DAT complete biology

flash of far red after red flash:

effect on red light reversed->night length restored to before state. **in series of alternating flashes, only last one affects perception of night length: red shortens, far-red restores

urine formation

(filtration, secretion, and reabsorption) *filtration: the fluid that goes through glomerulus (afferent arteriole=>glomerulus=>efferent) to the rest of the nephron is called filtrate; particles that are too large to filter through (blood and albumin) remain in circulatory system; passive process; driven by hydrostatic pressure of blood. so glomerulus->filtrate pushed into bowmans *secretion: substances such as acids, bases, and ions (K+) are secreted by both passive/active transport; secreted from peritubular capillaries *reabsorption: glucose, salts, aa, and water are reabsorbed from filtrate and return to blood; takes place namely in PROXIMAL convoluted tubule (active) *concentration: when dehydrated volume of fluid in bloodstream is low so you need to make small amounts of concentrated urine=>ADH prevents water loss by making distal tubule permeable to water. when blood pressure is low=> aldosterone increases reabsorption of Na+by distal nephron which increases water retention

primary structure of roots

(from outside of root to center) 1. epidermis: lines outside surface of root. in zone of maturation, epidermal cells produce root hair. when zone of maturation ages, root hair die. new epidermal cells from zone of elongation becomes cell of new zone of maturation, forms new root hairs to continue absorption of water. old epidermis functions to protect root. 2. cortex: makes up bulk of root, storage of starch, contains intercellular spaces to provide aeration of cells for respiration. 3. endodermis: ring of tightly packed cells at inner most portion of cortex. a band of fatty material (suberin) impregnates endodermal cell walls to form encircling band called *casparian strip: creates water-impenetrable barrier between cells. all water passing through endodermis must pass through endodermal cells, not between. controls movement of water into center of root and prevents water from moving back out to cortex 4. vascular cylinder (stele): makes up tissues inside endodermis (phloem, xylem, pericycle). outer part consists of one or several layers of cells (pericycle: from which lateral root arise). inside pericycle are vascular tissue. *dicot: xylem cells fill center of vascular cylinder (shape X with phloem-sieve tube members and companion cells- in the spaces of X *monocot: groups of xylem and phloem alternate in a ring with the pith in the middle

glycocalyx

a carbohydrate coat that covers outer face of cell wall of some bacteria and outer face of plasma membrane (some animal cells). it consists of glycolipids attached to plasma membrane and glycoproteins such as recognition proteins. it may provide adhesive capabilities, a barrier to infection, or markers for cell to cell recognition

artificial selection

a form of directional selection carried out by humans when they breed favorable traits (not natural selection)

one-gene-one polypeptide hypothesis

defines a gene as the DNA segment that codes for a particular polypeptide

savannas

grasslands with scattered trees. similar to tropics in that they have high temperature, but they get very little rainfall

community

group of populations living in same area

amniotes

group of tetrapods that have a terrestrially adapted egg; supported by several extraembryonic membranes

facultative anaerobe

grows in presence of oxygen but can switch to anaerobic metabolism when oxygen is absent

seed plants include:

gymnosperms (conifers) and angiosperms (flowering plants).

fresh water biomes

ponds, lakes, streams, and rivers. hypotonic to organisms, affected by climate/weather variations

habitat

type of place where organism usually lives; including other organisms as well as physical, chemical environment

rhizomes

underground stems that can sprout to produce new shoots and roots for the plant

phagocytosis

undissolved material (solid) enters cell; white blood cell engulfs. plasma membrane wraps outward around

origin of life

universe: 12-15 bya solar system: 4.6 bya earth: 4.5 bya microfossils of prokaryotes: 3.6 bya photosynthetic bacteria: 2.3 bya eukaryotes: 1.5 bya

platyhelminthes

unsegmented flatworms that are invertebrates. lack specialized nervous, circulatory, and respiratory systems. o2 and co2 transport is by diffusion

endocytosis

uses ATP and is an active process

chemiosmosis in chloroplasts

uses H+ gradient to generate ATP 1. H+ ions accumulate inside thylakoids: H+ are released into lumen when water is split by PSII. H+ is also carried into lumen from stroma by cytochrome between PSII and PSI 2. pH and electrical gradient is created: about pH~5 3. ATP synthase generates ATP: phosphorylate ADP + Pi==> ATP (3 H+ is required for 1 ATP) 4. calvin cycle produces 2G3P using NADPH and CO2 and ATP: at the end of ETC following PSI, 2e- produces NADPH

Thyroxin

increases the basal metabollic rate

endocrine system

synthesize and secretes hormones into bloodstream

adrenaline and noradrenaline

synthesized in the adrenal medulla

plant hormones: gibberellins

(GA): group of hormones that promote cell growth (flower and stem elongation), synthesized in young leaves, roots, and seeds then transported to other parts of the plant. can act together with auxin to stimulate growth. involved in inhibition of aging in leaves, promotes fruit development and seed germination (gibberellin is released from embryo, moves through endosperm to aleurone layer. aleurone then secretes digestive enzymes amylase to break down endosperm starch into sugars->nourishment->germination commences. high conc of gibberellins causes bolting (rapid elongation of stems)

plant hormones: auxin

(IAA-indoleacetic acid): promotes plant growth (elongation of cells) by increasing H+ conc in primary cell walls->activates enzymes that loosen cellulose fiber (increase cell wall plasticity) thus turgor pressure expands cells to grow. produced at tips of shoots and roots (apical meristem). *in concert with other hormones, influences plant response to light (phototropism) and gravity (geotropism). it is modified tryptophan AA. after synthesis it is actively transported from cell to cell in a specific direction (polar transport) by means of chemiosmotic process. it inhibits lateral buds when it is produced at terminal bud of growing tip. moves unidirectional from shoot to root

blood vessels

(arteries, veins, and capillaries) *arteries: thick-walled, muscular, elastic, pump oxy blood away from heart (except for pulmonary arteries that transport deoxy blood from heart to lungs). wrapped in smooth muscle typically innervated by sympathetic NS *arterioles: very small, wrapped in smooth muscle, constrict/dilate to regulate BP and reroute blood-major determinant of pressure *capillaries: have smallest diameter-single layer of endothelial cells across which gases, nutrients, enzymes, hormones, and waste diffuse *venules: small blood vessels that lead back to veins; very thin and porous; drain blood from capillary bed->venules combine->veins *veins: larger veins often have valves that aid in transport of deoxy blood back to heart due to fighting gravity (except for pulmonary veins and umbilical vein that carry oxy blood)

digestion: large intestine

(colon) reabsorption of water and salts to form feces; 1.5m long. *feces stored at end of LI in the rectum->anus *at beginning is appendix, which in herbivores is large cecum (cellulose digestion) with the help of bacteria *bacteria (eg E. coli) a symbion in LI=main source of Vit K (also Vit B)

excretion in humans

(lungs, liver, skin, and kidney) *lungs: CO2 and H2O gas diffuse from blood and are continuously exhaled *liver: processes nitrogenous wastes, blood pigment wastes, other chemicals, urea products *skin: sweat glands in skin excrete water and dissolved salts/ regulate body temperature *kidney: three regions 1. outer cortex 2. inner medula 3. renal pelvis which drains to ureter *each has many nephrons. kidneys->ureter->bladder->urethra. functions to excrete wastes, maintain homeostasis of blood fluid, volume, and solute composition. helps control plasma pH

double capillary beds

(portal system) occur in glomerulus, capillaries that surround loop of Henle, small intestine, liver, and hypothalamus and anterior pituitary gland. *capillary bed pools into another capillary bed (cap bed 1->drains into portal vein->cap bed 2->drains into vein that returns blood to heart) without first going to heart (transport products in high concentration without spreading to rest of body)

structure of skin: hypodermis

(subcutaneous) not part of skin; areolar and adipose tissue; fat storage; pressure sensing nerve endings; passage for blood vessels

porphyrins

(tetrapyrroles) 4 joined pyrrole rings. often complex with metal as with porphyrin heme complexes with iron in hemoglobin, and chlorophyll with Mg

must be true for HWE:

* p + q = 1 (all alleles sum to 100%) * p2 + 2pq + q2 = 1 (all individuals sum to 100%)

invertebrate respiration: arthropods

**80% of all living species!! insects, spiders, crustaceans etc *grasshopper: series of chitin-lined respiratory tubules called trachae open to surface in openings called spiracles through which oxygen enters and Co2 exits. no oxygen carrier is needed due to direct distribution and removal of respiratory gases between air and body cells; diffusion across moistened tracheal endings *spiders: book lungs, stacks of flattened membranes enclosed in internal chamber

plant respiration

**photosynthesis produces glucose and gives off oxygen while respiration requires oxygen to degrade glucose **plants undergo aerobic respiration similar to animals *glucose->2ATP + 2 pyruvic acid *gases diffuse into air space by entering and leaving through stomata of leaves or lenticels in woody stems *anaerobic respiration takes place in simple plants when molecular oxygen is lacking

all digestive enzymes cleave

**specific bonds

cardiac muscle structure and function:

**striated appearance (sarcomeres); one or TWO central nuclei; cells separated by intercalated discs that have gap junction to allow action potentials to chain flow via electrical synapse; involuntary; lots of mitochondria. both smooth and cardiac muscle are myogenic: capable of contracting without stimuli from nerve cells

nitrogen as a waste product

*aquatic animals excrete NH3 or NH4 directly into water *mammals convert NH3 to urea *birds, insects, reptiles convert urea to uric acid (insoluble in water, water conservation, excreted as solid)

skeletal muscle

**striated muscle, **voluntary movement **fibers are multinucleated cells: 1. myofibrils: filaments divided into sarcomeres 2. sarcomeres: individual contractile units separated by a border (Z-line) 3. sarcoplasmic reticulum: stores Ca2+; surrounds myofibrils 4. sarcoplasm: cytoplasm 5. sarcolemma: plasma membrane of muscle cells; can propagate ap. **invaginated by T-tubules: channel for ion flow **wraps several myofibrils together to form a muscle cell/muscle fiber 6. mitochondria: present in large amounts in myofibrils

DNA replication: Primase is an enzyme that creates a small strip of RNA primer off of which DNA polymerase can work since it can only add to an existing strand

*DNA replication requires an RNA primer *every okazaki fragment has an RNA primer, these RNA strips are later replaced with DNA by DNA polymerase I

anterior pituitary hormones

*PRL (prolactin) *GH

parathyroid hormones

*PTH increases blood Ca2+

thyroid hormones

*T4 (thyroxin) *T3 (triiodothyronine) both increase cellular metabolism *calcitonin- lowers blood Ca2+

digestive systems: unicellular organisms

*amoeba: food capture: phagocytosis-> food vacuoles-> fuse with lysosomes *paramecium: cilia sweep food into cytopharynx. food vacuole forms and moves toward anterior end of cell

general categories of living organisms

*autotrophic anaerobes (chemosynthetic bacteria) *autotrophic aerobes (green plants, photoplankton) *heterotrophic anaerobes (yeast) *heterotrophic aerobes (amoebas, earthworms, humans)

organization of vertebrate skeleton

*axial skeleton: basic framework (skull, vertebral column, rib cage) *appendicular skeleton: bones of appendages, pectoral and pelvic girdles *bone organization: **sutures: immovable joints (holds together bones of skull **moveable joints: bones that move relative to each other. ligaments-bone to bone connectors; stengthen joints. tendons-muscle to bone; bend skeleton at moveable joints **origin: point of attachment of muscle to stationary bone **insertion: point of attachment of muscle to bone that moves **extension: straightening of joint **flexion: bending of joint

molecular genetics of bacteria

*bacteria are prokaryotes with no nucleus or organelles *single circular as DNA molecule that is tightly condensed and called a nucleoid *no histones or other associated proteins *replicate DNA in both directions from single point of origin *reproduce by binary fission: chromosome replicates, cell divides into two cells: each cells bearing one chromosome *lacks a nucleus so lacks microtubules, spindle, centrioles *plasmids: short, circular DNA outside the chromosome which carry genes that are beneficial but not essential for survival and replicate indepently *episomes: are plasmids that can incorporate into the bacterial chromosome

liver functions

*blood storage *blood filtration: kupfer cells phagocytize bacteria picked up in intestines *carbohydrate metabolism: liver maintains normal blood glucose levels via gluconeogenesis (production of glycogen and glucose from noncarb precursors), glycogenesis, and storage of glycogen. **all carbs absorbed into blood are carried by portal vein to the liver. absorbed galactose and fructose are converted to glucose, then stored as glycogen. *protein metabolism: liver deaminates aa, forms urea from ammonia in blood, synthesizes plasma proteins and nonessential amino acids *detoxification: detoxified chemicals, excreted by the liver as part of bile (or polarized to be excreted by kidneys) *erythrocyte destruction: kupfer cells destroy irregular erythrocytes (but most are destroyed by spleen) *vitamin storage: stores vit A, D, B12. also stores iron by combining it with apoferritin->ferritin *glycogenesis (formation of glycogen) and glycogenolysis (if blood glucose levels decrease->glycogen broken down to glucose for release) *when liver mobilizes fat or protein for energy, blood acidity increases (ketone bodies are produced->ketosis/acidosis results) *blood supply: hepatic portal vein supplies blood as does hepatic artery (oxygenates liver); blood leaves via hepatic vein->vena cava *digestive (produces bile); transport (synthesizes blood plasma proteins important in clotting)

plant responses to stimuli

*cant move, must change growth pattern **tropism: growth pattern in response to an environmental stimulus **phototropism: response to light (achieved by hormone auxin). auxin is produced in apical meristem->moves downward by active transport into zone of elongation->generate growth by stimulating elongation. stem grows straight when all sides of apical meristem are equally illuminated. but when not equally illuminated, auxin moves more toward shady side (grow more)->stem bends toward light **gravitropism (geotropism): response to gravity by stems and roots (auxin and gibberellins involved). if stem is horizontal, auxin concentrates on lower side=>stem bends upward. if root is horizontal, auxin is produced at apical meristem and moves up in root and concentrates on lower side. however, auxin inhibits growth in roots due to higher auxin at root than stems->lower side grows less, root curls down **thigmotropism: response to touch (eg vines wrap around object they contact)

domain bacteria distinct from archaea and eukaryote by these features: **bacteria are prokaryotes

*cell wall (peptidoglycan) *bacterial DNA is not associated with histone *ribosome activity inhibited by antibiotics

plant divisions that produce seeds:

*coniferophyta *anthophyta

eye structure and function

*cornea: focuses light *pupil: diameter controlled by iris *lens: controlled by ciliary muscles; focuses image *retina: light sensitive cells **cones: high intensity illumination; sensitive to color. **rods: low intensity; important in night vision; no color. rod pigment rhodopsin is struck by photons from light, causing hyperpolarization transduced into neural ap sent to brain. photoreceptor cells synapse to bipolar cells->ganglion cells-> axons of ganglion cells bundle to optic nerve. point at which optic nerve exits is blind spot (no photoreceptors here) *fovea: densely packed with cones; important for high acuity vision *eye has vitrous humor: jelly like, maintains eye shape and optical properties. *aqueous humor: anterior chamber, eye produces it

gene cloning

*cut at restriction site to get linear piece of DNA *add genes, close plasmid *add to something like bacteria to replicate it; bacteria dislike plasmids so only fraction of them get taken up by some bacteria *use antibiotic resistance gene to determine which bacteria were transformed that will survive on a certain medium *plasmids will get reproduced **if making a prokaryotic gene product in mammalian cell: *need to add polyA tail for the mRNA to survive **if making eukaryotic gene product in prokaryotic cell: *need to make sure no introns *use reverse transcriptase on the mRNA product to get the desired DNA fragment

9. eukaryotes formed

*endosymbiotic theory: eukaryotic cells originated mutually among prokaryotes (mitochondria, chloroplast establish resident inside another prokaryote) *evidence: thylakoid membranes of chloroplasts resembe photosynthetic membranes of cyanobacteria, mitochondria and chloroplasts have their own circular DNA not wrapped with histones, ribosomes of these organelles resemble those of bacteria, they reproduce independently via process similar to binary fission, two membranes

adrenal gland (inner-medulla) hormones

*epinephrine (adrenalin) *norepinephrine (noradrenalin) **secreted by blood vessels, liver and heart. increases blood glucose, vasoconstriction (sympathetic)

cellular components of the blood

*erythrocytes (RBCs): transport O2 (up to 4) on Hb, catalyze conversion of CO2 and H2O to H2CO3-lack nucleus/organelles to maximize Hb content *leukocytes (WBCs): larger and phagocytize foreign matter and organisms. **diapedesis: process by which WBCs become part of the interstitial fluid (slip through the endothelial lining) *platelets/thrombocytes: cell fragments involved in blood clotting-lack nuclei; stick to damaged epithelium; attract more. **convert fibrinogen (inactive) to fibrin (active). derived from *megakaryocytes

ovary hormones

*estrogen: menstrual cycle, secondary sex** *progesterone: menstrual cycle, pregnancy**

regulatory mechanisms for endotherms

*evaporation: body heat is removed as liquid evaporates (endergonic) *metabolism: muscle cx and other metabolic activities generate heat *surface area: vasodilation or vasoconstriction of extremity vessels results in heat retention or removal (blood flow to ears reduce body temp, countercurrent exchange keeps central parts of body warm)

differences in development

*external development: fish and amphibians have external fertilization in water; reptiles, birds, and some mammals aka monotremes. have internal fertilization then lay eggs. no placenta *non placental internal development: certain animals (eg marsupials, tropical fish) with no placenta either, limited exchane of food and o2 between mother/young *placental internal development: eg humans. major components are umbilical cord and placenta system: O2 received directly from mother (fetal lungs not functional until birth) and nutrients; CO2 and metabolic wastes removed. placenta and umbilical cord form from outgrowths of amnion, chorion, allantois, and yolk sac. amnion contains amniotic fluid as shock absorber; placenta formation begins with chorion; blood vessels of allantois wall enlarge and become umbilical vessels (connect fetus->developing placenta); yolk sac (site of early development of blood vessels) becomes associated with umbilical vessels. aka viviparous in mammals, results in live birth

recap of urine formation

*filtration occurs in renal corpuscle *reabsorption/secretion mostly in proximal tubule *filtrate becomes more concentrated as it moves down loop of henle (water passive out of tube) *more dilute as it moves up loop (passive and active transport of salts out, but not water) *distal convoluted tubule dumps into collecting duct *filtrate more concentrated again as it descends to collecting duct (bc surrounding medulla is salty, H20 leaves) *collecting duct leads to renal calyx *empties into renal pelvis *drains to ureter

means of asexual repro in fungi:

*fragmentation (breaking up hyphae), budding (small hyphal outgrowth), and asexual spores 1. sporangiospores: produced in sac-like capsules (sporangia) that are each borne on a stalk called sporangiophore 2. conidia: formed at tips of specialized hyphae, not enclosed inside sac; hyphae bearing conidia called conidiophores

stages of sexual reproduction in fungi:

*fungi are primarily haploid but form temporary diploid structures for sexual repro 1. plasmogamy: fusing of cells from two different fungal strains to produce single cell with nuclei of both strains. a pair of haploid nuclei, one from each strain is called dikaryon. *dikaryotic hypha is hypha containing dikaryon 2. karyogamy: fusing of two haploid nuclei of a dikaryon to form single diploid nucleus 3. meiosis: of diploid nucleus restores haploid condition; daughter cells develop into haploid spores which germinate into haploid hyphae (has one fungal strain)=> merge into dikaryon and repeat

domain eukarya: kingdom fungi

*fungi grows as filaments (hyphae), mycellium is a mass of hyphae; some fungi have septum which divide filament into compartments containing single nucleus. cell walls contain chitin. those without septa are coenocytic (multinucleate) *fungi are either parasites/ saprobes (decomposers) absorbing food products due to digestive enzymes. parasitic fungi have hyphae (haustoria) that penetrate hosts

pancreas (alpha cells) hormones

*glucagon (secreted by liver and increases blood glucose)

adrenal gland (outer-cortex) hormones

*glucocorticoids (cortisol) increases blood glucose *mineralocorticoids (aldosterone) increases reabsorption of Na+ and excretion of K+ (the adrenal glands lie above the kidneys and each has an outer cortex and an inner medulla)

immune system: nonspecific 2nd line of defense

*innate immunity. WBCs (leukocytes): all originate from bone marrow but some multiply and become non naive in the lymph nodes (lymph drainage act as a sewer system of antigens; cell recognizes antigen, goes from naive -> activated; multiplies 1. phagocytes are wbcs that engulf pathogens by phagocytosis. they include neutrophils and monocytes. monocytes enlarge into large phagocytic cells called macrophages. other white blood cells called natural killer cells (NK cells) attack abnormal body cells such as tumors of pathogen-infected body cells 2. complement: is a group of about 20 proteins that complement defense reactions 3. interferons: substances secreted by cells invaded by viruses that stimulate neighboring cells to produce proteins that help them defend against the viruses 4. inflammatory response: following events occur *histamine is secreted by mast cells, wbcs found in CT *vasodilation stimulated by histamine, increases blood supply to the damaged area and allows for easier movement of wbcs through blood vessel walls *phagocytes attracted to the injury by chemical gradients of complement, arrive and engulf pathogens and damaged cells *complement helps phagocytes engulf foreign cells, stimulate basophils to release histamine, and help lyse cells

immune system: nonspecific 1st line of defense

*innate immunity: generalized protection 1. skin: physical and hostile barrier covered with oily and acidic (pH 3-5) secretions from sweat glands 2. antimicrobial proteins: lysozyme (saliva, tear) which break down cell wall of bacteria 3. cilia: line the lungs and sweep invaders out 4. gastric juice: stomach kills most microbes 5. symbiotic bacteria: digestive tract and vagina outcompetes many other organisms

pancreas (beta cells) hormones

*insulin (secreted by liver, muscles, fat and decreases blood glucose)

lymph vessels

*lymphatic system is an open secondary circulatory system-transports excess interstitial fluids (lymph) through the cx of adjacent muscles and some walls of larger lymph vessels have smooth muscle *proteins and large particles that cant be taken up by capillaries removed to lymph; also monitors blood for infection *valves prevent backflow-fluid returns to blood circulatory system through two ducts located in shoulder region (thoracic and right lymphatic duct) *lymph nodes contain phagocytic cells (leukocytes) that filter the lymph and serve as immune response centers

5 types of sensory receptors:

*mechanoreceptors: touch *thermoreceptors: temperature *nocireceptors: pain *electromagnetic receptors: light *chemoreceptors: taste, smell, blood chemistry **respond strongly to own stimuli and weakly to others. neural pathways separate and terminate in the CNS Note: all nerves not directly inside the brain or spinal cord are all part of the PNS. cranial and spinal nerves come OUT of those structures; and are part of the PNS

human respiration controlled by

*medulla oblongata: signals the diaphragm to contract

in plants:

*meiosis in sporangia which produces haploid spores *spores undergo mitosis to become multicellular which is then called a gametophyte and is haploid *the gametes fuse to produce a diploid cell (zygote 2n) that grows by mitosis to become a sporophyte *cells in sporophyte stage (sporangia) undergo meiosis to produce haploid spores which germinate and repeat the life cycle *described above is the alternation of generations: alternation of diploid and haploid stages

pineal hormone

*melatonin: circadian rhythms

summary of seed plant reproduction:

*microsporangium: produces numerous microspore mother cells, which divide by meiosis to produce 4 haploid cells. microspores-male=>mature into pollen grains (represent gametophyte generation) which divides into 3 cells (in flowering plants) or 4 cells (in conifers). one is vegetative (tube) cell that controls growth of pollen tube, others=sperms *megasporangium: called nucellus produces megaspore mother cell->meiosis->4 haploid cells, one survives to become megaspore (female gametophyte generation). megaspore->mitosis->one egg (in flowering plants) or two eggs (in conifers). one/two tissue layers (integuments) surround megasporangium. ovule (integument + nucellus + megaspore daughter cells); micropyle is opening through integuments for pollen access to egg *once pollen grain contacts megasporangium, tube cell (of sperm) directs growth of pollen tube through the micropyle and toward egg=>fertilization (zygote)=>embryo (beginning of sporophyte generation); integuments=seed coat

invertebrate respiration: annelids

*mucus secreted by earthworm provides moist surface for gaseous exchange by diffusion *circulatory system brings oxygen to cells and waste products CO2 back to skin for excretion

eye disorders:

*myopia: nearsightedness *hyperopia: farsightedness *astigmatism: irregularly shaped cornea *cataracts: lens becomes opaque->light cannot enter *glaucoma: increase in pressure of eye due to blocking of outflow of aqueous humor

