MCAT - bio

dna repair

cells have developed several mechanisms to deal with dna damage. first, cell cycle checkpoints are activated, and arrest cell cycle progression. in eukaryotes, checkpoint pathways function at phase boundaries (such as the G1/S transition, and the G2/M transition), and can also be activated within some phases. extensive dna damage can induce apoptosis in eukaryotes, but before this happens, cells try to repair the dna damage. this is important so that defective dna isn't passed onto daughter cells. there are several types of dna repair. direct reversal homology-dependent repair double-strand break repair sos repair?ked

cell cycle

cells reproduce themselves by first doubling everything in the cytoplasm and the genome and then splitting in half. some cells continually go through a cycle of growth and division, traditionally discussed in 4 phases. S (synthesis) phase is when the cell actively replicates its genome. M phase includes mitosis and cytokinesis. mitosis is the partitioning of cellular components (genes, organelles, etc) into 2 halves. cytokinesis is the physical process of cell division. btwn M phase and S phase, there are 2 "gap" phases, G1 and G2. the gap phases plus S phase together form the part of the cell cycle btwn divisions, known as interphase. see pg 208/phone for cell cycle the cell spends most of its time in interphase, busily metabolizing and synthesizing materials. some cells are permanently stuck in interphase (G0). in fact, the more specialized a cell becomes, the less likely it is to remain capable of reproducing itself. examples are neurons, blood cells, and cells on the surface of the skin. they must be replenished by reproduction of less specialized precursor cells called stem cells. all the blood cells, for ex, are derived from a single type of stem cell found in the bone marrow. during interphase, the genome is spread out in a form that is not visible w a light microscope without special stains, and dna is accessible to the enzymes of replication. by the end of S phase, the nucleus contains 2 complete copies of the genome. the cell now has twice the normal amount of dna. mitosis is divided into 4 phases: prophase, metaphase, anaphase, and telophase. a mnemonic is I pee on the mat. where I is for interphase. the first sign of prophase is that the genome becomes visible upon condensing into densely packed chromosomes, instead of diffuse chromatin. (the chromosomes condense so that they can be separated without tangling.) observing a human cell under the light microscope at the beginning of prophase, one can see 46 differently shaped chromosomes. upon closer observation, one notes that each chromosome actually consists of 2 identical particles joined at a centeromere. these 2 particles are the 2 copies of a chromosome, known as sister chromatids. when mitosis is complete, each new daughter cell will have 46 chromosomes, each consisting of a single chromatid, separated from its sister. spending a little more time starting at the nucleus, you might notice that the jumble of 46 chromatid pairs actually consists of 23 homologous pairs of identical appearing sister chromatid pairs (23 pairs of pairs). homologous chromosomes are different copies of the same chromosome, one from your mother and the other from your father. to repeat: sister chromatids are identical copies of a chromosome, attached to each other at the centromere. homologous chromosomes are equivalent but nonidentical and do not come anywhere near each other during mitosis. other important events occur during prophase. the nucleolus disappears, the spingle and kinetochore fibers appear, and the centriole pairs begin to move to opposite ends of the cell. so now the cell has 2 MTOCs, called asters (stars) bc of the star-like appearance of microtubules radiating out. also at the end of prophase, the nuclear envelope converts itself into many tiny vesicles. (this stage of prophase is also referred to as prometaphase. it is the last event in prophase and is rather dramatic; once the nuclear membrane is disintegrated into vesicles, the spindle fibers can attach to the centromeres of the chromosomes and the cell can enter metaphase.) metaphase is simple: all the chromosomes line up at the center of the cell, forming the metaphase plate. the chromosomes line up in the center of the cell bc the kinetochore of each sister chromatid is attached to spindle fibers that attach to MTOC at opposite ends of the cell. so each member of a pair of chromatids is pulled toward the opposite pole of the cell. during anaphase, the spindle fibers shorten, and the centromeres of each sister chromatid pair are pulled apart. the cell elongates, and cytokinesis begins with the formation of a cleavage furrow, which is accomplished by a ring of microfilaments encircling the cell and contracting. in telophase (telos is greek for end), a nuclear membrane forms around the bunch of chromosomes at each end of the cell, the chromosomes decondense, and a nucleolus becomes visible within each new daughter nucleus. each daughter nucleus has 2n chromosomes. cytokinesis is complete, and the cell is split in 2. see pg 209/phone for phases

cones

color, aCuity. concentrated in fovea. 3 types, blue light, green, red

x-linked dominant traits

harder to identify. a female will display an x-linked dominant phenotype if she has one or 2 copies of the allele on her X chromosomes. a male will express the phenotype if he inherited the affected allele from his mother. while these traits still tend to affect males more than females, this trend is less obvious than for x-linked recessive traits

if antibodies to a viral capsid protein are ineffective in blocking infection, what might this indicate about the virus?

it suggests that the virus is enveloped, so the antibody cannot reach its epitope on the capsid surface in infectious virus

acetylcholine is a neurotransmitter in several areas in the body including

neuromuscular junction, pre and postganglionic parasympathetic neurons, and preganglionic sympathetic neurons

para long pre

parasympathetic preganglionic neuron sends a long axon to a small ganglion which is close to the effector while in the sympathetic system, the preganglionic axon is relatively short, and there are only a few ganglia, these sympathetic ganglia are quite large. the sympathetic postganglionic cell sends a long axon to the effector

conservative replication

parental ds-dna would remain as-is while an entirely new double-stranded genome was created

colon

part of excretory system. large intestine reabsorbs water and ions (Na+, calcium, etc) from feces. in this sense it doesn't really excrete anything, but merely processes wastes already destined for excretion. colon also capable of excreting excess ions (sodium, chloride, calcium) into the feces, using active transport

respiratory zone

parts of respiratory system that participate in actual gas exchange

tricuspid valve

valve btwn right atrium and right ventricle

varicose veins

when the venous valves that prevent back flow of blood (from veins to heart) fail, these result bc inc venous pressure

if an enzyme that degrades an mRNA is injected into the cytoplasm of a cell and all translation ceases, is the cell prokaryotic or eukaryotic?

it could be either. mrna and translation are found in the cytoplasm of both prokaryotes and eukaryotes, so the cell could be either

nucleolus

(little nucleus) a region within the nucleus which functions as a ribosome factory. there is no membrane separating the nucleolus from the rest of the nucleus. it consists of loops of dna, rna polymerases, rRNA, and the protein components of the ribosome. [would you expect th nucleolus to be larger in cells that are actively synthesizing protein, or in quiescent cells? - the nucleolus is largest in cells that are producing large amounts of protein. the increased size reflects increased synthesis of ribosomes.] [what role would the loops of dna in the nucleolus play? - the dna will serve as template for ribosomal rna production] the nucleolus is the site of transcription of rRNA by rna pol 1. transcription of mrna and rRNA is performed by other polymerases in other areas of the nucleus. [does a similar "division of labor" exist in the prokaryotic cell? - no. bacteria have only a single kind of rna pol which is responsible for all transcription] the ribosome is partially assembled while still in the nucleolus. the protein components of the ribosome are not produced in the nucleolus; they are transported into the nucleus from the cytoplasm (remember that all translation takes place in the cytoplasm). after partial assembly, the ribosome is exported from the nucleus, remaining inactive until assembly is completed in the cytoplasm. this may serve to prevent translation of hnRNA.

parasitic bacteria

(under domain archaea?) parasitic bacteria can either be obligate, meaning that they must be inside a host cell to replicate, or facultative, meaning that they can live and replicate inside or outside of a host cell. in either case, the designation as a parasite means that damage is being done to the host cell. however in order to ensure a continued supply of energy and cellular materials needed to survive and reproduce, parasitic bacteria need to modulate the course of that damage. [how is this model similar to viruses? - viruses are obligate intracellular parasites. they don't have the option to replicate outside of a host cell, but must also balance the damage that is done to the host cell against what is needed for more virus to be made] T cells (lymphocytes involved in immunity) are responsible for monitoring cellular contents; people who are T cell deficient have a hard time fighting off these types of bacterial infections, just as they would also struggle with viral infections. mycobacteria, the genus of bacteria which encompasses the cause of tuberculosis as well as other diseases, has members which are obligate and others which are facultative, whereas the sexually transmitted disease chlamydia is caused solely by an obligate parasitic bacteria

symbiotic bacteria

(under domain archaea?) symbiotic bacteria coexist with a host, where both the bacterial cell and the host cell derive a benefit. an example of this would be the Rhizobia genus, which is responsible for the fixing of nitrogen in the nodules that exist on the roots of legumes. without these bacteria the legume plants would not be able to grow, as they would be unable to derive the necessary nitrogen from the soil on their own. similarly, Cyanobacteria are responsible for nitrogen fixing in marine environments. some of the bacterial flora in the human gut is also composed of symbionts which aid the human body in defending against other pathogenic strains. [what other functions do the bacteria in the gut have? - the gut flora is responsible for the production of vitamin K, which is necessary for blood clotting and in feeding off of undigested material from what humans have consumed; they are one of the final stages in processing our solid waste for excretion] due to their close relationship with their host cells, these bacteria often have smaller genomes with a more limited number of cellular products that are made, since the host cells can provide some of what the bacteria need. this can often mean that the symbiotic bacteria don't survive long outside of the host environment.

