What happens to immature B cells that bind to normal cell surface proteins? What about those who bind to normal soluble proteins?

They undergo apoptosis. They become anergic (unresponsive). Only immature B cells that undergo maturation without binding to any proteins will be circulated into blood. This selection process occurs in the bone marrow or lymph nodes. Similar to T cells, who also become anergic when binding to normal proteins. However, this occurs in the thymus or lymph nodes.

How do aldosterone and ADH work together?

They work to elevate BP. First, aldosterone causes sodium reabsorption, which results in increased plasma osmolarity. Then, this causes ADH to be secreted which results in increased water reabsoprtion.

What is the prosthetic group contained on the pyruvate dehydrogenase complex (PDC)?

Thiamine pyrophosphate (TPP).

Ground substance

Thick, viscous material of extracellular matrix. Composed of proteoglycans, which are composed of large macropolymers consisting of protein core with many attached carbohydrate chains called glycosaminoglycans (GAGs).

Cytochrome C reductase

Third protein complex in ETC. accepts electrons from ubiquinone (coenzyme Q) and passes electrons on to cytochrome C.

How does activity of isocitrate dehydrogenase change with the needs of the cell?

This is an enzyme in the Kreb's cycle that causes an exergonic reaction (-delta G). In the presence of ATP, the enzyme is inhibited.

Which will have more particles in solution? 0.5 moles of NaCl (i = 2) or 1 mole of sucrose (i =1)?

This will result in the same number of particles. Can be calculated by iM. therefore, the two will have the same effect on a colligative property.

halpoinsufficiency

a diploid organism only has a single functional copy of a gene, which is not enough to support a normal state.

pH of stomach

about 2

When does high transcription of Z,Y, and A genes occur? high or low levels of glucose/lactose?

absence of glucose and presence of lactose.

function of colon

absorb water and minerals, form and store feces until time of defecation

Function of NADPH (produced in PPP - pentose phosphate pathway)

acts as reducing agent in many anabolic processes. It also aids in neutralizing reactive oxygen species.

The nitrogenous bases

adenine, guanine, cytosine, thymine, uracil

names of the nucleosides (nitrogenous bases linked to ribose)

adenosine, guanasine, thymidine, cytidine, and uridine.

Examples of cells derived from fibroblasts

adipocytes, chondrocytes, and osteocytes.

Annealing

aka hybridization. binding of two complementary DNA strands.

What plasma proteins are synthesized in the liver

albumin, globulins, fibrinogens, other clotting factors.

What are the 5 key hormones that involve the kidneys?

aldosterone, ADH, calcitonin, PTH, and erythropoietin. Of these, only erythropoietin is produced by the kidneys.

Nonpolar, hydrophobic amino acids

aliphatics (glycine, alanine, valine, leucine, isoleucine, and proline), phenylalanine, tryptophan, methionine. Usually found in interior of globular protein structures.

Types of glycosidic linkages that mammals can digest

alpha glycosidic linkages

2 most common types of secondary structures of proteins

alpha helix and beta pleated sheets

Two proteins that make up a microtubule

alpha-tubulin and beta-tubulin. Microtubules are dynamic and get longer or shorter by adding or removing tubulin monomers from the end. The other end does not elongate, as it is attached to microtubule organizing center (MTOC).

Examples of hydrophilic molecules that cannot pass through phospholipid membrane easily?

amino acids, carbohydrates, and ions.

Amino acid catabolism

amino group is removed and converted to urea for excretion. remaining carbon skeleton can be broken down to CO2 and H2O, or it can be coverted to glucose or acetyl CoA.

Residual volume

amount of air that remains in lungs after strongest possible expiration.

What is oxidized in glycolysis to produce NADH, and what does it become?

an aldehyde. It becomes a COOH.

What type of cells do enveloped viruses infect?

animal cells

adenohypophysis is the .... while neurohypophysis is the...

anterior pituitary gland, posterior pituitary gland. Mnemonic: Anterior = Adeno

if polypeptide folds once and forms beta pleated sheet with it self, would it be parallel or antiparallel?

antiparallel

Does DNA participate in parallel or antiparallel bonding?

antiparallel (5' of one strand binds to 3' of the other).

Small nuclear RNA (snRNA)

around 150 nucleotides long. Associate with proteins to form snRNP (small nucear ribonucleic particles) complexes in the spliceosome

Where does exchange of materials between blood and tissue occur?

capillaries Other vessels are too thick and muscular for exchange to occur.

Proper name of rod-shaped bacteria

bacillus/bacilli

Mechanism of action of thyroid hormone

binds to receptor in the cytoplasm of cells that regulates transcription in the nucleus (considering it is an AA derivative and not a steroid, this behavior is anomalous). Effect of this increases metabolic rate and body temperature.

holoenzyme

biochemically active compound composed of enzyme and coenzyme. Holo meaning "complete".

glycosidic linkage

bond between two sugar molecules that forms from a dehydration reaction that requires enzymatic catalysis.

Do fungi produce sexually or asexually?

both

Transfer RNA (tRNA)

carries an amino acid from the cytoplasm to the ribosome, adding it to a growing protein.

Ribozymes

catalytic RNAs.

Fatty acid synthase

catalyzes decarboxylation of malonyl-CoA, adding two carbons from malonyl-CoA to a growing fatty acid. This process requires NADPH (which is generated from pentose phosphate pathway). Will continue until fatty acid contains 16 C, and then additional enzymes will modify the fatty acid.

DNA polymerase

catalyzes elongation of daughter strand using parental template, and elongates the primer by adding dNTPs to its 3' end.

Hexokinase

catalyzes first step of glycolysis - phosphorylation of glucose using ATP to form G6P. Inhibited by G6P (feedback inhibition).

polyribosome

chain of ribosomes that attach to mRNA and initiate translation. Occurs in proks and euks

How does adding a reactant or product to a system in equilibrium affect Q and Keq?

changes Q (which is [products]/[reactants] at any given time), but does not change Keq (which is [products/reactants] at equilibrium).

epigenetics

changes in gene expression that are not due to changes in DNA sequences, but are either heritable or have a long term effect.

What cells secrete pepsinogen?

chief cells. Later converts to pepsin due to acidity of stomach, which is a protease.

Pancreatic enzymes activated by trypsin

chymotrypsinogen to chymotripsen, procarboxypeptidase to carboxypeptidase, and procolleganse to collegenase.

beta-oxidation of fatty acids

cleaves free fatty acids into 2 carbon acetyl CoA groups, which are used in Kreb's cycle to create ATP. Each beta oxidation produces 1 FADH2 and 1 NADH.

nucleosomes

cluster of histones in which DNA wraps around. These are the "beads" of the beads on a string model (DNA is the string)

Proper name of round bacteria

coccus/cocci

I gene (lac operon)

codes for repressor protein, which binds to the operator of the lac operon and prevents RNA pol from being able to bind. It can also function by binding to lactose.

Mucociliary escalator

columnar epithelial cells of upper respiratory tract have cilia on their apical surfaces which constantly sweep the layer of mucus toward the pharynx, where mucus containing pathogens and inhaled particles can be swallowed or coughed out.

T helpers

communicates with other cells by releasing special hormones called lymphokines and interleukins.

Competitive inhibitors

compete with substrate at active site. Resemble the structure of the substrate or, even more effectively, the transition state that is normally stabilized by the active site.

chylomicrons

composed of fat and lipoproteins, carried to organs via blood stream and lmphatic system. Is then hydrolyzed to free fatty acids, which are then used to generate energy.

Spliceosome

composed of proteins and small nuclear RNA (snRNA), which form snRNPs (small nuclear ribonucleic particles). Assembles around introns that need to be removed.

What does reaction rate depend on? (enzyme kinetics)

concentration of substrate and concentration of enzyme

tendons

connects bones and muscles.

viroids

consist of short piece of circular, single-stranded RNA with extensive self-complementarity. Do not typically code for proteins and lack capsids. Often produce siRNAs, silencing normal gene expression. Most viroid diseases found in plants.

Nucleus functions and number of membranes

contain and protect DNA, transcription, partial assembly of ribosomes. Has 2 membranes.

Amphipathic

contain both hydrophilic and hydrophobic regions (soap)

glycolipids

contain fatty acid groups and carbohydrate side chains. One of most common lipids in eukaryotic membranes.

Constitutive activity

continuous enzyme catalysis

topoisomerases

cut the strands of DNA to unwrap the helix after it becomes more tightly coiled due to the effect of helicase.

where does fatty acid anabolism take place?

cytoplasm (which allows it to be compartmentalized from enzymes that catabolize fatty acids)

Wobble hypothesis

due to the fact that there are 61 codons in mRNA and only 45 anticodons in tRNA, some anticodons have to bind to codons that are not exact matches. To compensate, the 5' base of the anticodon can often "wobble", binding to a base of the codon that is nonpreferential. For this to work, the other two bases must be matched correctly.

Three segments of small intestine

duodenum, jejunum, and ileum

Chaperones

family of proteins that folds a nascent protein into its correct 3 dimensional shape

Which stores more energy: fats or carbohydrates? why?

fats, because of greater packing ability (pack more tightly due to greater hydrophobicity), and greater energy content (because they are more reduced).

unsaturated fatty acid

fatty acid that contains at least one double bond, almost always in Z (cis) orientation.

Saturated fatty acid

fatty acid that is "saturated" with hydrogen, and does no contain any double bonds

Three major components of the prokaryotic flagellum

filament, hook, and basal structure

Tight junctions - define and give example

form seal between the membranes of adjacent cells that blocks the flow of molecules across the entire cell layer. Form bands around the entire cell. Example - epithelial cells in the gut.

closed complex (transcription)

formed when RNA polymerase holoenzyme (complete enzyme) recognizes a promoter and stops to unwind the DNA.

ligase

forms a chemical bond (e.g., DNA ligase)

fMet

formyl methionine. Is the first amino acid to be added to ribosome during translation in proks.

Central chemoreceptors

found in medullary respiratory control center, and monitor P(CO2) and pH of CSF.

MHC I (Major histocompatability complex I)

found on the surface of every nucleated cell in the body. Their role is to randomly pick up peptides from inside the cell and display them on the cell surface, exposing any possible infection within the cell to killer T cells that are monitoring it. Killer T cells are recruited to destroy it.

Glycerol

foundation of triglycerides. Contains 3 OH groups, which are esterified to fatty acids.

Freezing point depression equation

freezing point depression = -Kf x im Kf = solvent's freezing point depression constant i = the solute's van't hoff factor m = molal concentration of the solution. Same as boiling point elevation, but negative due to decreasing temperature.

How many copies of a chromosome would a gamete have if nondisjunction occurs?

either 2 or 0. Typically results in a zygote with trisomy or monosomy (because other parent will donate gamete with 1 copy of each chromosome).

When is the reducing power of all NADH and FADH2 generated by cellular respiration put to use?

electron transport/oxidative phosphorylation.

Telomeres

ends of chromosomes. Composed of distinct nucleotide repeat sequences that are often rich in guanine. Contains about 300 bp of single stranded DNA at the very end. telomeres contain protein caps that prevent activation of repair pathways.

first law of thermodynamics

energy not created or destroyed

What does a low Km say about an enzymatic reaction?

enzyme has a high affinity for the substrate (it requires much less substrate to get the reaction to 1/2 Vmax).

Pepsin

enzyme secreted by chief cells in the stomach wall. Catalyzes proteolysis. Originally in the form of pepsinogen, which is inactive form. Converted by gastric acidity.

reverse transcriptase

enzyme used by some retroviruses to make DNA from RNA (going against central dogma)

What is required for hydrolysis of carbohydrate to occur?

enzyme with specificity toward that carbohydrate. If the activation energy of this reaction were lower, it would occur spontaneously, not allowing for storage.

Lipases

enzymes that hydrolyze fats

Goblet cells

epithelial cells within respiratory tract or GI tract that secrete mucus.

What cells line the lumen of the GI tract?

epithelial cells.

why is euchromatin portion of chromatin more likely to undergo transcription/DNA replication?

euchromatin is lighter, less dense portion of DNA in chromatin. There is more space for DNA to interact with enzymes and proteins.

Is hnRNA (heterogeneous nuclear RNA) found in eukaryotes, prokaryotes, or both?

eukaryotes

eEF-1

eukaryotic elongation factor - plays role in elongating polypeptide being made in translation. Helps with entry of animo-acyl tRNA into A site and catalyzes release of GDP.

eEF-2

eukaryotic elongation factor. plays role in elongating polypeptide being made in translation. Is the translocase of euk translation.

What are eIFs? How are there activities controlled?

eukaryotic initiation factors - proteins involved in initiating and regulating translation. They are controlled by post translational modification.

eRF3

eukaryotic release factor 3. ribosome-dependent GTPase that helps eRF1 release completed polypeptide in translation.

eRF1

eukaryotic release factor. Recognizes all 3 stop codons and allows for release of polypeptide formed in translation with the help of eRF3.

photoreactivation

example of a direct reversal of a mutation. In this case, pyrimidine dimers that formed due to UV radiation can be reversed with exposure to visible light.