DNA organization

*nucleosome: DNA is coiled around bundles of 8/9 histone proteins (beads on a string). *while not in process of division, chromatin exists as either of two types: 1. euchromatin: loosely bound to nucleosomes, actively being transcribed 2. heterochromatin: areas of tightly packed nucleosomes where DNA is inactive (condensed = darker). contains a lot of satellite DNA (large tandem repeats of noncoding DNA *transposons: (jumping genes) DNA segments that can move to new location on same/ different chromosome; 2 types: insertion sequences that consist of only one gene that codes for enzyme that just transports it (transposase). complex transposons that code for extra: replication, antibiotic resistance, etc. insertion of transposons into another region could cause mutation with little to no effect

all living things have:

*one or more cells *plasma membrane *genetic material in DNA form *mechanisms of using RNA and ribosomes to translate genetic material into proteins and enzymes

phosphorus cycle

*required for manufacturing of ATP and all nucleic acids a. reservoirs: rocks and ocean sediments (erosion transfers P to water and soil) b. assimilation: plants absorb inorganic PO43- (phosphate) from soil; animals obtain organic phosphorous when they eat c. release: plants and animals release phosphorous when they decompose, and animals excrete in waste products

testis hormone

*testosterone: spermatogenesis, secondary sex char

foraging behavior

*optimize feeding (minimize energy spent and risk) 1. herds, flocks, schools: several advantages, uses cooperation (carry out a behavior more successfully as a group) a. concealment: most individuals in flock are hidden from view b. vigilance: in a group, individuals can trade off foraging and watching for predators c. defense: a group of individuals can shield their young or mob their predator 2. packs: enable members to corner and successfully attack large prey 3. search images: help animals find favored or plentiful food based on specific and/or abbreviated target image. ex: spotting a police car, book on shelf color without reading title

O2 saturation of Hb also depends on CO2 pressure, pH, and temp of the blood

*oxygen dissociation curve shows the percentage of Hb bound with O2 at various partial pressures of O2 *curve is shifted right (ie oxygen is released easier, low O2 affinity) by an increase of CO2 pressure, H+ concentration, or temp (and vise versa) *CADET face right! (CO2, Acid, 2,3-DPG, Exercise, and Temperature)

digestive systems: invertebrates

*physical breakdown: cutting and grinding in mouth; churning in dig tract *chemical breakdown: enzymatic hydrolysis-> smaller nutrients-> pass through semipermiable membrane to gut cells to be further mobilized **cnidarians: hydra-intracellular and extracellular digestion **annelids: earthworms- one way dig tract. (crop=food storage, gizzard=grind food, intestine=contains typholosole to increase surface area for absorption **arthropods: also have jaws for chewing and salivary glands

digestion in plants and fungi

*plants have no digestive system, but intracellular processes similar to animals do occur **intracellular digestion: store primarily starch in seeds, stems, and roots; when nutrients are required, polymers are broken down (into glucose, fatty acid, glycerol, and aa) by enzymatic hydrolysis **extracellular digestion: several plants must obtain nutrient from environment *fungi: rhizoids of bread mold, secrete enzymes into bread, producing simple digestive products which are then reabsorbed by diffusion into rhizoid *venus flytrap: enzymes digest trapped fly (serves as nitrate source); **still autotrophic

repair mechanisms

*proofreading: DNA polymerase checks base pairs *mismatch repair: enzymes repair things DNA polymerase missed *exision repair: enzymes remove nucleotides damaged by mutagens

5. organic molecules were concentrated/isolated into protobionts

*protobionts=precursors of cells. like cells, metabolically active but unable to reproduce. *microspheres/liposomes and coacervates=spontaneously formed lipid or protein bilayer bubbles-are experimentally and abiotically produced protobionts that have some selective permeable qualities

circulation in invertebrates

*protozoans: movement of gas through simple diffusion within cell *cnidarians: body cells 2 walls thick, therefore all cells in direct contact with either internal or external environment (ex=hydra) *arthropods: open circulatory system: pump blood into internal cavity called hemocoel (cavities called sinuses), which bathe tissues in oxygen and nutrient containing fluid (hemolymph). this fluid returns to pumping mechanism (heart) through holes called ostia *annelids: aka earthworms. have closed circulatory system-blood is confined to vessels. also seen in certain mollusks (octopus and squid) and vertebrates. **away from heart= aorta->arteries->arterioles->capillaries. **back to heart= capillaries->venules->veins *Note: human and birds hearts have 4 chambers, reptiles and amphibians hearts have 3, fish hearts have 2, crocs and gators have 4 chambers!

bowmans capsule leads to renal tubule

*proximal convoluted tubule: active reabsorption of glucose, ions, aa. **drugs, toxins etc secreted into filtrate; H+ ions secreted in as well via antiport with Na+ *loop of henle (majority of nephron) **descending: only permeable to water (this water picked up by vasa recta so medulla stays salty) **ascending: makes renal medulla salty-actively pumps out Na+, K+, Cl-; impermeable to water! *this process allows reabsorption of 99% of filtrate->concentrated urine **distal convoluted tubule: more reabsorption of glucose, ions, water, etc (cortex not salty) *filtrate: Na+ and Ca2+ get reabsorbed into body, K+/H+/HCO3- secreted out via tubule. distal tubule empties to... **collecting duct: collects remaining filtrate. is ordinarily impermeable to water unless ADH acts on it. *descents to medulla (salty part), where ADH/vasopressin can make MORE water leave from the urine by increasing permeability of collecting duct->urine even more concentrated. 1 collecting duct is shared by many nephrons. *also, aldosterone acts on distal conv tubule and collecting duct: increases Na+ reabsorption, K+ secretion and water passively follows Na+

regulation of eukaryotic gene expression

*regulatory proteins: repressors and activators, influence RNA pols attachment to promoter region *nucleosome packing: methylation of hisones (tighter packing = preventing transcription); *acetylation of histones (uncoiling and transcription proceeds) *RNA interference: short interfering RNAs (siRNAs) block mRNA transcrptions (fold nack within itself = dsRNA), translation, or degrade existing mRNA. *siRNAs: dsRNA gets chopped up, then made single stranded. the relevant strand will bind to DNA (prevents transcription) or mRNA (signals destruction)

nitrogen cycle

*required for amino acid and nucleic acids a. reservoirs: atmosphere (N2), soil (NH4+, NH3, NO2, NO3) b. assimilation: plants absorb nitrogen as either NO3- or NH4+, animals obtain nitrogen by eating plants/animals **nitrogen fixation: nitrogen fixing bacteria in soil (N2->NH4+); lightning + UV (N2->NO3-) **nitrification: NH4+->NO2- and NO2- ->NO3- by nitrifying bacteria c. release: denitrifying bacteria (convert NO3->N2; denitrification), detrivorous bacteria convert organic compounds back to NH4+ (ammonification), animals excrete NH4, urea, or uric acid, decay (nitrogen in the form of NH3 is released from dead tissues)

carbon cycle

*required for building organic materials. basis for this is photosynthesis and respiration a. reservoirs: atmosphere (CO2), fossil fuels (coals, oil), peat, cellulose b. assimilation: plant uses CO2 in photosynthesis, animals consume plants (this is carbon fixing-reduced from its inorganic form of CO2 to organic compounds) c. release: release CO2 through respiration and decomposition and when organic material is burned

functions of skin

*thermoregulation, protection, environmental sensory input, excretion, immunity (specialized cells of the epidermis are components of immune system), blood reservoir (vessels in dermis hold up to 10% of the blood in resting adult), vit D synthesis (UV radiation activates skin molecule that is a precursor to vit D

skeletal muscle types

*type I (slow twitch): lots of myoglobin, lots of mitochondria, aerobic endurance *type IIA (fast twitch): endurance but not as much as type I (anaerobic endurance) *type IIB (fast twitch): low myoglobon, lots of glycogen and power **skeletal muscle generally doesnt undergo mitosis to create new muscle cells (hyperplasia), but will increase in size (hypertrophy)

lamarck theory

*use and disuse: body parts can develop with increased usage, unused parts are weakened *inheritance of acquired characteristics: body features acquired during lifetime can be passed down to offspring (incorrect) *natural transformation of species: organisms produced offspring with changes, transforming each later generation slightly more complex (incorrect) *natural selection: survival of the fittest aka darwinism now called neo-darwinism (synthetic theory of evolution

secondary structure of stems and roots

*vascular cambium: becomes cylinder of tissue that extends the length of stem and root. cells on the inside differentiate into secondary xylem, and those on the outside into secondary phloem. over years, secondary xylem accumulate and increase girth of stem and root. *outside of cambium later, new secondary phloem are added yearly. as a result, tissues beyond the secondary phloem are pushed outward as xylem increases its girth. these tissues include the primary tissue (epidermis and cortex) break apart and shed. in order to replace shed epidermis, cork cambium produces new cells on the outside (cork cells- impregnated with suberin). on the inside, phelloderm may be produced. together, the cork/cork, cambium/phelloderm are called *periderm. *in stem of dicots/conifers, cork cambium originates from cortex just inside epidermis. in root, it originates from pericycle. **wood: formed from xylem tissues at maturity (dead), only the more recent secondary xylem produced from vascular cambium remain active to transport water (sapwood). older xylem located at center (heartwood) functions only as support. **annual rings: alternation of growth (active vascular cambium divides) and dormancy due to season in secondary xylem tissue. size of rings->rainfall history. number of rings->age of tree

pyrimidines

1 ring: thymine and cytosine (single ring) 3H bonds

sources of variations

1. mutation 2. sexual reproduction 3. diploidy 4. outbreeding 5. balanced polymorphism

sliding filament model

1. ATP binds to myosin head: converted to ADP+Pi, which remain attached to head 2. Ca2+ exposes binding sites on actin: binds troponin->tropomyosin exposes attachment sites 3. cross bridges between myosin heads and actin filaments form 4. ADP + Pi are released-> sliding motion of actin bring Z lines together (Cx, power stroke) 5. new ATP attaches to myosin head, causes cross bridges to unbind: new phosphorylation breaks cross bridge *without new ATP, the cross bridges remain attached to myosin head...this is why corpses are stiff **strength of cx of single muscle fiber cannot be increased, but strength of overall cx can be increased by recruiting more muscle fibers

types of lymphocytes

1. B cells (antibodies): originates and mature in bone marrow (B cell for bone); response to antigens. plasma membrane of B cells contains *antigen receptor-antibodies (immunoglobulins) = are proteins; specific to each antigen, 5 classes (IgA, IgD, IgE, IgG, IgM) cariation in Y-shaped protein constant region and variable regions). *antibodies inactivate antigens upon binding-> mark for macrophage or natural killer cell phagocytosis, lysis by complement proteins, agglutination of antigenic substance, or chemical inactivation (if a toxin) *when antigen bound to B cell-> proliferation (2 copies) into daughter B cells (assisted by helper T) a. plasma cells: B cells that release specific antibodies that circulate in blood b. memory cells: long-lived B cells that do not release antibodies in response to immeduate antigen invasion; instead they circulate the body, proliferate, and respond quickly (via antibody synthesis) to eliminate subsequent invasion by same antigen 2. T cells (foreign): originates in bone marrow but mature in thymus gland (T for thymus). T cells have antigen receptors but **do not make antibodies. they check molecules displayed by nonself cells. in the thymus, if a T cell binds to a self-antigen, it is destroyed. if not, released for work in lymphoid tissue. discrimination of self and nonself are as follows: a. MHC markers on plasma membrane of cells distinguish between self and nonself cells b. when body cell is invaded by pathogen (nonself), it displays a combination of self and nonself markers. T cells interpret this as nonself **cancer cells or tissues transplant cells are often recognized as nonself by T cells due to the combination 3. natural killer cells: attack virus-infected cells or abnormal body cells (tumors)

similarities between archaea and eukaryotes:

1. DNA of both archaea and eukaryotes are associated with histone; not bacterial DNA 2. ribosome activity is not inhibited by antibiotics (streptomycin and chloramphenicol) unlike bacteria

checkpoints: cell specific regulations

1. G1 checkpoint: aka restriction point, the most important. at the end of the G1 phase, if cell is not ready to divide, it may arrest here = G0 phase: nerve and muscle cells remain here, rarely divide after maturing and never proceed or wait until it is ready 2. G2 checkpoint: end of G2 phase, evaluates accuracy of DNA replication and signal whether to begin mitosis 3. M checkpoint: during metaphase, ensures microtubules are properly attached to all kinetochores, prevents anaphase if they are not

male reproductive cycle

1. GnRH-> FSH + LH (also called ICSH, interstitial cell stimulating hormone-> testosterone and androgens from testis 2. FSH and testosterone->influence sertoli cells to promote development of sperm (nourish sperm during development-spermatogenesis) *hormone and gamete production are constant unlike female

virus components

1. a nucleic acid (RNA/DNA may be double/single stranded 2. capsid: protein coat that encloses the nucleic acid (capsomeres assemble to form the capsid) 3. enelope: surrounds capsid of some viruses; it incorporates phospholipid/ protein obtained from cell membrane of its host **viruses usally specific to a type of cell and bind to specific receptors and species. host range is the range of organisms that a virus can attack

some common neurotransmitters

1. acetylchonline: secreted at the neuromuscular junctions->muscle cx/relaxation. inhibitory everywhere else (PNS) 2. epinephrine, norepinephrine, dopamine, and serotonin: aa derived, secreted between neurons of CNS (SNS) 3. gamma aminobutyric acid (GABA): inhibitory NT among brain neurons

social behavior

1. agonistic behavior: (aggression and submission) ex: dog wagging tail a. originates from competition from food, mates, or territory b. agnostic behavior is ritualized, so injuries and time spent in contests are minimized 2. dominance hierarchies: indicate power and status relationship in a group; minimize fighting for food/mates a. pecking order 3. territoriality: active possession and defense of territory-ensures adequate food/place to mate 4. altruistic behavior: seemingly unselfish behavior that appears to reduce fitness of individual-when an animal risks its safety in defense of another in order to help another individual rear its young a. actually increases inclusive fitness (fitness of individual plus relatives who share some identical genes) b. kin selection: natural selection that increases inclusive fitness c. ex: squirrels alarm when predator comes, risky to self but saves kin=kin selection d. ex: haplodiploid reproductive system of bees-males are haploid (unfertilized egg of queen) and female workers and queen are diploid (fertilized eggs). females are highly related to each other (same father whose genes all come from a queen mother and same queen). inclusive fitness of female workers is greater is she promotes production of sisters

cell doctrine or theory

1. all living organisms are composed of one or more cells 2. the cell is the basic unit of structure, function, and organization in all organisms 3. all cells come from preexisting, living cells 4. cells carry hereditary info

humans supplement natural body defenses by:

1. antibiotics: are chemicals derived from bacteria/fungi that are harmful to other microorganisms 2. vaccines: stimulate production of memory cells from inactivated viruses or weakened bacteria (artificially active immunity) 3. passive immunity: transferred antibodies from another individual (ex: newborns from mother) a. acquired immediately, but short-lived and nonspecific b. gamma globulin (blood containing antibodies) can confer temporary protection against hepatitis and other diseases

responses of immune system are categorized into two kinds of reactions:

1. cell-mediated response: effective against infected cells. uses mostly T cells and responds to any nonself cell, including cells invaded by pathogens. nonself cell binds T cell-> clonal selection-> chain of events: a. produce cytotoxic T cells (destroy) and helper T cells b. helper T cells bind macrophages (macrophages engulf pathogens=whole is nonself) c. helper T cells then produce interleukins to stimulate proliferation of T cells and B cells and macrophages 2. humoral response (antibody mediated response): responds to antigens or pathogens that circulate in lymph or blood (bacteria, fungi, parasites, viruses, blood toxins). basically the B cell stuff. humor is body fluid and the following events occur: a. B cells produce plasma cells b. B cells produce memory cells c. macrophage and helper T cells (in cell-mediated of macrophages engulf-nonself) stimuate B cell production d. general progression: naiive-> mature->plasma->ab

communication in animals

1. chemical: chemicals used for communication are pheromones. chemicals that trigger reversible behavioral changes are called releaser pheromones; those that cause long term physiological (and behavioral) changes are called primer pheromones. pheromones may be smelled or eaten. ex: doe in heat-releaser pheromones. ex: queen bees and aunts secrete primer pheromones to prevent development of reproductive capability 2. visual: during displays of aggression (agonistic behavior) or during courtship. ex: aggression-wolves baring teeth/submission-laying on back. 3. auditory: ex: whale sound, elephant infrasound, frog calls 4. tactile: common in social bonding, infant care, grooming, and mating

structure of bone

1. compact bone: highly organized, dense bone that doesnt appear to have cavities from outside: osteoclasts burrow tunnels (**Haversian canals) throughout. osteoclasts are followed by osteoblasts, which lay down new matrix onto tunnel walls forming concentric rings (lamellae). osteocytes trapped between the lamella (lacunae) exchange nutrients via canaliculi. the haversian canals also contain blood and lymph vessels and are connected by volkmann's canals. the entire system of lamellae and haversian canals is called an osteon** (haversian system). compact bone is filled with yellow bone marrow that contains adipose cells for fat storage 2. spongy (cancellous) bone: less dense and consists of an interconnecting lattice of bony spicules (trabeculae); filled with red bone marrow (site of RBC development) **bone growth occurs at cartilagenous epiphyseal plates that are replaced by bone in adulthood. bone increases in length but also in diameter along the diaphysis as well. most of the Ca2+ in body is stored in bone matrix as hydroxyapatite. bones can be made from a combination of compact and spongy

genetic variations of bacteria

1. conjugation: donor produces a bridge (pilus) and connects to a recipient. sends chromosome or plasmid to recipient and recombinant can occur. the **F plasmid allows pilus to occur. once the recipient receives, it is now F+ and can donate as well. **R plasmids provide bacteria with antibiotic resistance. 2. transduction: DNA is introduced into genome by a virus. when virus is assembled during lytic cycle, some bacterial DNA is incorporated in place of viral DNA. when the virus infects another host, the bacterial DNA part that it delivers can recombine with the resident DNA 3. transformation: bacteria absorb DNA from surrounds and incorporate into genome

common groups of bacteria

1. cyanobacteria: photosynthetic like plants. contain accessory pigment phycobilins; some have specialized cells called heterocysts that produce nitrogen-fixing enzyme. **known as blue-green algae (not related to other prokaryotic algae groups 2. chemosynthetic: autotrophs; some are nitrifying bacteria (no2- to no3- 3. nitrogen fixing: heterotrophs that fix n2. lives in nodules of plants (mutualism) 4. spitochetes: coiled bacteria that move with corkscrew motion, internal flagella between cell wall layers

angiosperms are divided into two groups

1. dicotyledons (dicots 2. monocotyledons (monocots)

kingdom plantae: adaptations for survival on land

1. dominant generation is diploid sporophyte generation (except primitive bryophyes: mosses, liverworts, and hornworts); provide two copies against genetic damage that plants were more susceptible to once out of water 2. cuticle: waxy covering that reduces desiccation (drying up/water loss) 3. vascular system reduces dependency on water (cells no longer need to be close to water)=> formation of specialized tissues: true leaves (centers for photosynthesis, true stems (support leaves), true roots (acquire water/anchor plant)). two groups of vascular tissues evolved: *xylem (water transport) and *phloem (sugar transport) 4. in primitive plant divisions (flagellated sperm require water to swim to eggs). in advanced division (coniferophyta and anthophyta) sperm is packaged as pollen (wind) 5. anthophyta: gametophyes are enclosed (protected) inside an ovary 6. adaptations: (in coniferophyta and anthophyta) of seasonal variations in availability of water and light. some are deciduous (shed leaves to prevent water loss through slow-growing seasons) others like desert plants will germinate, grow, flower, and produce seeds rapidly in brief periods of rain.

mammals: development is two stages

1. embryonic 2. fetal development *fetus is an embryo that resembles the infant form

classification of bacteria:

1. mode of nutrition/how they metabolize resources 2. ability to produce an endospore: resistant bodies that contain DNA and small amount of cytoplasm surrounded by a durable wall 3. means of motility (flagella: apical, posterior or engulf cell), corkscrew motion, or gliding through slime material 4. shapes: cocci (spherical), bacilli (rod shaped), spirilla/spirochetes (spirals 5. thick peptidoglycan cell wall (gram positive); think peptidoglycan covered with lipopolysaccharides (gram negative)

structure of the leaf

1. epidermis: protective layers, covered with cuticle (protective layer containing waxy cutin) which reduces transpiration (water loss through evaporation); may bear trichomes (hair, scales, glands, etc outgrowths) 2. palisade mesophyll: consists of parenchyma cells with chloroplasts and large surface area (specialized for photosynthesis). oriented and packed in at upper surface, but for dry habitat->both surfaces (leaf photsynthesis occurs here primarily) 3. spongy mesophyll: parenchyma cells loosely arranged below palisade mesophyll. numerous intercellular spaces provide air chambers CO2 to photsynthesizing cells, O2 respiring cells 4. guard cells: specialized epidermal cells control opening and closing of stomata (allow gas exchange) 5. vascular bundles: consist of xylem (water for photsynthesis) and phloem (transports sugar and by products of photosynthesis to other parts of plants). *bundle sheath cell surrounds vascular bundle->no vascular tissue exposed to intercellular space->no air bubbles that can enter to impede movement of water; also provide anaerobic environment for CO2 fixation in C4 plant

animal tissues: 4 types

1. epithelial: skin, internal covering 2. connective: bone, cartilage, blood 3. nervous 4. muscle

kingdom protista: algaelike (plantlike)

1. euglenoids: 1-3 flagella. pellicles=protein strips make up cell wall. heterotrophic in absence of light. eyespot permits phototaxis 2. dinoflagellates: 2 flagella. some are bioluminescent. others produce nerve toxin in filter feeding shellfish that causes illness to humans when eaten. **responsible for algal bloom called red tide: high concentrations of algae that can lead to toxin buildup, depletion of dissolved oxygen, and other harmful effects 3. diatoms: have tests (shells) that fit together like a box with a lid. contain silica 4. brown algae: multicellular and have flagellated sperm cells (giant seaweed) 5. rhodophyta: red algae (red accessory pigments phycobilins) multicellular and gametes do not have flagella 6. chlorophyta: green algae, have both chlorophyll a and b. cellulose cell walls, store energy as starch. some species have isogamous gamete (both sperm and egg) others are anisogamous (sperm/egg differ in size) others can have oogamous (large egg cell remains with the parent and is fertilized by small sperm). a lineage of chlorophytes, charophytes are believed to be the ancestor of plants

stages of embryonic development (sea urchin-echinoderm)