parallel evolution

2 species go through similar evolutionary changes due to similar selective pressures

theory of evolution by natural selection

1 in a population there are heritable differences btwn individuals 2 heritable traits (alleles of genes) produce traits (phenotypes) the affect the ability of an organism to survive and have offspring 3 some individuals have phenotypes that allow them to survive longer, be healthier, and have more offspring than others 4 individuals with phenotypes that allow them to have more offspring will pass on their alleles more frequently than those with phenotypes that have fewer offspring 5 over time, those alleles that lead to more offspring are passed on more frequently and become more abundant, while other alleles become less abundant in the gene pool 6 changes in allele frequency are the basis of evolution in species and populations

inc force of contraction 2 ways

1 motor unit recruitment 2 frequency summation. tetanus. contracting when Ca2+ still in cytoplasm so it builds on itself. but after refractory period

2 key features of clonal selection in B cells

1 recombination during development to produce many clones each w a single antigen recognition specificity 2 selection of a clone out of the many clones based on specific recognition of antigen by preexisting antibody genes

cell theory

1. all living organisms are composed of one or more cells and their products 2. cells are the monomer for any organism 3. new cells arise from pre-existing, living cells though these basic principles are still true, more modern extensions of cell theory also include the idea that no matter what the species, the chemical composition of cells is similar, that dna is the source of hereditary programming information passed from cell to cell, that an organism's activity is determined by the total activity of its cells, and that biochemical energy flow occurs within cells. these additional principles have been explored and verified due to vast improvements both in microscopy as well as biochemical and genetic testing all living organisms (which doesn't include viruses) can be classified as either prokaryotes or eukaryotes. the classification of organisms into these groups is based on examination of their internal cellular structure. representatives from both groups are able to carry out the basic biochemical processes of photosynthesis, the Krebs cycle, and oxidative phosphorylation to produce atp. the primary feature of prokaryotes that distinguishes them from eukaryotes is that they don't contain membrane-bound organelles (nucleus, mitochondria, lysosomes, etc). prokaryote means "before the nucleus," and the lack of a nucleus indicates that prokaryotes are evolutionarily the oldest domains. unlike viruses, however, prokaryotes possess all of the machinery required for life. they are true cells; true living organisms. the prokaryotes include bacteria, archer (extremophiles), and blue-green algae (cyanobacteria). the classification of living organisms, taxonomy, is an important part of biology bc it is used to determine the evolutionary relationship of organisms to one another. the largest taxonomic division is the domain. there are three recognized domains: Bacteria, Archea, and Eukarya. domains Bacteria and Archea include prokaryotic organisms, and Domain Eukarya includes eukaryotic organisms. each domain can be further subdivided into kingdoms. currently there are 3 well-recognized eukaryotic kingdoms (Animalia, Plantae, and Fungi), and great debate over the number of kingdoms that should be present in the other prokaryotic domains and in the single-celled eukaryotes (protists). the most basic and ancient of organisms, the prokaryotes see pg 148/phone for prokaryote

punnet square steps

1. determine the gametes that are possible from each parent in the cross. 2. draw a square w the possible gametes from each parent on 2 sides 3. fill in the square with the zygote genotypes that would result from each possible combination of gamete 4. determine the phenotype of each genotype 5. find the probability of each genotype and each phenotype see pg 238/phone for pic see pg 239/phone

excretory and homeostatic roles of the kidney

1. excretion of hydrophilic wastes 2. maintenance of constant solute concentration and constant pH 3. maintenance of constant fluid volume (important for blood pressure and cardiac output) these goals accomplished through 3 processes: 1 filtration - entails passage of pressurized blood over a filter (like a coffee filter). cells and proteins remain in the blood (like coffee grinds), while water and small molecules are squeezed out into the renal tubule (like java). during filtration, water, waste products, and useful small molecules like glucose are filtered into renal tubule. fluid in tubule is filtrate, and it will eventually be made into urine. 2 selective reabsorption - take back useful items (glucose water amino acids), while leaving wastes and some water in the tubule 3 secretion - this involves addition of substances to the filtrate. secretion can inc the rate at which substances are eliminated from the blood; bc not only are the substance filtered out, more of them are added to the filtrate after filtration last step in urine formation is concentration and dilution. involves selective reabsorption of water and is where we decide whether to make concentrate urine or dilute urine. after this step whatever remains in renal tubule gets excreted as urine

hardy-weinberg conditions in the real world

1. mutation: mutation is inevitable in a population. even if there are no chemical mutagens or radiation, inherent errors by DNA polymerase would over time cause mutations and introduce new alleles in a population. 2. migration: if migration occurs, animals leaving or entering the population will carry alleles with them and disturb the hardy-weinberg equilibrium 3. natural selection: for there to be no natural selection, there would have to be unlimited resources, no predation, no disease, and so no. this is not a set of conditions encountered in the real world. 4. non-random mating: if individuals pick their mates preferentially based on one or more traits, alleles that cause those traits will be passed on preferentially from one generation to another. 5. random drift: if a population becomes very small, it cannot contain as great a variety of alleles. in a very small population, random events can alter allele frequencies significantly and have a large influence on future generations.

respiratory system function

1. pH regulation. CO2 converted to carbonic acid in blood by carbonic anhydrase. CO2 exhaled by the lungs, carbonic acid decreased in the blood, pH increases. hyperventilation causes alkalinization, respiratory alkalosis. hypoventalization causes acidification of the blood, or respiratory acidosis. while the kidney regulates pH over a period of hours to days 2. thermoregulation. breathing can result in heat loss. from evaporative water loss which functions under the same principles as sweating. the respiratory structures are necessarily moist. liquid water absorbs heat as it changes into water vapor, and this heat is removed from the body during the process. dogs depend on panting for dissipation of excess heat bc they can't sweat. some animals conserve water and heat by using countercurrent exchange in nasal passages. the nasal passages warm and humidify the air entering the respiratory system and the exiting air is cooled and de humidified. breathing through the mouth like during exercise will bypass this mechanism and increase rates of heat loss. 3. protection from disease and particulate matter. mucociliary escalator and alveolar macrophages protect us from harmful inhaled particles

codominance

2 alleles are both expressed but are not blended. ex are alleles of gene for ABO blood group antigens

autosomal recessive

2 copies of the allele are required for the affected phenotype. no sex bias

bile and pancreatic secretions in duodenum

2 ducts empty into duodenum. pancreatic duct, delivers exocrine secretions of pancreas (digestive enzymes and bicarbonate). other is common bile duct which delivers bile. contains bile acids made from cholesterol in liver and normally absorbed and recycled. bile stored in gallbladder until needed. bile has 2 functions: vehicle for disposal (excretion) of waste products by the liver, and it is essential for the digestion of fats. bile ducts and pancreatic duct empty into the duodenum via the same orifice, known as sphincter of Oddi.