What does RNA polymerase lack that DNA polymerase has?

exonuclease activity. It is unable to remove mismatched nucleotides.

difference between exonuclease and endonuclease?

exonuclease witll cut a nucelic acid chain at the end. An endonuclease will cut a polynucleotide acid chain in th emiddle of the chain, usually at a particular sequence.

How can bacterial growth be described in ideal conditions?

exponential

T tubules

extensions of the membrane of cardiac muscle, allowing maximum entry of calcium into the cell in order to allow longer membrane depolarization.

exteroceptors vs interoceptors

exteroceptors are sensory receptors that detect stimuli from the outside world, while interoceptors are sensory receptors that respond to internal stimuli.

heterochromatin

dark regions of densely packed chromosomes - rich in repeats. Difficult for genes to be accessed within heterochromatin, and so they are usually turned off.

Summation

decision of a postsynaptic neuron whether to fire an action potential, based on adding the effect of all synapses impinging on a neuron, both excitatory and inhibitory.

Where are sensory receptors located in skin?

dermis

Van't Hoff equation

describes osmotic pressure. (π= MiRT) M= molarity R= .0821 L-atm/K-mol T in Kelvin

What are the effects of low pH in stomach?

destruction of microorganisms, acid catalyzed hydrolysis of many dietary proteins, and conversion of pepsinogen to pepsin.

How do viruses navigate between host cells?

diffusion (no flagella)

second law of thermodynamics

disorder, or entropy of the universe tends to increase.

Where does most secretion occur in nephron?

distal convoluted tubule. This is also how most drugs and toxins are secreted into urine.

Eight principal taxonomic categories

domain, kingdom, phylum, class, order, family, genus, species.

If surrounding pH is higher than the pKa of a molecule, will the molecule accept or donate H+?

donate

Van'f Hoff (or ionizability) factor

donated as i. Tells us how many ions one unit of a substance will produce in a solution. Example - for NaCl, i=2

How does cartilage receive nutrition and immune protection if is is avascular?

from surrounding fluid.

MicroRNA (miRNA) and small interfering RNA (siRNA)

function in RNAi (interference) in order regulate gene expression post transcriptionally. Can bind to specific mRNA molecules to affect translation.

noncoding RNA

functional RNA that is not translated into protein

What kind of cells do telomerase typically act on?

germl line, embryonic stem cells, some WBCs and some cancer cells (which help them immortalize).

Three hormones that can raise the blood sugar

glucoagon, epinephrine, and cortisol.

What does adrenal cortex secrete?

glucocorticoids (main one being cortisol) and mineralcorticoids (main one being aldosterone), and some sex hormones.

Enzyme that regulates pentose phosphate pathway (PPP)

glucose 6 phosphate dehydrogenase.

Storage unit for glucose in animals

glycogen

Would elevated glucagon levels (meaning low blood glucose) stimulate glycogen synthase or glycogen phosphorylase?

glycogen phosphorylase (catabolizes glycogen into glucose). Glycogen syntahse would not be helpful, as it would use up glucose 1 phosphate to store more glycogen.

Would elevated insulin levels (meaning high blood glucose) stimulate glycogen synthase or glycogen phosphorylase?

glycogen synthase (enzyme that creates glycogen from glucose-1-P). Glycogen phosphorylase would not be helpful, as it would catabolize glycogen into more glucose.

Are fungal adults haploid or diploid?

haploid. It produces a diploid zygote, but this zygote quickly enters meiosis forming haploid cells again. This undergoes repeated division by mitosis.

For what reasons are mtDNA used in evolutionary biology and population history studies?

high copy number (average of 5 copies per mitochondria), high mutation rate, doesn't undergo recombination, and has maternal inhertance.

TATA box

highly conserved DNA recognition sequence for the TATA box binding protein, which initiates transcription complex assembly at the promoter.

Polar, basic amino acids

histidine, arginine, lysine

How could one piece of RNA synthesize 2 different polypeptides?

hnRNA (heterogenous nuclear RNA) can accomplish this with differential splicing prior to becoming mRNA.

Primary transcript in eukaryotes

hnRNA (made by RNA pol II). This is modified extensively before translation, which is a main difference from translation in prokaryotes.

Microtubules

hollow rod making up cytoskeleton in animals - composed of two globular proteins (alpha-tubulin and beta-tubulin), polymerized noncovalently.

two pathways for double strand break (DSB) repair

homologous recombination and nonhomologous end-joining.

Nucleases

hydrolyze dietary DNA and RNA (pancreatic enzyme)

hydrolase

hydrolyzes chemical bonds. (hydrolysis entails breaking apart bonds while incorporating water).

protease

hydrolyzes peptide bonds (e.g. trypsin, chymotrypsin, and pepsin).

What dictates tertiary folding?

hydrophobic/hydrophilic interactions of R groups

where do SNPs occur most often?

in noncoding regions of DNA.

zymogen/proenzymes

inactive form of an enzyme. Enzyme precursor

Will increasing unsaturated fatty acids in a membrane cause an increase or decrease in membrane fluidity?

increase. Kinked structure, less van der waals interactions.

residue

individual AA when part of a polypeptide chain

At equilibrium, which is thermodynamically favored: individual AAs or peptide?

individual amino acids

Is lac operon inducible or repressible?

inducible (it catabolizes)

gene repressor proteins

inhibit transcription in euks.

3 stages of transcription

initiation, elongation, termination.

Three distinct stages of translation

initiation, elongation, termination.

Where does electron transport/oxidative phosphorylation occur?

inner mitochondrial membrane

Which is active process? expiration or inspiration?

inspiration

What is an important element of transposase DNA?

inverted repeats that flank the transposon gene (for example: GGCCAAT-transposase gene-ATTGGCC)

Colon is AKA the....

large intestine

Which daughter strand is continuously replicated during DNA replication? Which daughter strand is discontinuously replicated?

leading strand, lagging strand IMPORTANT TO MEMORIZE

The more specialized a cell becomes, the (blank) likely it is to be able to reproduce itself?

less. They are replenished by reproduction of stem cells.

Homeotherms

life forms with constant body temperatures.

euchromatin

lighter, less dense regions of chromatin. Genes within euchromatin are more easily activated.

cardiac muscle

lines heart

smooth muscle

lines organs

Alpha-glycosidic linkage

linkage between sugar molecules that points downward from anomeric carbon (carbon attached to 2 Os). Remember - fishies (alpha symbol) stay down, birdies stay up.

beta-glycosidic linkage

linkage between sugar molecules that points upward from anomeric carbon (carbon attached to 2 Os). Remember - fishies (alpha symbol) stay down, birdies stay up.

cholesterol

lipid that serves as a building block for hydrophobic steroid hormones, such as estrogen and testosterone. Contributes to membrane fluidity.

Accessory organs of GI tract

liver, gallbladder, and pancreas. Also salivary glands.

Digestive organs primarily involved in exocrine secretion?

liver, gallbladder, pancreas. Also performed by individual epithelial cells of the gut itself. (They dump secretions directly into the GI lumen via ducts).

fatty acid

long carbon chain (typically 14-18 carbons long) with carboxylic acid terminus.

Tropmyosin

long fibrous protein that winds around actin polymer within microfibril, blocking all myosin binding sites.

Long ncRNAs

longer than 200 nucleotides. Help control basal transcription. Can also play roles in post transcriptional regulation by controlling splicing and translation. Also function in imprinting and X chromosome inactivation.

Possible cycles of animal viruses

lytic cycle, lytic-like cycle called productive cycle, and lysogenic cycle (productive cycle does not occur in bacteria)

type of RNA that is used to construct protein

mRNA

primary transcript in prokaryotes

mRNA. Because of this, it is ready to be translated immediately, and this often occurs before transcription is even complete!

Monocytes

macrophages Undergo phagocytosis of debris and microorganisms, amoeboid motility, chemotaxis

rRNA (ribosomal RNA)

major component of ribosomes.

phospholipids

make up barrier between intracellular and extracellular environments in cellular membranes.

eukarya defining characteristics

membrane bound organelles

cofactors

metal ions or small molecules required for activity in many enzymes (many vitamins are precursors for cofactors, including vitamin B3 into NAD+)

Where does Kreb's cycle occur?

mitochondrial matrix

Where does PDC occur (pyruvate dehydrogenase complex)

mitochondrial matrix

where does fatty acid catabolism occur?

mitochondrial matrix

Inosine

modified adenine, which can act as a wobble base in tRNA anticodon. In doing so, it can bind to A, U, or C in mRNA codon.

uncompetitive inhibitor

molecule that inhibits catalytic activity of an enzyme by binding to the enzyme-substrate complex. (It cannot bind before the substrate is bound).

Creatine phosphate

molecule used for intermediate term energy storage. Its hydrolysis drives regeneration of ATP from ADP and Pi. This is necessary because glycolysis and TCA cycle are not fast enough to keep pace with rapid ATP utilization during extended contraction.

How does liver assist in lipid metabolism

molecules called chylomicrons exit intestine and enter the liver via hepatic portal vein. Degraded by lipases into triglycerides, glycerol, and cholesterol rich chylomicron remnants. These remnants are taken up by hepatocytes and combined with proteins to make lipoproteins (HDL, LDL, VLDL, etc.). They then reenter blood and are source of cholesterol and triglycerides for other tissues in the body.

glycosidic linkages in glycogen and starch

mostly alpha-1,4, but some alpha-1,6

Quaternary structure

mostly noncovalent interactions between subunits (not between chains on the same polypeptide). May also be disulfide bridges.

Animalia defining characteristics

multicellular, diploid, eukaryotic organisms; chemoheterotrophs that perform ingestive digestion.

kinetochores

multiprotein complexes that act as anchor attachment sites for spindle fibers.

What are two types of effectors?

muscles and glands

Intercalating agent

mutagen that causes errors in replication by inserting itself between base pairs in DNA.

intergenic regions

noncoding DNA - may assemble specific chromatin structures or regulate nearby genes. Examples are tandem repeats and transposons.

Electrical synapses. What type of junctions are between cells with electrical synapses. In what cells are they more common?

occur when the cytoplasms of two cells are joined by gap junctions. Action potentials spread directly from one cell to another through an electrical synapse. More common in smooth muscle and cardiac muscle.

Chromosome amplification

occurs when a segment of a chromsome is duplicated.

Sympatric speciation

occurs when a species gives rise to a new species in the same geographical area, such as through divergent selection.

double strand break

occurs when both backbones of DNA helix break due to a physical mutagen (such as ionizing radiation). As opposed to single strand breaks, these are very difficult to repair.

Translocations

occurs when recombination occurs between nonhomologous chromosomes (a segment of chromosome 4 may be swapped with a segment of chromosome 20). This may cause gene fusion, which could create a new gene product.

How many neurotransmitters can a presynaptic neuron release? How many can a postsynaptic neuron respond to?

one, several.

Transcription bubble

opening of dsDNA that forms when RNA pol is attached and unwinds it. Once a termination signal is detected, RNA polymerase is released, RNA is released, and transcription bubble closes.

photoautotrophs

organism who gets its energy from the sun and use only CO2 as carbon source.

Sarcomeres

overlapping arrangement of bands of thick and thin filaments in myofibrils.

short arms of chromosomes

p arms (long arms are q)

Example of a common tumor suppressor gene

p53 - induces apoptosis.

What are additional tasks done by respiratory system, other than ventilation and respiration?

pH regulation, thermoregulation, and protection from disease and particulate matter.

what enzyme converts triglycerides to fatty acids and monoglyceride?

pancreatic lipase

Where is PTH produced? What is its target and effect?

parathyroid. Opposite that of calcitonin (in other words, it causes increase of calcium ions in blood by breaking down bone, reabsorbing into gut, and reabsorbing into blood stream instead of urinating it out.

conservative replication

parental dsDNA remains as is, while an entirely new dsDNA is created. THIS WAS PROVEN FALSE BY MESELSON AND STAHL EXPERIMENT.

Interphase

part of cell cycle between divisions (includes gap phases plus S phase)

Mitosis

partitioning of cellular components (genes, organelles, etc.) into two halves prior to cell division

origin of replication (ORI)

pattern of nucleotides along DNA that attract specific proteins to recruit helicase, which will initiate replication.

Lysogenic cycle (viruses)

phage genome is incorporated into bacterial genome, now referred to as a prophage. The host in this situation is called a lysogen. The prophage remains dormant for a while, as it has a phage-encoded repressor protein that binds to phage promotors, blocking transcription of phage genes. It reproduces with each reproduction of host cell, and then eventually becomes activated. It then removes itself from the host genome (in a process called excision) and enters the lytic cycle.

Lytic cycle of phages

phages inject genome into bacterium. Early genes, such as hydrolase, are encoded immediately by ribosomes of the bacterium. This enzyme degrades the entire host genome. Multiple copies of the phage genome are reproduced using the dNTPs from the degraded host genome. Abundance of capsid proteins are also produced, which surround the new copies of phage genomes. Lysozyme is then produced (a late gene), which destroys bacterial cell wall, releasing newly formed phages.

What bonds of ATP are energy contained?

phosphoanhydride bonds

Most common lipids in eukaryotic membranes

phospholipids (most abundant), glycolipids, and cholesterol

Cytokinesis

physical process of cell division.