1. fertilization: sperm penetrate plasma membrane of secondary oocyte a. recognition: before penetration, sperm secretes proteins that bind with receptor that reside on glycoprotein layer (vitelline layer-zone pellucida in human) surrounding plasma membrane of oocyte ensures same species fertilization b. penetration: plasma membranes of sperm and oocyte fuse, sperm nucleus enters oocyte c. formation of fertilization membrane: vitelline layer forms fertilization membrane blocks additional sperm (due to cortical reaction: exocytosis of enzymes produced by cortical granules in egg cytoplasm during fertilization-slow block when seen in mammals d. completion of meiosis II in secondary oocyte: sperm penetration triggers meiosis II; ovum and polar body (discharged through plasma membrane) produced e. fusion of nuclei and replication of DNA: sperm and ovum nuclei fuse-> zygote (diploid-23 pairs in human) 2. cleavage: rapid cell divisions without cell growth; each cell = blastomere (less cytoplasm than original zygote) a. embryo polarity: egg has upper, animal pole and lower, vegetal pole (contain more yolk material which is denser than cytoplasm, settles at bottom; differentiates into extraembryonic membranes that protect and nourish embryo). b. polar and equatorial cleavages: early cleavages are polar, dividing egg into segments that stretch from pole to pole (segments of orange); others are parallel with equator c. radial and spiral cleavages: radial in deuterostomes forming (intermediate) cells at animal and vegetal poles that are aligned together, top cells directly above bottom cells. in protostomes (spiral determinate), cells formed on top are shifted relative to those below d. indeterminate and determinate cleavages: indeterminate (blastomeres can individually complete normal development if separated). determinate cannot develop into complete embryo if separated; each is differentiated into part of the embryo *note: fertilization takes place in the oviduct; embryo at blastula stage by the time it reaches the uterus for implantation 3. morula: successive cleavage results in solid ball of cells (~8+ cells stage) first 8 cells are totipotent (can develop into any type of cell) 4. blastula: cell division continues; liquid fills morula and pushes cells out to form circular cavity surrounded by single layer of cells. blastocoel is the cavity (~128 cells stage) mammalian blastocyst has an inner cell mass** in humans the blastula is called the blastocyst and implants into the endometrium 5. gastrulation: invagination into blastula, forming two layered embryo with an opening from outside into center cavity a. three germ layers: ectoderm, mesoderm, and endoderm (3rd layer is formed between outer and inner layer of invaginated embryo). give rise to all subsequent tissues. **note: some primitive animals eg sponges and cnidarian will develop mesoglea, a noncellular layer, instead of mesoderm b. archenteron: center cavity formed by gastrulation c. blastopore: opening into archenteron, becomes mouth (protostomes) or the anus (deuterostomes) 6. extraembryonic membrane development: in birds, reptiles, and humans (called amniotes), this develops as follows: a. chorion: outer membrane. birds and reptiles: membrane for gas exchange. mammals: chorion implants into endometrium, and later, the chorion and maternal tissue form the placenta (a blend of maternal and embryonic tissues across which gases, nutrients, and wastes are exchanged) b. allantois: sac that buds off from archenteron (cavity of gastrula forming primitive gut) that eventually encircles the embryo, forming layer below chorion. birds and reptiles: initially stores waste products as uric acid. later fuses with chorion-> membrane for gas exchange with blood vessels below. mammals: allantois transports waste products to placenta; eventually forms umbilical cord between embryo and placenta: transporting gases, nutrients, and wastes. becomes urninary bladder in adults c. amnion: encloses amniotic cavity, a fluid-filled cavity that cushions the developing embryo, much like the coelom cushions internal organs in coelomates d. yolk sac: in birds and reptiles, yolk sac membrane digests enclosed yolk. blood vessels transfer nutrients to embryo. in placental mammals, yolk sac is empty, as umbilical cord/placenta delivers nutrients 7. organogenesis: cells continue to divide after gastrulation -> differentiate-> develop into specific tissues and organs. in chordates: a. notochord: cells along dorsal surface of mesoderm layer form notochord, a stiff rod that provides support in lower chordates. vertebrae of higher chordates are formed from nearby cells in mesoderm b. neural tube: in ectoderm later directly above notochord, layer of cells forms neural plate. plate indents, forming neural groove, then rolls up into a cylinder, the neural tube. this develops into the CNS. additional cells roll off top of neural tube and form neural crest (which form teeth, bones, muscles of skull, pigment cells in skin, and nerve tissue)

joint types

1. fibrous: connect bones without allowing any movement (ex: skull, pelvis, spinous process and vertebrae) 2. cartilaginous: bones attached by cartilage, allow little movement (ex: spine and ribs) 3. synovial: allow for much more movement; most common; filled with synovial fluid which acts as a lubricant (ex: carpals, wrist, elbow, humerus and ulna, shoulder and hip joints, knee joint)

notable exceptions to the general embryonic development patters

1. frog: amphibian a. gray crescent: sperm penetrates frog egg-> reorganization of cytoplasm-> pigmented cap of animal pole rotates towards point of penetration while gray, crescent-shaped region forms opposite the point of penetration. spemann found in early cleavage, each individual cell could develop into a frog only if it had a small portion of gray crescent b. gastrulation: blastopore forms at border between gray crescent and vegetal pole. during gastrulation, cells migrate over top edge (dorsal lip-formed from same region previously occupied by gray crescent) of and into blastopore in process called involution; blastocoel disappears and replaced by a different cavity (the archenteron). bottom edge of blastopore-> ventral lip, side -> lateral lip c. yolk: more extensive than sea urchin; cells from vegetal pole rich in yolk material form yolk plug near dorsal lip 2. bird: a. blastodisc: yolk of bird egg is very large, not involved in cleavages; cleavages only occur in blastula that consists of flattened, disc-shaped region that sits on top of yolk (blastodisc) b. primitive streak: when gastrulation begins, invagination occurs along line called primitive streak (rather than a circle). as cells migrate into here, results in an elongated blastopore rather than circular as in sea urchins and frogs 3. humans and most other mammals: a. blastocyst: blastula stage consisting of two parts-outer ring of cells (trophoblast) and inner mass of cells (embryonic disc) *inner cell mass goes on to form the epiblast and hypoblast; epiblast is what gives rise to endo/epi/mesoderm b. trophoblast: accomplishes implantation by embedding into endometrium; produces human chorionic gonadotropin (HCG) to maintain estrogen and progesterone production from corpus luteum (which in turn maintains endometrium); it later forms the chorion (later forms placenta) c. embryonic disc: within cavity created by trophoblast, inner cell mass culsters at one pole and flatten into embryonic disc (analogous to blastodisc of birds and reptiles). primitive streak develops-> gastrulation -> development of embryo and extraembryonic membranes (except chorion)

four stages in growth and development of animal

1. gametogenesis (sperm/egg formation) 2. embryonic development (fertilization of egg until birth) 3. reproductive maturity (puberty) 4. aging process to death

hormones involved in the digestive process

1. gastrin: produced by stomach lining when food reaches or upon sensing food 2. secretin: produced by cells lining duodenum when food enters; stimulates pancreas to produce bicarbonate (neutralizes the chyme) 3. cholcystokinin: produced by SI in response to fats; stimulates gallbladder to release bile and pancreas to release its enzymes 4. gastric inhibitory phase: produced in response to fat/protein digestates in duodenum; mild decrease of stomach motor activity

plant tissues: 3 distinct major groups

1. ground tissues: 3 kinds differ by nature of cell walls. *parenchyma: most common. thin cell walls. function in storage, photosynthesis, and secretion (eg mesophyll cells in leaf). *collenchyma: thick but flexible cell walls, serve mechanical support functions. *sclerenchyma: thicker walls than collenchyma, also provide mechanical support. 2. dermal tissue: epidermis cells that cover outside of plant parts: guard cells that surround stomata, hair cells, stinging cells, and glandular cells; in aerial portions of the plants epidermal cells secrete waxy protective substance: cuticle. Note: roots do not have cuticle- would prevent them from absorbing water! 3. vascular tissue: consists of xylem and phloem-> form vascular bundles

prezygotic isolating mechanism

1. habitat isolation: species do not encounter 2. temporal isolation: species mate/flower during different seasons/time 3. behavioral isolation: does not perform correct courtship rituals 4. mechanical isolation: male/female genitalia are not compatible 5. gametic isolation: male gametes do not survive in environment of female gametes (gametes dont recognize each other)

factors involved in opening and closing of stomata

1. high temps = close 2. low CO2 inside = open = photosynthesis 3. close at night, open during day (CO2 is low during daylight because used by photosynthesis. could be response to CO2 levels: high at night due to respiration, low during day because used for photosynthesis 4. stomata opening accompanied by diffusion of K+ into guard cell->create gradient->more water moves in 5. K+ enter->unbalanced charge state. Cl- cannot come in or H+ gets pumped out

postzygotic isolating mechanisms

1. hybrid inviability: zygote fails to develop properly and dies before reaching one another 2. hybrid sterility: hybrids become functional adults but cannot reproduce 3. hybrid breakdown: hybrids produce offspring that have reduced viability/fertility (hybrids children cant reproduce)

CO2 carried in blood in three forms:

1. in physical solution 2. as bicarbonate ion 3. in carbamino compounds (combined with Hb and other proteins) *majority as bicarbonate ion

factors that influence development

1. influence of egg cytoplasm: cytoplasmic material distributed unequally in egg, non-uniform distribution of cytoplasm (think gray crescent in frogs and yolk in bird eggs) results in embryonic axes, such as animal and vegetal poles. when cleavages divide egg-> daughter cells have different quality of cytoplasmic substances (cytoplasmic determinants). -> unique substances influence subsequent development of each daughter cell 2. embryonic induction: influence of one cell/group of cells over neighboring cells; organizers (controller cells) secrete chemicals that diffuse among neighboring cells, influence their development (dorsal lip functioning as a primary organizer) of blastopore induces notochord development in nearby cells. second dorsal lip grafted to embryo-> two notochords developed 3. homeotic genes: control of development by turning on and off other genes that code for substances that directly affect development. *mutant* homeotic genes in fruit flies-> wrong body parts in wrong places. *homeobox (unique DNA segment-180 nucleotides) identifies a particular class of genes that control development 4. apoptosis: programmed cell death that is part of normal cell development. essential for development of nervous system, operation of immune system, and destroying tissue (webbing) between fingers and toes. damaged cells also undergo this, if dont cancer may develop. regulated by protein activity (rather than at transcription/translation level) apoptosis proteins are present but inactive in normal cell. mammals: mitochondria play important role in apoptosis. characteristics of apoptosis: changes include blebbing, cell shrinkage, nuclear fragmentation, chromatin condensation and chromosomal DNA fragmentation. there is no cellular rupturing, no inflammatory response. the dead cells are engulfed. typically affects single cells.

two groups of chordates

1. invertebrate chordates (lancelets, tunicates) 2. vertebrate (sharks, fish, amphibians, reptiles, birds, and mammals) have vertebrae that enclose the spinal cord *note: reptiles have leathery eggs

cells of the epidermis

1. keratinocytes: produce the protein keratin that helps waterproof the skin 2. melanocytes: transfer skin pigment melanin to keratinocytes 3. langerhans cells: interact with helper T-cells of immune system 4. merkel cells: attach to sensory neurons and function in touch sensation

animal movement

1. kinesis: an undirected (without direction) change in speed of an animals movement in response to a stimulus; slow down in favorable environment and speed up in unfavorable environment. ex: animals scurrying when rock is lifted up 2. taxis: directed movement in response to stimulus. movement is either toward/away from stimulus. phototaxis is the movement toward light. ex: moths moving toward light, sharks moving toward food odors 3. migration: long distance, seasonal movement of animals. usually in response to availability of food/degradation of environmental conditions. ex: migration by whales, birds, elk, insects, and bats to warmer climates

domain eukarya: 4 kingdoms

1. kingdom protista 2. kingdom fungi 3. kingdom plantae 4. kingdom animalia

prophase I: has 5 steps

1. leptotene: chromosomes start condensing 2. zygotene: synapsis begins; synaptonemal complex forming 3. pachytene: synapsis complete, crossing over 4. diplotene: synatopnemal complex disappears, chiasma still present 5. diakinesis: nuclear envelope fragments, chromosomes complete condensing, tetrads ready for metaphase

molecular genetics of viruses: replication

1. lytic cycle: virus penetrates cell membrane of host and uses host machinery to produce nucleic acids and viral proteins that are then assembled to make new viruses-these viruses burst out of the cell and infect other cells **DNA virus: DNA is replicated and form new viral DNA which is transcribed to produce viral proteins (DNA and viral proteins assemble to form new viruses) **RNA virus: RNA serves as mRNA which is translated into protein (protein + RNA => new virus) **retroviruses: (HIV) ssRNA viruses that use reverse transcriptase to make DNA complement of their RNA which can go on to manufacture mRNA or go into the lysogenic cycle (which becomes incorporated into the DNA host) 2. lysogenic cycle: viral DNA is incorporated into DNA of host cell; dormant state (provirus/prophage if bactera) remain inactive until receives external stimuli. when triggered, begins lytic cycle.

some groups of archaea:

1. mathanogens: obligate anaerobes that produce CH4 as by product of obtaining energy from H2 to fix CO2 2. extremophiles: live in extreme environment: *halophiles (salt lover) high salt environment. most are aerobic and heterotrophic; others anaerobic and photosynthetic with pigment (bacteriorhodopsin) *thermophiles (heat lover) are sulfur-based chemoautotroph in very hot places. others live in high acid/base/pressre environments

causes of change in allele frequencies

1. natural selection 2. gene flow: introduction or removal of alleles from population when individuals leave (emigration) or enter the population 3. genetic drift: random increase/ decrease of allele by chance. small population = larger effect *founder effect: allele frequencies in group of migrating individuals are (by chance) not the same as that of their population origin *bottleneck: occurs when population undergoes a dramatic decrease in size (natural catastrophe) making them vulnerable to genetic drift 4. nonrandom mating: individuals choose mates based upon their particular traits (mates choose nearby individuals) 5. mutations

types of phagocytes

1. neutrophils: function in destruction of pathogens in infected tissues; drawn to infected or injured areas by chemicals in process called chemotaxis; slip between endothelial cells of capillary (into tissue) via diapedesis 2. monocytes: move into tissues (diapedesis) where they develop into macrophages 3. eosinophils: work collectively to surround and destroy multicellular parasites 4. dendritic cells: responsible for the ingestion of pathogens and stimulate acquired immunity 5. mast cells: function in allergic response, inflammatory response (histamine release), anaphylaxis

replication of telomere: 2 problems can occur

1. not enough template strand where primase can attach 2. last primase is removed; in order to change RNA to DNA, there must be another DNA strand in front of the RNA primer. DNA pol cannot build after removing RNA primer, ultimately that RNA is destoyed by enzymes that degrade RNA left on the DNA. a section of the telomere is lost with each replication cycle as a result. **prokaryotic DNA is circular so not telomeres thus this is not an issue

interactions between organisms and their environment

1. osmoregulation: a. freshwater fish: live in hypoosmotic environment which causes excess intake of water; thus the fish seldom drink and excrete dilute urine b. saltwater fish: live in hyperosmotic environment; constantly drinking and excreting salt across their gills c. arthropods: secrete solid uric acid crystals to conserve water d. plants: possess waxy cuticles on lead surface and stomata and have stomata on the lower leaf surfaces only; leaves shed in winter; desert plants have extensive root systems, fleshy stems, spiny leaves, extra cuticles, and few stomata 2. thermoregulation a. cold-blooded (poikilothermic): vast majority of plants and animals; body temp is close to that of surroundings so metabolism is radically affected by environmental temp b. warm-blooded (homeothermic): make use of heat produced by respiration; physical adaptations like fat, hair, and feathers retard heat loss (mammals and birds)

female reproduction system

1. ovary: ova or eggs, are produced. each female has two ovaries 2. oviduct: eggs move from ovary to uterus through oviduct (fallopian/ uterine tube); one for each ovary; swept by fimbrae 3. uterus: fertilized ovum implants (attaches) on the inside wall aka endometrium of the uterus. development of embryo occurs here until birth 4. vagina: at birth, fetus passes through cervix (opening in the uterus), through and out of body

evidence for evolution

1. paleontology: fossils (actual remains, petrification, imprints, molds, casts) 2. biogeography: geography to describe distribution of species. continental drift of pangea 3. embryology: similar stages of development (ontogeny) among related species helps establish evolutionary relationships (phylogeny) 4. comparative anatomy: describes two kind of structures that contribute to identification of evolutionary relationship *homologous structures: body parts that resemble one another in different species from common ancestor *analogous structure: body parts that resemble one another in different species because they evolved independently as adaptation to their environments 5. molecular biology: examines nucleotide and amino acid sequences of DNA and proteins from different species 6. comparative biochemistry: organisms with common ancestor= common biochemical pathways

hormone types

1. peptide: synthesized in rough ER and modified in golgi (requires vesicle to cross membrane) acts on surface receptors typically via secondary messengers (cyclic AMP) *manufactured in rough ER as larger preprohormone-> cleaved in ER lumen to prohormone->cleaved again in golgi to final form *receptor-mediated endocytosis: protein stimulates production of second messengers (G-protein->cAMP-produced from ATP; IP3-produced from membrane phospholipids which triggers Ca release from ER) **anterior pituitary: FSH, LH, ACTH, hGH, TSH, prolactin **posterior pituitary: ADH and oxytocin **parathyroid: PTH **pancreas: glucagon and insulin 2. steroid: synthesized from cholesterol in smooth ER; hydrophobic = freely diffuse but require protein transport molecule to dissolve in blood; intracellular receptors *direct stimulation: "steroid" diffuses past plasma membrane and binds receptor in cytoplasm->hormone and receptor transported to nucleus-> binds activated portion of DNA **adrenal gland (cortex): glucocorticoids and mineralicorticoids (aka cortisol and aldosterone) **gonadal hormones aka from testis and ovaries: estrogen, progesterone, and testosterone **estrogen and progesterone are also produced by the placenta 3. tyrosine derivatives: formed by enzymes in cytosol or on rough ER *thyroid hormones: lipid soluble; require protein carrier in blood; bind to receptors in nucleus *catecholamines: (epinephrine and norepinephrine) water soluble; dissolve in blood; bind to receptors on target tissue and mainly act via second messenger **thyroid hormones: T3 and T4 aka thyroxine **catecholamines formed in adrenal medulla: epinephrine and norepinephrine

4 methods for material to cross capillary wall:

1. pinocytosis 2. diffusion through capillary cell membrane 3, movement through pores in the cells (fenestrations) 4. movement through space between cells

process of blood clotting

1. platelets contact exposed collagen of damaged vessel and cause neighboring platelets to form platelet plug 2. both the platelets and damaged tissue release clotting factor; thromboplastin 3. thromboplastin converts inactive plasma protein prothrombin to thrombin (active) 4. thrombin converts fibrinogen into fibrin 5. fibrin threads coat damaged area and trap blood cells to form a clot

process of fertilization in angiosperms

1. pollen lands on sticky stigma (female). pollen tube (elongating cell) that contains vegetative nucleus grows down the style toward an ovule; two sperm cells inside pollen tube. 2. ovule within ovary (consist of megaspore mother cell surrounded by nucleus + integuments). megaspore mother cell=>meiosis 4 haploid megaspores; one survives=>mitosis x3=8 nuclei=>6 nuclei undergoes cytokinesis and form plasma membranes (embryo sac). at the micropole of embryo sac are 3 cells (egg and 2 synergids). at the other end of micropyle are 3 antipodal cells. in the middle are polar nuclei (2 haploid cells) 3. pollen tube (2 sperm cells) enters embryo sac through micropyle; 1 sperm cell fertilizes egg (form diploid zygote); nucleus of second sperm fuses with both polar nuclei=>triploid nucleus->mitosis->endosperm (provide nutrient). **double fertilization is fertilization

natural selection

1. populations possess an enormous reproductive potential 2. population size remain stable 3. resources are limited 4. individuals compete for survival 5. there is variation among individuals in a population 6. much variation is heritable 7. only the most fit individuals survive 8. evolution occurs as favorable traits accumulate in the population

list of animal phyla:

1. porifera (parazoa): sponges; feed by filtering water through sponge wall of flagellated cells (choanocytes-flagella creates a flow of water for feed filter). water exits through osculum opening. choanocytes pass food to amoebocytes (digesting and distribute nutrients). sponge wall contains spicules (skeletal needles made from CaCO3 or SiO2. sessile (fixed). used in development and research of antibiotics 2. cnidaria: hydrozoans, jellyfish, sea anemones, corals; two body forms (medusa-floating, umbrella-shaped body with tentacles; polyp-sessile cylinder-shaped with rising tentacles). some alternate between during medusa/polyp in life cycle. *cnidoblasts: specialized cells located in the tentacles and bodywalls of cnidaria; interior of cnidoblasts filled with stinging organelles (nematocysts) 3. platyhelminthes: three types of acoelomate flatworms; *free living flatworms (planarians-carnivores in marine or freshwater). *flukes are internal animal parasites/external parasites that suck tissue fluids/blood. *tapeworms are internal parasites that often live in digestive tract of vertebrates; appear segmented (but these segments aka proglottids only develop secondarily for reproduction->not considered true segmented animal). tapeworms do not have a digestive tract, only need to absorb predigested food around them. other platyhelminthes have a saclike gut 4. nematoda: roundworms: pseudocoelomate with complete digestive tract; free-living soil dwellers help decompose and recycle nutrients (causes trichinosis in human, when ingested via incompletely cooked meat) 5. rotifera: multicellular with specialized organs enclosed in pseudocoelom, complete digestive tract; filter-feeder 6. mollusca: snail, octopus (highly developed NS with complex brain), squids (most have shells), bivalves (2 part shells eg clams and mussels); no shell in octopus, small and internal shell in squid. mollusks have coelomate bodies, complete digestive tract, usually open circulatory system with internal cavity called hemocoel. exoskeletons are CaCO3. *class gastropoda: largest molluscan class: examples are slugs and snails; characterized by a single shell *class cephalopoda: octopus and squid; have high O2 demands, giant nerve fibers, closed circulatory systems *class bivalvia: clams, mussels, scallops, oysters 7. annelida: segmented worms (leeches-have suckers at both ends for attachment and movement and are predators of small animals/blood parasites; earthworms and polychaete worms-mostly marine, exhibit variety of lifestyles). septa divide the coelem into separate compartments. 8. arthropoda: spiders, insects, crustaceans; jointed appendages, well-developed nervous system; specialized body segments, exoskeleton (chitin). two kinds of life cycles: *nymph (small version of adult, change shape as growth proceeds) *larvae are maggots specialized for eating; when they reach certain size they enclose themselves within a pupa (cocoon) to undergo metamorphosis into adults (specialized to disperse and reproduce). classes include: *insects: three pairs of legs, spiracles, tracheal tubes for breathing. more species than any other class on earth *arachnids: four pair of legs and "book lungs" (spiders and scorpians) *crustaceans (subphylum) segmented body with variable number of appendages and have gills. crab, shrimp, lobster, crayfish and barnacles 9. echinodermata: sea stars, urchin, sand dollars; coelomate deuterostomes; complete digestive tract; adults have radial symmetry but are bilateral when young; some features are bilateral (ancestors are believed to have been bilateral) 10. chordata: 4 main features (sometimes just temporary during embryonic development) *notochord: provides dorsal, flexible rod that functions as support; replaced by bone during development in most vertebrates, it becomes nucleus pulposus of intervertebral disc; derived from mesoderm. defines primitive axis of embryo. *dorsal hollow nerve cord: forms basis of nervous system. in some chordates, becomes brain and spinal cord. *pharyngeal gill slits: provide channels across pharynx to outside body; slits become gills for O2 or filter-feeding; slit disappear during embryonic development in others. in fish, gill pouch -> fish gills. in mammals, gill pouch -> eustachian tubes in ears. *muscular tail: such tail lost during embryonic development in humans and many other chordates

transmission of nerve impulse

1. resting potential: normal polarized state of neuron, -70mV 2. action potential: stimulus->gated ion channels let Na+ into the cell, depolarizing it. if the threshold level is reached (-50mV), it will cause an ap that will result in opening of voltage gated Na+ channels down the entire length of the neuron. *all or nothing event! 3. repolarization: in response to Na+ flow in, more gated ion channels let K+ out of the cell, restoring polarization, but the Na+ and IN and the K+ are OUT 4. hyperpolarization: by the time the channels close, too much K+ is released (-80mV) 5. refractory period: neuron will NOT respond to new stimulus until Na+/K+ pumps return the ions to their resting potential locations (outside/inside respectively) if absolute. if relative, abnormally large stimuli can create an ap. note that refractory period is what prevents an ap from moving backwards, even though ions are theoretically rushing in and diffusing in both directions

glands of the skin

1. sebaceous (oil) glands: connected to hair follicles; absent in palms and soles 2. sudoriferous (sweat glands) **eccrine (most of body) regulate temp through perspiration; eliminate urea **apocrine: armpits, pubic region, and nipples; secretions are more viscous 3. ceruminous (wax) glands: found in ear canal; produce wax-like material as barrier to entrance 4. mammary (milk) glands

three types of neurons

1. sensory (afferent): receive initial stimulus (ex: neurons in retina of eye) afferent->brain 2. motor (efferent): stimulate effectors which are target cells that elicit some response (ex: neurons may stimulate the muscles, sweat glands, or cells in the stomach to secrete gastrin) brain->motor 3. association (interneuron): located in spinal cord and brain. receive impulses from sensory and send impulses to motor neurons. they are integrators, as they elevate impulses for appropriate response. about 99% of nerves are interneurons

types of muscle response

1. simple twitch: response of a single muscle fiber to brief stimulus; latent, cx, relax *latend period: time between stimulation and onset of cx; lag *contraction *relaxation (absolute refractory period): unresponsive to stimulus 2. summation and tetanus: *summation: contractions combine and become stronger and more prolonged (repeated action potentials summate) *tetanus: continuous sustained cx; muscle cannot relax; will release if maintained (in tetanus, rate of muscle stimulation so fast that twitches blur into one smooth constant) 3. tonus: state of partial cx; muscle never completely relaxed

regulation of cell cycle: limitations

1. surface to volume ratio: when ratio is large, exchange becomes much easier. when small, exchange is hard and leads to cell death or cell division to increase SA 2. genome to volume ratio: genome size remains constant throughout life; as cell grows, only volume increases

purines

2 rings: adenine and guanine (double ring) 2H bonds

male reproduction system

1. testis: each consists of seminiferous tubules for production of sperm and interstitial cells (*leydig cells) produces male sex hormones (testosterone = androgen) secreted in the presence of LH; sertoli cells stimulated by FSH surround and nurture sperm (also secrete peptide hormone:*inhibin-acts on pituitary gland to inhibit FSH release); testis contained in scrotum-about 2 degrees C lower than body temp here for sperm production 2. epididymis: coiled tube, one attached to each testis; site for final maturation and storage of sperm 3. vas deferens: transfer sperms from one epididymis to urethra 4. seminal vesicles: two glands, during ejaculation secrete into vas deferens: provide mucus (liquid for sperm), fructose as ATP, and prostaglandins (stimulate uterine contractions that help sperm move into uterus) 5. prostate gland: secretes milky alkaline fluid into urethra; neutralizes acidity of urine that may still be in urethra, also vagina acidity. also neutralizes seminal fluid (too acidic from metabolic waste of sperm) 6. bulbourethral glands aka cowpers: secrete small amount of fluid unknown function into urethra 7. penis: transport semen (fluid containing sperm and secretions) into vagina 8. sperm: compact packages of DNA specialized for effective male genome delivery *sperm head: haploid (23 chromosomes); at tip is acrosome (a lysosome containing enzyme-hyaluronidase- which are used to penetrate egg. originates from golgi body vesicles that fused together). only nuclear portion of sperm enters the egg *midpiece: flagellum (9+2 microtubule array) lots of mitochondria *tail: remainder of flagellum; sperm is propelled by whiplike motion of tail and midpiece

important characteristics of animal kingdom

1. tissue complexity: eumetazoa (functioning cells organized into tissues). diplobasltic/triploblastic layers of tissue (ecto, meso, endoderm). another group is parazoa (cells not organized into true tissues=>organs do not develop 2. body symmetry: radial symmetry (one orientation front and back) with circular body pattern; bilateral symmetry (dorsal-top, ventral-bottom, head-anterior, tail-posterior 3. cephalization: in animals with bilateral symmetry (greater nerve tissue connection at anterior end as organisms increase in complexity) eg brains have developed and sensory organs 4. gastrovascular cavity: guts (digestion of food). one opening-sacline, limited processes. two openings (digestive tract), specialized activities as food travels through 5. coelem: more advanced animals develop this cavity derived from mesoderm; fluid-filled coelem cushions internal organs. acoelomate animals lack a coelem. psuedocoelomate animals have a cavity (but not completely lined by mesoderm derived tissue) 6. segmentation: sometimes repetitive and sometimes specialized (seen in: arthropods, annelids, chordates 7. protostomes and deuterostomes: cleavage (cell divisions in zygotes early development); archenteron (the primitive gut that forms during gastrulation in the developing blastula. it develops into the digestive tract of an animal; its opening will either be mouth or anus). coelem will either develop from splitting of mesodermal tissue at side of archenteron or directly from outpouching in archenteron wall

movement in lower forms

1. unicellular locomotion: *protozoans and primitive algae: cilia or flagella by means of power stroke and recovery stroke *amoeba: extend pseudopodia; advancing cell membrane extends forward 2. invertebrate locomotion: *hydrostatic skeletons **flatworms: bilayered muscles, longitudinal and circular, contract against hydrostatic skeleton. cx causes hydrostatic skeleton to flow longitudinally, lengthening animal **segmented worms (annelids): advance by action of muscles on hydrostatic skeleton. bristles in lower part of each segment aka setae, anchor worm in earth while muscles push ahead