■ Four-chambered heart: structure and function

2 kinds of chambers involved in pumping blood, atria and ventricles. atria are reservoirs or "waiting rooms" where blood can collect from the veins before getting pumped into the ventricles. the muscular ventricles pump blood out of the heart at high pressures into the arteries. the system circulation and the pulmonary circulation are separated within the heart, so the right and left sides of the heart each high one atrium and one ventricle. the right atrium receives deoxygenated blood from the systemic circulation (from the large veins: the inferior vena cava and superior vena cava) and pumps it into the right ventricle. from right ventricle blood passes through the pulmonary artery to the lungs. oxygenated blood from the lungs returns through the pulmonary veins to the left atrium and is pumped into the left ventricle before being pumped out of the heart in a single large artery, the aorta, to the systemic circulation. requires blood supply of its own. the very first branches from the aorta are coronary arteries, which branch to supply blood to the wall of the heart. they are called coronary bc they encircle the heart forming a crown shape. deoxygenated blood from the heart collects in coronary veins, which merge to form coronary sinus, located beneath a layer of fat on the outer wall of the heart. a sinus is an open space, in the case of the cardiovascular system, it is a pool of low pressure blood. blood in the coronary sinus is the only deoxygenated blood that doesn't end up in the inferior vena cava or superior vena cava. instead the coronary sinus drains directly into the right atrium.

enteric nervous system

2 networks nerouns. myenteric plexus and submucosal plexus. myenteric plexus is found btwn circular and longitudinal muscle layers and helps regulate gut motility. submucosal plexus is found in submucosa and helps regulate enzyme secretion, gut blood flow, and ion/water balance in the lumen. in areas where these functions are minimal (esophagus or anus), the submucosal plexus is sparse branch of autonomic nervous system. can operate independently of other 2 branches of autonomic nervous system but both of those branches can modulate the activity of this nervous system

cell-mediated immunity and T cell

2 types of T cells: T helpers (CD4 cells) and T killers (cytotoxic T cells, CD8 cells where CD means cell differentiated marker.) the role of the T helper is to activate B cells, T killer cells, and other cells of the immune system. hence the T helper is the central controller of the whole immune response. it communicates with other cells by releasing special hormones called lymphokines and interleukins. t helper cell is the host of HIV the virus that causes AIDS. role of T killer cell is to destroy abnormal host cells namely: 1 virus-infected host cells 2 cancer cells 3 foreign cells like cells of a skin graft given by incompatible donor T in T cell stands for thymus where they develop in childhood. different T cells specific for particular antigen like with B cells. but only B cells make antibodies. if a t helper is specific for an antigen it will activate B cells or T killers to destroy it. major histocompatibility complex MHC class I and II. MHC I randomly picks peptides and display them on cell surface. allows T cells to monitor cell contents. MHCII cells are antigen presenting cells APCs, including macrophages and B cells. role is to phagocytize particles or cells, chose them up and display fragments using MHC II display system which t helpers then recognize (bind to). after a t helper is activated by antigen displayed in MHC II it will activate B cells (and stimulate proliferation of T killer cells) that are specific for that antigen. the activated B cells mature into plasma cells and secrete antibodies specific for the antigen note that full activation of T cells only occurs when the T cell binds to both antigen (displayed on MHC I or II) and the MHC molecule itself

■ Stomach oStorage and churning of food oLow pH, gastric juice, mucal protection against self-destruction o Production of digestive enzymes, site of digestion oStructure (gross)

3 purposes, partial digestion fo food, regulated release of food into small intestine, and destruction of microorganisms. ph 2, secret HCl. effects of this: 1 destruction of microorganisms, 2 acid catalyzed hydrolysis of many dietary proteins 3 conversion of pepsinogen to pepsin pepsin - enzyme catalyzes proteolysis (protein digestion). secreted as pepsinogen, which is an inactive precursor that must be converted to the active form pepsin. this conversion is catalyzed by gastric acidity. inactive form is zymogen. most zymogens activated by proteolysis. pepsinogen is unique bc activated by acidic proteolysis (autocleavage) instead of proteolytic cleavage by another enzyme churn food to expose to acidity and enzymes sphincters - lower esophageal sphincter prevents reflux of chyme (food + gastric secretions) into esophagus. the pyloric sphincter prevents passage of food from stomach into duodenum. opening of pyloric sphincter (stomach emptying) is inhibited when small intestine already has large load of chyme. stretching or excess acidity in duodenum inhibits further stomach emptying, by causing pyloric sphincter to contract. this effect is mediated by nerves connecting duodenum and stomach and by hormones like cholecystokinin cck secreted by epithelial cells in the wall of the duodenum. cck stimulates peristalsis in intestine and inhibits stomach emptying. gastrin - hormone secreted by g cells in stomach. stimulates acid and pepsin secretion and gastric motility. stimulated by food in stomach and parasympathetic stimulation. small molecule histamine (secreted in response to both stomach stretching and to gastrin) binds to parietal cells to stimulate acid release. ulcer healing drugs block binding of histamine to its receptor (H2 receptor) on parietal cells. results in less gastric acidity allows ulcers to heal.

■ Small Intestine o Absorption of food molecules and water o Function and structure of villi o Production of enzymes, site of digestion o Neutralization of stomach acid o Structure (anatomic subdivisions)

3 segments duodenum jejunum and ileum surface area from 1 length 2 villi 3 microvilli. villi are multicellular macroscopic projections in wall of small intestine microvilli are microscopic foldings of cell membranes of individual intestinal epithelial cells. lumen surface of small intestine is known as the brush border due to brush like appearance of microvilli villus 3 important structures 1 capillaries which absorb dietary monosaccharides and amino acids. capillaries merge into veins, form hepatic portal vein, transports blood containing amino acid and carbohydrate nutrients from the gut to the liver. 2 villus also contains small lymphatic vessels called lacteals, which absorb dietary fats. the lacteals merge to form large lymphatic vessels, which transport dietary fats to the thoracic duct which empties into bloodstream 3 Peyer's patches are part of immune system. collections of lymphocytes dotting villi that monitor GI contents and confer immunity to gut pathogens and toxins duodenal enzymes - dueodenal enterokinase (enteropeptidase) activates pancreatic zymbogen trypsinogen to trypsin. other duodenal enzymes are peculiar in that they are not truly secreted, but rather do their work inside or on the surface of the brush border epithelial cells. these are brush border enyzymes. role is to hydrolyze smallest carbohydrates and proteins like disaccharides and dipeptides into monosaccharides and amino acids. duodenal hormones - cholecystokinin CCK (deals w fats in duodenum), secretin (neutralizes HCl? in duodenum), and enterogastrone (dec stomach emptying)

cross of heterozygotes at 2 alleles

9:3:3:1

■ Nervous and endocrine control

ANS doesn't initiate action potentials in the heart but it does regulate the rate of contraction. the intrinsic firing rate of the SA node is about 120 beats per min. normal HR is only 60-80 bc the parasympathetic nervous system continually inhibits depolarization of the SA node. in particular, vagus nerve (a cranial nerve) contains preganglionic axons which synapse in ganglia near the SA node. postganglionic neurons innervate the SA node, releasing acetylcholine ACh. ach inhibits depolarization by binding to receptors on the cells of the SA node. the constant lvl of inhibition provided by the vagus nerve is known as vagal tone. in simmary the role of the parasympathetic system in controlling the heart is to modulate the rate by inhibiting rapid automaticity sympathetic system can also influence the heart. at rest most nervous input is from the vagus. sympathetic system kicks in when inc cardiac output is needed during fight or flight respnse. sympathetic system affects heart in 2 ways - 1 sympathetic postganglionic neurons directly innervate the heart, releasing norepinephrine. 2 epineprhine secreted by the adrenal medulla binds to receptors on cardiac muscle cells. effect of sympathetic activation is stimulatory. HR incs, and so does the force of contraction

endoskeleton vs exoskeleton

An endoskeleton allows the body to move and gives the body structure and shape. An exoskeleton is an external feature that supports and protects an animal's body. Insects, crustaceans, and other invertebrates, like shelled mollusks, have exoskeletons. ?

■ Adaptive immune system cells o T-lymphocytes o B-lymphocytes

B cell - mature into plasma cell and produce antibodies T cell - kill virus-infected cells, tumor cells, and reject tissue grafts; also control immune response

what kind of synthetic rna would give rise to a mixture of polyproline, polyhistidine, and polythreonine?