Hypophysis is another name for...

pituitary gland

What requires net energy input: polysaccharide synthesis or hydrolysis?

pollysaccharide synthesis

primary structure of protein

polypeptide chain.

secondary structure of protein

polypeptides are folded into shapes and stabilized by hydrogen bonding between backbone NH and CO groups.

Gap junctions - define and give example

pore-like holes connecting cells. Allow ions to flow back and forth between them. Also allow for exchange of amino acids and carbohydrates, but not polypeptides and organelles. Example: smooth muscle and cardiac muscle

Cis stack

portion of golgi apparatus closest to the rough ER.

Trans stack

portion of golgi apparatus furthest from the rough ER.

two ways of altering genetic expression outside of the central dogma

post translational modification and DNA methylation.

dispersive theory of replication

postulated that genomes were composed of scattered pieces of new and old DNA. THIS WAS PROVEN FALSE BY MESELSON AND STAHL EXPERIMENT.

Driving force of blood flow

pressure difference between arteries and veins

Vapor pressure

pressure exerted by a gaseous phase of a liquid that evaporated from the exposed surface of a liquid. Weaker intermolecular forces = higher vapor pressure (more volatile)

Reciprocal control

prevents two opposing reactions from occurring at the same time.

ORgans involved in excretion

primarily kidneys, but also liver, large intestine, and skin.

Exocytosis

process by which a secretory vesicle containing proteins leaves golgi apparatus, fuses with plasma membrane, and then releases its contents to the extracellular environment. Hormones and digestive enzymes are examples.

Oxidation

process by which carbohydrates are broken down to CO2. AKA burning or combustion.

Phagocytosis

process by which large particulate matter is engulfed by the cell (such as when macrophages of immune system engulf bacteria and viruses). This matter ends up in phagocytic vesicle, which fuses with lysosomes for degradation.

how are chromosomes oriented in prokaryotes?

prokaryotes have a single, circular chromosome.

4 phases of mitosis

prophase, metaphase, anaphase, and telophase (PMAT).

transposase

protein that "cuts and pastes" transposons (transposable elements). A transposase gene is always incorporated in transposon DNA.

Difference between proteins synthesized on cytoplasmic ribosomes and on ribosomes of rough ER

proteins created from cytoplasmic ribosomes will move toward peroxisomes, mitochondria, nucleus, or head to the cytoplasm. From rough ER, they will secrete to extracellular environment, become intermembrane proteins, or head toward ER, Golgi apparatus, or rs.

What enzyme converts polysaccharides to disaccharides

ptyalin and pancreatic amylase

reactants in PDC (pyruvate dehydrogenase complex)

pyruvate, Coenzyme A, and NAD+

What does K'eq represent?

ratio of products to reactants at equilibrium.

exergonic reactions

reactions that occur spontaneously (negative delta G).

Causes of double strand breaks

reactive oxygen species, ionizing radiation, UV light, or chemical agents

isomerase

rearranges bonds within a molecule to form an isomer

Which of the following stores energy, like compressing a spring? oxidation or reduction?

reduction

Path of sound to hearing:

sound waves - auricle - external auditory canal - TM - malleus - incus - stapes - oval window - perilymph - endolymph - basilar membrane - auditory hair cells - tectorial membrane - neurotransmitters stimulate bipolar auditory neurons - brain - perception

Proper name of spiral-shaped bacteria

spirillum/spirilla or spirochete/spirochetes.

what does deltaGº' represent?

standard free energy change of a system with equal concentrations of products and reactants at a pH of 7. Can predict spontaneity of reaction at ideal (lab) conditions, but cannot predict spontaneity under actual conditions.

What can be digested in the mouth? what can't be?

starch, fat can be. Proteins cannot be. lysozyme of saliva also attacks bacteria.

Make up of hydrophobic hormones

steroid hormones that bind to receptors in cellular interior. Differ from hydrophilic hormones, which are either peptides or amino acid derivatives.

How does gastrin work?

stimulates secretion of histamine, which binds to parietal cells to stimulate acid release. Ranitidine is a histamine receptor antagonist, which prevents acid release.

triacylglycerol

storage form of fatty acid. AKA triglyceride or fat. Stored in adipose cells.

Functions of endoskeleton

support body, framework for movement, protect organs, store calcium, synthesize formed elements of blood (RBCs, WBCs, platelets. This is called hematopoiesis).

Apical surface

surface of plasma membrane exposed to the body exterior or the cavity of an internal organ.

What glands are located in dermis?

sweat and oil glands (sudoriferous and sebaceous).

what does it mean when delta G = 0?

system is at equilibrium

mismatch repair pathway (MMR)

targets mismatched bases in DNA that were not corrected by DNA pol during replication.

How does transcription know when to stop?

terminator sequences of DNA.

Are catalysts consumed in a reaction or regenerated for future reactions?

regenerated.

centromere

region of chromosome to which spindle fibers attach during cell division. Made up of heterochromatin and repetitive DNA sequences.

open complex

region of single stranded DNA where RNA pol is bound to the promoter. Open complex forms after RNA pol binds to promoter, unwinding the DNA to a single strand.

Is the Trp operon a repressible enzyme or an inducible enzyme?

repressible (so it is turned on until in the presence of tryptophan)

Would saturated or unsaturated fatty acid have more van der waals interactions with bilayer membrane?

saturated fatty acid, because it is not bent, allowing for better fit and greater interaction.

Elongation (in proks)

second aminoacyl-tRNA enters the A site and hydrogen bonds with the second codon. Requires hydrolysis of one phosphate from GTP. Elongation factor EF-Tu contains a GTPase to do this. EF-T then removes the remaining GDP from EF-Tu, allowing it to reset. Then, peptidyl transferase activity of large ribosomal subunit (the 23S rRNA) catalyzes the formation of a peptide bond between fMet and second amino acid. In this reaction, tRNA is the leaving group, and leaves the ribosome. Next, translocation occurs, which moves the empty tRNA into the E site, the tRNA attached to the polypeptide into the P site, and the next codon to be translated into the A site. These steps occur over and over again.

open reading frame

section of mRNA that is responsible for coding protein - starts with start codon, ends with stop codon.

Calyx (kidneys)

see image

summary of sensory modalities

see image.

Interoception

sense that helps you understand and feel what's going on inside your body. For example, pH receptors and aortic arch baroreceptors

Mechanoreceptors

sensory receptors that respond to mechanical disturbance. Include Pacinian corpuscles, auditory hair cells, vestibular hair cells, etc.

nuclear envelope

separates contents of the nucleus into a distinct compartment, isolated from other organelles and from the cytoplasm. Composed of 2 lipid bilayer membranes. Allows for DNA replication, transcription, sand splicing to occur in nucleus while translation occurs in the cytoplasm.

Anticodon

sequence of three ribonucleotides located on tRNA that is complementary to the mRNA codon on which it translates.

Do mutations typically have greater effect on autosomes or sex chromosomes? why?

sex chromosomes, because autosomes are present in double copies and sex chromosomes are not.

PIWI-interacting RNAs (piRNAs)

short (20-30 nucleotides long). Work with PIWI proteins to prevent transposons from mobilizing.

SNPs

single nucleotide polymorphisms. occur 1 in every 1000 bp or so.

Subunit

single polypeptide chain that is part of a large complex containing many subunits. (example: hemoglobin has 4 of these)

SSBPs

single stranded binding proteins - protect unstable, single stranded DNA that has been unpackaged for replication, keeping the strands separated.

A site (ribosome)

site of ribosome at which each new tRNA delivers its amino acid. AKA Aminoacyl-tRNA site (hence the A)

P site (ribosome)

site of ribosome at which growing polypeptide chain, still attached to tRNA, is located during translation. AKA Peptidyl-tRNA site, hence the P.

E site (ribosome)

site of ribosome where now-empty tRNA sits prior to its release from the ribosome. AKA the Exit-tRNA site, hence the T.

Amino acid acceptor site

site of tRNA at which its amino acid binds. Located on 3' end of tRNA. ALWAYS composed of CCA.

Levels of skeletal muscle organization

skeletal muscle, fascicle, myofibers, myofibrils, sarcomere.

Three types of muscle

skeletal, cardiac, smooth

snRNP

small nuclear ribonucleic particles (composed of snRNA and proteins). Participate in spliceosome to splice out introns by hydrogen bonding to conserved nucelotides.

Initiation (translation in prokaryotes)

small ribosomal subunit (30S) binds two initiation proteins called IF1 and IF3. This complex then binds to mRNA transcript. Next, first aminoacyl-tRNA (amino acid is fMet) joins at P site with initiation factor call IF2, which is also bound to GTP. Finally, the 50S subunit complmetes the complex. This is powered by GTP hydrolysis.

Muscle twitch

smallest measurable muscle contraction

skeletal muscle

voluntary muscle

How many FADH2, NADH, and Acetyl CoA groups would be formed from beta oxidation of lauric acid (12 carbon free fatty acid)

would be 5 cleavages - so would produce 5 FADH2 and 5 NADH. However, it would form 6 Acetyl CoA groups, as the last cleavage forms 2 Acetyl CoA groups. These are then used in Kreb's cycle.

Flux (diffusion)

the rate of diffusion.

Does molarity change with temperature? does molality?

yes, no.

Ohm's Law in terms of hemodynamics (blood flow).

ΔP = QR Similar to V = IR ΔP = pressure gradient between arterial system and venous system. Q = blood flow R = resistance

Three types of cells in islets of langerhans

α cells secrete glucagon in response to low blood sugar. β cells secrete insulin in response to high BS. δ cells secrete somatostatin, which inhibits many digestive processes.

How do transposons work?

they code for transposase protein, which cuts an element of DNA (a transposon sequence) and pastes it to another location. Sometimes transposon sequences are completely excised and removed, sometimes they are duplicated and moved while still maintaining its original location.

codon

three letter code of DNA that allows for construction of an amino acid.

RNA polymerase II

transcribes hnRNA (so ultimately mRNA). Also makes most snRNA and some miRNA. (eukaryotes).

RNA polymerase I

transcribes most rRNA (in eukaryotes).

Three mechanisms by which bacteria increase genetic diversity

transduction, transformation, and conjugation.

2 main types of noncoding RNA

transfer RNA (tRNA) and ribosomal RNA (rRNA)

phosphorylase

transfers a phosphate group to a molecule from inorganic phosphate (e.g. glycogen phosphorylase)

Path of protein created in rough ER

transported through vesicles that bud from ER to the Golgi apparatus, then to the plasma membrane or lysosome.

3 main physiological lipids

triglycerides (fats), phospholipids, and cholesterol

signal amplification

turns one signal molecule into multiple second messenger molecules

synonyms (in terms of codons)

two codons that code for the same AA.

mRNA

type of RNA that carries genetic information to ribosomes, allowing for production of polypeptides

Missense mutation

type of point mutation in which one AA is replaced by another AA.

What kind of fatty acid increases membrane fluidity?

unsaturated, as kinks disrupt orderly packing of phospholipid bilayers.

Transition state

unstable, transient intermediate that must be reached by input of activation energy before reactions can occur

What is located at 5' end of mRNA?

untranslated region (UTR), which is important in initiation and regulation of translation.

helicase

unwinds dsDNA and separates the strands in preparation for DNA replication (however, it only pulls the DNA strands apart, creating more tension on either side of the ORI - picture pulling on 2 ropes that are coiled around each other apart. Topoisomerase are required to relieve this)

Upstream elements of protein coding genes in euks

upstream control elements (UCEs) 200 bases upstream of initation site, core promoter containing building sites for basal transcription complex and RNA polymerase II (about 50 bases upstream of initation site), and TATA box 25 bases upstream (-25).

Substances excreted in urine

urea, sodium, bicarbonate, and water.

DNA gyrase

uses energy from ATP to twist the circular chromosome of prokaryotes into supercoils.

Mnemonic for remembering length of pre and post ganglionic neurons of autonomic system.

"para long pre". Parasympathetic preganglionic neurons are long. this means para post are short. Sympathetic are the opposite.

How many high energy phosphate bonds would be required in translation of a polypeptide that is 20 amino acids long?

(20*2)...aminoacyl-tRNA synthesis + (19*2)...elongation steps + 1....initiation. Total is 79, which is close to 4^n.

Hardy-Weinberg equation

(p+q)^2 = 1, or (p^2 + 2pq + q^2) = 1. This calculates population frequency of alleles. Let's say G and g are the alleles available in equal frequencies in a population. p represents frequency of G allele in a population, q represents frequency of g allele in population. P^2 represents frequency of GG genotype in population, 2pq represents frequency of Gg genotype in population, and q^2 represents frequency of gg genotype in population.

autophagy

(self eating). Process by which damaged organelles are degraded in lysosomes by hydrolases.

Main takeaways of electron transport/oxidative phosphorylation

1) NADH and FADH2 are oxidized by beginning of the ETC. 2) Electron released by ETC allows protons to pump back out into the mitochondria 3) energy from protons forms ATP. 4) Occurs in inner mitochondrial membrane

Three types of endocytosis

1) Phagocytosis 2) Pinocytosis 3) Receptor-mediated endocytosis

Main takeaways of pyruvate dehydrogenase complex

1) Pyruvate is decarboxylated to form acetyl group. 2) Acetyl group is then attached to coenzyme A, a carrier that can transfer the acetyl group into the Kreb's cycle. 3) a small amount of NADH is produced. 4) occurs in mitochondrial matrix 5) requires oxygen, but does not use it directly

The three meanings of "reduce"

1) Remove oxygen 2) Add electrons 3) Add hydrogen

Types of cells T killer cells target?