6 fungi groups:

1. zygomycota: lack septa, except filaments bordering reproductive filaments; reproduce sexually by fusion of hyphae from different strains, followed by plasmogamy, karyogamy, meiosis: haploid zygospores are produced=> germinate into new hyphae (eg bread molds) 2. glomeromycota: lack septa, do not produce zygospores; mutualistic associations with roots of plants (mycorrhizae) 3. ascomycota: have septa; reproduce sexually by producing haploid ascospores. after plasmogamy of hyphae from different strains, dikaryotic hypha produces more filaments by mitosis; karyogamy and meiosis occurs in terminal hyphal=>4 haploid cells=> mitosis to produce 8 haploid ascospores in a sac called ascus; often grouped together into fruiting body ascocarp (yeast). the spores release and germinate into hyphae, cycle repeats 4. basidiomycota: septa, reproduce sexually by producing haploid basidiospores. plasmogamy-> mitoisis->fruiting body (basidiocarp) such as mushroom; karyogamy occurs in terminal hyphal cells called basidia, followed by meiosis to produce 4 haploid basidiospores 5. deuteromycota: imperfect fungi, artificial group (no sexual reproductive cycle). penicillium produces penicillin 6. lichens: mutualistic associations between fungi and algae. provide nitrogen if algae is nitrogen fixing. fungus (usually ascomycete) provides water and protection (pigments from UV light, or toxic chemicals) from environment

triglycerides

3 fatty acid chains attached to a glycerol backbone

major plant division: pterophyta

3 groups: 1. ferns: produce cluster of sporangia called sori that develop on undersurface of fern fronds (meiosis => spores) 2. horsetails: include extinct woody trees; hollow, ribbed stems that are joined at nodes; stobili bear spores. stems, branches, and leaves are green (photosynthetic) and have rough texture due to silica (SiO2) 3. whisk ferns: branching stems without roots. leaves reduced to small appendages or absent. absence of roots/ leaves is considered *secondary loss: lost as whisk ferns diverged from ancestors

TOTAL energy from 1 glucose

36 ATP but in prokaryotes 38 ATP ( not actual yield, mitochondrial efficiency varies) difference because prokaryotes have no mitochondria so dont need to transfer pyruvate into mitochondrial matrix-they use the cell membrane for respiration

electron tomography

3D model buildup using TEM data. can look at objects in 3D and see objects relative to one another. cant be used on living things

digestion in humans

4 groups of molecules encountered: 1. starches->glucose 2. proteins->amino acids 3. fats->fatty acids 4. nucleic acids->nucleotides

Hb structure

4 polypeptide subunits, each has a heme cofactor (organic molecule with iron atom center) *each iron atom can bind with one O2 molecule *via cooperativity: one O2 binds-> rest bind easier (this is why Hb has a sigmoidal shape. likewise one O2 released-> the rest release easier

blood

4-6 liters in the human body; is a connective tissue *55% liquid (plasma) and 45% cellular components-plasma is an aqueous mixture of nutrients, salts, gases, wastes, hormones, and blood proteins (immunoglobulins, albumin, fibrinogen, clotting factors)

DNA backbone

5' to 3' phosphodiester bonds form phosphate backbone

ribosomes

60S+40S=80S prokaryote=50S+30S=70S. the two subunits produced inside the nucleolus moved into the cytoplasm where they are assembled into a single 80S ribosome. made of rRNA +protein, function to make proteins

air

80% nitrogen, 20% oxygen

human genome

97% of human DNA does not code for protein product; noncoding DNA: regulatory sequences, introns, repetitive sequences never transcribed etc. tandem repeats abnormally long stretches of back to back repetitive sequences within an affected gene (huntingtons)

stroke volume

=EDV-ESV. volume of blood pumped out of the heart with each beat. formula subtracts the end systolic volume (blood in the ventricle at the end of the contraction/systole) from the end diastolic volume (volume of blood in the ventricle just before contraction)

cardiac output (CO)

=Stroke volume * heart rate *stroke volume = volume of blood discharged from the ventricles with each Cx *cardiac output = volume discharged from ventricle each minute *stroke volume = end systolic volume - end diastolic vol

RNA

A,U,G,C. functional usage-varies per type: mRNA linear, tRNA clover, rRNA globular

plant hormones: abscisic acid

ABA: growth inhibitor. in buds it delays growth and forms scales, maintains dormancy in seeds. dormancy can be broken by increase in gibberellins or mechanistic response to environmental cues

plants DO have mitochondria

BUT the ATP from photosynthesis comes from the chloroplast (not mitochondria) and is used to drive photosynthesis further aka the calvin cycle. photosynthesis primarily makes glucose for the plants own mitochondria to use as energy!

CUT the PYE

C, T, and U are pyrimidines

tRNA

C-C-A-3' end of tRNA attaches to amino acid, and the other portion is the **anticodon which base pairs with the codon in mRNA. *wobbles: exact base pairing of the third nucleotide in the anticodon and third nucleotide in the codon is often not required, allowing 45 different tRNAs to base pair with 61 codons that code for amino acids. transports amino acid to its mRNA codon

plant hormones: ethylene

CH2=CH2: gas that promotes ripening of fruit; production of flowers; influences leaf abscission (aging and dropping of leaves); apoptosis. together with auxin, can inhibit elongation of roots, stems, and leaves. stimulates ripening by enzymatic breakdown of cell walls. ethylene is why ripe fruit in proximity to a spoiled one will also cause it to spoil

oxygen diffuses from alveolar air into blood

CO2 diffuses from blood into lungs

excretion in annelids

CO2 excretion directly through moist skin *nephridia (metanephridia) occur in pairs within each segment of annelids (earthworms). interstitial fluids enter a nephridium through ciliated opening *nephrostome and concentrate through collecting tubule due to selective secretion into surrounding coelomic fluid. blood that surrounds tubule reabsorbed. water, salts, urea are excreted through excretory pore

gas exchange in humans

CO2 is transported as HCO3- in the plasma, catalyzed by carbonic anhydrase located in the RBC. some CO2 mixes directly with plasma as gas, or binds with Hbs in RBCs

bulk flow of CO2

CO2 mainly transported as HCO3- ions in plasma, liquid portion of the blood. produced by carbonic anhydrase in RBCs. CO2 can also directly mix with plasma (as CO2 gas) or bind Hb inside RBCs.

excretion in arthropods

CO2 released from tissues-> tracheae (which are continuous with external air through spiracles) *malphigian tubules: occurs in arthropods (terrestrial insects). tubes attached to mid digestive tract (midgut) collect body fluids from hemolymph that bathe the cells; fluids are deposited into midgut. fluids include N wastes. as fluid passes through hindgut, retained materials pass out of walls and wastes continue down the tract for excretion through anus

cyclin-dependent kinases (Cdks)

Cdk enzyme activates proteins that regulate cell cycle by phosphorylation; Cdks are activated by protein cyclin

DNA replication: second chromatid containing a copy of DNA is assembled during interphase

DNA is unzipped and each strand serves as a template for complementary replication. semiconservative replication= one strand of the two is old, the other is new

Bohr effect

Hb O2 binding affinity decreases under conditions of low pH (high CO2 and H+)-> oxygen loads released by Hb *decrease in CO2 or increase in pH will result in Hb binding more O2

transport proteins

Hb carries o2, cytochromes carry electrons

1. size

N, total number of individuals in population

ozone depletion

O2+UV in atmosphere->O3 is ozone which absorbs UV radiation, preventing it from reaching surface of earth (UV damages DNA). CFCs (chlorofluorocarbans) enter upper atmosphere and break down O3

autosomal recessive genetic disorders

PKU; inability to produce proper enzyme for phenylalanine breakdown leading to degradation product phenylpyruvic acid accumulation. cystic fibrosis; fluid buildup in tracts. tay-sachs; lysosome defect where cant break down lipids for normal brain function. sickle-cell; defective Hb due to substitution mutation.

Pfr appears to reset circadian rhythm clock:

Pfr is active form of phytochrome; maintains accuracy by resetting clock

Pr is the form of phytochrome synthesized in plant cells:

Pr is synthesized in leaves

flash of red during night:

Pr->Pfr->shorter night period measured->circadian rhythm reset

DNA finger printing

RFLPs at crime scene compared to RFLPs of suspects

Coenzyme Q

Ubiquinone is a soluble carrier dissolved in the membrane that can be fully reduced/ oxidized, it passes electrons in chain

receptor mediated

a form of pinocytosis; specific molecules (ligands) bind to receptors; proteins that transport cholesterol in blood (LDL) and hormones target specific cells by this

species

a group of individuals capable of interbreeding

clade

a group of species that includes a common ancestor and all of its descendants aka monophylum

red tide

a harmful algal bloom caused predominantly by dinoflagellates

aldosterone

a mineralocortocoid isolated from the adrenal cortex. mineralocortocoids are involved with water and salt balance. stimulates kidney cells to reabsorb sodium ions and water from the filtrate, which results in a rise in blood volume and pressure

homologous chromosomes

a pair of chromosomes that contains the same genetic material (gene for gene). each parent contributed 1 of the chromosomes in the pair and thus different alleles may exist for a gene (dominant and recessive or incomplete dominance like color blending, or codominance such as blood type

sere

a particular stage of an ecosystem

reflex arc

a rapid, involuntary response to a stimulus involving two or three neurons, but brain DOES NOT integrate the sensory and motor activities. instead synapse in spinal cord** ex: knee jerk (patellar) reflex

turner syndrome

a type of aneuploidy with nondisjunction in the sex chromosome. gametes (single, from one parent) can be XX/XY or O (no chromosome) leading to XO sterile, physically abnormal; Klinefelter (XXY)

cast

a type of fossil formed when a mold is filled in

6. population growth

a. biotic potential: maximum growth rate under ideal conditions (unlimited resources and no restrictions). factors that contribute: age at reproductive maturity, clutch size (number of offspring produced at each reproduction), frequency of reproduction, reproductive lifetime, survivorship of offspring to reproductive maturity b. carrying capacity (K): maximum number of individuals of a population that can be sustained by a habitat c. limiting factors: density-dependent (limiting effect becomes more intense as population density increases-competition, spread of disease, parasites, predation) and density-independent (occur independently of density of population such as natural disasters or big temp changes) **growth rate of pop: r=(births-deaths)/N **change: deltaN/deltat=rN=births-deaths **intrinsic rate: of growth is when the reproductive rate (r) is maximum (biotic potential) d. expontential growth: occurs whenever reproductive rate (r) is greater than zero (J-shaped) e. logistic growth: occurs when limiting factors restrict size of population to the carrying capacity of habitat. when pop size increases-> growth rate decreases and reaches 0 when pop size reach carrying capacity(K)-> S-shaped **population cycle: fluctuations in pop size in response to varying effects of limiting factors. when pop grows over carrying capacity, it may be limited (lower) than the initial K due to the damage caused to the habitat-> lower new carrying capacity K or it may crash to extinction

hydrologic cycle (water cycle)

a. reservoir: oceans, air, groundwater, glaciers b. assimilation: plants absorb water from soil; animals drink and eat other organisms c. release: plants transpire; animals and plants decompose

simple and complex reflexes

a. simple: automatic 2 nerve (afferent/efferent) response to stimulus controlled at spinal cord (lower animals) b. complex: automatic response to significant stimulus (controlled at brain stem or even cerebrum) ex: startle response: controlled by the reticular activating system

predation: another form of community interaction

a. true predator: kills and eats another animal b. parasite: spends most of its life living on host, host usually doesnt die until parasite completes one life cycle c. parasitoid: an insect that lays its eggs on host (insect or spider). after eggs hatch, larvae obtain nourishment by consuming hosts tissues. host eventually dies, but not until larvae complete development and begin pupation d. herbivore: animal that eats plants. granivores are seed eaters-eat whole seed leaving it not viable. grazers- animals that eat grasses. browsers-eat leaves and eat only part of it->weakening it in process

mitosis: cytokinesis

actually begins during the later stages of mitosis. most sources indicate it begins towards the end of anaphase. this is the division of cytoplasm to form 2 cells. it begins with a cleavage furrow where actin and myosin microfilaments shorten and pull plasma membrane into the center (animals) for plants, a cells plate is formed by vesicles from golgi bodies migrating to fuse the cell plate. then there is out growth and it merges with the PM separating the two new cells. the cells dont actually separate from each other, middle lamella cements adjacent cells together

gel electrophoresis on proteins

add SDS: denatures, linearizes, adds negative charge

cholesterol

adds rigidity to membrane of animal cells under normal conditions (but at low temps it maintains its fluidity) sterols provide similar function in plant cells. prokaryotes do not have cholesterol, use hopanoids instead

trial and error learning (operant conditioning)

another form of associative learning that occurs when animal connects its own behavior with environmental response, reward.

left ventricle

after going through left AV (aka mitral or bicuspid) valve, blood from left ventricle goes to aorta through the aortic semilunar valve into rest of body: *aorta->arteries->arterioles->capillaries->tissues get what they want->venules->veins->superior and inferior vena cava->cycle repeats *left AV valve prevents backflow into atrium, aortic semilunar valve prevents it into ventricle

insulin

after large meals, stores glucose as glycogen, glucagon is the opposite effect and turns on glycogen dehydration. insulin activates PFK enzyme, glucagon inhibits it

left atrium

after lungs the oxy blood enters left atrium via pulmonary veins

MTOCs

aka centrosomes. pair of these lay outside nucleus. in animal cells, each MTOC contains a pair of centrioles. recall that plants do have MTOCs called centrosomes, but they are NOT composed of centrioles

major plant division: coniferophyta

aka gymnosperms (naked seeds): cone-bearing (pines, firs, spruces, junipers, redwoods, cedars); pollen bearing male + ovule bearing female cones; seeds produced in unprotected megaspores near surface of reproductive surface of reproductive structure. fertilization and seed development are lengthy (requires one to three years)

root cap

aka root tip, protects apical meristem behind it. secretes polysaccharides that moisten soil, permitting root growth

protists

all are eukaryotes and are classified based on locomotion

excretion in protozoans and cnidarians

all cells in contact with external aqueous environment *water soluble wastes (ammonia, CO2) exit by simple diffusion *protists such as paramecium and amoebas: possess contractile vacuole for excess water excretion by active transport

polyploidy

all chromosomes undergo meiotic nondisjunction and produce gametes with twice the number of chromosomes. common in plants

biotic

all living things that directly or indirectly influence the life of the organism

contraction

all or nothing response 1. action potential of neuron releases acetylchonline when meets neuromuscular junction 2. action potential then generated on sarcolemma and throughout T-tubules 3. sarcoplasmic reticulum releases Ca2+ 4. myosin cross bridges form: result of Ca2+ binding to troponin on actin helix

gene pool

all the alleles for any given trait in the population

(p,q)

allele frequencies for each allele

hardy-weinberg equilibrium

allele frequencies remain constant from generation to generation = no evolution. requires the following conditions: 1. no mutation 2. all traits are neutral (no natural selection) 3. population must be isolated (no gene flow) 4. large population (no genetic drift) 5. mating is random 6. no net migration

porins

allow passage of certain ions and small polar molecules. aquaporins increase rate of h2o passing in kidney and plant root cells. these tend to not be specific

density-dependent inhibition

cells stop dividing when surrounding cells density reaches maximum

forward mutation

already mutated organism mutates again even more

ecological footprint

amount of raw land necessary to sustain an individuals lifestyle habits

ATP

an RNA nucleotide (due to its ribose sugar) unstable molecule because the 3 phosphates in ATP are negatively charged and repel one another. when one phosphate group is removed during via hydrolysis, more stable molecule ADP results. the change from a less stable molecule to a more stable one always releases energy. provides energy for all cells by transferring phosphate from ATP to another molecule

positive feedback

an action intensifies a condition so that it is driven further beyond normal limits (labor contraction, lactation, and sexual orgasm)

reverse transcriptase

an enzyme seen in retroviruses in which RNA is the genetic material. DNA is then made from the RNA and incorporated into the host cell.

mold

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

observational learning

animal copies behavior of another without having experienced any feedback themselves a. all monkeys followed lead of first by washing off potato in water

CAM photosynthesis

another add on to C3, crassulacean acid metabolism; almost identical to C4. 1. PEP carboxylase fixes CO2 + PEP to OAA; OAA==>malic acid 2. malic acid is shuttled into vacuole of cell 3. at night, stomata are open (opposite of normal) PEP carboxylase is active, malic acid accumulates in vacuole 4. during the day, stomata are closed. malic acid is out of vacuole and converted back to OAA which requires 1ATP, releasing CO2 and PEP ** overall advantages are can proceed during day while stomata are closed which reduces water loss. occurs in cacti, crassulacea plants (dicotyledon family)

Rh factor

another blood antigen (protein on surface of RBCs); mother might attack Rh+ in second fetus (erythroblastosis fetalis) aka hemolytic disease *first child is fine but during first childhood blood exposure-> antibodies to Rh attack second child

spatial learning

another form of associative learning. animal associates attributes of landmark with reward of identifying and returning to that location a. ex: wasps able to associate pinecones with location of nest (lost upon removal)

meristems

are areas in plants where active mitosis occurs, due to this cell division, it is also where growth occurs. lateral meristems can be at tip of lateral growth in plant. apical meristems are responsible for vertical growth and found at root and shoot (apex) tips

enzymes

are globular proteins that act as catalysts. substrate specific, unchanged during rxn, catalyzes in both forward and reverse directions, temp and pH affect enzyme function, active site and induced fit is how enzymes bind

integral proteins

are hydrophobic; use detergent to destroy membrane and expose these proteins

glycolipids

are like phospholipids but with a carb group instead of phosphate. lipids are insoluble so they are transported in the blood via lipoproteins

ECL cells

are neuroendocrine cells in the dig tract; gastrin stimulates them to release histamine which in turn stimulates parietal cells to produce gastric acid

domain archaea

are prokaryotes but differ from bacteria, the other major category of prokaryotes *archaeal cell walls contain various polysaccharide, NOT peptidoglycan (as in bacteria), cellulose (as in plants), or chitin (as in fungi). *phospholipid components: glycerol is different (uses an isomer of the one in bacteria/eukaryotes), and the hydrocarbon chain (fatty acid) is branched (rather than straight chain) with ether-linkages instead of ester-linkages

antibodies

are released from plasma cells, are specific for an antigen, and a single B lymphocyte produces only one ab type

vascular bundles

arrangement of vascular tissue (xylem and phloem) in stems. dicots= organized in a circle. monocots= scattered

character displacement (niche shift)

as a result of resource partitioning, certain traits allow for more success in obtaining resources in their partitions-> reduces competition-> divergence of features (character displacement) such as different beak of birds on same island.