CCACCACCACCA... this would yield polyproline if read as CCA, CCA etc. but if read as CAC, CAC, etc it would give rise to polyhistidine. if it were read as ACC, ACC, ACC, it would encode polythreonine

■ Muscular control o Peristalsis

GI peristalsis - contraction of circular smooth muscle at point A prevents food located at point B from moving backward. then longitudinal muscles at point b contract w result shortening of gut so it is pulled up over food like a sock. food moves toward point C. circular smooth muscles at point b contract to prevent food from moving backward...

conjugation mapping (bacteria)

Hfr bacteria provide a mechanism of mapping the bacterial genome. by allowing Hfr cells to conjugate in the lab and stopping the conjugation process after different time intervals, researchers can figure out the order of the genes on the bacterial chromosome by analyzing recipient cells to see hat genes were transferred. for ex, you have 2 strains of e coli. one is a normal Hfr bacterium. the other is F- and auxotrophic for arginine, leucine, and histidine (F- Arg- Leu- His-). you allow conjugation to begin and stop it after 2 minutes. you find that all the recipients are now F- Arg- Leu- His+. then you take another bunch of bacteria and allow conjugation to proceed for 5 minutes. now all the recipients are F- Arg+ Leu- His+. you do the experiment a third and final time, allowing 8 minutes of conjugation, and find the recipients to be F- Arg+ Leu+ His+. (what is the arrangement on the genome of the enzymes responsible for synthesis of each amino acid, relative to the site of F plasmid integration? - the experiments showed that the ability to make histidine was transferred in a short time. after a slightly longer time, the ability to make both histidine and arginine was transferred. lastly, the ability to make leucine were transferred. so the arraignment on the genome (the map) must be: His-Arg-Leu-plasmid integration site.)

law of segregation

Mendel's law that states that the 2 alleles of an individual are separated and passed on to the next generation singly.

neuromuscular junction and impulse transmission

NMJ. synapse btwn axon terminus (synaptic knob) and a myofiber. nmj is not a single point, but rather a long trough or invagination of the cell membrane; the axon terminus is elongated to fill the long synaptic cleft. the purpose of this arrangement is to allow the neuron to depolarize a large region of the postsynaptic membrane at once. the postsynaptic membrane (myofiber cell membrane) is known as the motor end plate. ACh is the neurotransmitter at the NMJ impulse transmission at the NMJ is typical of chemical synaptic transmission: an action potential arrives at the axon terminus, triggering the opening of voltage gated Ca2+ channels; the resulting increase in intracellular Ca2+ triggers the release of vesicles of acetylcholine. the postsynaptic membrane contains ACh receptors which are ligand gated sodium channels. binding of ach to its receptor results in postsynaptic sodium influx, which depolarizes the postsynaptic membrane. this depolarization is known as an end plate potential. smallest measurable end plate potential caused by exocytosis of a single acetylcholine vesicle, is known as a miniature end plate potential MEPP. ach continues to stimulate postsynaptic receptors until it is destroyed. this is done y acetylcholinesterase, which hydrolyzes ACh to choline plus an acetyl unit. action potential similar to neuronal one, summation needed, threshold needed, voltage gated sodium channels open. shape of ap on graph is also similar. transverse tubules T-tubules - deep infoldings that allow action potential to depolarize entire cell not just membrane. sarcoplasmic reticulum. sequesters and release Ca2+. active transporters in it remove calcium from sarcoplasm (myofiber cytoplasm). then when action potential travels down t tubular network it depolarizes the cell and with it the sarcoplasmic reticulum. the sarcoplasmic reticulum contains voltage gated calcium channels which allow calcium to rush out into sarcoplasm upon depolarization. this causes troponin tropomyosin to change conformation, allowing myosin to bind actin. actin and myosin fibers slide across each other and muscle fiber contracts. when cell repolarizes, calcium actively sequestered and contraction ended.

classical dominance

The masking of a recessive allele by a dominant one

esophagus

Tube connecting the pharynx (throat) to the stomach

pleiotropism

a gene's expression alters many different, seemingly unrelated aspects of the organism's total phenotype

inborn errors of metabolism

a huge group of genetic diseases that involve disorders of metabolism. most of these are due to a single mutation in a single gene that codes for some sort of metabolic enzyme. symptoms are caused by either the build-up of a toxic compound that can't be broken down or by the deficiency of an essential molecule that cannot be synthesized. bc cellular metabolism is crucial, many symptoms are possible and a wide range of systems can be affected. inborn errors of metabolism are typically organized into groups of disorders, depending on what type of metabolic pathways they affect: carbohydrate, amino acid, urea cycle, organic acids, fatty acid oxidation, mitochondrial, porphyrin, purine or pyrimidine, steroid, peroxisomal function, or lysosomal storage

pinocytosis

a type of endocytosis. means cell drinking. is the nonspecific uptake of small molecules and extracellular fluid via invagination. primitive eukaryotic cells obtain nutrition in this manner, but virtually all eukaryotic cells participate in pinocytosis.

pores and porins

a pore is a tube through the membrane which is so large that it is not selective for any particular molecule. rather all molecules below a certain size may pass. (also a molecule which is just barely small enough to cross may not cross if it has the wrong charge on its surface.) pores are formed by polypeptides known as porins. we have studied pores in the double nuclear membrane, the outer mitochondrial membrane, and the gram-negative bacterial outer membrane. the eukaryotic plasma membrane does not have pores, bc pores destroy the barrier function of the membrane, allowing solutes in the cytoplasm to freely diffuse out of the cell. (are porins and ion channels found in the same membranes? - no. porins are large holes, and ion channels are small, usually regulated channels. if porins and ion channels were found in the same membrane, the ion channels would be useless, bc ions would flow in an unregulated manner through the pores)

phagocytosis

a type of endocytosis. means cell eating. it refers to the nonspecific uptake of large particulate matter into a phagocytic vesicle, which later merges with a lysosome. thus, the phagocytksed material will be broken down. the prime example of phagocytic human cells are macrophages ("big eaters") of the immune system, which engulf and destroy viruses and bacteria. (note: this is not an invagination.)

autosomal dominant

a single copy of the allele will confer the trait or disease phenotype. no sex bias

epistasis

a situation where expression of alleles for one gene is dependent on a different gene. for ex, a gene for curly hair cannot be expressed if a different gene causes baldness

organelle

a small structure within a cell that carries out specific cellular functions. most organelles are bounded by their own lipid bilayer membrane. the membrane acts like a plastic bag to seal off the contents of the organelle from the rest of the cytoplasm and control what enters and exits. a summary of the major animal cell organelles is given in the table on pg 174/phone

osmosis

a special type of diffusion in which solvent diffuses rather than solute. for ex, if a chamber containing water and a chamber containing a solution of sucrose are connected directly, sucrose will diffuse throughout the entire volume until a uniform concentration is reached. however if the 2 chambers are separated by a semipermeable membrane that allows water but not sucrose to cross, then diffusion of sucrose btwn the chambers cannot occur. in this case, osmosis draws water into the sucrose chamber to reduce the sucrose concentration as well as the volume in the water chamber. ignoring gravity, water will flow into the sucrose chamber until the concentration is the same across the membrane. the plasma membrane of the cell is a semipermeable membrane that allows water- but not most polar solutes - to cross by osmosis. (if a cell is placed in a hypotonic solution (solute concentration lower than in the cell), what will happen to the cell? - water will flow into the cell through the plasma membrane until the cell volume increases to the point that the cell bursts) see pg 193/phone for pic, diffusion vs osmosis the term tonicity is used to describe osmotic gradients. if the environment is isotonic to the cell the solute concentration is the same inside and outside. a hypertonic solution has more total dissolved solutes than the cell, a hypotonic solution has less. you may also hear the terms isoosmotic, hyperosmotic, and hypoosmotic. the tendency of water to move down its concentration gradient (into cells) can be a powerful force, able to cause cells to explode. this tendency (of water to move to where there are more particles) along with the inability of those particles to cross the membrane is what accounts for the difference in fluid lvls in the beaker at the bottom right hand corner of pic on pg 193. the large difference in fluid lvls may be a rather extreme example, but it is conceptually accurate: just as osmotic forces can cause a cell to rupture, they can overcome gravity, as shown.

pure-breeding strain

a strain in which animals of like phenotypes perpetuate those phenotypes in their progeny. for ex if mating yellow plants w yellow plants always produces yellow progeny, yellow is a pure-breeding strain

syncytium

a tissue in which the cytoplasm of different cells can communicate via gap junctions

stabilizing selection

a type of natural selection. both extremes of a trait are selected against, driving the population closer to the average. ex birds that are too large or too small are eliminated from a population bc they cannot mate

facilitated diffusion: carriers

a type of passive transport. carrier proteins also can transport molecules through membranes by facilitated diffusion, but they do so by a mechanism different from that of ion channels. carrier proteins don't form a tunnel through membranes like ion channels do. instead, carriers appear to bind the molecule to be transported at one side of the membrane and then undergo a conformational change to move the molecule to the other side of the membrane. some carriers, called uniports, transport only one molecule across the membrane at a time. other carriers termed symptoms carry two substances across a membrane in the same direction. anti ports, on the other hand, carry 2 substances in opposite directions.

which may result from inc pulmonary capillary hydrostatic pressure?