1) Virus infected host cells 2) cancer cells 3) foreign cells such as the cells of a skin graft given by incompatible donor Side note - T cells have specific targets!

Main takeaways from Kreb's cycle

1) acetyl group formed from pyruvate dehydrogenase complex is added to oxaloacetate to form citric acid. 2) Citric acid is decarboxylated and isomerized to recreate original oxaloacetate 3) A modest amount of ATP, a large amount of NADH, and a small amount of FADH2 are formed 4) occurs in mitochondrial matrix 5) requires oxygen, but does not use it directly

What are the three things a cell may do when telomeres become too short (they shrink with each replication)

1) activate repair pathways 2) apoptosis 3) enter senescent state (alive but not dividing)

3 steps of amino acid activation (tRNA loading) Page 166

1) amino acid reacts with ATP to form aminoacyl AMP. PPi is the leaving group 2) The pyrophosphate leaving group is hydrolyzed to 2 orthophophates (delta G <<0 for this reaction). 3) tRNA loading, an unfavorable reaction, is driven forward by destruction of high energy aminioacyl-AMP bond created in step 1.

The three meanings of "oxidize"

1) attach an oxygen (or increase the number of bonds to oxygen) 2) remove electrons 3) Remove hydrogen

Three important structures of villus in gut.

1) contains capillaries, which absorb dietary monosaccharides and amino acids. MErge to form hepatic portal vein, transporting these nutrients to the liver. 2) lacteals - small lymphatic vessels that absorb dietary fats. Merge to form large lymphatic vessels, which transport dietary fats to thoracic duct. 3) Peyer's patches - part of the immune system. collection of lymphocytes dotting vill that monitor GI contents and confer immunity to gut pathogens and toxins.

What 4 strategies are used to cope with cold weather?

1) contraction of skeletal muscles 2) insulation from skin, which conserves heat generated by metabolism. Fat helps. 3) Heat loss by conduction is minimized by constriction of blood vessels in dermis (cutaneous vasoconstriction). Occurs in response to cold weather or activation of sympathetic nervous system. 4) contrivances such as blankets.

4 ways of regulating enzyme activity

1) covalent modification. 2) proteolytic cleavage. 3) Association with other polypeptides. 4) Allosteric regulation.

Genes with their own promoter that code for proteins important in the regulation of the lac operon:

1) crp gene - located at a distant site, codes for catabolite activator protein (CAP), and helps couple the operon to glucose levels in the cell (CAP binds to operon in absence of glucose). 2) I gene: located at a distant site, codes for Lac repressor protein.

Three factors that stabilize the tense configuration of hemoglobin (which has low affinity for oxygen)

1) decreased pH 2) increased CO2 in blood 3) increased temperature HOT ACID is bad for hemoglobin This effect is known as Bohr effect

In a pedigree: 1) what is represented by a diamond? 2) What is represented by a circle? 3) What does shading in represent? 4) What does a square represent?

1) diamond represents unborn child 2) circle represents female 3) shading represents someone affected by a trait 4) Square represents a male

Functions of circulatory system

1) distributes nutrients from digestive tract, liver, and adipose (fat) tissue) 2) transport oxygen from the lungs to the entire body and carbon dioxide from the tissues to the lungs. 3) Transport metabolic waste products from tissues to the excretory system (i.e. the kidneys) 4) Transport hormones from endocrine glands to targets and provide feedback 5) Maintain homeostasis of body temperature 6) Hemostasis (blood clotting). This does not address a need of a multicellular organism per se, but rather is necessitated by the presence of the circulatory system itself.

Excretory and homeostatic roles of the kidney

1) excretion of hydrophilic wastes 2) maintenance of constant solute concentration and constant pH 3) maintenance of constant fluid volume (important for BP and cardiac output)

4 steps of oxidative catabolism of glucose

1) glycolysis 2) pyruvate dehydrogenase complex 3) kreb's cycle 4) oxidative phosphorylation/electron transport

Two ways to increase venous return? (and what does this affect?)

1) increase total volume of blood in circulatory system by retaining water (urinating less). 2) Contraction of large veins can propel blood toward the heart. Higher venous return stretches the heart muscle, which causes it to contract more forcefully (increasing cardiac output!). This is called the Frank-Starling mechanism.

Factors that determine if a reaction will occur spontaneously?

1) intrinsic properties of reactants and products (delta Gº') 2) concentrations of reactants and products (RTlnQ) 3) temperature (in a lab setting).

How does DNA methylation affect gene expression?

1) it can physically block genes from transcriptional proteins 2) Certain proteins bind methylated CpG (5'C---phosphate---3'G of DNA strand that is often methylated) groups and recruit chromatin remodeling proteins that change the winding of DNA around histones.

Why might free exonucleases present in a cell? Give 2 reasons.

1) mRNA is often degraded rapidly. This regulates mRNA activity, which regulates gene expression. 2) They offer a way of degrading viral RNA that do not have 5' methylated guanine cap and 3' poly-A tail.

Three functions of larynx

1) made entirely of cartilage and thus keeps airway open. 2) contains epiglottis, which seals trachea during swallowing to prevent the entry of food. 3) contains vocal cords, which are folds of tissue positioned to partially block flow of air and vibrate, producing sound.

Three types of point mutations

1) missense mutation 2) nonsense mutation 3) silent mutation

Two reactions catalyzed by splicesome in order to eliminate introns

1) one end of an intron is attached to a conserved adenine within that same intron, forming a loop 2) exons are joined together, releasing this loop.

How is RNA different from DNA?

1) single stranded (except in some viruses 2) contains ribose instead of 2' deoxyribose 3) contains uracil instead of thymine

Similarities between skeletal muscle and cardiac muscle

1) thick and thin filaments organized into sarcomeres, giving striated appearance. 2) T-tubules 3) Troponin-tropomyosin regulates contraction 4) Length tension relationship works same way, but more significant in cardiac muscle.

Why does water tend to leak out of intercellular clefts of capillary walls and into tissues?

1)Hydrostatic pressure created by heart squeezes water out of capillaries 2) High osmolarity of tissues tends to draw water out of bloodstream.

Examples of innate immunity

1)skin barrier 2) tears, saliva, blood contain lysozyme 3) acidity of stomach 4) WBCs phagocytosis 5) complement system - group of about 20 blood proteins that can nonspecifically bind to surface of foreign cells, leading to their destruction

How many chromosomes do prokaryotes have? how many origins of replication?

1, 1

Kf of water (freezing point depression constant)

1.9°C/mol

How many protons are pumped into intermembrane space when 1 NADH travels through ETC?

10 protons (this creates 2.5 ATP, as each ADP + Pi -> ATP reaction requires 4 protons).

If there are 1000 wolves in a population, out of which there are 100 homozygotes of an autosomal allele h and 200 heterozygoes, what is the frequency of the h allele?

1000 wolves means 2000 alleles present. 100 homozygotes accounts for 200 h, 200 heterzygotes accounts for 200 h. 400/2000 = .20

How many carbons are added at a time in fatty acid synthesis

2

how many net ATP and NADH are produced in glycolysis, per glucose molecule?

2 ATP and 2 NADH.

Which steps in prokaryotic translation require high energy phosphate bonds? how many HEPB do each of these steps require?

2 HEPBs are hydrolyzed for the formation of each aminoacyl-tRNA, 2 HEPBs are hydrolyzed for each elongation step (1 for each new aminoacyl-tRNA entrance to A site and 1 for translocation), and 1 HEPB is hydrolyzed during intiation to position tRNA and mRNA on the ribosome. Number of HEPBs required comes out to about 4^n, with n being number of peptides.

What products come out of glycolysis?

2 NADH, 2 H+, 2 H2O, 2 net ATP, and 2 pyruvate.

If mitochondria were once a prokaryotic cell, then why does mtDNA code for such few proteins? (the prokaryote that codes for the least amount of proteins still codes for WAY more than mtDNA does)

2 possible reasons: 1) no selective pressure for mtDNA to create proteins anymore because of presence of nuclear DNA 2) genes originally coded by mtDNA may have migrated to nuclear genome.

How many pairs of autosomes are there? How many total chromosomes are there?

22 (making up 44 chromosomes). There are 46 total chromosomes - the remaining two are the sex chromosomes.

number of chromosomes in human genome

24 (22 autosomes, 2 sex chromosomes)

distance between rungs of base pairs

3.4 Angstroms between each pair

Age of oldest fossils.

3.5 billion years old - primitive prokaryotic cell walls found in stromatolites (layered mats formed by colonies of proks).

total ATP produced by one glucose in eukaryotes? in prokaryotes?

30 ATP, 32 ATP respectively.

Genes coded by mitochondrial DNA

37 total genes. 13 are protein coding (the proteins involved in ETC), two code for rRNA, and the rest code for tRNAs. Nuclear genes control mtDNA replication, transcriptin, and translation.

pKa of a carboxylic acid functional group

4

How many cells are produced from single diploid parent cell during meiosis?

4 haploid cells are produced.

How many protons are required in proton pump to facilitate ADP + Pi -> ATP reaction?

4 protons

Initiation complex (eukaryotic translation)

43S pre-initation complex forms, composed of 40S small ribosomal subunit, Met-tRNA(met), and several eukaryotic initiation factors (eIFs). This complex is recruited to the 5' capped end of transcript by initiation complex of proteins (more eIFs). Scans mRNA for start codon; once found it recruits the large ribosomal subunit (60S) and translation begins.

Cytochrome C

4th membrane bound protein in ETC. Accepts electrons from cytochrome C reductase and passes them on to cytochrome C oxidase.

How many types of DNA polymerases do prokaryotes have? which ones are important to memorize?

5 DNA pol III and DNA pol I.

What sequences initiate translation in eukaryotes?

5' UTR sequences - a common one is the Kozak sequence, which is typically located a few nucleotides upstream of start codon.

Cytochrome C oxidase

5th and final membrane bound protein complex of ETC. Accepts electrons from cytochrome C. Reduces O2 to H2O.

For each glucose oxidized in cellular respiration, what are the products of Krebs cycle?

6 NADH, 2 FADH2, and 2 GTP (3, 1, and 1 per pyruvate). Also produces 4 CO2 per glucose.

How many protons are pumped into intermembrane space when 1 FADH2 travels through ETC?

6 protons (this creates 1.5 ATP, as each ADP + Pi -> ATP reaction requires 4 protons

How large are prokaryotic ribosomes? and their individual subunits?

70S. Small subunit is 30S and large subunit is 50S (S stands for Svedbergs, which is measure of sedimentation rate (how quickly something will sink in a gradient during centrifugation)).

How many histones are in a nucleosome?

8

How large are eukaryotic ribosomes? and their individual subunits?

80S. large subunit is 60S and small subunit is 40S (S stands for Svedbergs, which is measure of sedimentation rate (how quickly something will sink in a gradient during centrifugation)).

Arrangement of microtubules in cilia and flagella of euk cells. What binds the microtubules together?

9+2 arrangement - 9 pairs of microtubules in a ring around two lone microtubules in the center. Microtubules bound by dynein, which causes movements of filaments past one another.

Using second law of thermodynamics and free energy equation, is it favorable for delta G to be < or > 0?

< 0. Increase in entropy is more favorable, which would lead to delta G < 0 according to the free energy equation.

Genotype

A DNA sequence of the alleles a person carries. (Bb DNA sequence)

the purines

A and G (contain 2 rings)

Motile (bacteria)

A bacterium which possesses one or more flagella.

Thrombus

A blood clot (essentially a scab) circulating in the bloodstream.

Gene

A length of DNA that codes for a particular gene product. Fundamental unit of inheritance.

Transition (point mutation)

A purine is replaced by another purine (or pyrimidine is replaced by another pyrimidine).

Pleiotropism

A single gene effects a number of phenotypic traits.

Hapten

A small molecule that becomes antigenic when associating with a larger carrier molecule.

Sex pilus

A special pillus attaching F+ (male) and F- (female) bacteria which facilitates the formation of conjugation bridges.

Anagenesis

A species simply becomes another by changing so much over time. Different from cladogenesis, in which branching occurs from one species to create two different species.

Haploid

A species with only one copy of each chromosome.

Schwann cells

A type of glial cell that exist in conjunction with neurons, wrapping layers of specialized membrane around the axons. Creates myelin sheath in peripheral nervous system. (similar cells called oligodendrocytes myelinate the axons in the CNS).

Operon

A unit of linked genes that are thought to regulate other genes that produce a protein. Contain a coding sequence for enzymes and upstream regulatory sequences.

Signal sequence

AA sequence of some proteins at N-terminus (secreted and lysosomal proteins). Recognized by signal recognition particle, which binds to the ribosome. Rough ER has SRP receptors that dock the ribosome, feeding newly translated polypeptides into the rough ER. This signal sequence is then removed by signal peptidase, and transported to golgi apparatus (and eventually to the plasma membrane).

tRNA loading

AKA amino acid activation. Two high energy phosphate bonds are hydrolyzed to provide energy to attach an amino acid to its tRNA molecule. An aminoacyl-tRNA synthetase specifically matches the appropriate AA to the tRNA.