2. primordial seas form:

as earth cooled, gases condensed, sea with water and minerals

reabsorption

as the filtrate flows through the renal tubule, most of the water and nutrients are reabsorbed into the blood. the concentrated fluid that remains is called urine

protein synthesis: mRNA processing

before leaving the nucleus, pre-mRNA undergoes several modifications: 1. 5' cap (-P-P-P-G-5'): the sequence is added to the 5' end of the mRNA; guanine with 2 phosphate groups=> GTP; providing stability for mRNA and point of attachment for ribosomes. 2. a poly-A tail (-A-A-A..A-A-3'): sequence is attached to the 3' end of the mRNA. tail consists of 200A; provide stability and control of movement of mRNA across the nuclear envelope. **in prokaryotes, polyA tail facilitates degradation! 3. RNA splicing: removes nucleotide segments from mRNA; before mRNA moves into cytoplasm, small nuclear ribonucleoproteins (snRNPs) and the spliceosome delete the introns and splice the exons **prokaryotes have no introns! 4. alternative splicing: allows different mRNAs to be generated from the same RNA transcript; by selectively removing differences of an RNA transcipt into different combinations=> each coding for a different protein product

protein synthesis: translation

assembly of amino acids based on reading of new RNA; uses GTP as its energy source. **aminoacyl-tRNA: in the cytoplasm, amino acid attaches to tRNA at 3' end, requires 1 ATP->AMP per amino acid 1. initiation: small ribosome unit attaches to 5' end of mRNA; tRNA-methionine attaches to start sequence of mRNA AUG, and large ribosomal unit attaches to form a complete complex. *requires 1 GTP 2. elongation: next tRNA binds to A site, peptide bond formation, tRNA without methionine is released, the tRNA currently in A site moves to P site (translocation) and the next tRNA comes into A site and repeats the process *requires 2 GTP per link 3. termination: encounters the stop codon UAG, UAA, UGA. polypeptide and the two ribosomal subunits all release once release factor breaks down the bond between tRNA and final amino acid of the polypeptide. while polypeptide is being translated, AA sequences are determining folding conformation. folding process assisted by chaperone proteins *requires 1 GTP 4. post-translation: translation begins on a free floating ribosome; signal peptide at the beginning of the translated polypeptide may direct the ribosome to attach to the ER, in which case the polypeptide is injected into the ER lumen. if injected, polypeptide may be secreted from the cell via Golgi. in general, post-translational modification (addition of sugars, lipids, phosphate groups to the AAs) may occur. **AA are placed starting from the 5' end of the mRNA and move all the way down to the 3' end. tRNA codons for matching are 3' to 5' **translation can occur simultaneously with transcription in prokaryotes, but not in eukaryotes. multiple ribosomes may simultaneously translate 1 mRNA **also note that in bacteria, the start codon is n-formylmethionine rather than methionine

if asked the number of chromatids...

assume they have already been doubled in this situation and dealing with mitosis **mitosis = no genetic variation

adhesion proteins

attach cells to neighboring cells, provide anchors for internal filaments and tubules. provides stability

two major methods of energy acquisition

autotroph and heterotroph

primary producers

autotrophs that convert sun energy into chemical energy; plants, photosynthetic protists, cyanobacteria, and chemosynthetic bacteria

backward mutation

back to original state

if phenotype skips generations

be suspicious of an autosomal recessive disorder

DNA replication

begins at special sites (origins of replication) in the middle of the DNA molecule (not the end) DNA strands separate to form replication bubbles that expand in both directions. thousands of these bubbles happen; speed up replicatin of 3 billion BP DNA molecule. **prokaryotes only have one origin of replication

secondary succession

begins in habitats where communities were entirely/partially destroyed by damaging event; begins on substrate that already bear soil (may contain native seed bank)

instinct

behavior that is innate, or inherited. ex: in mammals, care for offspring by female parents

stabilizing selection

bell curve, favors an intermediate

asexual reproduction

benefits from stable environment since offspring are clones; sexual reproductions advantage is variation

carrier proteins

bind to specific molecules, protein changes shape, molecule passed across. ex is glucose into cell.

receptor proteins

binding sites for hormones and other trigger molecules

Hb

binds CO with much greater affinity than Mb (also has 4 subunits vs 1)

98% of blood oxygen

binds rapidly and reversibly with protein Hb inside RBCs, forming oxyhemoglobin

central dogma of genetics

biological info cannot be transferred back from protein to either protein or nucleic acid. DNA to RNA to proteins

incomplete dominance

blending of expressions of alleles

multiple alleles

blood groups have 3 possible alleles leading to 4 possible genotypes

right ventricle

blood is squeezed through right AV/tricuspid valve into right ventricle which contracts and pumps blood into pulmonary artery through the pulmonary semilunar valve *when the ventricle cx, AV valve closes to prevent backflow *when ventricle relaxes, semilunar valve prevents backflow from pulmonary artery back into ventricles

pulmonary circuit

blood pathway from right side of heart to lungs to left side of heart *blood flows from pulmonary artery-> arterioles -> capillaries of the lungs-> collects in venules-> veins->pulmonary veins->left atrium

osmoregulation: fresh water fish

body is hypertonic to environment; water moves in=>rarely drink, constantly urinate, and absorb salts through gills

osmoregulation: marine fish

body is hypotonic to environment->water is constantly lost by osmosis, constant drinking, rarely urinate, and secrete accumulated salts through gills

know it is codominance when:

both alleles will show as dominant with capital letters

amphipathic

both hydrophilic and hydrophobic properties

codominance

both inherited alleles are completely expressed

mucoprotein

bound to carbohydrate

lipoprotein

bound to lipid

chromoprotein

bound to pigmented molecule

osteoclasts

break down bone. if the body needs calcium it breaks down bone. PTH will stimulate its activity, while Calcitonin tones down the blood calcium level by decreasing activity. they cannot carry out mitosis

peroxisomes

break down substances common in liver and kidney where they break down toxic substances. in plant cells, modify by products of photorespiration. in germinating seeds, it is called glyoxysomes break down stored fatty acids to help generate energy for growth. peroxisomes produce h2o2 which they then use to oxidize substrates. can also break down peroxide if necessary

fatty acids

broken down for energy via beta oxidation and takes place in the mitochondrial matrix. fatty acids in the blood combine with albumin which carries them. 2 ATP spent which activates the entire chain saturated fatty acids produce 1 NADH and 1 FADH2 for every cut into 2 carbons unsaturated fatty acids produce 1 less FADH2 for each double bond yields more ATP per carbon than carbohydrates, more energy in fats than sugars

acid rain

burning of fossil fuels (coal) releases into air SO2 and NO2. when they react with water vapor->sulfuric acid and nitric acid (HNO3)->kills plants and animals when they rain to earth

global climate change

burning of fossil fuels and forests increase CO2 in atmosphere->more heat trapped (greenhouse effect; normally a good thing for maintaining heat on earth but this is overkill)-> global temp rises-> raise sea level by melting ice and decrease agriculture output (affecting weather patterns)

8. oxygen and ozone layer + abiotic chemical evolution ended

by production of photosynthetic activity of autotrophs *UV light + oxygen => ozone layer

ion channels

called gated channels in nerve and muscle cells, respond to stimuli. note that these can be voltage-gated that respond to difference in membrane potential, ligand gated where chemical binds and opens channel, or mechanically gated which responds to pressure, vibration and temp

Pr accumulates at night:

cells keep making Pr at night, but there is no sunlight to convert Pr->Pfr *Pfr breaks down faster than Pr and is also converted back to Pr metabolically, thus Pr accumulates

sex-influenced

can be influenced by sex of individual carrying trait aka Bb female not bald, Bb male is bald

genetic basis of behavior

can be inherited through genes (innate-molded by natural selection-increase fitness) or learned. behavioral ecology is the study of behavior that seeks to explain how specific behaviors increase fitness

confocal laser scanning and fluorescence

can look at thin slices while keeping sample intact, can look at specific parts of cel via fluroescent tagging. can look at living cells, but only fluorescently tagged parts. fluorescence can cause artifacts. can be without fluorescence as well uses laser light to scan dyed specimen, then displays the image digitally

transport proteins

can use ATP to transport. active transport: sodium potassium pump to maintain gradients. facilitated diffusion.

facultative anaerobes

can use oxygen when its present but switch to fermentation/ anaerobic resp if it isnt

obligate anaerobes

cannot live in presence of oxygen

chloride shift

carbonic anhydrase is in RBCs to balance bicarbonate ions diffusing out of cells (because CO2 enters RBCs, carbonic anhydrase converts, bicarbonate diffueses out to plasma) *opposite in lungs: Cl- enters

storage proteins

casein in milk. ovalbumin in egg whites, and zein in corn seeds

amylase

catalyzes the reaction that breaks the alpha glycosidic bonds in starch

paracrine

cell signaling where target is nearby; autocrine is cell signaling via hormone/ chemical messenger that binds to receptors on same cell

aerobic respiration

cellular respiration in the presence of oxygen. this includes: glycolysis, pyruvate decarboxylation, krebs cycle, oxidative phosphorylation. water is the final product

control of respiration

central chemoreceptors in the medulla monitors H+ in the cerebrospinal fluid and peripheral chemoreceptors in the carotid arteries and aorta monitor arterial CO2, O2, and H+. in an active body, there is increased CO2 production; it enters plasma is converted to HCO3 and H+, the blood pH drops and respiratory rate increases. *O2 and pH mainly monitored by the peripheral chemoreceptors

ecological succession

change in composition of species over time. describes how one community is replaced by another gradually consisting of different species. as it progresses, diversity and total biomass increase. a final successional stage of constant species composition (climax community), is attained and unchanged until destroyed by catastrophic event

microevolution

changes in allele frequencies that occur over time within a population due to mutation, selection, gene flow and drift

antenna pigments

chlorophyll b, carotenoids, phycobilins (red algae pigment), xanthophylls which capture wavelengths that chlorophyll a does not, passes energy to chlorophyll a where direct light reaction occurs.

nucleus

chromatin is the general packaging structure of DNA around proteins in eukaryotes, the tightness depends on cell stage. chromosomes are tightly condensed chromatin when the cell is ready to divide. histones serve to organize DNA which coil around into bundled nucleosomes-8 histones. nucleolus is inside nucleus and are the maker of ribosomes. nucleus bound by double layer nuclear envelope with nuclear pores for transport. no cytoplasm in nucleus

duplications

chromosome segment is repeated on same chromosome

chromosomal abberations

chromosome segments are changed. includes duplications, inversions, and translocations

inversions

chromosome segments are rearranged in reverse orientation

meiosis II: metaphase II

chromosomes align on plate like in mitosis BUT now with half the number of chromosomes aka no extra copy

eukaryotic cells

chromosomes contain long, linear DNA with histone enclosed in the nucleus. have specialized organelles to isolate metabolic activities. 9+2 microtubule array of flagella and cilia

mitosis: metaphase

chromosomes line up single file at the center, each chromatid is complete with a centromere and a kinetochore. once separated, it is a chromosome. centrosomes are at opposite ends of the cell. once separated thats the end of metaphase. karyotyping performed here

cyclosis/streaming

circular motion of cytoplasm around cell transport molecules

major plant division: lycophyta

club mosses, spike mosses, and quillworts (herbaceous plants); club and spike mosses produce clusters of spore-bearing sporangia in conelike strucutre: strobili *resurrection plant (recover from dead appearance after watered, is a spike moss)

prosthetic group

cofactor strongly covalently bonds to enzyme

temperate coniferous

cold dry forests; vegetation has evolved adaptations to conserve water (needle leaves)

tundras

cold winters (ground freezes), top layer thaws during summer-> support minimal vegetation (grasses). but deeper soil (permafrost) remains permanently frozen. very little rainfall that cant penetrate frozen ground

sex-linked diseases

colorblindness and hemophilia

hybridization

complementary base pairs annealing

tight junctions

completely encircles each cell, producing a seal that prevents the passage of materials between cells; characteristic of cells lining the digestive tract

metalloprotein

complexed around a metal ion

biosphere

composed of all regions of earth that contain living things (atmosphere, hydrosphere, lithosphere, etc)

nephrons

composed of renal corpuscle and renal tubule. reabsorbs nutrients, salts, and water

sarcomere

composed of thin filaments (actin) and thick filaments (myosin) *Z-line: boundary of a single sarcomere; anchor thin filaments *M-line: center of sarcomere *I-band: region containing thin filaments (actin) only *H-zone: region containing thick filaments (myosin) only *A-band: actin and myosin overlapping (one end of overlap to the other end of overlap) **H and I-bands reduce during contraction while A-band does NOT

vertebrate skeleton

comprised of an endoskeleton. two major components are cartilage and bone: *cartilage: avascular connective tissue; softer and more flexible; (ex: ear, nose, larynx, trachea, joints). 3 types: 1. hyaline (most common-reduced friction/absorbs shock in joints) 2. fibrocartilage 3. elastic **from mesenchyme tissue->chondrocytes->produce collagen (present in tissue as triple helix with hydroxyproline and hydroxylysine, ground substance, and elastin fibers) composed primarily of collagen, receive nutrients via diffusion *bone: CT; hard and strong, while elastic and lightweight. functions: support of soft tissue, protection of internal organs, assistance in body movement, mineral storage, blood cell production, and energy storage in form of adipose cells in marrow. bone has 4 types of cells surrounded by extensive matrix: 1. osteoprogenitor/osteogenic: differentiate into osteoblasts 2. osteoblasts: secrete collagen and organic compounds upon which bone is formed. incapable of mitosis. as matrix released around them ->enveloped by matrix->differentiate into osteocytes (remember blast means build) 3. osteocytes: incapable of mitosis; exchange nutrients and waste material with blood 4. osteoclasts: destroy bone matrix, releasing minerals back to blood. develop from monocytes

community ecology

concerned with interaction of populations; such as interspecific competition (different species)

xylem

conduction of water and mineral and also functions in mechanical support; have second cell wall for additional strength; some places in walls of xylem cells have pits (absence of second cell wall). cells are dead at maturity (no cellular component-just cell walls). two kinds of xylem cells: 1. tracheids: long and tapered where water passes from one to another through pits 2. vessel elements: shorter and wider, have less or no taper at ends. a column of vessel elements (members) is called a vessel. perforations are where water passes through from one vessel member to the next (lack both first and second cell walls). perforations are an advantage vs tracheids- water moves more efficiently

taigas

coniferous forests (and trees with needles for leaves). very long cold winters and precipitation in form of heavy snow. **largest terrestrial biome

primary growth vs secondary growth

conifers and woody dicots undergo secondary growth in addition to primary growth. this extends the length. secondary growth increases girth and is the origin of woody plant tissues: occurs at the two lateral meristems: 1. vascular cambium (secondary xylem and phloem) 2. cork cambium: gives rise to periderm-protective material that lines outside of woody plant

central nervous system

consists of brain and spinal cord: *brain: outer gray matter (cell bodies) and inner white matter (axons)-forebrain, midbrain, hindbrain. **forebrain: largest and most important brain region. contains cerebral cortex (processes sensory input/important for memory and creative thought), olfactory bulb (smell), thalamus (relay for spinal cord and cerebral cortex), hypothalamus-visceral function (water balance, blood pressure, and temp regulation, hunger, thirst, sex) **midbrain: relay center for visual/ auditory impulses; motor control **hindbrain: posterior part of brain; cerebellum (maintenance of balance, hand-eye coordination, timing of rapid movements) pons (relay center to allow communication between cortex and cerebellum), medulla oblongata (breathing, heart rate, gastrointensinal activity)-the brainstem consists of midbrain + medulla oblongata + pons. connects the cerebrum with spinal cord *spinal cord: outer white/inner gray cell bodies. sensory info enters through the dorsal horn. all motor info exits through the ventral horn.

muscular system

consists of contractile fibers held together by CT

the seed: development

consists of embryo, seed coat, and some kind of storage material (endosperm or cotyledons-formed by digested material in endosperm). there are two cotyledons in dicot (pea), 1 cotyledon in monocot (corn). in many monocots the endosperm is the primary storage tissue, cotyledon functions to transfer nutrients from endosperm->embryo. *embryo: 1. epicotyl: (top portion of embryo) becomes shoot tip 2. plumule: are young leaves often attached to epicotyl; plumule can refer to both together 3. hypocotyl: becomes young shoot (below epicotyl and attached to cotyledons) 4. radicles: develops from below hypocotyls into root 5. a sheath called coleoptiles (in monocots) surrounds and protects epicotyl. in developing young plants, coleoptiles appear first as leaf, but the first true leaves are from the plumule within the coleoptiles

peripheral nervous system

consists of sensory branch and motor branch. motor consists of somatic and autonomic nervous systems *somatic: responsible for VOLUNTARY movement of skeletal muscles *autonomic: involuntary movement; innervates cardiac and smooth muscle: **sympathetic: fight or flight (higher BP and HR) **parasympathetic: rest and digest; non-emergency (lower heart rate, digestion, relaxation, sexual arousal)

neuron

consists of several dendrites, single (branched) axon, and cell body

detrivores

consumers that obtain energy by consuming dead plants/animals (detritus). smallest ones are decomposers (fungi and bacteria). also includes nematodes, earthworms, insects and scavengers (vultures, jackals, crab), saprophytes

recombinant DNA

contains DNA segments or genes from different sources. the transfer of these DNA segments can come from viral transduction, bacterial conjugation, transposons, or through artificial recombinant DNA technology. crossing over during prophase of meiosis produces recombinant chromosomes

nucleoprotein

contains histone or protamine, bound to nucleic acid

xylem

contains two cell types: tracheids and vessel members. conducts water and dissolved mineral absorbed from the soil, and mechanically supports the plant. the yearly xylem deposits make up the annual growth rings used to record the age of a plant

parapatric speciation

continuous population but it doesnt mate randomly: individuals more likely to mate with geographic neighbors. divergence may happen due to reduced gene flow since selection pressures vary across the populations range (different niches, adjacent but not isolated)

Lac operon (E. coli)

controls breakdown of lactose; regulatory gene produces active repressor (binds to operator) and blocks RNA polymerase. when lactose is available, lactose binds repressor and inactivates it => RNA polymerase can now transcribe. lactose induces the operon. the enzymes that the operon produces are said to be inducible enzymes. **Note: consists of three lac genes (Z, Y, A) which code for: B-galactosidase (converts lactose into glucose/galactose), lactose permease (transport lactose into cell), and thiogalactoside transacetylase. **also know that low glucose means high cAMP levels->cAMP binds to CAP binding site of promoter-> RNA polymerase more efficiently transcribes -> lactose can be broken down. if lactose AND glucose are high, operon is shut off (cAMP is low, doesnt bind to CAP, bacteria uses one sugar at a time and prefers glucose).

slow block to polyspermy

cortical reaction in sea urchins where a sperm-proof fertilization membrane is formed when the cortical granules in the egg fuse with the plasma membrane. as enzymes are released, biochemical reactions harden the vitelline layer and allow no further sperm from entering

osmolarity gradient

created by exiting/ entering of solutes; increases from cortex to medulla

rough ER

creates glycoproteins by attaching polysaccharides to polypeptides as they are assembled by ribosomes. in eukaryotes the rough ER is continuous with the outer nuclear membrane

Protein synthesis: transcription

creation of RNA molecules from DNA template. prokaryotes are polycistronic. eukaryotes are monocistronic. 1. initiation: RNA pol attaches to promoter region of DNA and unzips the DNA into two strands. a promoter region for mRNA transcription often contains the sequence TATA (box). most common sequence of nucleotides at promoter region is called a consensus sequence; variations from it cause less tight RNA pol binding which leads to a lower transciption rate. 2. elongation: RNA pol unzips DNA and assembles RNA nucleotides using one strand of DNA template; only one strand is transcribed 3. termination: when RNA pol reaches a special sequence often AAAAAAA in eukaryotes. **transcription is occurring in the 3' to 5' direction of the DNA template strand (but synthesis of the RNA strand is as always 5' to 3')

lethal gene

cross between Aa and Aa, we get AA:2Aa:aa. if "aa" was lethal, we would have AA and Aa as 1:2 ratio.

batesian mimicry

deceptive: harmless species has evolved to imitate the warning signals of a harmful species directed at a common predator

nuclear lamina

dense fibrillar network inside nucleus of eukaryotic cells. provides mechanical support also helps regulate DNA replication, cell division, chromatin organization

right atrium:

deoxy blood enters via superior and inferior vena cava

counter current multiplier

descending loop permeable to water and ascending is permeable to salts/ ions; this makes the medulla very salty and facilitates water reabsorption

niche

describes all biotic and abiotic resources in the environment used by an organism. when an organism is said to occupy a niche, certain resources are consumed or certain qualities of environment are changed in some way by presence

3. dispersion

describes how individuals in a population are distributed; may be clumped, uniform, or random

ecosystem

describes interrelationships between organisms in a community and their physical environment

ecological efficiency

describes the proportion of energy represented at one trophic level that is transferred to the next. on average, an efficiency of 10% is transferred to the next. 90% is for metabolism and to detrivores when they die

4. age structure

description of the abundance of individuals of each age

anchoring junctions

desmosome: keratin filaments inside attach to adhesion plaques which bind adjacent cells together via connecting adhesion proteins, providing mechanical stability. in animal cells. present in tissues like skin, epithelium, cervix, uterus

parthenogenesis

development of egg without fertilization; resulting adult is haploid (honeybees, some lizards)

sexual dimorphism

differences in appearance of males and females which becomes a form of disruptive selection

zone of maturation

differentiation; cells mature into xylem, phloem, parenchyma, or epidermal cells (root hairs may grow here).

pinocytosis

dissolved material (liquid) plasma membrane invaginates

metabolic vs respiratory acidosis/alkalosis

distinguishable by the cause of the imbalance *respiratory from breathing issues, metabolic from anything else *respiratory acidosis comes from inadequate ventilation: we dont clear enough CO2 and it builds up, so more H+ ends up getting formed-> pH drops in tissues *respiratory alkalosis: comes from breathing too rapidly: we are losing CO2 too quickly, H+ and HCO3- start combining to form more CO2, pH rises. *metabolic acidosis and alkalosis are not due to breathing issues: you may alter breathing to compensate, but the cause is not breathing related

osteoblasts

do not carry out mitosis. they do secrete collagen and build bone

day-neutral plants

do not flower in response to daylight changes but rather temperature or water.

dumb kings play chess on fine green sand

domain kingdom phylum class order family genus species

unsaturated

double bonds, better for health . have lower melting points than saturated

chromosomal genetic disorders

downs, turner (XO), Klinefelter (XXY), cri du chat (deletion on chromosome 5. note* turners doesnt typically cause mental retardation, but downs, kline, and cri du chat do

bone formation

during FETAL stage of development: *endochondral ossification->cartilage->bone (ex: long bones, limbs, fingers, toes) *intramembranous ossification: undifferentiated CT replaced by bone (ex: flat bones, skull, sternum, mandible, clavicles)

X-inactivation

during embryonic development in female mammals, one of two X chromosomes does not uncoil into chromatin==> barr body which cannot be expressed. thus, only the genes on the other X chromosome will be expressed. either one can be inactivated = genes in the female will not be expressed similarly, so all cells in a female mammal not necessarily functionally identical as in calico cats

meiosis II: anaphase II

each chromosome is pulled into 2 separate chromatids and migrate to opposite poles of the cell

human population growth

enabled by: increase in food supply, reduction in disease (medicine), reduction in human wastes, habitat expansion (advancements now allow inhabitance of previously uninhabitable places)

transport of water

enter root through root hairs by osmosis. there are two pathways for water to go to center of the root: 1. water moves through cell walls and intercellular spaces from one to another without ever entering cells. this pathway is called apoplast (nonliving portion of cells) 2. water moves through cytoplasm of one cell to another (symplast-living portion) through plasmodesmata (small tubes that connect cytoplasm of adjacent cells) *once water reaches endodermis, it can only enter by symplast (due to casparian strips blocking) into the stele (vascular cylinder) and is selectively permeable (K+ pass, Na+ is blocked-common in soil but unused in plants). once through endodermis, apoplast pathway takes over to reach xylem (which is the major conduction pathway via tracheids and vessels)

cooperativity

enzyme becomes more receptive to additional substrate molecules after one substrate molecule attaches to an active site-example is Hb binding to additional oxygen even though not an enzyme

uncompetitive inhibition

enzyme inhibitor binds only to the formed E-S complex, preventing formation of product (Vmax lowered and Km too)

telomerase

enzyme that attaches to the end of template strand and extends the template strand by adding short sequence of DNA over and over, allowing for elongation of the lagging strand to continue. however, the end will still not be enough for primase to attach but this loss of unimportant segment will not cause any problem. telomerase carries an RNA template and binds to flanking 3' end of the telomere that compliments part of its RNA template, synthesizes to fill in over the rest of its template

at daybreak, light rapidly converts accumulated Pr to Pfr:

equilibrium is maintained

waxes

esters of fatty acids and monohydroxylic alcohols

pollution

eutrophication is the process of nutrient enrichment in lakes and subsequent increase in biomass (lakes polluted with fertilizer runoff-> abundant nutrients (especially phosphates) stimulates *algal blooms (massive algae/phytoplankton growth) which respire and deplete oxygen and breakdown and detrivous bacteria deplete even more oxygen-> many animals die of oxygen starvation

phyletic gradualism

evolution occurs by gradual accumulation of small changes; but unlikely to be valid because intermediate stages of evolution are missing (no fossils); fossils only reveals major changes in groups of organisms

coevolution

evolution of one species in response to new adaptation that appear in another species

coevolution

evolution of one species in response to new adaptations that appear in another species (predator/prey)

punctuated equilibrium

evolutionary history consists of geologically long periods of stasis (stability) with little or no evolution followed by geologically short periods of rapid evolutions. absence of fossils revealing intermediate stages of evolution is considered data that confirms rapid evolutionary events

C4 photosynthesis

evolved from C3, when CO2 enters leaf it is absorbed by mesophyll cells then moved to bundle sheath cells; instead of being fixed by Rubisco into PGA, CO2 combines with PEP to form OAA by PEP carboxylase in the mesophyll. OAA: has 4C==> C4 photosynthesis OAA==> malate and then transported through plasmodesmata into bundle of sheath cell. Malate==> pyruvate + CO2 (CO2 can be used in calvin, pyruvate moved back to mesophyll then==> PEP ** overal purpose is to move CO2 from mesophyll to bundle sheath cell. minimizes photorespiration and water loss from stomata(leaf pores). found in hot, dry climates. requires one additional ATP which becomes AMP. C3 typically occurs in mesophyll cells, but in C4 it occurs in bundle-sheath cells. occurs in corn and sugarcane

Haldane effect

explains CO2s dissociation curve. we pick up CO2 in tissues where its been generated, and get rid of it at the lungs and grab oxygen instead. Hb without oxygen acts as blood buffer by accepting H+-> this reduced to Hb has higher capacity to form carbamino Hb rather than the oxygen carrying kind.

extranuclear inheritance

extranuclear genes are found in mitochondria and chloroplasts. defects in mitochondrial DNA can reduce cells ATP production. mitochondria passed to the zygote all come from the mother, so all related diseases are mother inherited. Note that mitochondria have their own 70S ribosomes that make mitochondrial proteins within the mitochondrial matrix!

nondisjunction

failure of one or more chromosome pairs or chromatids to separate during mitosis: anaphase. or meiosis: homologous chromosomes to separate during meiosis I or sister chromatids to separate during meiosis II; result in trisomy or monosomy; for example down syndrome note** specifically during anaphase!!