acculmulation of intersitial fluid in the lungs fluid accumulation in the alveoli decreased oxygenation of the blood due to excess fluid slowing O2 diffusion if the hydrostatic pressure is high enough, all of these will result

does ACh always inhibit postsynaptic cells? if not how can different responses be elicited by the same neurotransmitter?

ach is the neurotransmitter released by all autonomic preganglionic neurons, all parasympathetic postganglionic neurons, and all somatic motor neurons. in most cases it is stimulatory, ie causes an action potential to occur, causes an effect in an organ. whether a neurotransmitter or inhibitory depends only of the nature of the receptor on the postsynaptic cell

sliding filament model of muscle contraction

actin and myosin filaments overlap w each other in sarcomeres. contraction occurs when the thin and thick filaments slide across each other, drawing the z lines of each sarcomere closer together and shortening the length of the muscle cell. filament sliding powered by atp hydrolysis. myosin is an enzyme that uses energy of atp to create movement. (myosin atpase) each myosin monomer contains a head and a tail. the head attaches to a specific site on an actin molecule (myosin binding site). when its attached, myosin and actin are said to be connected by a cross bridge. contractions occurs when angle btwn head and tail dec. filament sliding occurs in 4 steps. 1 binding of myosin head to myosin binding site on actin, aka cross bridge formation. myosin has ADP and Pi bound. 2 power stroke, myosin head moves to low energy conformation, pulls actin chain toward center of the sarcomere. adp released. 3 binding of a new atp molecule necessary for release of actin by the myosin head (key!!) ** 4 atp hydrolysis occurs immediately and myosin head is cocked (set in high energy conformation). another cycle begins when myosin head binds to a new binding site on the thin filament thin filament also contains troponin tropomyosin complex that prevents contraction when Ca2+ isn't present. tropomyosin is a long fibrous protein that winds around the actin polymer blocking all the myosin binding sites. troponin is a globular protein bound to the tropomyosin that can bind Ca2+. when troponin binds Ca2+ troponin undergoes a conformational change that moves tropomyosin out of the way, so that myosin heads can attach to actin and filament sliding can occur.

order of events of action potential

action potential reaches end of axon at synaptic knob depolarization of presynaptic membrane voltage-gated calcium channels open neurotransmitter is released from the presynaptic cell neurotransmitter cross the synaptic cleft neurotransmitter binds to ligand-gated ion channels on the postsynaptic membrane membrane depolarization of postsynaptic cell voltage gated sodium channels open action potential initiated neurotransmitter in the synaptic cleft is degraded and/or removed

if the ratio of adenine to thymine in a DNA virus isn't one to one, what can be said about the genome of this virus?

adenine base pairs with thymine in double stranded dna. thus for every A there should be one T for a 1:1 ratio of A to T. if the ratio differs from this, the genome must be single stranded dna, or rna, which has no T

in an experiment, facultative anaerobic bacteria that are growing on glucose in air are shifted to anaerobic conditions. if they continue to grow at the same rate while producing lactic acid, then the rate of glucose consumption will: A. increase 16 fold B. decrease 16 fold C. decrease 2 fold D. not change

aerobic respiration produces 32 atp per glucose in prokaryotes compared to only 2 atp per glucose in fermentation. if the rate of growth is to remain the same, the rate of atp production must remain the same to drive biosynthetic pathways forward. since fermentation produces 1/16 the amount of atp per glucose, the rate of glucose consumption must increase 16fold to maintain the rate of growth at the same lvl. the answer is A. (in reality the growth rate would probably decrease)

sensory neurons

afferent neurons. to cns

homologous recombination

after dna replication, the genome contains identical sister chromatids. homologous recombination is a process where one sister chromatid can help repair a DSB in the other. first, the dub is identified and trimmed at 5' ends to generate a single-stranded dna. this is done by nucleases (which break phosphodiester bonds) and helices (to unwind the dna). many proteins bind these ends and start a search of the genome to find a sister chromatid region that is complementary to the single-stranded dna. once found, the complementary sequences are used as a template to repair and connect the broken chromatid. this requires a "joint molecule," where damaged and undamaged sister chromatids cross over. DNA polymerase and ligase build a corrected dna strand. see pg 94/ phone for pic

hardy-weinberg equilibrium

after one generation this is reached. in which allele frequencies no longer change. since allele frequencies don't change and genotype frequencies can be calculated from allele frequencies, it follows that genotype frequencies also don't change over time. (genotype frequencies of F2 and after will be the same as genotype frequencies of the F1 generation)

semiconservative replication

after replication, one strand of the new double helix is parental (old) and one strand is newly synthesized daughter dna

membrane structure (eukaryotes)

all of the membranes of the cell are composed of lipid bilayer membranes. the 3 most common lipids in eukaryotic membranes are phospholipids, glycolipids, and cholesterol, of which phospholipids are the most abundant. an example of a phospholipid is phosphatidyl choline w 2 long hydrophobic fatty acids esterified to glycerol, along w a charged phosphoryl choline group. thus phospholipids have portions that are distinctly hydrophilic and hydrophobic. glycolipids, w fatty acids groups and carbohydrate side chains, also have hydrophilic and hydrophobic regions. when fatty acids or phospholipids are mixed w water, they spontaneously arrange themselves w the hydrophobic tails facing the interior to avoid contact w water and the hydrophilic regions facing outward toward water. fatty acids form small micelles, but due to steric hindrance, phospholipids arrange themselves spontaneously into lipid bilayer membranes. since the lipid bilayer is the lowest energy state for these molecules, the bilayer membrane can reseal and repair itself if a small portion of membrane is removed. the interior of the lipid bilayer membrane is very hydrophobic, w water largely excluded. hydrophilic molecules such as ions, carbohydrates, and amino acids are not soluble in this environment, making the membrane a barrier to the passage of these molecules. nonpolar molecules such as CO2, O2, and steroid hormones can cross the membrane easily. water can also pass through the membrane but does so through specialized protein channels. see pg 186/phone for pic see pg 186/phone for pic in addition to lipids, proteins are a major component of membranes. in some cases, such as the mitochondrial inner membrane, there is a higher protein than lipid concentration. some proteins act to mediate interactions of the cell w other cells. other proteins called cell-surface receptors bind extracellular singalong molecules such as hormones and relay these signals into the cell so that it can respond accordingly. channel proteins selectively allow ions or molecules to cross the membrane. in general, membrane proteins are classified as peripheral or integral. integral membrane proteins are actually embedded in the membrane, held there by hydrophobic interactions. membrane crossing regions are called transmembrane domains. integral membrane proteins may have a complex pattern of transmembrane domains and portions not within the membrane. (at which point in the secretory pathway would the insertion of transmembrane domains into the membrane occur? - it occurs in the RER as the protein is translated and threaded across the ER membrane). peripheral membrane proteins are not embedded in the membrane at all, but rather are stuck to integral membrane proteins, held there by hydrogen bonding and electrostatic interactions. see pg 187/phone for pic see pg 187/phone for pic the current understanding of membrane dynamics is termed the fluid mosaic model, bc the membrane is seen as a mosaic of lipids and proteins that are free to move back and forth fluidly. according to this model, lipids and proteins are free to diffuse laterally, in 2 dimensions, but are not free to flip-flop. phospholipid head groups and hydrophilic protein domains are restricted from entering the hydrophobic membrane interior just as hydrophilic molecules in the extracellular space are. thus the membrane is said to have polarity. this just means that the inside face and the outside face remain different. we have already discussed one such difference: all glycosylations are found on the extracellular face. so the "fluid" in "fluid mosaic" means that things are free to move back and forth, but in 2 dimensions only. one exception is that some proteins are anchored to the cytoskeleton and thus cannot move in any direction. (phospholipids can be covalently attached to a fluorescent tag and then integrated into a lipid bilayer. if one cell has a red fluorescent tagged lipid in its plasma membrane and another cell has a green fluorescent tagged lipid in its membrane, what will happen if the 2 cells are fused together? - after a short period of time, the red and green tagged lipids will diffuse laterally and mix. an even distribution of the tags will be seen across the surface of the new hybrid cell) the fluidity of a membrane is affected by the composition of lipids in the membrane. the hydrophobic van der Waals interactions btwn the fatty acid side chains are a major determinant of membrane fluidity. saturated fatty acids, lacking any double bonds, have a very straight structure and pack tightly in the membrane, w strong can der Waals forces btwn side chains. unsaturated fatty acids, w one or more double bonds, have a kinked structure and pack in the membrane interior more loosely. cholesterol also plays a key role in maintaining optimal membrane fluidity by fitting into the membrane interior. (if the percentage of unsaturated fatty acids in a membrane is increased, will membrane fluidity inc or dec at body temp? - unsaturated fatty acids w a kinked structure have fewer van der Waals interactions, and therefore allow a more fluid membrane structure. inc the unsaturated fatty acids will inc membrane fluidity) see pg 188/phone for pic