Glycocalyx

AKA capsule. Only exist in some bacteria. Sticky layer of polysaccharide "goo" surrounding the bacterial cell and often surrounding an entire colony of bacteria, making it less susceptible to attack from immune system. Also enables adherence.

NADH dehydrogenase

AKA coenzyme Q reductase. First membrane bound complex of ETC. Passes electrons to coenzyme Q (AKA ubiquinone), oxidizes NADH.

melting (DNA)

AKA denaturation. Separation of DNA strands.

Type II fibers

AKA fast twitch fibers. Separated into type IIA and type IIB fibers. Contract quickly.

Type IIA fibers

AKA fast twitch oxidative fibers. Somewhat resistant to fatigue. Maintain activity around 30 minutes or so (not as much as slow twitch but much greater activity that type IIB).

Capsule (bacteria)

AKA glycocalyx. Sticky layer of polysaccharide "goo" surrounding the bacterial cell and often surrounding an entire colony of bacteria, making it less susceptible to attack from immune system. Also enables adherence.

Type I fibers

AKA red slow twitch or red oxidative fibers because of high myoglobin content. Surrounding capillary network, good oxygen delivery. Due to this, fibers are able to maintain contraction for extended periods of time without fatigue.

Amino acid activation

AKA tRNA loading. Two high energy phosphate bonds of ATP are hydrolyzed to provide energy to attach an amino acid to its tRNA molecule. An aminoacyl-tRNA synthetase specifically matches the appropriate AA to the tRNA.

Coenzyme Q

AKA ubiquinone 2nd membrane bound protein in ETC. receives electrons from Coenzyme Q reductase (AKA NADH dehydrogenase) and passes electrons to cytochrome C reductase. Oxidezes FADH2 to FAD.

Type IIB fibers

AKA white fast twitch fibers due to lack of mitochondria. Fibers contract very quickly and with great force. Fatigue very quickly as well. Used for explosive force, such as jump shots or pole vaults.

What molecule is responsible for regulating PDC? (pyruvate dehydrogenase complex)

AMP. In the presence of AMP, PDC is stimulated

What favorable reaction do cells use to drive unfavorable reactions? (reaction coupling)

ATP hydrolysis

what is adenylate?

ATP. -ylate represents acidic phosphate group. TTP is called thymidylate.

What is PFK allosterically regulated by?

ATP. More ATP actually causes decrease in glycolysis, although it is a reactant.

Describes method of nutrition of fungi

Absorptive - means that digestion of nutrients occurs outside the fungal cell.

Thin filaments of myofibrils?

Actin

Proteins within myofibrils?

Actin and myosin

Duodenal enterokinase (AKA enteropeptidase)

Activates pancreatic zymogen trypsinogen to trypsin. Secreted by duodenal cells.

Motor unit recruitment

Activation of motor neurons (a single motor neuron innervates a group of myofiber), in order to cause muscle contraction. Recruitment of more motor neurons leads to larger twitch.

Forced expiration

Active process of expiration that occurs during exertion. Abdominal muscles contract. Expiration is usually passive.

Respiration

Actual exchange of gases (between either the lungs and the blood or the blood and the other tissues in the body).

Function of DNA pol I (in prokaryotes)

Adds nucleotides to RNA primer during DNA replication. Has low processivity (efficiency). Also capable of 3' to 5' exonuclease activity (proofreading errors). Eliminates RNA primer with 5' to 3' exonuclease activity, while simultaneously adding DNA in 5' to 3' activity.

anti-parallel beta pleated sheets

Adjacent polypeptide chains run in opposite directions

parallel beta pleated sheets

Adjacent polypeptide chains run in same direction

ACTH

Adrenocorticotropic hormone. Secreted by anterior pituitary. Stimulates increased activity of adrenal cortex, causing release of cortisol. In controlling the concentration of another hormone, it is a tropic hormone.

Repolarization

After depolarization occurs, resting cell membrane potential of -70 mV is restored.

Platelet plug

Aggregation of platelets to broken site of damage to blood vessel wall.

Polar, neutral amino acids

Alcohols (serine, threonine), Amides (glutamine, asparagine), cysteine, tyrosine. Capable of hydrogen bonding with water, but unable to act as an acid or base.

Hormones that adjust osmolarity and volume of urine in nephron.

Aldosterone and ADH. Function at distal portion of nephron (DCT and collecting duct).

rules regarding being a autotroph, heterotroph, chemotroph, and/or phototroph

All bacteria are either a chemotroph OR a phototroph and is either an autotroph OR a hetertroph.

What do parasympathetic postganglionic neurons release? What do sympathetic postganglionic neurons release?

All release acetylcholine, most release norepinephrine.

Law of independent assortment

Alleles of one gene will separate into gametes independently of alleles for another gene. (i.e. shape and color of pea are independent of each other).

What is the main difference between allosteric regulation and cooperativity?

Allosteric regulation bonding takes place at alternate sites from the active site, while cooperative bonding takes place at an active site, making other active sites more compatible with the substrate.

Nuclear pores

Allow passage of materials into and out of nucleus that are less than 60 kD in size. Only small molecules allowed to pass through pores, unless the molecule contains what...? A: nuclear localization sequence.

Tidal volume

Amount of air that moves in and out of lungs with normal breathing.

Reaction rate (enzyme kinetics)

Amount of product formed per unit time (mol/sec). Depends on concentration of substrate and enzyme

Protobionts

An aggregation of microspheres (proteinoid and water droplet), liposomes (lipids and microspheres), and coacervates (molecules that contain polysaccharides, polypeptides, and nucleic acids) that resemble a precursor to the prokaryotic cell. Lacks an organized mechanism of heredity.

Difference between endocrine and exocrine glands

An endocrine gland secretes its products, for example hormones, directly into the blood. An exocrine gland secretes its products, (for example enzymes), into ducts that lead to the target tissue.

Mixed type inhibition

An inhibitor can bind to an unoccupied enzyme or bind to an ES complex.

Repressible enzymes

Anabolic enzymes with suppressed activity in the presence of its product.

Basal body of cilia or flagella in euk cells

Anchors cilium or flagellum to the plasma membrane - contains same structure as a centriole (ring of 9 triplets of microtubules)

ACE

Angiotensin converting enzyme, which converts angiotensin I to angiotensin II in the lungs in order to raise blood pressure. Angiotensin II raises blood pressure by vasoconstriction and aldosterone relase.

Frank-Starling mechanism

Another mechanism of increasing cardiac output. If the heart muscle is stretched, it will contract more forcefully. This stretching occurs when more blood enters the heart (increased venous return).

Alimentary canal

Another name for GI tract or gut.

Main difference between anterior and posterior pituitary glands

Anteiror pituitary gland is a normal endocrine gland, controlled by hypothalamic tropic hormones. Posterior pituitary is composed of axons which descend from hypothalamus, secreting hormones (these are called neuroendocrine cells).

Carrier

Antigenic large molecule that may carry a small molecule to elicit an antibody response. The small molecule on its own would not be enough to elicit this response. This small molecule is also called a hapten.

What is the typical pressure in the vena cava?

Approximately 0 mm Hg. This is because the pressure throughout the blood vessels slowly dissipates as it travels from the heart, through the arteries, through the capillaries, through the veins, and then ultimately to the vena cava.

Renal tubule

Area of kidney where water and small molecules are squeezed into during filtration.

Cross bridge (skeletal muscle)

Area of skeletal muscle where myosin head binds to actin at myosin binding site.

Why is the loop of henle considered a countercurrent multiplier?

Ascending and descending limbs go in opposite directions and have different permeabilities. Descending limb is permeable to water but not ions. Ascending limb is the opposite, although it actively pumps ions into renal medullary interstitium (which contributes to its saltiness).

Polar, acidic amino acids

Aspartate, glutamate

Thomas Hunt Morgan

Associated a specific gene and its subsequent phenotype (eye color in the fruit fly) with a specific chromosome (the X chromosome).

Flavoprotein

Association of FAD with a protein. commonly involved in redox reactions, such as AA catabolism.

AV node

Atrioventricular node - electrical relay station in the heart. Impulse is delayed slightly at the AV node, and then passes from the node tot he ventricles via the conduction pathway again (to the AV bundle, AKA the bundle of His).

Why is AV valve so important?

Atrioventricular valve stops blood from flowing from ventricle to atrium. It is a one way valve. Important because ventricular pressure is high and atrial pressure is low.

What defines epithelial cells?

Attached to a basement membrane.

What is difference between autonomic afferent (sensory) neurons and somatic afferent neurons?

Autonomic sensory neurons can synapse in PNS (at autonomic ganglia) with autonomic efferent neurons in what is called "short reflex". First synapse of somatic afferent neurons is always in CNS. They are otherwise very similar.

Axial vs. appendicular endoskeleton

Axial is composed of skull, vertebral column and rib cage. Appendicular is everything else (think of appendages).

Lymphocytes

B cell - mature into plasma cell and produce antibodies T cell - kill virus infected cells, tumor cells. Control immune response

the pyramidines

C and T (contain 1 ring. Mnemonic is CUT the Py).

molecular formula of all simple sugars

C(n)H(2n)O(n)

Secondary structure in which hydrogen bonding occurs between distant amino acids or between amino acids on different polypeptide chains.

Beta-pleated sheets

Intercostal muscles

Between ribs, contract during inspiration, further expanding chest cavity.

Vertebrata defining characteristics

Bilateral symmetry, cephalization, endoskeleton w/ vertebral column, four limbs (or fins), a closed circulatory system, 2,3, or 4 chambered hear, respiratory system, excretory system w/ kidneys, mostly separate sexes.

noncompetitive inhibitors (enzyme kinetics)

Bind to allosteric site, causing decrease in catalytic activity.

Activator proteins (eukaryotic transcription)

Bind to enhancer regions (which are regions of DNA far from promoter that regulate transcription), causing the enhancer region to loop around and get closer to transcription site.

Attachment or adsorption (viruses)

Binding of virus tot he exterior of a bacterial cell wall.

Signal recognition particle (SRP)

Binds to the ribosome, recognizes signal sequence on N terminal of a nascent polypeptide. Docks onto rough ER, pushing translated protein into the rough ER for processing.

Hemostasis

Blood clotting

Lipoproteins

Blood protein composed of fats, cholesterol, and carrier proteins. Transport lipids through the blood stream.

Fibrinogen

Blood protein essential for blood clotting (hemostasis). Converted to fibrin by thrombin protein - fibrin holds platelet plug together and dries, forming scabs.

Albumin

Blood protein that is essential for maintenance of oncotic pressure (oncotic pressure is osmotic pressure in capillaries due only to plasma proteins)

Immunoglobulins

Blood protein that plays key role in immune system.

Boiling point elevation equation

Boiling point elevation = Kb x im Kb = solvent's boiling point elevation constant i = the solute's van't hoff factor m = molal concentration of the solution. Same as freezing point depression, but positive due to increasing temperature.

Bone remodeling

Bone is continually degraded and remade by osteoblasts and osteoclasts.

Where do formed elements of blood develop from?

Bone marrow stem cells

Examples of long bones

Bones of the limbs

Codominance. Define and give example

Both alleles are expressed, neither is dominant nor recessive. Example are blood antigens - antigen A and antigen B may both be expressed.

How are PFK and F-1,6-bpase regulated to prevent futile cycling (wasteful combination of glycolysis and gluconeogenesis)

Both of these enzymes are allosterically regulated by glycolytic intermediates that stimulate one and inhibit the other (example, AMP activates PFK into glycolysis and inhibits F-1,6-bpase from gluconeogenesis).

Respiratory bronchioles

Brach of alveolar duct. Made up of smooth muscle, just like terminal bronchioles, but one important difference: has a few alveoli scattered in its walls, allowing it to perform gas exchange.

Enteric nervous system

Branch of autonomic nervous system that helps to control digestion via innervation of the gastrointestinal tract, pancreas, and gall bladder. Regulates blood flow, gut movements, and the exchange of fluid from the gut to and from its lumen.

Canaliculi

Branch out from central (Haversian) canal of compact bones, pooling into spaces called lacunae (lakes).

Pulmonary capillaries (or alveolar capillaries).

Branching of large pulmonary arteries eventually become pulmonary capillaries. Just wide enough to permit passage of RBCs, permit diffusion of gases between blood and alveolus.

Catabolism

Breaking down molecules

Conjugation bridge (bacteria)

Bridge that forms between male bacteria and female bacteria, allowing for transfer of fertility factor (single circular DNA molecule that allows for exchange of genetic information between bacteria). This exchange is unidirectional.

What enzyme converts dipeptides and tripeptides to amino acids?

Brush border peptidases.

Chemoautrotrophs

Build organic macromolecules from CO2 using energy of chemicals. Obtain energy by oxidizine inorganic molecules like H2S.

Anabolism

Building up molecules.

Fascicles

Bundles of connective tissue that hold conttractile tissue together. Allow flexibility in muscle.