krebs cycle citric acid cycle tricarboxylic acid cycle (all the same thing)

fate of pyruvate that is produced in glycolysis. in krebs, acetylcoa merges with oxaloacetate to form citrate, cycle goes with 7 intermediates 3 NADH, 1 FADH2, 1 ATP (via sub phos) and 2 CO2 are produced per turn. two round of TCA cycle can occur. total 6 NADH, 2 FADH2, 2 ATP (technically GTP), 4 CO2 these ATP are produced via sub level phos. takes place in mitochondrial matrix like pyruvate decarb. CO2 that is produced here is what animals exhale when they breathe

carotenoids

fatty acid carbon chains with conjugated double bonds and 6 membered carbon rings at each end. pigments which produce colors in plants and animals. carotenes and xanthophylls are subgroups

directional selection

favors traits that are at one extreme of a range of traits. traits at opposite extremes are selected against. after many generations get changes in allele frequencies

scleroproteins

fibrous, structural, like collagen

photorespiration

fixation of oxygen by rubisco (can also fix CO2) produces no ATP or sugar. Rubisco is not efficient or fast because it will fix both CO2 and O2 at the same time if both are present. peroxisomes break down the products of this process

calvin cycle

fixes CO2, repeats 6 times, uses 6CO2 to produce glucose. C3 photosynthesis = dark reaction occurs in the stroma 1. carboxylation: 6CO2 + 6RuBP ==> 12PGA RuBisCo= most common protein in the world, aka RuBP carboxylase catalyzes this reaction. PGA is 3C molecule 2. reduction: 12ATP +12NADPH converts 12PGA ==>12G3P or 12PGAL; energy is incorporated; by products (NADP+ and ADP) go into noncyclic photophosphorylation 3. regeneration: 6ATP convert 10G3P==> 6RuBP which allows the cycle to repeat 4. carbohydrate synthesis: 2 remaining G3P are used to build glucose: 6CO2 + 18ATP + 12NADPH + H+ ==> 18ADP + 18Pi + 12NADP+ + 1 glucose (2G3P) 5. this is the "dark reaction" but it cannot occur without light because it is dependent on the high energy molecules produced from the light reaction (ATP and NADPH)

excretion in platyhelminthes

flame cells (protonephridia): distributed along branched tube system; wastes exit through pores of tube

biogeochemical cycles

flow of essential elements: environment-> living things-> environment

long-day plants

flower in spring and early summer when daylight is increasing

short-day plants

flower late summer and early fall when daylight is decreasing

major plant division: anthophyta (angiosperms)

flowering plants, dominant land plant form. major parts of flower: 1. pistil: female reproductive structure (3 parts: ovary (egg bearing), style, and stigma) 2. stamen: male reproductive structure (pollen bearing anther and stalk, filament) 3. petals: (and sometimes the sepals too) function to attract pollinators

digestion: small intestine

food goes from stomach to small intestine through the pyloric sphincter-first 25cm =duodenum, continues breakdown of starches and proteins as well as remaining food types (fats and nucleotides); ileocecal valve between SI and large intestine. structure is duodenum (most digestion), jejunum, then ileum (jejunum and ileum mostly for absorption). 90% of digestion and absorption occurs in SI. **structure: wall has finger like projections called villi that increase SA for greater digestion/absorption. each villi has a lacteal=(lymph vessel surrounded by capillary network); both function for nutrient abs. villi have microvilli, more SA. *goblet cells secrete mucus to lubricate and protect from mech/chem damage *duodenum has a pH~6 mainly due to bicarbonate ions secreted by pancreas **enzyme origin: small intestine-proteolytic enzymes: proteases, maltase and lactase, phosphatases/nucleosidases (nucleotides); lipase **pancreas: secretes bicarbonate; also acts as exocrine gland releasing major enzymes from acinar cells via pancreatic duct->duodenum *trypsin and chymotripsin (proteases), lipase, pancreatic amylase, deoxy and ribonucleases *all exist as zymogens/proenzymes (inactive) first. trypsin gets activated, then activates the other enzymes *these enzymes are in an alkaline solution (pancreatic duct->duodenum) **liver: produces bile (no ezymes, emulsifies fats) stored in gall bladder, flows thru bile duct which merges with pancreatic duct **remainder of small intestince (6m) absorbs breakdown products (villi and microvilli) *amino acids and sugars->capillaries *fatty acids and glycerol->lymphatic system **chyme moves through intestines via peristalsis as well. segmentation (second type of intestinal motion) mixes chyme with dig juices

channel proteins

for hydrophilic substances that are polar and charged

root

form of root. dicots= taproot (large, single root). monocots= fibrous system (many fine roots)

sympatric speciation

formation of new species without presence of geographic barrier *balanced polymorphism: natural selection due to polymorphism *polyploidy: possession of more than normal two sets of chromosomes *hybridization: two different forms of a species (closely related species) mate and produce along a geographic boundary called the hybrid zone (more genetic variations = hybrid can live beyond range of wither parent

3. complex molecules were synthesized:

formation of organic soup from inorganic, energy from uv light, heat, radiation which yielded acetic acid, formaldehyde, and amino acids

zone of cell division

formed from dividing cells of apical meristem

P700

forms pigment cluster (PSI) special chlorophyll a molecule

P680

forms pigment cluster (PSII) special chlorophyll a mol

extracellular matrix

found in animals, in area between adjacent cells (beyond the PM and glycocalyx); occupied by fibrous structural proteins, adhesion proteins, and polysaccharides secreted by cells; provide mechanical support and helps bind adjacent cells. note that cells adhere to the ECM is two ways: focal adhesions-conecction of ECM to actin filaments in the cell. and hemidesmosomes: connection of ECM to intermediate filaments as in keratin

plastids

found in plant cells. chloroplasts=site of photosythesis, leucoplasts=can specialize to store starch, lipid, protein as amyloplasts, elaioplasts, proteinoplasts respectively. or serve general biosynthetic functions. chromoplasts sore carotenoids

cell walls

found in plants (cellulose), fungi (chitin), protists/archaea (polysaccharides), and bacteria (peptidoglycans). provides support. sometimes a secondary cell wall developes beneath the primary one

(p2, q2)

frequency of homozygous

hydrostatic pressure

from heart contracting causes blood to move through arteries. blood pressure drops as it reaches the capillaries, and reaches near zero in the venules. blood continues to move through veins because of pumping of the heart assisted by movements of adjacent skeletal muscles, expansion of atria each time heart beats, and falling pressure in chest when a person breathes.

polar region

frozen with no vegetation or terrestrial animals

albumins and globulins

functional and act as carriers or enzymes

diffusion between alveolar chambers and blood

gas exchange across moist, sac membranes of alveoli. oxygen diffuses through alveolar wall, through pulmonary capillary wall, into blood, and into RBCs (CO2 is opposite)

peripheral membrane protein

generally hydrophilic; held in place by H-bonding and electrostatic interaction. disrupt/ detach by changing salt conc or pH to distrupt these interactions

endotherms

generate their own body heat aka homeotherms/warm blooded

gene

genetic material on a chromosome for a trait

sexual reproduction

genetic recombination (crossing over, independent, random joining of gametes)

genetic variation

genetic recombination during meiosis and sexual reproduction originates from 3 events: 1. crossing over during prophase I 2. independent assortment of homologues during metaphase I (which chromosome goes into which cell) 3. random joining of gametes aka germ cells: which sperm fertilizes which egg. genetic composition of the gamete affects this.

single nucleotide polymorphisms (SNPs)

genome of humans differs roughly one of every 1000 nucleotides

aneuploidy

genome with extra or missing chromosome, often caused by nondisjunction. down syndrome = trisomy 21

amoebas

genus of protozoa, shapeless and unicellular

renal corpuscle

glomerulus (sieve) surrounded by bowmans capsule; afferent arteriole=> into glomerulus; efferent arteriole=> out of glomerulus *after efferent arteriole passes back out of the glomerulus it webs around the entire nephron structure as the peritubular capillaries and vena cava before dumping back into the renal branch of renal vein.

myoglobin of muscle

has hyperbolic curve (structure doesnt do allosteric cooperative binding, single subunit) saturates quickly and releases in very low oxygen "emergency muscle" situations

chlorophyll a

has porphyrin ring=alternating double and single bonds, double bonds critical for light reactions, complexed with Mg atom inside

ear structure and function

has three main parts: outer, middle and inner ear; transduces sound energy into impulses *outer ear: auricle/pinna and auditory canal; direct sound into external auditory canal-> *middle ear: amplifies sound; tympanic membrane aka eardrum begins the middle ear and vibrates at same frequency as incoming sound=>ossicles (malleus, incus, stapes)-> *inner ear: wave moves through the cochlea (vibration of ossicles exert pressure on fluid). as wave moves through pressure alternates, moving the vestibular membrane in and out; this movement is detected by hair cells=not actual hair but specialized stereocilia, of the organ of corti=>transduced to neural signal-> ap. the inner ear also has semicircular canals responsible for balance (fluid and hair cells sense orientation and motion)

pol 1 and pol 3

have 3' to 5' exonuclease: breaks phosphodiester backbone on a single strand of DNA and removes a nucleotide. in this case, exonuclease can only remove from the 3' end of the chain

prokaryotes

have a PM, DNA molecule, ribosomes, cytoplasm, and cell wall. in prokaryotes: 1. no nucleus 2. single circular naked DNA no chromatin 3. 50S+30S=70S; 4. cell walls made of peptidoglycan; archaea made of polysaccharides-many have sticky capsules on wall 5. flagella are constructed from flagellin not microtubules in prokaryotes

allosteric enzymes

have both an active site for substrate binding and an allosteric site for binding of an allosteric effector

cancer cells

have defied all of cell regulation and are called transformed cells. cancer drugs that inhibit mitosis do so by disrupting the ability of microtubules to separate chromosomes during anaphase thus stopping replication

mitochondria

have outer membrane, intermembrane space with H+, inner membrane where oxidative phosphorylation occurs, and mitochondrial matrix where krebs cycle occurs

diatoms

have unique glass like walls consisting of silica embedded in an organic matrix

heart contraction

heart is a large muscle, but unlike skeletal, not anchored to bone. its fibers form a net and the net contracts upon itself, which squeezes blood into arteries

cardiac output

heart rate * stroke volume. the volume of blood pumped by the ventricle (per min)

sex-linked recessive genetic disorders

hemophilia; abnormal blood clotting. color blindness. duchenne muscular dystrophy.

primary consumers

herbivores (long digestive tract with greater surface area and time for more digestion; symbiotic bacteria in dig tract break down the cellulose which the herbivore itself cannot), eat primary producers

2pq

heterozygous

tropical rain forest

high (but stable) temperature and humidity, heavy rainfall, tall trees with branches at top->little light to enter). most diverse biome *epiphytes are plants that grow commensally on other plants (like vines)

meiosis I: metaphase I

homologous pairs are spread across metaphase plate. microtubules are attached to kinetochores of one member of each homologous pair. microtubules from other site attach to second member of pair **independent assortment and genetic variation

meiosis I: anaphase I

homologues within tetrads uncouple and pulled to opposite sides=disjunction

tropic hormones

hormone that stimulates endocrine gland to grow and secrete its hormones aka one hormone causes another hormone to do something. secreted by anterior pituitary gland: ACTH, FSH, LH

deserts

hot and dry; most extreme temp fluctuations (hot day, cold night); growth of annual plants is limited to short period following rare rain, plants and animals adapt to conserve as much water as possible

5. survivorship curves

how mortality of individuals in a species varies during their lifetimes a. type I: most individuals survive to middle age and die more quickly after this age (humans) b. type II: length of survivorship is random (invertebrates-hydra) c. type III: most individuals die young, with few surviving to reproductive age and beyond (oysters)

autosomal dominant genetic disorders

huntingtons; degenerate nervous system disease

lipids

hydrophobic molecules. functions to insulate, store energy, structural and endocrine

Mb curve

hyperbolic

be suspicious for X-linked recessive disorders

if a father doesnt have the phenotype, none of his daughters display it

recap of humoral response:

imagine a bacterial infection: 1. inflammation, macrophages and neutrophils engulf the bacteria 2. interstitial fluid flushed into lymphatic system where lymphocytes are waiting in lymph nodes 3. macrophages process and present bacterial antigen to B-lymphocytes 4. with help of helper T cells, B cells differentiate into plasma and memory cells 5. memory cells prepare for event of same bacteria ever attacking again (secondary response) 6. plasma cells produce antibodies released to blood to attack the bacteria

immune system: specific 3rd line of defense

immune response targets specific antigen **acquired immunity-develops after body has been attacked 1. major histocompatability complex: mechanism by which immune system is able to differentiate between self and nonself. MHC is a collection of glycoprotein that exists on membranes of all body cells. the proteins of single individual are unique (20 genes, each with 50+ alleles, unlikely to have same cells with same MHC set as someone else). antigen presentation 2. lymphocytes: primary agents of immune response, leukocytes that originate in bone marrow but concentrate in lymphatic tissues such as lymph nodes, thymus gland, and spleen

mosaicism

in cells that undergo nondisjunction in mitosis during embryonic development; fraction of body cells have extra or missing chromosome

DNA replication final notes

in prokaryotes, the 'good' strand is methylated after replication so it doesnt accidentally repair the wrong strand. in all cases of repar, ligase must come in to seal the backbone. energy for elongation is provided by two additional phosphates attached to each new nucleotide. breaking the bonds holding the two extra phosphates provides chemical energy for the process

contractile vacuoles

in single-celled organisms that collect and pump excess water out of the cells (prevent bursting). active transport. found in protista like amoeba and paramecia, organisms live in hypotonic environment

triglycerides how they work

in the lumen of the small intestine are broken down via lipases into monoacylglycerides + fatty acids, which are then absorbed into the enterocytes=cell lining of the small intestine. there, they are reassembled into triglycerides, and then along with cholesterol, proteins, and phospholipids, are packaged into chylomicrons which move on to the lymph capillary for transport to the rest of the body where they are stored as adipose tissue

pyruvate decarboxylation

in the mitochondrial matrix. pyruvate to AcetylCoA, producing 1 NADH and 1 CO2. NET: 2 NADH + 2 CO2 catalyzed by PDC enzyme (pyruvate dehydrogenase complex)

photic zone

in water=light penetrates; all aquatic photosynthesis

eukaryotes

include all organisms except for bacteria, cyanobacteria and archaeabacteria

microtubule organizing centers

include centrioles and basal bodies. 9x3 array. plant cells lack centrioles and its division is by cell plate instead of cleavage furrow. note that plant cells do have MTOCs

epinephrine functions

increase heart rate and respiratory rate. increase blood glucose and blood flow to skeletal muscle. increase the rate of glycogenolysis. constrict blood vessels to decrease blood supply to digestive tract and kidneys. dilate the pupils, increase blood flow to the brain and blood pressure

flowering plants

initiate flowering in response to changes in photoperiod

fixed action patters (FAP)

innate behaviors following a regular, unvarying patter. initiated by a specific stimulus called sign stimuli (released when between members of same species) and completed even if original intent of behavior cannot be fulfilled a. ex: goose methodically rolling egg back to nest even if it slips away or is removed b. ex: male stickleback fish defending territory against any object with red underside c. ex: swimming action of fish/flying actions of locusts

imprinting

innate program for acquiring specific behavior only if appropriate stimulus is experienced during critical period. once acquired, trait is irreversible a. ex: goslings accepting any moving object as mother during first day of life b. ex: salmon hatch in freshwater, migrate to ocean to feed, return to birthplace to breed based on imprinted odors associated with birthplace

night length is responsible for resetting the clock:

interrupt daylight with brief dark period->no effect. but flashes of red and far red during night period can reset the clock. only the last flash effects the night length. *red=shorter night length *far red=restores night length

mutation

introduce new allele

reverse transcriptase

introns often prevent transcriptions; this enzyme makes DNA molecule directly from mRNA. DNA obtained from this manner is complementary DNA (cDNA) which lacks introns that suppress transcriptions

nucleoid

irregular shaped region within the cell of prokaryote that contains almost all of genetic material

membrane of an unstimulated neuron

is **polarized, although a high concentration of Na+ is present outside the cell and a high concentration of K+ is present inside the cell (the inside is actually negative due to the negatively charged proteins and nucleic acids residing in the cell). additionally, neuron membranes are selectively permeable to K+ as opposed to Na+, which helps to maintain polarization

glycogen

is a glucose polymer, stored 2/3 in liver and 1/3 in muscles. all cells capable of producing and storing glycogen but only muscle and liver cells have large amounts

amebocyte

is a mobile cell in the body of invertebrates such as echinoderms, mollusks or sponges. they move by pseudopodia (a temporary protrusion of the cytoplasm-actin of amoeba, serving for locomotion or the engulfment of food)

Cytochrome C

is a protein carrier in the ETC, common in many living organisms, used for genetic relation. Note: cytochromes have nonprotein parts like iron that accept/donate electrons for redox.

the diaphragm

is a skeletal muscle innervated by the phrenic nerve. it is also the only organ that all mammals have, and without which no mammal can survive

mitochondrial DNA

is an exception to the universality of genetic code

food web

is an expanded more complete version of food chain

urine

is hypertonic to the blood and contains a high urea and solute concentration

DNA polymerase 3

is pure replication, eukaryotes have different polymerases. can do some proofreading; if it makes a mistake it will go back and use this to replace it. **summary: pol 3 mainly replicates the DNA 5' to 3' but can also proofread via 3' to 5' exonuclease

meiosis I

is reduction division. homologous chromosomes pair at plate, migrate to opposite poles (no separation of sister chromatids)

fetal Hb curve

is shifted left of adult-has higher binding affinity to grab O2 from maternal blood

gametogenesis in humans

it is the meiotic cell divisions that produce eggs (oogenesis) and sperm (spermatogenesis). egg contains most of the cytoplasm, RNA, organelles, and nutrients needed by developing embry 1. oogenesis: begins during embryonic development; oogonia (fetal cells)->(mitosis) primary oocytes->(meiosis) and remain at **prophase I until puberty (one primary oocyte during each menstrual cycle-28 days, stimulated by FSH) continue its development through remainder of meiosis I within follicle (protects and nourishes oocyte)-> (completion of meiosis I) secondary oocyte=most of cytoplasm and polar body (small cytoplasm; may or may not dividue but products disintegrate) formed; now arrested at metaphase of meiosis II until ovulation 2. ovulation: releases secondary oocyte from vesicular follice (caused by **LH surge). if fertilized by sperm-> (finishes meiosis II) ovum/egg (diploid once completely fertilized) and polar body (degenerate) 3. spermatogenesis: begins at **puberty within seminiferous tubules of testes. spermatogonia cells-> (mitosis) primary spermatocytes-> (meiosis) 2 secondary spermatocytes-> (meiosis II) => 4 spermatids **sertoli cells: in seminiferous tubules provide nourishment to spermatids as they differentiate into mature spermatozoa (aka sperm). they complete maturation (gain motility and are stored) in the epididymis

northern blotting

just like the southern blot, but for RNA fragments

nucleoside

just the sugar and base

primary structure of stems

lack endodermis and casparian strips (not needed, these tissues specialized for water absorption) 1. epidermis: contain epidermal cells covered with waxy (fatty) cutin which forms protective later called cuticle 2. cortex: ground tissue types that lies between epidermis and vascular cylinder (many contain chloroplasts) 3. vascular cylinder: consists of xylem, phloem, and pith. in dicots and conifers, xylem and phloem are grouped in bundles (xylem inside, phloem outside) that ring a central pith area. a single layer of cells between the xylem and phloem may remain undifferentiated and later become the vascular cambium

central vacuole

large, occupy most of plant cell interior. exert turgor when fully filled to maintain rigidity. also store nutrients, carry out functions performed by lysosomes in animal cells. have a specialized membrane known as the tonoplast

cerebrum

largest part of the brain with two hemispheres connected by corpus callosum (thick nerve bundle). cerebrum has outer portion (cerebral cortex-gray matter) and inner portion (medulla-white matter). cerebrum contains sensory, motor, association areas *divided by lobes: **frontal: conscious thought, voluntary skeletal muscle movement **parietal: sensory areas- temp,touch, pressure, pain **temporal: sensory-hearing and smelling **occipital: sensory-vision

DNA replication: DNA polymerases move from the 3' to 5' direction only, synthesizing a new strand that is antiparallel (5' to 3')

leading strand: works continuously as more DNA unzips (synthesized 5' to 3') lagging strand: for the 5' to 3' template strand, the DNA polymerase has to go back to the replication fork and work away from it. it produces fragments at a time called **okazaki fragments via continuous replication. DNA ligase connects okazaki fragments

habituation

learned behavior that allows animal to disregard meaningless stimuli a. sea anemones disregarding repeated feeding stimulation with a stick b. if stimulus no longer regularly applies, response will recover over time-spontaneous recovery

protein

least desirable source of energy, only when carbs and fat unavailable. most amino acids are deaminated in the liver, then converted to pyruvate or acetylcoa or other intermediates. they enter cellular respiration at these various points (varies by aa) oxidative deamination removes ammonia molecule directly from aa. ammonia is toxic to vertebrates: fish excrete, insects and birds convert to uric acid, mammals convert to urea for excretion.

chloroplast

light-dependent and light independent reactions occur here. have double membrane like mitochondria and nucleus 1. outer membrane: PM (phospholipid bilayer) 2. intermembrane space 3. inner membrane: also phospholipid bilayer**chloroplasts have 3 phospholipid bilayers! 4. stroma: fluid material that fills area inside inner membrane; calvin cycle occurs here fixing CO2==>G3P 5. thylakoids: suspended within stroma (stacks); individual membrane layers are thylakoids; entire stack is granum membrane of thylakoids contain PSI + PSII, cyctochromes, and other e- carriers. also a phospholipid bilayer 6. thylakoid lumen: interior of the thylakoid; H+ accumulates here Note: gradient uses ATP synthase to move the accumulated H+ from thylakoid lumen to stroma; H+ move from inside to outside to generate ATP via synthase

stereomicroscope

light-visible light for surface of sample. can look at living samples, but low resolution vs compound light

compound microscope

light-visible light for thin section of sample. can look at some living samples (single cell layer). may require staining

cryoSEM

like SEM but no dehydration so you can look at samples in more natural form. cant use on living; samples frozen for prep which can cause artifacts

food chain

linear flow chart of whos eaten by whom

prostaglandins

locally acting autocrine/paracrine lipid messenger molecules that have physiological effect (eg contract/ relax smooth muscle)

AV node

located in lower wall of the right atrium/interatrial septa; sends impulse through bundle of His->passes between both ventricles->branches into ventricles via the purkinje fibers which results in contraction

locus

location on chromosome where gene is located

scanning electron microscope

look at surface of 3D objects with high resolution. cant use on living; preparation is extensive sample has to be dried and coated and is costly

transmission electron

look at very thin cross-sections in high detail. can look at internal structures, very high resolution, but cant be used on living things. preparation is extensive and costly

ADH and Oxytocin

made by the hypothalamus and stored in the posterior pituitary gland

microfilaments

made up of actin and involved in cell motility. skeletal muscle, amoeba, cleavage furrow

microtubules

made up of protein tubulin, provide support and motility for cellular activities. spindle apparatus which guide chromosomes during division. in flagella and cilia: 9+2 array; 9 pairs and 2 singlets in center. in all animal cells and lower plants like mosses and ferns

smooth muscle structure and function

mainly involuntary, ONE central nucleus; LACK STRIATION; stimulated by ANS** (ex: lining of bladder, uterus, dig tract, blood vessel walls). no sarcomere organization: intermediate filaments attached to dense bodies spread throughout cell. thick and thin filaments attached to intermediate filaments contract->intermediate filaments pull dense bodies together->smooth muscle length shrinks. two types of smooth muscle: 1. single-unit: aka visceral, connected by gap junctions, contract as single unit (stomach uterus, urinary bladder) 2. multi-unit: each fiber directly attached to neuron; can contract independently (iris, bronchioles,etc). in addition to neuronal response, can respond to: hormones, change in pH, O2, CO2 levels, temperature, ion concentration

phosphate buffer system

maintains pH of internal fluids of all cells; H2PO42- and HPO42- act as acid and base (amphoteric) able to act as both acid and base

balanced polymorphism

maintenance of different phenotypes in a population (one is usually best and increased in allele frequency). however, polymorphisms (coexistence or two or more different phenotypes) can exist and be maintained: *heterozygote advantage: heterozygous condition bears greater advantage than either homozygous conditions. sickle cell (AA,AS,SS). AS is 14% in africa because it has resistance against malaria *hybrid vigor: (heterosis) superior quality of offspring resulting from crosses between two different strains of plants. hybrid superior quality results from reduction of loci with deletion of recessive homozygous conditions and increase in heterozygous advantage *frequency-dependent selection: (minority advantage) least common phenotypes have a selective advantage. common phenotypes are selected against. rare will increase in frequency and will be selected against and repeat.

domain eukarya: kingdom plantae

major plant divisions: 1. bryophytes 2. lycophyta 3. pterophyta 4. coniferophyta 5. anthophyta (angiosperms)

brownian movement

particles move due to kinetic energy, spreads small suspended particles throughout cytoplasm

mitochondria

make ATP, also fatty acid catabolism (beta oxidation) fatty acids are made in the cytosol. also have their own circular DNA and ribosomes. have a double layered membrane.

autotrophs

manufacture their own organic materials. uses light or chemicals (photo vs chemo) such as H2S, NH3, NO2-, NO3-

outbreeding

mating with unrelated partners. mixing different alleles leading to new allele combinations

chemiosmosis in mitochondria

mechanism of ATP generation that occurs when energy is stored in the form of a proton concentration gradient across a membrane. krebs produces NADH/FADH2, they are oxidized so they lose electrons. H+ transported from matrix to intermembrane space, pH and electric charge gradient is created, ATP synthase uses the energy in this gradient to create ATP by letting the protons flow through the channel. remember that increase in H+ means pH goes down.