bicuspid valve

aka mitral valve. valve btwn left atrium and left ventricle

stop codons

aka nonsense codons, since they don't code for any amino acid

tight junctions

aka occluding junctions bc they do not just join cells at one point, but form a seal btwn the membranes of adjacent cells that blocks the flow of molecules across the entire cell layer. they are not spots where cells are stuck together but rather bands running all the way around the cells. intestinal epithelial cells are involved in the active transport of glucose and other molecules from one side of epithelium to the other. a tight seal btwn these cells is required to prevent the 2 compartments from mixing. tight junctions also block the flow of molecules within the plane of the plasma membrane. for example, the surface of the plasma membrane facing the intestinal lumen, termed the apical surface, has different membrane proteins than the plasma membrane on the other side of the cell facing the tissues beneath, called the basolateral surface. (will a transmembrane protein inserted into the apical surface of an intestinal epithelial cell diffuse in the plane of the plasma membrane to reach the basolateral surface of the cell? - no. it is free to move around on the apical surface, but the tight junctions prevent it from diffusing to the basolateral surface.)

protease

aka proteolytic enzyme. protein that does the cutting in proteolysis

androgens and estrogens

all hormones involved in development and maintenance of male characteristics are androgens, while those involved in development and maintenance of female characteristics are estrogens. the primary androgen produced in the testes is testosterone. it is converted into dihydrotestosterone within the cells of target tissues. the primary estrogen produced in the ovaries is estradiol. testosterone is required in the testes for spermatogenesis. after birth the lvl of testosterone falls to negligible lvls until puberty at which time it increases and remains high for the remainder of adult life. elevated levels of testosterone are responsible for the development and maintenance of male secondary sexual characteristics (maturation of genitalia, male distribution of facial and body hair, deepening of the voice, and increased muscle mass). the pubertal growth spurt and fusion of the epiphyses also result. the role of estrogen in the female is analogous to the role of testosterone in the male. beginning at puberty, estrogen is required to regulate the uterine cycle and for the development and maintenance of female secondary sexual characteristics (maturation of genitalia, breast development, wider hips, and pubic hair). estrogen causes the fusion of the epiphyses in females. during puberty and adult life, sex steroid production is controlled by the hypothalamus and anterior pituitary. gonadotropin releasing hormone from the hypothalamus stimulates pituitary to release the gonadotropins: follicle-stimulating hormone (FSH) and lutenizing hormone (LH). in men Lh acts on interstitiaL cells to stimulate testosterone production, and fSh stimulates the Sustenacular cells. in women fsh stimulates the granulose cells to secrete estrogen and lh stimulates formation of corpus lute and progesterone secretion. feedback inhibition by the steroids inhibits the production of gonadotropin releasing hormone and lh and fsh. inhibin, produced by sustenacular cells and the granulosa cells provides further feedback regulation of fsh production.

transposons

aka transposable elements. both prokaryotes and eukaryotes have mobile genetic elements in their genomes. its thought that many eukaryotic transposons are degenerate (old and defective) retroviruses. "genetic mobility" means that these short segments can jump around the genome. transposons can cause mutations and chromosome changes such as inversions, deletions, and rearrangements there are 3 common types of transposons, each with a different structure. 1 IS element. simplest type. is composed of a transposase gene flanked by inverted repeat sequences. the structure of an example inverted repeat is shown on pg 88/phone. 2 some transposons are more complex, in that they also contain additional genes. for ex some transposons contain genes for antibiotic resistance. 3 finally, composite transposons have 2 similar or identical IS elements w a central region in between see pg 88/phone for pic of all those all transposons contain a gene that codes for a protein called transposase. this enzyme has "cut and paste" activity, where it catalyzes mobilization of the transposon (excision from the donor site) and integration into a new genetic location (the acceptor site). sometimes the transposon sequence is completely excised and moved, and sometimes its duplicated and moved, while still maintained at the original location. the inverted repeats are important for this mobilization. see pg 89/phone for pic many mobilizations have no effect bc the transposon inserts into a relatively unimportant part of the genome. however, transposons can cause mutations if they jump into an important part of the genome when transposons are mobilized, they can insert in any part of the genome, and this can affect gene expression or cause mutations. they can jump into a promoter and turn gene expression off. they can jump into a protein-coding region and disrupt (or mutate) the sequence. they can also jump into regulatory parts of the genome and ramp up gene expression at a nearby site. in addition to jumping around the genome, transposons can cause structural changes to chromosomes when they work in pairs. directionality of the transposon is important here, as it determines what happens to the chromosome. if a chromosome has 2 transposons with the same direction, the transposons can line up beside each other, so they are parallel. this causes the chromosomal segment btwn them to loop around. recombination occurs btwn the transposons, and this causes deletion of the dna btwn the 2 transposons. the original chromosome therefore completely loses the dna segment btwn the transposons (a deletion). the segment of dna that is lost takes one transposon with it, meaning it can actually jump back into the genome somewhere else, causing chromosome rearrangement: one chunk of a chromosome has moved to a new location in the genome. see pg 90/phone if a chromosome has 2 transposons with inverted orientations, they can again pair and align with each other. after recombination, the sequence of dna between the 2 transposons ends up inverted see pg 90/phone diploid organisms have 2 copies of each gene, and generally a mutation in one copy is tolerated as long as the other copy of the gene is normal. however, if a deletion removes the normal copy of the gene, the only remaining copy is the mutated version. this is referred to as loss of heterozygosity. this makes the locus hemizygous: there is only one gene copy in the diploid organism. if the remaining allele is mutant or defective, all gene expression of the normal gene product is lost. for ex, hereditary retinoblastoma is a type of retinal cancer common in young children. it occurs when a child receives a flawed copy of the tumor suppressor Rb1 from one parent, and a loss of heterozygosity event leads to loss of the normal allele (from the other parent). with no functional Rb protein (due to having only one copy of Rb1, and it being a flawed or mutant copy), the child almost invariably develops retinoblastoma

incomplete dominance

alleles display neither dominant nor recessive patterns of expression. phenotype of a heterozygote is a blended mix of both alleles. alleles for that trait are given different, upper-case letters.

southern blotting

allows you to detect the presence of specific sequences within a heterogeneous sample of dna. allows you to isolate and purify target sequences of dna for further study

conjugation (bacteria)

although bacteria reproduce asexually, they have developed conjugation to exchange genetic information. in conjugation, bacteria make physical contact and form a bridge btwn the cells. one cell copies dna, and this copy is transferred through the bridge to the other cell. a key to bacterial conjugation is an extrachromosomal element known as the F (fertility) factor. bacteria that have the F factor are male, or F+, and will transfer the F factor to female cells. bacteria that do not contain the F factor are female, F-, and will receive the F factor from male cells to become male. [if all cells in a population are F+, will conjugation occur? - no. conjugation occurs only btwn F+ (male) and F- (female)] the F factor is a single circular dna molecule. although much smaller than the bacterial chromosome, the F factor contains several genes, many of which are involved in conjugation itself. [which cell will produce sex pili: the male cell of the female cell? - the male cell contains the F factor that encodes the genes for pili production and will produce pili] after the male cell produces sex pili and the pili contact a female cell, a conjugation bridge forms. the F factor is replicated and transferred from the F+ to the F- cell. dna transfer btwn F+ and F- cells is unidirectional; it occurs in one direction only. although the F factor is an extrachromosomal element, it does sometimes become integrated into the bacterial chromosomes through recombination. a cell with the F factor integrated into its genome is called an Hfr (high frequency of recombination) cell. [will an Hfr cell undergo conjugation with an F- cell? - yes. all of the genes of the F factor are still present and expressed normally in the Hfr cell] when an Hfr cell performs conjugation, replication of the F factor dna occurs as in F+ cells with the extra chromosomal F factor. since the F factor dna is integrated in the bacterial genome in Hfr cells, replication of F factor dna continues into bacterial genes, and these too can be transferred into the F- cell see pg 159/phone for pics

anatomy of respiratory zone

alveolus - where gases diffuse alveoli are tiny sacs w very thin walls, so thin they're transparent. wall of the alveolus is only one cell thick, except where capillaries pass across its outer surface. the duct leading to the alveoli is an alveolar duct, and its walls are entirely made of alveoli. the alveolar duct branches off a respiratory bronchiole. this is a tube made of smooth muscle, just like the terminal bronchioles, but w one difference: respiratory bronchiole has a few alveoli scattered in its walls. this allows it to perform gas exchange, so its part of the respiratory zone.