Conjugation

Bacteria make physical contact and form a bridge between cells. One cell copies DNA, and this copy is transferred through the bridge to the other cell. Male uses F (fertility) factor to form conjugation bridge to female bacteria without F factor. Female bacteria become male after receiving this fertility factor.

Mesophiles

Bacteria that favor mild temperatures, similar to the ones humans and other organisms favor (30°C). Most bacteria are mesophiles.

Obligate aerobes

Bacteria which require oxygen

3 types of prokaryotes

Bacteria, archea (extremophiles), and blue-green algae (cyanobacteria).

Stationary phase

Bacterial cells cease to divide for lack of nutrients. The maximum population for that environment (carrying capacity), has been reached.

Why might a bacteriophage inject its DNA, while animal viruses do not?

Bacteriophages need to puncture cell wall.

Binary fission

Bacterium grows in size until it has synthesized enough cellular components for two cells, then replicates its genome and dives in two.

How does a bacterium withstand osmotic pressure? How do animal cells do so?

Bacterium have a cell wall that prevents lysis from osmotic pressure. Animal cells continuously pump ions across the cell membrane.

Auxotroph

Bacterium that cannot survive on minimal growth medium (which is just glucose added to agar). Requires auxillary (additional) trophic substance to live. Auxotrophy results from a mutation in a gene coding for an enzyme in a synthetic pathway.

Glomerulus

Ball of capillaries at site of Bowman's capsule, where filtration occurs.

Bolus

Ball of food moving through GI tract

Osteon

Basic unit of compact bone structure. Sometimes referred to as Haversian system.

Loose connective tissues

Basically packing tissues, including areolar tissue (soft material between most cells throughout body) and adipose tissue.

Why do codons have to be 3 letters (bases) long?

Because 3 bases allows for enough combinations of letters to account for the 20 amino acids (4^3 = 64, while 4^2 = 16).

Why are specific cell types or specific species susceptible to viral infection?

Because a virus binds to specific surfaces depending on its surface, and the receptors on cell surfaces.

Why would a reaction rate vs [S] graph by sigmoidal? (shape of an S)

Because increase in [S] causes cooperative binding, making the curve steeper as more is added.

Why does FADH2 produce fewer ATP than NADH in the ETC?

Because it bypasses NADH dehydrogenase of the ETC, so less protons are pumped.

Why is the SA node considered the pacemaker of the heart?

Because it has way more Na+ leak channels than any other portion of the heart, allowing it to reach voltage threshold before other portions of the heart.

Why is DNA pol termed "processive"

Because it is able to add tens of thousands of templates before falling off.

Why is the genetic code said to be degenerate?

Because multiple codons can code for different proteins.

Why would alpha helix structures often be found in transmembrane regions?

Because of the hydrogen bonding that occurs within an alpha helix (between CO and NH groups), the polar elements of the structure are not going to interact with the hydrophobic elements within a cell, and the structure becomes suitable for a hydrophobic environment. Must contain AAs with hydrophobic R groups.

Actin and myosin filament sliding reaction is spontaneous outside of myofiber. So why isn't it spontaneous within the myofiber?

Because of toponin-tropomyosin complex, which prevents contraction in the absence of Ca2+.

Why are prokaryotes able to harness more ATP from NADH produced in glycolysis?

Because prokaryotes do not have membrane bound organelles, NADH does not need to be shuttled to a mitochondrion and does not bypass NADH dehydrogenase (1st protein complex of ETC). Therefore, it pumps more protons, generating more ATP.

Why are PDC and Kreb's cycle unable to occur without oxygen?

Because they rely on byproducts from the ETC (NAD+ and FAD), and the ETC requires oxygen.

Why are X-linked DOMINANT traits harder to identify?

Because they will likely be expressed fairly equally in males and females.

Why is it important that the inner membrane of the mitochondria be impermeable to H+?

Because transfer of H+ from mitochondrial matrix to intermembrane space via protein complexes in ETC causes proton gradient, which can then sufficiently power ATP synthase, creating ATP. Without impermeability, proton gradient would not be sufficiently formed.

How does fatty acid synthesis begin?

Begins with acetyl CoA being converted to malonyl-CoA via acetyl-CoA carboxylase (this requires ATP). Malonyl-CoA is required for fatty acid synthesis to begin.

What configuration are all sugars found in animals?

D

The codon GTC in DNA is transcribed in RNA as _ _ _, which the ribosome translates into what AA? (chart is located on page 136).

CAG, coding for glutamine (note the opposite bases from the DNA, but same order).

What stimulates gallbladder contraction and bile release?

CCK and parasympathetic response.

What happens to calcitonin level when serum [Ca+2] level is peaking above normal levels?

Calcitonin level is increased, halting Ca+2 production. It regulates [Ca+2]

What do thrombin and fibrinogen depend on for activation for hemostasis (blood clotting)?

Calcium, vitamin D.

Tolerant anaerobes

Can grow in the presence of oxygen, but do not use it in their metabolism

Oxidative stress - how is it good, how is it bad?

Can include increased levels of peroxides or free oxygen, causing production of reactive oxygen species. This can damage DNA, cellular proteins, and lipid bilayers. This damage can activate oncogenes, linking it to cancer. Also used by immune system - activated phagocytes may produce reactive oxygen species to kill pathogens.

Endocytosis (viruses)

Can only occur in cells without cell walls (animal cells). Host cell engulfs the virus and internalizes it.

Why does inflammation occur?

Capillaries dilate, increasing the size of the intercellular clefts of the capillary walls. This allows more space for WBCs to migrate into tissues. Plasma proteins and a lot of water are lost into the tissues as a result. Termed edema. Fluid, proteins, and WBCs are eventually returned to blood stream via lymphatic system.

Where is the viral genome located?

Capsid head

Anomeric carbon

Carbon of a carbohydrate that is attached to two O atoms (stereogenic carbon that forms linkage of straight chain carbohydrate).

Which types of muscles are striated?

Cardiac and skeletal. Just think of striated as the opposite of smooth.

Uniports

Carrier proteins that transport one molecule across the membrane at a time.

Antiports

Carrier proteins that transport two substances across a membrane in opposite directions.

Symports

Carrier proteins that transport two substances across a membrane in the same direction.

coronary veins

Carry deoxygenated blood from the heart, which merge to form coronary sinus (which is located beneath of layer of fat underneath the heart). Coronary sinus drains directly into right atrium.

Inducible enzymes

Catabolic enzymes that are stimulated by high quantities of its substrate.

Enzyme contained in peroxisomes, and its main function

Catalase - converts H2O2 to H2O and O2.

Phosphofructokinase

Catalyzes third step in glycolysis - the transfer of a phosphate group from ATP to F6P in order to form F1,6bP.

frameshift mutation

Cause a change in the reading frame of DNA. Insertions or deletions would cause this. These are very serious.

Excitatory post synaptic potentials (EPSPs)

Caused by excitatory neurotransmitters, which depolarize postsynaptic membrane.

Inhibitory post synaptic potentials (IPSPs)

Caused by inhibitory neurotransmitters, which hyperpolarize postsynaptic membrane.

How do noncompetitive inhibitors affect Vmax and Km?

Causes decrease in Vmax but typically causes Km to stay the same.

Where are all parasympathetic preganglionic neurons located?

Cell bodies are in the brainstem or the sacral (lowest portion) portion of the spinal cord. Hence, it is known as craniosacral system (as opposed to sympathetic system, which is known as thoracolumbar system).

Where are all sympathetic preganglionic efferent neurons located?

Cell bodies are in thoracic or lumbar regions of spinal cord. This is why sympathetic system is often referred to as thoracolumbar system (different from parasympathetic system, which is craniosacral system).

M phase

Cell cycle phase that involves mitosis and cytokinesis. Mitosis is the partitioning of cellular components (genes, organelles, etc.) into two halves. Cytokinesis is physical process of cell division.

Peritrichous

Cell has multiple flagella

Sarcolemma

Cell membrane of myofiber (skeletal muscles that make up fascicles). Made up of plasma membrane and additional layer made up of polysaccharide and collagen. This additional layer helps the cell fuse with tendon fibers.

Hfr (high frequency of recombination) cell.

Cell with fertility factor (single circular DNA molecule that allows for exchange of genetic information between bacteria) incorporated into its genome. Can still transfer F factor to a F- bacterial cell, often causing recombination between the F factor and the previously F- cell's genome.

Osteoblasts

Cells which make bone by laying down collagen and hydroxyapatite. osteoBlasts Build.

Formed elements

Cellular elements in blood.

Soma

Central cell body of the neuron, where nucleus is located. Where most of biosynthetic activity of the cell takes place.

Voltage gated ion channel

Channel protein of a membrane opens in response to a change in electrical potential across the membrane.

Ligand gated ion channel

Channel protein that opens to a specific neurotransmitter.

two types of proteins that allow for facilitated diffusion.

Channel proteins and carrier proteins.

Perforating (or Volkmann's) canals

Channels that run perpendicular to central canals to connect osteons.

Pedigrees

Charts that depicit inheritance of a trait.

neuromuscular junction. Where are these located? what neurotransmitter is involved?

Chemical synapse between neurons and skeletal muscle. Acetylcholine is released when action potential reaches the synapse. It binds to postsynaptic acetylcholine receptor, opening Na+ channel, depolarizing the post synaptic cell membrane.

All fungi are (blank)? (chemo/photo auto/heterotrophs)?

Chemoheterotrophs

Macula densa

Chemoreceptors located in distal convoluted tubule of nephron, which stimulate JG cells of afferent arteriole to release renin in response to low osmolarity of filtrate. Doing so increases BP. Also causes dilation of afferent arteriole.

Hormones secreted by duodenum.

Cholecystokinin, secretin, and enterogastrone

Metaphase

Chromosomes line up in center of the cell, forming metaphase plate. Kinetochore of each sister chromatid is attached to spindle fibers that attach to MTOC at opposite ends of the cell.

Plasmid

Circular piece of dsDNA in prokaryotes, much smaller than the genome. Referred to as extrachromasomal genetic elements. Encode advantageous gene products, such as antibiotic resistance Often capable of autonomous replication. Also orchestrate bacterial exchange of genetic information (conjugation).

Osteichthyes

Class of vertebrates. Bony fish, lay eggs without shells, cold blooded (ectothermic), with a 2-chambered heart, respire via gills, ancestors of amphibians. Example - tuna, bass

Chondrichthyes

Class of vertebrates. Cartilaginous fish, lay eggs or have live young, cold-blooded (ectothermic) with a 2-chambered heart, respire via gills, evolved from a side-branch from Agnatha. Example is sharks.

Reptiles

Class of vertebrates. Develop as an embryo surrounded by amnion, born in shelled egg or alive, dwell on land, cold-blooded (ectothermic), with a 3-chambered heart, respire using lungs, ancestors of birds and mammals.

Aves

Class of vertebrates. Develop in shelled amniotic eggs, have two wings and a lightweight honeycomb skeleton, warm-blooded (endothermic) with a 4-chambered heart, respire using lungs, descended from reptiles.

Mammalia

Class of vertebrates. Internal fertilization, most have live young, feed offspring via mild from mammary glands, have hair and large brains, warm-blooded (endothermic) with a 4-chambered heart, respire using lungs, descended from reptiles in a separate branch from Aves.

Agnatha

Class of vertebrates. Jawless, similar to ancestral vertebrates. Example is lampreys

Amphibia

Class of vertebrates. Water-dwelling larvae and land-dwelling adults, lay eggs without shells, cold-blooded (ectothermic), with a 3 chambered hear, respire via lungs and/or skin, ancestors of reptiles.

Plaque (growth media)

Clear area in bacterial lawn. Plaques result from death of bacteria that are caused by lytic viruses or toxins.

Transfusion reaction

Clumping and destruction of red blood cells bearing an antigen that a person has the antibody against. May lead to death of recipient. For example, type B blood type will likely have transfusion reaction if type A blood is received. These antibodies develop from birth, which is unusual. The rhesus factor antibody does not develop from birth - it develops from exposure.

Coenzyme

Cofactor in the form of an organic molecule that aids in enzymatic activity.

Psychrophiles

Cold loving bacteria. Thrive at very low temperatures, near 0°C.

Two principal ingredients of bone

Collagen and hydroxyapatite

What is spongy bone always surrounded by?

Compact bone

Peptidoglycan

Complex polymer made of sugars and amino acids that makes up bacterial cell wall.

Polygenism - define and example

Complex traits that are influenced by many different genes. Height is a good example, as it is affected by frowth factors, receptors, hormones, bone deposition, etc.

cytochrome

Composed of heme bound to protein (all of the protein complexes involved in ETC are cytochromes).

Inner membrane of mitochondria

Composed of lipid bilayer. Completely impermeable. Densely folded into structures called christae, which extend into the matrix. Site of oxidative phosphorylation.

Outer membrane of mitochondria

Composed of lipid bilayer. smooth, contain large pores called porin proteins, allows for continuity between cytoplasm and intermembrane space.

Nonelectrolytes

Compounds that do not dissociate into ions.

Lamellae

Concentric rings of bone surrounding Haversian canal within compact bone.

Significance of oxaloacetate in cellular respiration (book says to. memorize)

Condenses with acetyl unit of acetyl CoA to form citrate in citric acid cycle. Oxaloacetate is derived from previous citric acid cycle, and is constantly recycled.