K-selected population

members have low reproductive rates and are roughly constant (at K) in size (ex. human pop). have a carrying capacity that pop levels out at. carrying capacity is a density dependent factor

producing seeds:

microsporangia produces microspores (male spores) and macrosporangia produce the macrospores (female spores)

cytoskeleton

microtubules, microfilaments, intermediate filaments. in eukaryotic cells, aids in cell division, cell crawling, and the movement of cytoplasm and organelles

law of independent assortment

migration of homologues within one pair of homologous chromosomes does not influence the migration of homologues of other homologous pairs

juxtaglomerular apparatus

monitors filtrate pressure in distal convoluted tubule via granular cells->secrete renin->angiotensin cascade->tells to make aldosterone

4. polymers and self-replication

monomers->polymer (dehydration condensation) *proteinoids are abiotically produced polypeptides

domain eukarya: kingdom animalia

monophyletic: can all be traced back to one common ancestor. diverse kingdom but all member share these characteristics: multicellular, heterotrophic, dominant diploid generation, motile at some part of their life cycle, 2-3 layers of tissues form during embryonic development

major plant division: bryophyes

mosses, liverworts, and hornworts. gametes are produced in gametangia (protective structures) on gametophytes, dominant haploid stage of life cycle of bryophytes. *antheridium (male gametangium) produces flagellated sperm that swim through water. *archegonium (female) produces egg. zygote grows into diploid structure (still connected to gametophyte). they are anchored by rhizoids rather than roots. **in mosses, this structure is a stalk bearing capsule which contains haploid spores produced by meiosis=> spores dispersed by wind and germinate and grow into haploid gametophyes which produces antheridium + archegonium *lacks true root, true leaves, true stems (lack vascular tissues) so must remain in/near water

anchorage dependence

most cells only divide when attached to an external surface such as neighboring cells or side of culture dish

filtration in kidneys

most filtration occurs in the glomerulus. blood pressure forces water, salt, glucose, aa, and urea into bowmans capsule. proteins and blood cells are too large to cross the membrane. they remain in the blood. the fluid that enters the renal tubes called the filtrate

if no skip in generation of phenotype

most likely an autosomal dominant disorder

cohesion-tension theory

most water movement is explained by this; major contributor (osmosis and capillary action are minor) consists of: 1. transpiration: evaporation of water from plants, removes water from leaves=> causing negative pressure (tension) to develop within leaves and xylem 2. cohesion: attraction between like substances (water); so water within xylem cells behaves as a single, polymerlike column from roots to leaves 3. bulk flow: when a water molecule is lost from a leaf by transpiration, it pulls up behind an entire column of water molecules (generated by transpiration, which is itself caused by heat action of the sun, so technically sun drives sap ascent)

transport vacuoles

move materials between organelles or organelles and the PM

respiration

movement of gases in and out; also means cellular respiration producing ATP within mitochondria

osmosis in plants

moves from soil through root and ito xylem by gradient (continuous movement of water out of root by xylem, and high mineral inside stele) this osmotic force (root pressure) can be seen as *guttation, formation of small droplets of sap (water and minerals) on ends of leaves in morning. but mostly, root pressure too small to have major effect on water transport

skeleton muscle

multinucleated, voluntary and striated. normally does not undergo mitosis, contains thick myosin protein filaments that slide past the thin actin protein filaments

obligate aerobes

must have oxygen to live

7. primitive autotrophic prokaryotes

mutation, heterotroph gained ability to produce its own food=>cyanobacteria

gap junctions

narrow tunnels between animal cells (connexins) prevent cytoplams of each cell from mixing, but allow passage of ions and small molecules. tissues like heart have these to pass electrical impulses

plasmodesmata

narrow tunnels between plant cells

mitosis: checkpoints

near the end of G1: cell growth assessed and favorable conditions checked. if fails, enters G0 stage end of G2: checks for sufficient mitosis promoting factor (MPF) levels to proceed M checkpoint: metaphase checkpoint during mitosis that triggers start of G1

glial cells

nervous tissue support cells; capable of cellular division *oligodendrocytes: produce myelin in CNS; wrap many times around axons *shwann cells: produce myelin in PNS. myelin sheaths act as insulators and are separated by **nodes of Ranvier. instead of traveling continuously down axon, action potential jumps from node to node (aka salutatory conduction) speeding up the impulse. **only vertebrates have myelinated axons. myelinated axons appear white (white matter); neuronal cell bodies appear gray (gray matter) *microglia: phagocytes of the CNS *ependymal: use cilia to circulate CSF *satellite cells: support ganglia which are groups of cell bodies in the PNS *astrocytes: physical support to neurons of CNS; maintain mineral and nutrient balance

nervous system vs endocrine

neuronal communication is rapid/direct/specific. hormonal is slower/spread through body and affects many cells/tissues in different ways/longer lasting

nonsense mutation

new codon codes for a stop codon

missense mutation

new codon codes for new AA => minor or fatal results as in sickle cell (valine, new; for glucine, old)

silent mutation

new codon still codes from the same AA

budding

new individual splits off from existing one (hydra)

cladogenesis/ branching evolution

new species branches out from parent species

zone of elongation

newly formed cells absorb water and elongate. responsible for our perception of growth

realized niche

niche that an organism occupies in absence of competing species is its *fundamental niche. when competitors are present, one/both species may be able to coexist by occupying their realized niches, that part of their existence where niche overlap is absent (occupy areas of niche that dont overlap so no competition for resources)

nucleotide consists of

nitrogen base, five carbon sugar deoxyribose, phosphate group

neutral mutation

no change in protein function

saturated

no double bonds

smooth ER

no ribosomes. synthesizes lipids and steroid hormones for export. in liver cells, smooth ER has functions to break down toxins, drugs, and toxic by-products from cellular rxns. smooth and striated muscle have smooth ERs called sarcoplasmic reticulums that store and release ions like calcium

what takes place in the chloroplast:

noncyclic, cyclic, photolysis, calvin, chemiosmosis **remember that it is the thylakoid membrane, not the outer or inner chloroplast membranes that absorb light!

abiotic

nonliving-temp, climate, light, water availability, topology

cofactors

nonprotein molecules that assist enzymes

prions

not viruses or cells. these are misfolded versions of proteins in the brain that cause normal version to misfold as well. fatal

cell division

nuclear division (karyokinesis) followed by cytokinesis. in diploid cells, there are two copies of every chromosome, foming a pair or homologous chromosome. humans have 46 chromosomes, 23 homologous pairs, a total of 92 chromatids-depending on stage of division.

mitosis: telophase

nuclear division, nuclear envelop develops, chromosomes condense to chromatin and nucleoli reappear

meiosis II: prophase II

nuclear envelop disappears and spindle develops etc. no chiasmata and no crossing over

meiosis II: telophase II

nuclear envelop reappears and cytokinesis occurs which results in 4 haploid cells **each chromosome = 1 chromatid

meiosis I: telophase I

nuclear membrane develops. each pole forms a new nucleus that has half the number of chromosomes. goes from homologous pair to each chromosome = 2 sister chromatids. **reduction to haploid **interphase may occur in between meiosis I and II depending on the species

rRNA

nucleolus is an assemblage of DNA actively being transcribed into rRNA. as ribosome, has 3 binding sites: one for mRNA, one for tRNA that carries a growing polypeptide chain (P site); and one for the second tRNA that delivers the next amino acid (A site). *termination sequences include: UAA, UGA, UAG. together with proteins, rRNA forms ribosomes. ribosome is assembled in nucleolus but large and small subunits are exported separately to the cytoplasm

DNA is a polymer of

nucleotides

RNA is a polymer of

nucleotides that contain ribose, thymine replaced by uracil which pairs with adenine, usually single stranded

meiosis I: prophase I

nucleus disassembles, nucleolus disappears and nuclear envelop breaks down, chromatin condenses, spindle develops. microtubules begin attaching to kinetochores. **crossing over means genetic recombination! *synapsis: homologous chromosomes pair up. these pairs are referred to as tetrads=group of 4 chromatids or bivalents *chiasmata: region were crossing over occurs for non-sister chromatids *synaptonemal complex: protein structure that temporarily forms between homologous chromosomes: gives rise to the tetrad with chiasmata and crossing over

mitosis: prophase

nucleus disassembles: nucleolus disappear, chromatin condenses into chromosomes, and nuclear envelope breaks down. mitotic spindle is formed and microtubules composed of tubulin begin connected to kinetochores

flower parts

number of petals, sepals, stamens, and other parts. dicots= in 4s, 5s or multiples. monocots= in 3s or multiples

ectotherms

obtain body heat from environment aka poikilotherms/cold blooded **invertebrates, amphibians, reptiles, fish

heterotrophs

obtain energy by consuming organic substances produced by autotrophs *parasites: obtain energy from living tissue of host *saprobes (saprophytes): obtain energy from dead, decaying matter which contributes to organic decay=decomposer

6. primitive heterotrophic prokaryotes

obtained materials by consuming other organic substances (pathogenic bacteria)

lactic acid fermentation

occurs in human muscle cells, other microorganisms. pyruvate-->lactate and NADH-->NAD+ lactate is transported to liver for conversion back to glucose once surplus ATP is available

alcohol fermentation

occurs in plants, fungi (yeasts), and bacteria (botulinum) pyruvate--> acetaldehyde + CO2, then acetaldehyde-->ethanol and NADH-->NAD+ acetaldehyde is the final electron acceptor! thus forming ethanol

glycolysis

occurs in the cytoplasm cellular aerobic respiration that is decomposition of glucose into pyruvate in the cytosol. 1 glucose molecule has 6C and is split into 2 pyruvates-each with 3C 2 ATP added, 2 NADH produced, 4 ATP produced, 2 pyruvate formed NET: 2 ATP + 2 NADH + 2 pyruvate (+2 H2O + 2H+) ATP is produced here via substrate level phosphorylation: direct enzymatic transfer of a phosphate to ADP, no extraneous carriers needed. Notes: hexokinase phosphorylates glucose, important because then it cant diffuse out and tricks the gradient. PFK (enzyme) adds the second phosphate, makes fructose 1,6-biphosphate-this is irreversible and commits to glycolysis-major regulatory point!

anaerobic respiration

occurs in the cytosol. includes glycolysis and fermentation. aerobic respiration regenerates NAD+ via O2, which is required for continuation of glycolysis, without O2, there would be no replenishing-NADH accumulates, cell would die with no new ATP so fermentation occurs

primary succession

occurs on substrates that never previously supported living things (volcanic islands, lava flows). essential and dominant characteristic of primary succession is soil building

associative learning

occurs when an animal recognizes (learns) that events are connected. a form called classical conditioning occurs when animal performs behavior in response to substitute stimulus rather than normal stimulus a. ex: dogs salivate when presented with food

disruptive selection

occurs when environment favors extreme or unusual traits while selecting against common traits. short and tall are favored while average is selected against

fertilization

of two haploid gametes = fertilization or syngamy resulting in a diploid zygote

teichoic acids

on cell wall of bacterium are used as recognition and binding sites by bacterial viruses that cause infections. also provide cell wall rigidity and only found on gram-positve bacteria!

epistasis

one gene affects phenotypic expression of the second gene. pigmentation: one gene controls whether on/off, second gene controls color or amount. if first gene codes for no pigment, then the second gene has no effect

law of segregation

one member of each chromosome pair migrates to an opposite pole so that each gamete is haploid aka each gamete has only one copy of each allele. this occurs in anaphase I

hemizygous

one single copy of a gene instead of two (male has XY chromosome = hemizygous)

anagenesis/ phyletic evolution

one species replaces another, straight path evolution

aphotic zone

only animal and other heterotrophs

control of stomata

open vs closed: affects gas exchange, transpiration, sap ascent, photosynthesis *when stomata are closed: CO2 not available, cannot photosynthesize *when stomata are open: CO2 can enter leaf, photosynthesize but plant risks desiccation from transpiration **guard cells: two surrounds the stomata. cell walls of guard cells do not have the same thickness (thicker when border the stomata). guard cell expands when water diffuses in. due to the irregular thickness and radial shape, the sides with thinner cell walls expand more and creates opening (stoma). when water diffuses out, kidney shape collapses and stoma closes

regulation of prokaryotic gene expression: operon

operon: control of gene transcription, consists of: 1. promoter: sequence of DNA where RNA polymerase attaches to begin transcription 2. operator: region that can block action of RNA polymerase if occupied by repressor protein 3. structural genes: DNA sequences that code for related enzymes 4. regulatory genes: located outside of operon region, produces **repressor proteins. others produce **activator proteins that assist the attachment of RNA polymerase to the promoter region

apoenzyme

or apoprotein, is the tern for when it is not combined with cofactor

oparin and haldane:

organic soup theory; if there was O2 (very reactive) no organic molecules would have formed. *oparins hypothesis was that origin of the earths environment was reducing (providing chemical requirements to produce complex molecules form simple building blocks. in an oxidizing environment you would break complex molecules apart

negative feedback

original condition is canceled so that conditions are returned to normal

female reproduction cycle

ovarian cycle (ovary) and menstrual cycle (uterus) 1. mentrual cycle: divided into follicular, ovulation, luteal, menstruation **hypothalamus and anterior pituitary initiate: monitor estrogen and progesterone in blood: low level->hypothalamus->GnRH->FSH and LH (via anterior pituitary -negative feedback)-> follicle developes-> FSH stimulate follicle to secrete estrogen-> lots of estrogen (positive feedback on anterior pituitary) -> LH surge-> ovulation (follicle is now *corpus luteum-maintained by LH which along with estrogen begins to decrease after ovulation), secretes-> estrogen and progesterone-> development of endometrium (thickens in preparation for implantation of fertilized egg) *IF NO IMPLANTATION: negative feedback on anterior pituitary from increases estrogen and progesterone-> terminates production of FSH and LH (due to decreased GnRH from hypothalamus)-> corpus luteum (no longer maintained by LH) disintegrates-> *corpus albicans, no estrogen and progesterone-> endometrium shed during mentruations flow phase *IMPLANTATION: if implantation occurs->embryo (placenta) secretes chorionic gonadotropin (HCG)-> maintain corpus luteum-> production of estrogen and progesterone remains high-> endometrium stays-> HCG is later replaced by progesterone from placenta 2. ovarian cycle: a. follicular phase: development of egg and secretion of estrogen from follicle b. ovulation: midcycle release of egg c. luteal phase: secretion of estrogen and progesterone from corpus luteum after ovulation **estrogen=thicken endometrium **progesterone=development and maintenance of endometrial wall

cellular respiration

overall an oxidative, exergonic process (delta G=-686kcal/mole). external respiration is entry of air into lungs and gas exchange between alveoli and blood; internal respiration is exchange of gas between blood and the cells + intracellular respiration processes. during respiration, high energy H atoms removed from organic molecules (dehydrogenation). C6H12O6 + 6O2 + 6H2O + energy.

photosynthesis

overall: 6CO2 +6H2O --> C6H12O6 + 6O2 begins with light absorbing pigments in plant cells; able to absorb energy from light; chlorophyll a, b, and carotenoids (red, orange, yellow). light is incorporated into electrons. excited electrons are unstable and re-emit absorbed energy; energy is then reabsorbed by electrons of nearby pigment molecule. the process ends when energy is absorbed by one of two special chlorophyll a molecules (P680 and P700)

desertification

overgrazing of grasslands that border deserts transform the grasslands into deserts-> agricultural output decreases, or habitat available to native species are lost

diffusion between blood and cells

oxygen diffuses out of RBCs, across blood capillary walls, into interstitial fluids, and across cell membranes (CO2 opposite)

bulk flow of oxygen

oxygen transported through body within Hb containing RBCs

fetal circulation

oxygenated, nutrient-rich blood from placenta carried to fetus via umbilical vein -> half enters *ductus venosus (allows blood to bypass the liver)-> carried to inferior vena cava-> RA-> RV ->ductus arteriosus (conducts some blood from the pulmonary artery to the aorta. *other half enters liver/portal vein->RA->foramen ovale (allows blood to bypass pulmonary circulation by entering the left atria directly from the right atria since there is no gas exchange in fetal lung)->LA->LV->aorta

leaf venation

pattern of veins in leaves. dicots= netted (branching pattern). monocots= parallel

macroevolution

patterns of changes in groups of related species over broad periods of geologic time. patters determine phylogeny: evolutionary relationships among species and groups of species

capacitation

penultimate step in maturation of the spermatozoa while in the vagina, allows for egg penetration

membrane proteins

peripheral=loosely attached to one side surface. integral=embeds inside membrane, transmembrane=type of integral all the way through both sides

new ATP formed via

phosphorylation: ADP+phosphate using energy from energy rich molecule like glucose

Nitrogen fixation in plants

plants require n2 to grow. atmospheric n2 is converted into NH4+ or NO3- to be utilized by plants. nitrogen fixing bacteria are located in root swellings called nodules. plants that contribute to nitrogen fixation include the legume family. peas, peanuts, soybeans, and beans are examples. in nitrogen fixation, n2 is converted to NH3

storage vacuole

plants store starch, pigments, and toxic substances

growth factor

plasma membrane has receptors for growth factors that stimulate cell for division (such as damaged cell)

glycogen

polymer of alpha glucose molecules. stores energy in animal cells

starch

polymer of alpha glucose molecules. stores energy in plant cells

cellulose

polymer of beta glucose. structural molecules for walls of plant cells and wood

chitin

polymer similar to cellulose but each beta glucose has a nitrogen containing group attached to a ring. structural molecule in fungal cell walls, exoskeleton of insects

allopatric speciation

population is divided by geographic barrier. interbreeding between two resulting populations is prevented. gene frequencies in two populations can diverge due to natural selection, mutation, genetic drift. if gene pool is sufficiently divergant, will not interbreed when barrier is removed, new species formed. this form of speciation can be through dispersal (group is isolated by being physically removed from the original location of the larger group) or vicariance (group is isolated by a geographic barrier but in the same overall location of the larger group).

diploidy

presence of two copies of each chromosome. in heterozygous conditions, recessive allele is stored for later generations. more variations are maintained in gene pool

transmission across the synapse

presynaptic cell->postsynaptic cell *electrical: ap travels along membranes of gap junction (less common); fast, in cardiac and visceral smooth muscle *chemical: most typical in animal cells; unidirectional 1. Ca2+ gates open: depolarization allows Ca2+ to enter the cell via VDCCs = voltage dependent calcium channel-also found in beta cells! 2. synaptic vessels release neurotransmitter: influx causes release into cleft 3. neurotransmitter binds with postsynaptic receptors: diffusion (via brownian motion) and binding 4. postsynaptic membrane is excited or inhibited. two possible outcomes: **Na+ gates open, membrane is depolarized=>excitatory postsynaptic potential (EPSP), if threshold potential is succeeded, ap is generated. **K+ gates open, membrane becomes hyperpolarized=>inhibitory postsynaptic potential (IPSP) it becomes more difficult to generate an ap 5. neurotransmitter is degraded and recycled: broken down by enzymes in cleft and recycled

structure of skin: dermis

primarily CT; collagen and elastic fibers; contains hair follicles, glands, nerves, and blood vessels 1. papillary region: top 20% 2. reticular region: dense connective tissue, collagen and elastic fibers; packed with oil glands, sweat gland ducts, fat, and hair follicles; provides strength, and elasticity (stretch marks are dermal tears)

secondary consumers

primary carnivores, eat primary producers

first time immune system is exposed to an antigen=

primary response, requires 20 days to reach full potential

penetrance

probability that an organism with a specific genotype will express a particular phenotype

Pr and Pfr are in equilibrium during daylight:

red light is present as sunlight Pr->Pfr and far red is also present (Pfr->Pr)

convergent evolution

two unrelated species that share similar traits by environment (analogous traits)

oxidative phosphorylation

process of ADP--> ATP from NADH and FADH2 via passing of electrons through various carrier proteins; energy doesnt accompany the phosphate group but comes from the electrons in the ETC establishing an H+ gradient that supplies energy to ATP synthase. NADH makes more energy than FADH2, more H+ is pumped across per NADH (both are coenzymes, 3:2 yield) final electron acceptor is oxygen-combines with native H+ to form water. carriers extract energy from NADH and FADH2 while pumping protons into the intermembrane space- ATP synthase uses this gradient to make ATP as it shuttles H+ back into the inner matrix

trp operon (E. coli)

produces enzyme for tryptophan sythesis; regulatory genes produce an inactive repressor => RNA pol produces enzymes. when tryptophan is available, no longer need to synthesize it internally: it binds to inactive repressor and activates repressor=> able to bind operator and block RNA pol. tryptophan is corepressor

note on prokaryotes and protein sythesis:

prokaryotes generally have ready to go mRNA upon transciption. it is only in eukaryotes that you need the step of mRNA processing. since prokaryotes dont need to process their mRNA first, translation can begin immediately/simultaneously. in both prokaryotes and eukaryotes, multiple RNA polymerases can transcribe the same template simultaneously

RNA world hypothesis

proposes that self-replacing ribonucleic acid molecules were precursors to current life. RNA stores genetic info like DNA and catalyzes chemical reactions like an enzyme protein. may have played a major role in the evolution of cellular life. RNA is unstable compared to DNA, so more likely to participate in chemical rxns due to its extra hydroxyl group

phytochrome

protein modified with light absorbing chromophore. two forms: 1. Pr (P660-red) 2. Pfr (P730-far red) they are reversible. when exposed to red light: Pr->Pfr and vise versa

saprophytism

protists and fungi that decompose dead organic matter externally and absorb nutrients

kingdom protista: protozoa (animal like)

protists are heterotrophs; consume living cells or dead organic matter; unicellular eukaryotes 1. rhizopoda: ameobas that move by extensions of their cell body called pseudopodia; phagocytosis 2. foraminifera: aka forams, have tests (shells) usually made of calcium carbonate 3. apicomplexans: parasites of animals; apical complex (complex of organelles located at an end of the cell) no physical motility. form spores which are dispersed by hosts that complete their life cycle (malaria caused by sporozoan) 4. ciliates: use cilia for moving and other functions; have specialized structures: mouths, pores, contractile vacuoles, two kinds of nuclei. most complex of all cells (paramecium)

kingdom protista: fungus like

protists resemble fungi 1. cellular slime molds: funguslike and protozoalike characteristics: spores germinate into amoebas which feed on bacteria. when no food, amoebas aggregate into single unit slug (individual cells of slug mobilize into stalk with capsule at top to release spores = germinate and repeat cycle) their stimulus for aggregation is cAMP secretion (secreted by the amoebas that first experience food deprivation) 2. plasmodial slime molds: grow as single, spreading mass (plasmodium) feeding on decaying vegetation; when no food, stalks bearing spore capsules form, haploid spores released from capsule germinate into haploid amoeboid/ flagellated cells, fuse to form diploid = grow into plasmodium 3. oomycota: water molds, miders, white rusts; either parasites of saprobes; form filaments (hyphae) which secrete enzymes that digest surrounding substances like fungi do. hyphae lacks septa (cross wall) which is in true fungi that partition filaments into compartments; so they are coenocytic (lack septa) containing many nuclei within a single cell; cell walls are made of cellulose rather than chitin of fungi

invertebrate respiration: cnidaria

protozoa and hydra: *direct with environment: large surface areas and every cell is either exposed to environment or close to it-> simple diffusion of gases directly with outside environment (eg flatworms) *small animals only

intermediate filaments

provide support for maintaining cell shape like keratin.

endoplasmic reticulum

provides channel through cytoplasm, provides direct continuous passageway from PM to nuclear membrane

DNA probe

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

Km is the Michaelis constant

raised Km=substrate binding worse lowered Km=substrate binding better

adaptive radiation

rapid evolution of many species from a single ancestor; occurs when ancestral species is introduced to an area where diverse geographic/ecological conditions are available for colonization

R-selected population

rapid exponential pop growth, numerous offspring, fast maturation, little postnatal care (ex: bacteria). generally found in rapidly changing environments affected by density independent factors. characterized by opportunistic species (eg grasses, insects that quickly invade a habitat, reproduce, then die)

dendrites

receive info and transfer it to cell body

temperate grasslands

receive less water (and uneven seasonal occurrence of rainfall) and are subject to lower temperatures than savannas (eg north american prairie)

sex-linked

refers to single gene resides on sex chromosome; when male XY receives a X from mother, whether it is dominant or recessive will be expressed because there is no copy on the Y chromosome

species richness

reflects the diversity of a community in regards to the total number of different species present

cardiac cycle

regulated in terms of rate by autorhythmic cells of the ANS, but contractions are initiated independently of the ANS. instead the heart contract automatically: *SA (sinoatrial node) or pacemaker (located in upper wall of right atrium) is a group of specialized cardiac muscle cells that initiates by contracting both atria and sending delayed impulse to stimulate AV (atrioventricular node) **spreads contraction to surrounding cardiac muscles via electrical synapses made from gap junction **pace of SA node is faster than normal heartbeat but parasympathetic vagus nerve innervates SA node (also increases digestive activity of intestines); slows contractions

symbiosis

relationship between two species *mutualism: beneficial/beneficial *commensalism: beneficial/neutral *parasitism: beneficial/detrimental

basophils

release histamine for inflammatory response

short tandem repeat (STR)

repeat of 2-5 nucleotides and different between all individuals except identical twins