which one of the following proteins would not be found within the nucleus? A. a protein component of the large ribosomal subunit B. a factor required for splicing C. a histone D. an aminoacyl tRNA synthetase

aminoacyl trna synthetases are enzymes that function in the cytoplasm to attach amino acids to their respective trnas. they are never needed in the nucleus and wouldn't be found there (choice D is correct). the protein components of ribosomes are synthesized in the cytoplasm and then imported into the nucleus to be assembled in the nucleolus (choice A would be found in the nucleus and can be eliminated). splicing occurs in the nucleus, so anything involved in splicing would be found there (choice B can be eliminated). histones are used for dna packaging and would be found in the nucleus (choice C can be eliminated)

epithelium

an epithelial cell layer is a layer of cells which lies "upon nipples" of a type of extracellular connective tissue called basement membrane (epi means "upon," and -thele means "nipple," in the sense of a small bump). the basement membrane is a strong molecular sheet made of collagen. under the microscope the basement membrane under the epithelial cells has "bumps" which make epithelial cell layers easy to recognize. the intestinal wall is lined w a type of tissue called epithelium. the layer of epithelial cells in the gut forms a tight seal, preventing items from moving freely btwn the intestinal lumen and the body; this is accomplished by tight junctions. epithelial cells in the skin are held together tightly but do not form a complete seal; this is accomplished by desmosomes. some specialized cell types, such as heart muscle cells, are connected by holes called gap junctions that allow ions to flow back and forth btwn them. see pg 207/phone for cell junctions

adh and bp

an inc in adh would lead to increased retention of water, increased blood volume, increased bp ace inhibitors rectify high bp. angiotensin converting enzyme is the enzyme that converts angiotensin I into angiotensin II, a very powerful vasoconstrictor and stimulator of aldosterone release. ACE is part of the pathway to increase bp; inhibiting it would thus dec bp. dec in aldosterone rectifies high bp. aldosterone causes increased sodium reabsorption at the distal tubule; not only does water passively follow the salt as it is reabsorbed, but the resulting increase in blood osmolarity triggers the release of adh, leading to additional water retention. this increases blood volume and pressure. therefore, a decrease in aldosterone would cause opposite effects and a reduction in blood pressure.

capsule

another attribute which only some bacteria have is the capsule or glycocalyx. this is a sticky layer of polysaccharide "goo" surrounding the bacterial cell and often surrounding an entire colony of bacteria. it makes bacteria more difficult for immune system cells to eradicate. it also enables bacteria to adhere to smooth surfaces such as rocks in a stream or the lining of the human respiratory tract

endocytosis and exocytosis

another mechanism used to transport material through the plasma membrane is within membrane-bound vesicles that fuse with the membrane. exocytosis is a process to transport material outside of the cell in which a vesicle in the cytoplasm fuses with the plasma membrane, and the contents of the vesicle are expelled into the extracellular space. the materials released are products secreted by the cell, such as hormones and digestive enzymes. endocytosis is the opposite of exocytosis: generally, materials are taken into the cell by an invagination of a piece of the cell membrane to form a vesicle. again the cytoplasm is not allowed to mix with the extracellular environment. the new vesicle which is formed is called an endosome. there are 3 types of endocytosis: 1 phagocytosis 2 pinocytosis 3 receptor-mediated endocytosis see pg 201/phone for pic

hormones in female reproductive system

anterior pituitary and the hypothalamus play a role in the menstrual cycle by regulating the secretion of estrogen and progesterone from the ovary. estrogen and progesterone then regulate the events in the uterus. summary: 1 GnRH from the hypothalamus stimulates the release of fsh and lh from the anterior pituitary. 2 under the influence of fsh the granulosa and thecal cells develop during the follicular phase and secrete estrogen. secretion of GnRH, fsh, and lh is initially inhibited by estrogen; however, estrogen, which increases throughout the follicular stage, reaches a threshold near the end of this phase and has a positive effect on lh secretion. 3 this sudden surge in lh causes ovulation. after ovulation lh induces the follicle to become the corpus lute and to secrete estrogen and progesterone (this marks the beginning of the secretory phase). if pregnancy doesn't occur, the combined high lvls of estrogen and progesterone feedback to strongly inhibit secretion of GnRH, fsh, and lh. when lh secretion drops, the corpus lute regresses, no longer secretes estrogen or progesterone, and menstruation occurs.

temperature for bacterial growth

anther characteristic of bacteria used to categorize them is their ability to tolerate environmental variables, such as temperature. though bacteria as a group can grow at a wide range of temperatures, each species has an optimal growth temperature. if the temperature is too high or too low, bacteria fail to grow and may be killed, hence the use of boiling to kill bacteria and refrigeration to slow bacterial growth and prevent food spoilage. most bacteria favor mild temperatures similar to the ones that humans and other organisms favor (30 degrees celsius); they are called mesophiles (moderate temperature lovers). thermophiles (heat lovers) can survive at temps up to 100 degrees Celsius in boiling hot springs or near geothermal vents in the ocean floor. bacteria that thrive at very low temps (near 0 degrees C) are termed psychrophiles (cold lovers).

■ Arterial and venous systems (arteries, arterioles, venules, veins) o Structural and functional differences o Pressure and flow characteristics

arteries are vessels that carry blood away from heart at high pressure, and vessels that carry blood back toward the heart at low pressure are veins. as arteries pass farther from the heart the pressure of blood decreases and they branch into increasingly smaller arteries called arterioles. the arterioles then pass into capillaries, very small vessels just wide enough for single blood cell. arterioles have smooth muscle in their walls that can act as a control valve to restrict or increase the flow of blood into the capillaries of tissues. the capillaries have thin walls made of a single layer of cells and are designed to allow the exchange of material btwn the blood and tissues. after passing through capillaries, blood collects in small veins called venues, and then into the veins leading back to the heart. except for the largest vessels near the heart, veins lack a muscular wall.

prions

as infectious agents, prions don't strictly follow the central dogma bc they are self-replicating proteins. (why does this violate the central dogma? - the central dogma states that information flows in its nucleotide form from dna to rna (transcription) and then in its amino acid form from rna to protein (translation). prions take both transcription and translation out of the process and have proteins being shaped based on other proteins hence the term "self-replicating"). the prion itself is a misfolded version of a protein that already exists. see pg 145/phone when the normally folded protein (designated PrPc) comes into contact with the prion (designated PrPSc), the prion acts as a template; the shape of the normal protein is altered and it too becomes infectious. prions are responsible for a class of diseases in mammals referred to as the transmissible spongiform encephalopathies (TSEs). these diseases cause degeneration in the nervous system, especially the brain where characteristic holes develop, and are always fatal. the misfolded proteins are found in the nervous tissues and are very resistant to degradation by chemicals or heat, making them hard to destroy. bovine spongiform encephalopathy (BSE, commonly called mad cow disease) is the prion disease found in cows; this was originally transmitted to cows from sheep bc all types of tissue from sheep, including the brain, is used as a supplement in the feed for other farm animals. though much less common, the disease kuru follows a similar transmission path in humans; it is only found in a limited number of tribes where consumption of the body, particularly of the brain, is part of honoring the dead (since identification of the transmission route, this practice has stopped and kuru has virtually disappeared) however prion diseases can also be genetically linked, through mutations in the gene that codes for the prion protein. for ex, fatal familial insomnia (FFI) is an autosomal dominant condition inherited on chromosome 20, and Creutzfeldt Jakob disease (CJD) is also inherited. it is also possible for these diseases to arise spontaneously (through mutation) in someone with no prior family history. in general, however, prion diseases are very rare, striking only 1-2 people per million whether transmitted, inherited, or spontaneously arising, prion diseases are characterized by their very long incubation periods, which can be several months to years in animals and several years to decades in humans. the misfolded proteins cause the destruction of neurons, particularly in the central nervous system, leading to loss of coordination, dementia, and death. diagnosis is difficult, in part bc of the long incubation periods and in part bc the symptoms can be indicative of other conditions