Internodal tract

Conducting fibers in the heart which transmits action potentials very rapidly without contracting from SA node to AV node.

What shaped cells line the conduction zone? What shaped cells line the respiratory zone?

Conduction zone: columnar epithelial cells. Too thick for gas exchange. Respiratory zone: single layer of thin, delicate, squamous (flat) epithelial cells. This is called squamous epithelium. Allows gas exchange.

Ligaments

Connect bone to bone. Dense connective tissue.

Polar fibers

Connect microtubules to the aster (the microtubules that radiate out from the centriole). Whole assembly is called mitotic spindle.

Hepatic portal vein

Connects capillary bed of intestinal wall to capillary bed of liver. Amino acids and glucose are absorbed into digestive tract and then carried to the liver by this vein.

Connective tissue

Consists of cells and the materials they secrete. Derived from a single progenitor, the fibroblast. Connective tissue is primarily extracellular material with a few cells scattered in it. Incluces areolar tissue, fat, tendons, ligaments, cartilage, bone.

Dermis

Consists of various cell types embedded in a connective tissue matrix. Contains blood vessels that nourish both the dermis and epidermis. Contains sensory receptors, which convey information about touch, pressure, pain, and temperature. Compsed of sudoriferous (sweat) glands, sebaceous (oil) glands, and hair follicles.

What provides the basal level of pressure in arterial system?

Constant level of norepinephrine released by millions of sympathetic postganglionic axons innervating precapillary sphincters. This constant input is known as adrenergic tone.

Precapillary sphincters

Constrict arteriolar smooth muscle, causing resistance of blood flow to increase.

Lysosomes functions and number of membranes

Contain acid hydrolases which digest various substances. 1 membrane.

gram positive bacteria

Contain thick peptidoglycan layer outside of the cell membrane and no other layer beyond this. Introduction of gram stain binds to peptidoglycan wall readily, causing dark color. Due to less protection than gram negative bacteria, they stain strongly when exposed to Gram staining and are often less resistant to antibiotics.

Composite transposon

Contain two similar or identical IS elements (transposase with inverted repeats on flanks) with a central region in between them.

Melanin

Contained in epidermal epithelial cells. Brown pigment, produced by specialized cells called melanocytes, help absorb UV light of sun.

Vitamins

Contained in foods. Not substrates, but rather serve catalytic role as enzyme cofactors or prosthetic groups.

Lingual lipase

Contained in saliva, used for fat digestion.

Complex transposon

Contains a transposase DNA sequence and another gene (or multiple genes), which are all sandwiched between inverted repeats.

wild type strain

Contains all the characteristics normal to that particular species.

Minimal medium (growth medium)

Contains only glucose in addition to agar.

[-] RNA viruses

Contains single stranded RNA genome that is complementary to the RNA required to be translated into viral proteins. If translated by host ribosomes, useless polypeptides would be made. Must carry RNA-dependent RNA pol in capsid AND encode it too.

[+] RNA viruses

Contains single stranded RNA genome, which host ribosomes immediately encode viral proteins from. Must encode RNA-dependent RNA pol (and do not have to carry it) in order to replicate the RNA needed for viral replication (host cells do not contain RNA dependent RNA polymerase, as RNA pol usually uses DNA for transcription).

Hypothalamic pituitary portal system

Contains special miniature circulatory system for efficient transport of hypothalamic releasing and inhibiting facotrs to the anterior pituitary.

Vagal tone

Continual inhibition of SA node by vagus nerve.

Ostoclasts

Continually destroy bone by dissolving hydroxyapatite crystals. Is a large phagocytic cousin of macrophage. osteoClasts Crumble.

constitutive secretory pathway

Continuous, unregulated vesicle secretion of proteins from golgi apparatus (as opposed to regulated secretory pathway used by pancreatic cells for example).

What is an irreversible process involving pyruvate?

Conversion of pyruvate to acetyl CoA in PDC is irreversible. Once Acetyl Coa is formed, gluconeogenesis cannot occur. Therefore, this step is regulated.

Carbonic anhydrase

Converts CO2 to H2CO3 in presence of water, which breaks down to H+ and HCO3-. These products are then excreted in urine or exhaled in lungs in order to maintain optimal pH.

Outer and inner regions of kidney?

Cortex and medulla respectively.

Basic cell theory

Crafted by Robert Hooke in 1655: 1) All living organisms are composed of one or more cells and their products 2) Cells are the monomer for any organism 3) New cells arise from pre-existing, living cells

Sulfur containing amino acid that is polar.

Cysteine

If antibodies to a viral capsid protein are ineffective in blocking infection, what might this indicate about the virus?

The virus is likely enveloped.

Two primary means of cancer prevention

1) Detect cell damage and halt cell growth/division until it can be prepared 2) Trigger programmed cell death.

number of base pairs in human genome? in bacterial genome?

roughly 10^9 and 10^6 respectively.

Oxidoreductase

runs redox reactions (includes oxidases, reductases, dehydrogenases, and others).

In what ways is the activity of Na+/K+ ATPase important?

1) It creates resting membrane potential. 2) It maintains osmotic balance between interior and exterior of cell. 3) Provides sodium concentration gradient that is necessary for secondary active transport to occur.

By what mechanisms may an antibody remove an antigen from the body?

1) May directly inactivate the antigen 2) May induce phagocytosis by macrophages and neutrophils 3) Can activate complement system to form holes in the cell membrane and lyse the cell.

Examples of covalent modification of a protein

- Acetylated - Formylated - Alkylated - Glycosylated - Phosphorylated - Sulphated - Addition of fatty acid - Linkage to another protein (ubiquitination for example).

Kb of water (boiling point elevation constant)

0.5°C/mol

How many ATP are ultimately generated from a molecule of NADH produced in glycolysis (in eukaryotes)? Why does this value differ from the amount of ATP synthesized from NADH produced in the other steps of cell respiration?

1 NADH from glycolysis creates 1.5 ATP. This is because glycolysis is done in the cytoplasm, and must be transported to the mitochondria via the glycerol phosphate shuttle. This shuttle dumps the NADH at ubiquinone in the ETC, bypassing NADH dehydrogenase. Therefore, the NADH only causes 6 protons to be pumped in ETC, translating to production of only 1.5 ATP (as opposed to 10 protons and 2.5 ATP).

Products of PDC (pyruvate dehydrogenase complex)

1 acetyl CoA, 1 CO2, 1 NADH, and 1 H+ per pyruvate (double everything per glucose).

What is the mass of a liter of water?

1 kg

What is 1 Angstrom equal to?

1 x 10^-10 meter

What percentage of blood do leukocytes and platelets account for?

1%

3 ways that carbon dioxide is transported in the blood

1) 73% of CO2 is transported via conversion of CO2 to carbonic acid via carbonic anhydrase, which can dissociate into bicarbonate and proton. These compounds are water soluble and can be carried in the blood. 2) 20% of CO2 is transported simply by being stuck to hemoglobin. It does not bind to oxygen binding sites, but binds elsewhere. 3) 7% of CO2 can be dissolved in blood and carried from the tissues to the lungs as is.

5 factors that contribute to GI motility

1) Automaticity - in other words it contracts without external stimulation, due to spontaneous depolarization. 2) Functional syncytium, meaning that when one cell has an action potential and contracts, the impulse spreads to neighboring cells. 3) Contains its own nervous system, known as enteric nerovous system. 4) GI motility is increased or decreased by hormonal input. 5) Parasympathetic nervous system stimulates motility and causes sphincters to relax, allowing food through the gut.

Steps of contractile cycle

1) Binding of myosin head to myosin binding site on actin, AKA cross bridge formation. At this stage, myosin as ADP and Pi bound 2) Power stroke, in which myosin head moves to low energy conformation and pulls actin chain towards the center of the sarcomere. ADP is released. 3) Binding of a new ATP molecule is necessary for the release of actin by the myosin head (This is KEY!) 4) ATP hydrolysis occurs immediately and the myosin head is "cocked" (set in high energy conformation, like the hammer of a gun). Another cycle begins when myosin head binds to new binding site of thin filament.

Difference between cardiac muscle and skeletal muscle

1) Cadiac muscle cells are not structurally syncytial (they have only one nucleus). All cardiac muscle cells are interconnected by gap junctions called intercalated disks, which allow action potentials to propagate throughout the entire heart without nuclei or cytoplasm being shared. Only ions can pass through. So this is called functional syncytium. 2) Cardiac muscle cells are connected to several neighbors via intercalated discs. 3) Some of calcium required for cardiac muscle contraction comes from extracellular environment, through voltage gated calcium channels, rather than all calcium coming from sarcoplasmic reticulum (intracellular structure). 4) Cardiac muscle contraction depends on acetylcholine as an inhibitory neurotransmitter to slow heart rate. Skeletal muscle contraction depends on acetylcholine as a stimulatory neurotransmitter. 5) Action potential in cardiac muscle depends on not only voltage gated sodium channels, but also voltage gated calcium channels (slow channels, which cause a plateau in AP).

Order in which tRNAs move through the sites of a ribosome

A-->P-->E

which of the following would best describe the effect of thiamine deficiency on cellular metabolism in humans? A) rate of glycolysis would increase B) glcyolysis would proceed anaerobically to maintain ATP production at normal levels C) Glucose consumption would slow, and ATP production would increase D) Acetyl-CoA would be provided by fatty acid metabolism, so the Krebs cycle would proceed uninhibited

A. TPP is required in both Kreb's cycle and PDC, so a deficiency would cost a lot of ATP. Glycolysis would increase to make up for this.

Divergent selection

Form of natural selection in which average members of a population are eliminated, leaving two extreme groups. This causes the population to diverge into two different species.

Epistasis - define and example

Expression of alleles for one gene is dependent on another gene. Example: Allele for curly hair cannot be expressed if different gene with allele for baldness is present.

Are disulfide bridges likely to be found in extracellular proteins or interior of cells?

Extracellular proteins, as this is an oxidizing environment. Such an environment allows SH and SH to oxidize to S-S linkage. Interiors of cells are reducing environments, as they contain antioxidants.

Fertility factor (bacteria)

Extrachromosomal element that is copied and transferred from male bacteria (containing F factor) to female bacteria (which does not contain F factor yet) via conjugation bridge. Single circular DNA molecule.

How is fructose-1,6-bisphosphatase positively regulated? negatively regulated? (page 109)

F-1,6-BPase is an enzyme that drives gluconeogenesis. Not positively regulated (according to chart in textbook). Negatively regulated by F-2,6-phosphate and AMP;

Appendix

FInger like appendage of cecum. Composed of lymphatic tissue.

linkage

Failure of genes to display independent assortment. In other words, they may be expressed together. This only occurs when genes are on the same chromosome.

Lymph nodes

Filter lymph. Important part of immune system because they contain millions of WBCs that can initiate immune response against foreign materials picked up in lymph.

Spleen

Filters blood and is site of immune cell interactions, just like lymph nodes. Destroys aged RBCs.

Cecum

First part of large intestine.

Primary immune response

First response to an antigen during an infection. Slow due to immune system's lack of preparation for the event.

Inuslin processing: an example of post-translational modification

First step in image uses signal peptidase in ER. Note how disulphide bonds then form. Next step in image uses proprotein convertase. Last step involves carboxypeptidase.

Prophase I

First step in meiosis. Chromosomes condense, nuclear envelope breaks down. Unlike mitotic prophase, chromosomes pair with each other in process termed synapsis. This forms a bivalent, or tetrad.

Locus

Fixed position on a chromosome on which there is a gene.

Amphitrichous

Flagellum located at both ends of cell

Monotrichous

Flagellum located at only one end of cell

Two primary bone shapes

Flat and long

Pulmonary circulation

Flow of blood from right side of heart to lungs and back to the left side of the heart

Systemic circulation

Flow of blood from the left side of the heart to the rest of the body and back again to to the right side of the heart.

Filtrate

Fluid filtered into tubule, eventually becomes urine

Pulmonary edema

Fluid in lungs resulting from increased blood pressure. This happens because pressure increases within pulmonary capillaries, and fluid (blood plasma) is forced out of capillaries into lung tissue.

Lymph

Fluid in lymphatic vessels, which is filtered by numerous lymph nodes throughout the lymphatic system.

Microvilli (GI tract)

Folds on plasma membranes of apical surfaces that face into the lumen, increasing the surface area.

When does diploid become haploid in meiosis (in animals)?

Following meiosis I. Homologous chromosomes are separated in this phase due to tetrad structure that forms. In mitosis, homologous chromosomes are not separated, so they remain diploid.

What stimulates gastrin secretion in the stomach?

Food and parasympathetic stimulation.

Chyme

Food mixed with gastric secretions

Saturation kinetics of facilitated diffusion (How would graph of flux vs increasing driving force for diffusion look for both simple and facilitated diffusion?

For facilitated diffusion, proteins required eventually become saturated, hence the decline.

Channel proteins

Form a narrow opening in the membrane allowing for diffusion of a substance down the gradient. Are very selective.

Tertiary structure

Form from mostly interactions of R groups within a polypeptide. However, disulfide bridges also count.