DNA polymerase 1

replaces base pairs from the primer and does DNA repair. pol 1 also has a 5' to 3' exonuclease, to take off the primer and can also proofread with 3' to 5' when laying down a new chain. **summary: pol 1 primarily breaks down RNA primer via 5' to 3' exonuclease and replaces it with DNA (laid down between okazaki fragments mainly) via 5' to 3' polymerase while proofreading as it goes. can proofread via 3' to 5' exonuclease as well.

gonads

reproductive structure responsible for production of gametes. male=testis, female=ovaries

obligate anaerobes

require absence of oxygen to live

photoperiodism

response of plants to changes in photoperiod (relative length of daylight and night); plants maintain circadian rhythm; endogenous mechanism (internal clock that continues to keep time even if external cues are absent)

know it is incomplete dominance when:

respresented as such: A and A' in this case A' is not completely recessive and causes incomplete dominance together as AA'

restriction fragment length polymorphism (RFLPs)

restriction fragments between individuals are compared, fragments differ in length are observed because of polymorphism (different length in DNA sequences). inherited in mendelian fashion so often used in paternity suits, RFLP analysis used at crime scenes to match suspects

identical twins

result from indeterminate cleavage

fraternal twins

result from more than one egg being fertilized

capillary action in plants

rise of liquids in narrow tubes, contribute to movement of water up xylem; results from forces of adhesion (molecular attraction between unlike substances) between water and tube-> meniscus is formed at top of water column. no meniscus in active xylem since water forms a continuous column; capillary effect is minimal

digestion: mouth

salivary a-amylase breaks down (starch->maltose), chewing creates a bolus which is swallowed

tertiary consumers

secondary carnivores, eat secondary consumers

exocrine system

secrete substances into ducts (ex gallbladder) (pancreas is both exocrine and endocrine)

digestion: stomach

secretes gastric juice (dig enzymes and HCl)-food enters stomach through lower esophageal/ cardiac sphincter. the stomach contains exocrine glands (local secretion by way of duct) within gastric pits (indentations in stomach that denote entrance to the gastric glands, which contain secreting chief cells, parietal cells, and mucous cells (secrete mucus to prevent backwash) 1. storage: accordion like folds allow 2-4 L of storage 2. mixing: mixes food with water and gastric juice->chyme (creamy medium) 3. physical breakdown: muscles break food, HCl denatures proteins and kills bacteria 4. chemical breakdown: pepsin (secreted by chief cells) digests proteins; (pepsinogen activated by HCl, which is secreted by parietal cells) **peptic ulcers: caused by failure of mucosal lining to protect stomach. ulcers can be caused by excess stomach acid or H. pylori as well 5. controlled release: chyme->small intestine; controlled by the pyloric sphincter 6. stomach cells: **mucous cells: secrete mucus that lubricates and protects stomach's epithelial lining from acid environment. **chief cells: exocrine glands secrete pepsinogen (zymoegn is precursor to pepsin)-pepsinogen activated to pepsin by low pH in stomach; once active, begins protein digestion. **parietal cells: secrete HCl; intrinsic factor (B12 absorption). **G cells: secrete gastrin-a large peptide hormone which is absorbed into blood->stimulates parietal cells to secrete HCl (histamine also increases HCl secretion as well as gastrin)

germination and development of the seed

seed remains dormant at maturity until specific environment cues. others may have required dormancy period where germination wont happen regardless. *germination: begins with inhibition (absorption) of water->enymes activate->biochemical processes, respiration begin. absorbed water causes seed to swell and seed coat to crack->growing tips of radicle produce roots that anchor seedling->elongation of hypocotyl->young shoot formed. **in young seedling/plants, growth occurs at tips of roots and shoots (apical meristems); areas of actively dividing (meristematic) cells. this kind of growth is called primary growth: (produces tissues: primary xylem and primary phloem-> elongation). most plants (including most monocots) just have primary growth.

translocation

segment is moved to another chromosome. can be reciprocal (two nonhomologous chromosomes swap chunks) or Robertsonian (one chromosome from a pair becomes attached to another from a pair aka an extra chromosome 21 attached to 14 can cause downs as well, tripled 21 chunk)

industrial melanism

selection of dark colored melanic varieties in various species of moths (peppered moths) as a result of industrial pollution

SEVEnUP

seminiferous tubules->epididymis->vas deferens->ejaculatory duct->urethra->penis

fission

separation of organism into two new cells (amoeba)

steroids

sex hormones, cholesterol, corticosteroids- 4 ringed structure

synapomorphies

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

ecological pyramids

show relationships between trophic levels

Hardy-Weinberg law

shows us how a genotype and phenotype stability can be achieved in a population. this law examines population gene pools, not genotypes of individuals. assuming a large population, random mating, no net migration, no mutation, no natural selection, there should be no change in the gene pool of a population

Hb curve

sigmoidal

analogous traits

similar characteristics resulting from convergent evolution, therefore not derived from a common ancestor

western blot

similar method for proteins: *electrophoresis *blot to membrane *primary antibody specific to protein added to bind to that protein *secondary antibody enzyme conjugate will bind to primary and mark it with enzyme for visualization

meiosis II

similar to mitosis. chromosomes spread across metaphase plate and sister chromatids separate and migrate to opposite poles.

passive transport

simple diffusion, osmosis, dialysis, plasmolysis(movement of water out of a cell that results in its collapse), facilitated diffusion, countercurrent exchange (diffusion by bulk flow in opposite directions-blood and water in fish gills)

conjugated

simple protein + nonprotein

law of parsimony

simplest explanation is most likely correct

myoglobin

single chain/protein subunit, **stores O2 in muscle. has higher affinity for O2 than Hb. *Mb has no change in O2 binding over a pH range

prokaryotic cells

single chromosome is short, circular DNA usually without histone **but archaea have histoines**may contain plasmids. no nucleus, no organells. flagella consist of chains of protein flagellin instead of 9+2 microtubules **note: flagella use proton motive force to spin and give locomotion in bacteria (electrical gradient! not ATP!!)

pleiotropy

single gene has more than one phenotypic expression; sickle cell anemia leads to different health conditions

smooth muscle

single nucleated, found in walls of urinary bladder, digestive system, uterus, blood vessels, involuntary, non-striated, actin and myosin are present, but not organized into sarcomeres like seen in skeletal muscle

point mutation

single nucleotide changes causing substitution, insertion, or deletion. last two could cause frameshift mutation *transition mutation: purine to purine or pyrimidine to pyrimidine *transversion mutation: purine to pyrimidine or vise versa

cardiac muscle

single nucleus, has striations as well as complex junctions between adjacent individual cells called intercalated discs. it is involuntary

fragmentation and regeneration

single parent breaks into parts that regenerate into new individuals (sponge/planaria/starfish)

DNA replication: Helicase is the enzyme that unwinds DNA, forming a Y shaped replication fork

single stranded binding proteins attach to each strand of uncoiled DNA to keep them separate. Topoisomerases break and rejoin the double helix, allowing the prevention of knots

mRNA

single stranded template. since there are 64 possible ways (ways that 4 nucleotides can be arranged in triplet combinations) there are 64 possible codons. 3 of them are stop codons. therefore only 61 code for amino acids

deme

small local population eg all the beavers along specific portion of a river

phospholipid membrane permeability

small, uncharged, nonpolar molecules. polar can only if small and uncharged. and hydrophobic molecules can freely pass across the membrane

globular proteins

somewhat water soluble, many functions: enzymes, hormones, inter and intracellular storage and transport, osmotic regulation, immune response. mostly dominated by tertiary structure

allantois

special sac in bird egg that keeps N waste away from embryo

adipocytes

specialized fat cells that are white and contain a large lipid droplet composed primarily of triglycerides with a small layer of cytoplasm around it

centrifugation

spins and separates liquified cell and separates into layers based on density: nuclei is fastest to pellet out/most dense and the bottom layer, then microsomes/small vesicles, then ribosomes/viruses/larger macromolecules

chromosomal breakage

spontaneous or induced (mutagenic agents, x-rays) dificiency = lost fragment

plant hormones: cytokinins

stimulate cytokinesis aka cell division; stimulate and influences direction of organogenesis; stimulate growth of lateral buds (which weakens apical dominance-dominance growth of apical meristem); delay senescence (aging) of leaves. effects depend on target organ and presence or concentration of auxin. *structurally: variations of the nitrogen base adenine; include naturally occurring zeratin and artificially produced kinetin

cotyledons

storage tissue that provides nutrition to developing seedling. dicots= 2 cotyledons. monocots= 1 cotyledon

fats

store more energy than carbohydrates per carbon, their carbons are in a more reduced state

vestigial structures

structures that appear to be useless but had ancestral function

systematics

study of evolutionary relationships among organisms aka phylogenys

population ecology

study of growth, abundance, and distribution of populations

noncompetitive inhibition

substance inhibits enzyme by binding elsewhere than active site, substrate still binds but reaction is prevented from completing. Km is unchanged but Vmax is not

competitive inhibition

substance that mimics the substrate inhibits the enzyme by binding at the active site. can be overcome by increasing substrate connection. Km is raised but Vmax is not

recognition proteins

such as major-histocompatability complex on macrophage to distinguish between self and foreign; they are glycoproteins due to oligosaccharides attached

structure of skin: epidermis

superficial; avascular epithelial tissue (depends on dermis for oxygen and nutrients). layers from top down: 1. stratum corneum: 25-30 dead layers; filled with keratin and surrounded by lipids **lamellar granules make it water repellent 2. stratum lucidum: only in palms and soles of feet, and finger tips; 3-5 layers, clear/dead 3. statum granulosum: 3-5 layers of dying cells; lamellar bodies release hydrophobic lipids 4. stratum spinosum: strength and flexibility; 8-10 layers held together by (desmosomes-keratin involving adhesion proteins) 5. stratum basale (germinativum) contains merkel cells and stem cells that divide to produce keratinocytes; attached by basement membrane **the keratinocytes are pushed to the top layer. rise->accumulate keratin and die->lose cytoplasm/nucleus/other organelles->at outermost layer of skin, slough off body

chemiosmosis

takes place across the thylakoid membrane

ETC (electron transport chain)

takes place in the inner membrane/cristae (folds) of the mitochondria

noncyclic photophosphorylation

takes place in thylakoid membranes ADP + Pi + light --> ATP: light dependent reaction 1. photosystem II: electrons trapped by P680 in PSII are energized by light 2. primary electron acceptor: two excited electrons passed to primary e acceptor; primary because it is the first in chain of acceptor 3. ETC: consists of a plastoquinone complex (PSII) which contains proteins like cytochrome and cofactor Fe2+; analogous to oxidative phosphorylation 4. phosphorylation: 2e- move down chain = lose energy 5. photosystem I: e- transport chain terminates with PSI: they are again energized by sunlight and passed on to another primary e- acceptor. from this point foward it can go to cyclic or noncyclic path 6. NADPH: 2e- then pass down a short ETC with proteins like ferrodoxin to combine NADP+ + H+ + 2e- ==> NADPH (coenzyme) 7. splitting of water (photolysis): the loss of 2e- from PSII (initially) is replaced when H2O splits into 2e-, 2H+, and 1/2 O2. (H+ goes for NADPH formation and 1/2O2 that contributes to release as oxygen gas). this occurs at PSII: H2O + ADP + Pi + NADP+ + light ==> ATP + NADPH + O2 + H+

photolysis

takes place inside the thylakoid lumen; passes e- to the membrane for noncyclic photophosphorylation

southern blotting

technique to ID target fragments of known DNA sequence in a large population of DNA. *electrophoresis fragments first *separate DNA strands (usually with NaOH) *then transfer the SS DNA fragments to nitrocellulose membrane *add probe which will hybridize and mark it

gibbs free energy

tells us whether a given chemical reaction can occur spontaneously: G=H-TS. if delta G is negative, the reaction can occur spontaneously. likewise if delta G is positive, the reaction is nonspontaneous. chemical reactions can be coupled together if they share reaction intermediates. this principle of coupling reactions to alter the change in gibbs free energy is the basic principle behind all enzymatic action in biological organisms

food vacuoles

temporary receptacles of nutrients. merge with lysosomes which break down food

expressivity

term describing the variation of phenotype for a specific genotype

chaparral

terrestrial biome along california coastline characterized by wet winters, dry summers, scattered vegetation

stanley miller

tested the oparin theory and produced organic molecules. *miller and urey used ammonia, methane, water, and hydrogen sealed and simulated lightning. saw several organic molecules. amino acids, starting materials but NO nucleic acids!

fast block to polyspermy

the acrosomal reaction in sea urchins in which an electrical response occurs to change the membrane potential to prevent polyspermy

mitosis: anaphase

the chromosome number doubles here. microtubules shorten, each chromosome is pulled apart into two chromatids and chromosome number doubles. pulls the chromosomes to opposite poles=disjunction. at the end of this phase, each pole has a complete set of chromosomes, same as original cell before replication

systematic circuit

the circulation pathway through the body between left and right sides of heart

polygenetic inheritance

the interaction of many genes to shape a single phenotype with continuous variation aka height, skin color

resource partitioning

two species occupy same niche but pursue slightly different resources or securing their resources in different ways, individuals minimize competition and maximize success

marine biomes

the largest biome covering 3/4 of worlds surface. provides most of earths food and oxygen. includes *estuaries (where oceans and river meet), intertidal zones (where ocean meet land), continental shelves/littoral zone (shallow oceans bordering continents), coral reefs, and pelagic ocean (deep). relatively constant temp. *benthic zone: lowest layer of a body of water, including sediment surface and sub-surface layers. in ocean water (deep) light doesnt penetrate-most organisms are scavengers and detrivores *pelagic zone: the water that is neither close to shore nor the very bottom. it is broken down from top to bottom in layers. epiplagic (surface layer of water, only photic zone since enough light for penetration, nearly all primary production of ocean occurs here) all zones under are aphotic. mesoplagic (minimal O2). bathypelagic (pitch black, no plant life, most organisms here consume detritus. abyssopelagic (cold, high temp, most species have no eyes due to lack of light. hadopelagic (most life here exists in hydrothermal vents)

critical note

the majority of CO2 in the blood is transported in the form of bicarbonate. to a lesser extent, it can be transported bound to a Hb/plasma proteins, and to an even lesser extent simply dissolved in the plasma *CO2 is significantly more soluble in blood than O2

endomembrane system

the network of organelles and structures, either directly or indirectly connected that function in the transport of proteins and other macromolecules into or out of the cell. includes PM, ER, golgi, nuclear envelope, lysosomes, vacuoles, vesicles, endosomes but not mitochondria or chloroplasts

haloenzyme

the union of the cofactor and the enzyme

atrium

the upper chambers of the heart

note on photosystems

there are a few hundred in each thylakoid, have a reaction center containing chlorophyll a surrounded by antenna pigments that funnel energy into it

at anaphase I of meiosis:

there would be a total of 46 chromosomes if a cell has 46 chromosomes at the beginning because 23 chromosomes are pulled to each pole by independent assortment and no chromatids are separated at anaphase I

at anaphase of mitosis:

there would be a total of 92 chromosomes and 92 chromatids if a cell has 46 chromosomes at the beginning. even when pulled apart from sister chromatids, each one is now a complete chromosome

when T cells encounter nonself cells:

they divide and produce four kinds of cells: 1. cytotoxic T cells: killer T cells recognize and destroy by releasing perforin protein to puncture them (lysis) 2. helper T cells: stimulate activation of B cells, cytotoxic T cells, and suppressor T cells 3. suppressor T cells: play negative feedback role in immune system 4. memory T cells: similar function to memory B cells

mitosis: interphase

this begins after mitosis and cytokinesis are complete, and consists of G1, S and G2 phases. the whole cell cycle includes the M, G1, S, and G2 phases. during G1, cell increases size, and the G1 checkpoint ensures everything is ready for DNA synthesis. During S phase, second molecule of DNA replicated from the first, provides sister chromatids=DNA synthesis. During G2, there is rapid cell growth, preparation of genetic material for cellular division **more time is spent in interphase (G1, S, G2) than mitosis (over 90%). growth occurs in all 3 interphases

gel electrophoresis

this is after the DNA is cut up. agarose gel under an electric field for the separation of proteins based on charge and size. negative DNA moves toward positive anode from negative cathode. shorter DNA moves further than larger **distributes DNA based on size after electrophoresis, DNA can then be sequenced, or probed to identify location of specific sequence of DNA

cytoplasm

this is an area not a structure. metabolic activity and transport occur here. cyclosis is streaming movement within cell. everything is suspended within cytosol but the nucleus

domain eukarya: kingdom protista

this is an artificial kingdom used mainly for convenience; poorly understood. most are unicellular.

as O2 pressure increases, O2 saturation of Hb increases

this is ideal-in the lungs we are O2 rich and want to hang on to it, but in the tissues we are O2 poor (lower O2 pressure) so the Hb will release the O2 to the tissues

cytosol

this is just the gel like stuff. also known as cytoplasmic matrix. fatty acids made here

secretory phase of menstrual cycle

this is the final phase of the cycle; the corpus luteum produces progesterone which allows the endometrium to be receptive to implantation of the blastocyst

digestion: pharynx

this is where food and air passages cross; the epiglottis blocks trachea so only solid and liquid can enter the esoph

cyclic photophosphorylation

this replenishes ATP when calvin cycle consumes it. when excited 2e- from PSI join with proteins carriers in the first ETC and generate 1 ATP as they pass through; these 2e- are recycled into PSI and can take either cyclic or noncyclic path

1. earth and atmosphere form:

through volcanoes (CH4, NH3, CO, CO2, H2, N2, H2O, S, HCL, HCN, little to no O2)

heredity

to determine the probability of two or more independent events occurring together multiply the probabilities of each separate event

2. density

total number of individuals per area or volume occupied

secondary compounds

toxic chemicals produced in plants that discourage would be herbivores (tannins in oaks/nicotine/tobacco are toxic)

axon

transfers impulses away from cell body

transport of sugars in plants

translocation: movement of carbohydrate through phloem from a source (eg leaves) to sink (site of carbohydrate utilization). described by pressure-flow hypothesis: 1. sugars enter sieve-tube members: soluble carbs move from site of production (palisade mesophyll) to phloem sieve-tube members by active transport=>higher solute at source than at sink (root) 2. water enters sieve-tube members: water diffuses into source by osmosis to balance the lower water concentration from step 1 3. pressure in sieve-tube members at source moves water and sugars to sieve-tube members at sink through sieve tubes: when water enters the sieve-tube members, pressure build up since rigid cell walls do not expand. result: water and sugar move by bulk flow through sieve tubes 4. pressure is reduced in sieve-tube members at sink as sugar are removed for utilization by nearby cells: pressure begins to build up at sink (from bulk flow from source to sink). however, sink is where sugars are used->sugars removed from sieve-tube members by active transport-> increases water at sink->water diffuses out of cell->relieves pressure **cells store energy as insoluble starch. benefit of this = any cell can act as a sink and get the sugar and water transported there. likewise, by breaking down starch, any cell can act as a source (eg plant roots at night break down starch when photosynthesis activity is low, they act as a sugar source)

golgi

transport of various substances in vesicles. flattened sacs known as cisternae

phloem

transport sugar. made of cells called sieve-tube members (elements) that form fluid-containing columns (sieve tubes); cells are living at maturity (but lack nuclei and ribosomes). pores on end of member form sieve plates (areas where cytoplasm of one cell makes contact with next cell). sieve tubes are associated with companion cells (living parenchyma cells that lie adjacent to each sieve-tube member) and connected by plasmodesmata to maintain physiological support due to lack of nuclei in the sieve-tube members

general characteristics of hormone

transported throughout the body in blood; small amount = large impact; slower effect

the following are vascular plants (tracheophytes)

true root, leaves, and stems; germination of antheridium and archegonium (swim) produces diploid zygote into sporophyte (dominant generation) *lycophyta *pterophyta *coniferophyta *anthophyta

digestion: esophagus

tube leading to stomach, food travels by peristalsis

double helix

two antiparallel strands

phospholipid

two fatty acids and a phosphate group attached to a glycerol backbone

linked genes

two or more genes that reside on the same chromosomes and thus cannot separate independently because they are physically connected (inherited together). linked genes exhibit recombination about 18% of the time

mullerian mimicry

two or more harmful species that are not closely related, and share one or more common predators, have come to mimic each others warning signals

divergent evolution

two or more species that originate from common ancestor and become increasingly different over time (result of speciation)

parallel evolution

two related species made similar evolutionary changes after their divergence from common ancestor

competitive exclusion principle (Gause's principle)

two species compete for exactly the same resources (or occupy the same niche), one is likely to be more successful (no two species can sustain coexistance if they occupy the same niche)

phase-contrast

uses light phases and contrast. allows for detailed observation of living organisms (including internal structures) if thin. good resolution/contrast but not good for thick samples and produces "halo effect" around perimeter of samples

recombinant DNA technology

uses restriction endonucleases to cut up specific segments of DNA and leave it with sticky end (unpaired). these restriction enzymes *EcoRI; BamHI, normally used by bacteria to protect against viral DNA (protect their own DNA via methylation) *vector: such as plasmid because DNA molecule used as a vehicle to transfer foreign genetic material into another cell *to introduce foreign DNA into plasmid, the plasmid is treated with the same restriction enzyme so the same sticky ends bind. DNA ligase stabilizes the attachments; then the plasmid is introduced into bacterium by transformation. bacterium must be made competent to take up the plasmid by process of electroporation or heat shock+CaCl2 *after this process, bacteria can be grown to produce product, form clone library, etc. use antibiotic resistence/screen method to filter out the ones that dont have the recombinant DNA

PCR

uses synthetic primer (the primer may be RNA or DNA oligonucleotides) to clone DNA (rapidly amplify) *Taq polymerase (heat stable) + nucleotides + primers + salts (buffer) all necessary. attaches nucleotides to a DNA template, thus copying the DNA

allele

variance of genes such as different color

geographic variation

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

neutral variation

variation without selective value for example fingerprints in humans

phloem

vascular tissue consisting of sieve tubes through which sugars and other solutes are conducted

peripatric speciation

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

lysosomes

vesicles produced from golgi that contain digestive enzymes (low pH for function) break down nutrients, bacteria, cell debris. any enzyme that escapes from lysosomes remains inactive in the neutral pH of cytosol. functions in releasing contents into cell

bacteriophage

virus that only attacks bacteria.

temperate deciduous forests

warm summers, cold winters, and moderate precipitation. deciduous trees shed leaves during winter. soil is rich due to leaf shed. vertical stratification: plants and animals live on ground, low branches, and treetops. principal mammals hibernate through cold winter

aposematic coloration

warning coloration

invertebrate respiration: fish

water enters mouth, passes over gills, exits through operculum (gill cover). **countercurrent exchange between opposing movements of water and underlying blood maximizes diffusion of O2 into blood and CO2 into water

SNOW DROP

way to remember the blot techniques southern=DNA northern=RNA western=proteins

glucogenesis

we can produce glucose occurs in liver and kidney. liver is responsible for maintaining glucose concentration in the blood

insight

when animal exposed to new situation without prior experience, performs a behavior that generates positive outcome a. chimp stacks boxes to reach bananas previously out of reach

clonal selection

when antigen bind to B cell or when nonself binds to T cell->divide into daughter cells, only B and T cells that bears effective antigen receptor is selected and reproduces to make clones

flowering hormone: florigen

when flowering is initiated, this flowering hormone is produced in leaves and travels to shoot tips

repressible enzymes

when structural genes stop producing enzymes only in presence of an active repressor. unlike repressible enzymes, some genes are *constitutive (constantly expressed) either naturally or due to mutation

systole phase

when ventricles contract, backflow into ventricles causes semilunar valves to close

diastole phase

when ventricles relax, backflow into ventricles causes semilunar valves to close

adaptive radiation

where a number of different species emerge from a single ancestor. this exemplifies a divergent evolution. darwin's finches are an example

alveoli

where gas exchange between the circulatory system and the lungs occurs; surfactant reduces the surface tension (prevents water from collapsing alveoli). there are two types of epithelial cells in human alveoli: *type 1: structural support *type 2: produces surfactant

mutagenic agents include:

xrays, uv rays, radioactivity, chemical compounds which include colchicine (inhibits spindle formation causing polyploidy), mustard gas. these agents are generally also carcinogenic. proto-oncogenes stimulate normal growth; if mutated become oncogenes which lead to cancer