In what organelles are proteins modified?

In rough ER or golgi apparatus

Where does glycolysis occur?

In the cytoplasm, and it does not require oxygen

Does DNA methylation increase or decrease gene expression?

In the examples I have seen, it decreased gene expression. Acetylation has the opposite effect, increasing transcription.

Where is erythropoietin produced? What is its target and effect?

In the kidney. Causes increases synthesis of RBCs in bone marrow. Releasedwhen blood oxygen content falls.

How is fructose 2,6, bisphosphate controlled in regard to glycolysis?

In the presence of high blood glucose, insulin will activate PFK-2, forming more f-2,6-bp from F6P and stimulating glycolysis. With low blood glucose, glucagon will stimulate F-2,6BPase, which will break down F-2,6-BP into F6P, inhibiting glycolysis and stimulating gluconeogenesis.

Presbyopia

Inability to accomodate (focus). Results from loss of flexibility of lens, which occurs with aging.

Ischemia

Inadequate blood flow, results in tissue damage due to shortages of O2 and nutrients, and buildup of metabolic wastes. Different from hypoxia, which is when supply of oxygen is reduced even though there is adequate circulation.

Role of incisors, ciuspids, and molars

Incisors (front teeth) are for cutting, cuspids (canine teeth) are for tearing, and molars are for grinding.

Homo defining characteristics

Includes modern humans and species closely related to them (whihc are now extinct); this genus is approx 2.4 million years old and is differentiated from ancestors by an increase in cranial capacity.

Temporal prezygotic barrier

Individuals cannot mate due to differences in mating season

Mechanical prezygotic barrier

Individuals cannot mate due to differences in reproductive structures or genital organs

Behavioral prezygotic barrier

Individuals cannot mate due to differences in special rituals or courtship behaviors

Ecological prezygotic barrier

Individuals cannot mate due to different habitats, no access to each other.

Gametic prezygotic barrier

Individuals cannot mate due to incompatibility of sperm and egg.

Inhibitory neurotransmitter

Induce hyperpolarization of postsynaptic membrane (opposite of excitatory neurotransmitters, which depolarize the postsynaptic membrane).

subviral particles

Infectious agents that are even smaller ant simpler than viruses, including prions and viroids.

Chemotaxis

The process by which bacterial motion is directed toward attractants and deterred from toxins. Controlled by chemoreceptors, which bind attractants and repellents, transmitting a signal that causes the rod of the flagella to rotate in a specific direction.

Describe flow of blood into and out of heart

The right atrium receives deoxygenated blood from the inferior and superior vena cava, pumps it to right ventricle. Right ventricle pumps blood to pulmonary artery into the lungs, where blood is oxygenated and sent to left atrium through pulmonary veins. The oxygenated blood is then sent to the left ventricle. This is then pumped out to the aorta.

The interior of the ER is sometimes contiguous with what?

The space between the inner and outer nuclear membranes.

Hemodynamics

The study of blood flow.

Respiratory membrane

The three barriers that air must travel across to be transferred between air and blood. They includ alveolar epithelium, interstitial fluid, and capillary endothelium.

What does the structure of the most effective competitive inhibitors resemble?

The transition state that is normally stabilized by the active site of an enzyme.

Functional residual capacity

VOlume of air left in the lungs after a resting expiration.

Bicuspid (mitral) valve

Valve between left atrium and left ventricle.

Tricuspid valve

Valve between right atrium and right ventricle.

Forces that stabilize hydrophobic interactions of phospholipid bilayer

Van der waals forces

Coronary arteries

Very first branches from the aorta, which supply oxygenated blood to the wall of the heart.

Fibrous cartilage

Very rigid and is found in places where very strong support is needed, such as pubic symphysis and intervertebral discs of spinal column.

Bronchioles

Very small bronchi, contain no cartilage. Walls made of smooth muscle with diameters regulated to adjust airflow into the system.

Capillaries

Very small vessels, often just wide enough for a single blood cell to pass. Where exchange of materials between blood and tissues occur.

Exotoxins

Very toxic substances that are secreted by both Gram-negative and Gram-positive bacteria. Help bacteria compete with other bacterial species (such as in mammalian gut).

Endosome

Vesicle that forms during endocytosis.

Arteries

Vessels that carry blood away from the heart at high pressure

Veins

Vessels that carry blood toward the heart at low pressure

early gene (viruses). Give example.

Viral gene that is immediately encoded in a host cell (hydrolase is a good example, which hydrolyzes genome of bacteria).

Late gene (viruses). Give example.

Viral gene whose coding is delayed upon entering host cell (example is lysozyme, which waits until phages replicate before lysing the host cell).

Naked viruses

Viruses that do not have envelopes (covering of capsid derived from host cell membrane. All phages and plant viruses are naked, as their hosts have cell walls.

Total lung capacity

Vital capacity plus residual volume.

homology dependent repair pathways

When a single strand of DNA is damaged, the cell uses the information from the nondamaged, complimentary strand to repair.

Muscle fibers

When bundled, make up the fascicles. Also called myofibers. Each muscle fiber is a single skeletal muscle cell.

when is protein kinase A activated?

When there is low blood glucose, glucagon will activate PKA, deactivating PFK-2 and activating F-2,6-BPase. This will form F6P and stimulate gluconeogenesis.

Synaptic knobs

Where axons and action potentials terminate in neurons, connecting with target cells. Releases chemical messengers that travel across synaptic cleft to the target cell.

Intercalated discs

Where gap junctions are found in cardiac muscle - the connections between cardiac and muscle cells.

If a group of sea turtles lives most of the year disperesed over a large area of ocean without contact, except for mating once a year, is this considered a population?

Yes, because they reproduce

Trypsinogen

Zymogen which is converted to active form, trypsin, by enterokinase (an intestinal enzyme). Trypsin then activates many other pancreatic enzymes, including chymotrypsinogen to chymotripsen, procarboxypeptidase to carboxypeptidase, and procolleganse to collegenase.

Retroviruses

[+] RNA viruses that integrate into host genome as proviruses (lysogeny). Must encode RNA dependent DNA polymerase (reverse transcriptase) in order to code for DNA so that it can be incorporated into DNA of host cell. Does not need to carry reverse transcriptase in its capsid because the RNA in the capsid can be used for translation by the host cell.

3 domains of life

bacteria, archea, and eukarya

saponification

base catalyzed (NaOH for example) hydrolysis of triglycerides in fatty acid salts (soap - RCOO-Na+ for example) and glycerol.

Examples of wobble pairing in translation

base in anticodon - G, wobble base in codon - U. Base in anticodon - U Wobble base in codon - G Base in anticodon - I (inosine, which is modified adenine) Wobble base in codon - A, U, or C.

histones

basic, globular proteins that DNA wraps around.

Are histones basic or acidic?

basic. they are attracted to negatively charged, acidic DNA.

why is RNA less stable than DNA

because 2' hydroxyl group is capable of nucleophilically attacking the phosphate group of an RNA chain, causing hydrolysis while the rest of the chain acts as a leaving group.

Why is it okay that RNA is less stable than DNA?

because RNA is not used throughout a cell's entire life; it is meant to be transient and destroyed.

why are nucleic acids called "nucleic acids"?

because they are found in the nucleus and possess acidic phosphate groups.

glycosidic linkage of cellulose.

beta glycosidic bond

Lyase

breaks chemical bonds by means other than oxidation or hydrolysis (e.g. pyruvate decarboxylase).

Terpene

broad class of lipids built from isoprene units (C5H8)

What agents cause bronchoconstriction? bronchodilation?

bronchoconstriction is often caused by acetylcholine, histamine. Bronchodilation is caused by epinephrine.

What enzyme converts disaccharides into monosaccharides

bursh border disaccharidases (sucrase, lactase, maltase)

What does increasing the length of a fatty acid due to membrane fluidity?

decreases it.

structural determinants of membrane fluidity include...

degree of saturation, tail length, and amount of cholesterol

Free energy equation.

delta G = delta H - T delta S

Enthalpy equation

delta H = delta E - PdeltaV

How to calculate deltaG for a reaction in the body?

deltaG = deltaGº' + RTlnQ deltaGº' = free energy of system at equal concentrations of products and reactants at pH 7 Q = [products]/[reactants] (not necessarily at equilibrium) deltaG will be more negative/more likely to be spontaneous if [reactants] is greater than [products], as lnQ would be negative.

Equation relating deltaGº' to K'eq

deltaGº' = -RTlnK'eq (would be given on MCAT).

how is ribose modifed in DNA?

deoxy, meaning it is lacking an OH group at the 2' carbon.

dNTP

deoxyribonucleoside 5' triphosphate (building blocks of DNA, N stands for one of the 4 basic nucleosides).

flow summarizing structure of DNA in the nucleus.

deoxyribose-->add base-->nucleoside-->add three phosphates-->nucleotide--> polymerization using two phosphates--> oligonucleotide--> continue polymerizing--> single stranded polynucleotide--> H bond with antiparallel single stranded polynucleotide--> forms ds DNA--> coiling occurs--> ds helix--> wraps around histones--> nucleosomes-->packaging is completed--> chromatin.

Two networks of neurons in enteric nervous system

myenteric plexus (found between circular and longitudinal muscle layers and helps primarily regulate gut motility), and submucosal plexus (found in submucosa and helps to regulate enzyme secretion, gut blood flow, and ion/water balance in the lumen).

What is myopia? how is it corrected?

near sightedness. Occurs when too much curvature in lens or cornea causes light to be bent too much, focusing in front of the retina. Can be corrected with a concave, diverging lens which would cause light rays to diverge slightly before reaching the cornea.

delta G of spontaneous reaction is...

negative

If a mutation occurs in a muscle cell of an individual who then has many progeny, does this mutation increase genetic variation in the population?

no, because mutation must occur in the germ line to introduce a new allele into a population. Mutation in somatic cells cannot be passed on.

Do enzymes alter the concentration of reactants at equilibrium?

no, only the rate

When homologous chromosomes separate in meiosis, do all paternal and maternal chromosomes stay together in daughter cells?

no. Homologous chromosomes segregate randomly.

Prosthetic group

nonprotein molecule covalently bound to an enzyme as part of an active site. (example is TPP - thiamine pyrophosphate)

Another name for stop codons

nonsense codons.

Innate immunity

nonspecific protection the body provides against various invaders. Example is the barrier created by skin.

What is emmetropia? How is it corrected?

normal vision. Does not need to be corrected.

difference between nucleoside and nucleotide

nucleoside contains nitrogenous base and sugar. -tide contains nitrogenous base, sugar, and 1-3 phosphates.

Recombination frequency = ...

number of recombinants/total number of offspring (A recombinant is a phenotype that is not linked to another gene)

Most fungi are (blank), but yeast are (blank)? (type of aerobe/anaerobe)

obligate aerobes, facultative anaerobes.

germline mutations

occur in germ cells (which give rise to gametes)

somatic mutations

occur in somatic (non-gametic) cells and are not passed on to offspring.

Aldosterone

released by adrenal cortex of kidney when BP is low. Causes increased reabsorption of Na+ by distal nephron, which increases plasma osmolarity, leading to water retention and elevated BP. Low blood osmolarity, low blood volume, and angiotensin II also trigger aldosterone.

Heterotrophs

rely on organic nutrients for carbon source (glucose for example) created by other organisms.

What is the thermodynamic driving force of polymerization reaction during DNA replication?

removal and hydrolysis of pyrophosphate from each dNTP added to chain (3' OH group nucleophilically attacks the pyrophosphate group, replacing it).

Phosphatase

removes a phosphate group from a molecule

Blood enters kidney from ...

renal artery

Purified blood from kidney is returned to circulatory system by ....

renal vein

Two important types of endonucleases

repair enzymes - remove chemically damaged DNA from the chain. Restriction enzymes - found in bacteria. Destroy DNA of infecting viruses, restricting the host range of the virus.

theta replication

replication of prokaryotes - the circular chromosome of prokaryotes is replicated, which forms a replication bubble as always. When this occurs, the circle begins to look like a theta.

Pathway of respiratory zone

respiratory bronchioles -> alveolar ducts -> alveoli

Telomerase

ribonucleoprotein complex that contains RNA primer and reverse transcriptase. The reverse transcriptase converts the RNA primer to DNA, elongating the telomere.

What are nucleotides composed of?

ribose (or deoxyribose) sugar group, purine or pyrimidine base joined to carbon one of ribose ring, and 1-3 phosphate units joined to carbon five of ribose ring.

backbone of DNA

ribose + phosphate (called the backbone because it is invariant).

Shine-Dalgarno sequence

ribosome binding site on mRNA in prokaryotes. Located 10 bases upstream of the start codon (-10). Complementary to a pyrimidine rich region on the small subunit.

Rigor mortis

rigidity of skeletal muscles which occurs soon after death. Results from complete ATP exhaustion, which does not allow myosin heads to release actin. Therefore, muscle can neither contract or relax.

nuclear matrix/nuclear scaffold

role is analagous to role of cytoskeleton in cytoplasm: to support and provide overall structure. Also plays role in regulating gene expression.

The space between the nuclear membranes is continuous with....

the interior of the ER (ER lumen). The membrane of the ER is often contiguous with the outer nuclear membrane.