the lytic cycle of phages

as soon as the phage genome has entered the host cell, host polymerases and/or ribosomes begin to rapidly transcribe and translate it. one of the first viral gene products made is sometimes an enzyme called hydrolase, a hydrolytic enzyme that degrades the entire host genome. (hydrolase is an example of an early gene; one of a group of genes that are expressed immediately after infection and which includes any special enzymes required to express viral genes.) then multiple copies of the phage genome are produced (using the dNTPs resulting form degradation of the host genome), as well as an abundance of capsid proteins. next, each new capsid automatically assembles itself around a new genome. finally, an enzyme called lysozyme is produced. an example of a late gene, lysozyme is also present in human tears and saliva. it destroys the bacterial cell wall. bc osmotic pressure is no longer counteracted by the protection of the cell wall, the host bacterium bursts ("lyses," hence the name lytic), releasing about 100 progeny viruses, which can begin another round of the cycle. (if lysozyme were an early gene, would this be advantageous to the virus? - no the host cell would lyse before the phage had time to replicate and assemble). see pg 140/phone for lytic cycle

which one of following best describes selective reabsorption b in normal individuals the concentration of glucose which is filtered into the tubule is identical to the serum [glucose]. of the filtered glucose, 100% is reabsorbed by the epithelial cells of the tubule

as stated in the section on filtration, glucose is small enough that all of it freely passes through the glomerular basement membrane, as are ions, amino acids, and water. however even though glucose is filtered into the tubule, it must be reclaimed into the bloodstream or we would constantly lose glucose into the urine. 100% of filtered glucose is normally reclaimed and in no instance is glucose ever transported into the filtrate. note that in diabetes, the blood glucose llv is so high that the cotransporteris responsible for glucose reabsorption become saturated and large amounts of glucose are left in the urine

renal regulation of bp

at juxtaglomerular apparatus are juxtaglomerular cells, baroreceptors. dec in bp, secrete an enzyme called renin. renin catalyzes conversion of angiontensinogen into angiotensin I which is further converted to angiotensin II by angiotensin converting enzyme ACE in the lungs. angiotensin II is a powerful vasoconstrictor that immediately raises bp. it also stimulates release of aldosterone, which helps raise bp by inc sodium and indirectly water retention. macula densa cells are chemoreceptors, and monitor filtrate osmolarity in distal tubule. when filtrate osmolarity decreases, indicating reduced filtration rate, cells of macula dense stimulate JG cells to release renin. macula densa also causes direct dilation of afferent arteriole inc blood flow to and thus bp and filtration rate in the glomerulus.

energy storage in myofiber

atp provides energy for contraction and supplies must be regenerated by glucose catabolism. however glycolysis and tca cycle aren't fat enough to keep pace w rapid atp utilization during extending contraction. there is a need for an intermediate-term energy storage molecule. creatine phosphate is that molecule. during contraction, its hydrolysis drives the regeneration of atp from ADP + Pi. muscle is a highly aerobic tissue w abundant mitochondria. myoglobin is a globular protein and is similar to one of the 4 subunits of hemoglobin. the role of myoglobin is to provide an oxygen reserve by taking O2 from hemoglobin and then releasing it as needed. nonetheless during prolonged contraction supply of oxygen runs low and metabolism becomes anaerobic. lactic acid is produced and moves into bloodstream, causing a drop in pH. the liver picks up this lactate and converts it into pyruvate, which can be used in various pathways. cramps may result from exhaustion of energy supplies (temporary lack of atp) in muscle cells. rigor mortis is rigidity of skeletal muscles which occurs soon after death. it results from complete atp exhaustion; without atp myosin heads cannot release actin, and the muscle can neither contract nor relax.

bacterial shape

bacteria are often classified according to their shape. the 3 shapes and their proper names are: shape round rod-shaped spiral-shaped proper name (plural) cocci bacilli spirochetes or spirilla proper name (singular) coccus bacillus spirochete, spirillum see pg 149/phone for table

gram staining of the cell wall

bacteria can be classified according to 2 different types of cell wall. the method of classification is derived from the extend to which bacteria turn color in a procedure called Gram staining. the 2 groupings are gram-positive, which stain strongly (a dark purple) and gram-negative bacteria, which stain weakly (a light pink) gram-positive bacteria have a thick peptidoglycan layer outside of the cell membrane and no other layer beyond this. gram-negative bacteria have a thinner layer of peptidoglycan in the cell wall but have an additional out layer containing lipopolysaccharide. the intermediate space in gram-negative bacteria btwn the cell membrane and the outer layer is termed the periplasmic space, in which are sometimes found enzymes that degrade antibiotics. the increased protection of gram-negative bacteria from the environment is reflected in their weak staining, as well as in their increased resistance to antibiotics. see pg 150/phone for pic

nutrition for bacterial growth

bacteria can be classified according to their carbon source and their energy source. "troops" is a latin root meaning "eat." autotrophs utilize CO2 as their carbon source. heterotrophs rely on organic nutrients (glucose, for example) created by other organisms. chemotrophs get their energy from chemicals. phototrophs get their energy from light; not only plants but also some bacteria do this. each bacterium is either a chemotroph or a phototroph and is either an autotroph or a heterotroph. there are thus 4 types of bacteria: 1 chemoautotrophs build organic macromolecules from CO2 using the energy of chemicals. they obtain energy by oxidizing inorganic molecules like H2S. 2 chemoheterotrophs require organic molecules such as glucose made by other organisms as their carbon source and for energy. (we are chemoheterotrophs) 3 photoautotrophs use only co2 as a carbon source and obtain their energy from the sun (plants are photoautotrophs) 4 photoheterotrophs are odd in that they get their energy from the sun, like plants, but require an organic molecule made by another organism as their carbon source

genetic exchange btwn bacteria

bacteria reproduce asexually, but genetic exchange is evolutionarily favorable bc it fosters genetic diversity. bacteria have 3 mechanisms of acquiring new genetic material: transduction, transformation, and conjugation. note that none of these has anything to do with reproduction! transduction is the transfer of genomic dna from one bacterium to another by a lysogenic phage. transformation refers to a peculiar phenomenon: if pure dna is added to a bacterial culture, the bacteria internalize the dna in certain conditions and gain any genetic information in the dna. conjugation appears most likely to be related to normal bacterial function, however

bacterial life cycle

bacteria reproduce asexually. in asexual reproduction, there is no meiosis, no meiotic generation of haploid gametes, and no fusion of gametes to form a new individual organism. instead each bacterium grows in size until it has synthesized enough cellular components for 2 cells rather than one, replicates its genome, then divides in 2. this process in bacteria is also known as binary fission (fission means "to split"). [in prokaryotes, does reproduction increase genetic diversity? - no. each daughter cell is identical to the parent cell (assuming no mutation took place). if a eukaryote reproduces strictly by asexual reproduction, how will this affect the genetic diversity of a population? - many eukaryotes reproduce asexually. sexual reproduction allows for generation of new allelic combinations through meiotic recombination and random union of gametes. without this, diversity will decrease over time. how is asexual reproduction in a eukaryote different from asexual reproduction in a prokaryote? - in eukaryotes, asexual reproduction occurs through mitosis. prokaryotes don't go through mitosis.] although bacteria don't reproduce sexually, tho do possess a mechanism, termed conjugation, for exchanging genetic information. growth of bacterial populations is described in stages. under ideal conditions, bacterial population growth is exponential, meaning that the number of bacterial cells increases exponentially with time. this also means the log of the population size growths linearly with time, hence the name log phase. [if 10 bacteria in log phase are placed in ideal growth conditions and the doubling time is 20 minutes, how many bacteria will there be after 4 hours? - since 4 hours is equal to 240 minutes, the bacteria will divide 12 times. therefore, one bacterium will produce 2^12 = 4096 bacteria after 12 divisions. since there are 10 bacteria initially, the total after 4 hours will be 10 x 2^12 = 40960] see pg 157/phone for pic of graph prior to achieving exponential growth, bacteria that weren't previously growing undergo a lag phase, during which cell division doesn't occur even if the growth conditions are ideal. (if growth conditions are ideal, why wouldn't cell division occur immediately? - cells that aren't growing aren't actively producing components that are needed for cell division, such as dNTPs. the lag period is a time when biosynthetic pathways are very actively producing new cellular components so that cells can then begin to divide) (will bacteria that are transferred from a culture that is in log phase to a fresh new culture show a lag phase? - no, since they will have all the gear necessary for population growth at the ready) as metabolites in the growth medium are depleted, and metabolic waste products accumulate, the bacterial population passes from log phase to stationary phase (in cultures, the stationary phase is usually cloudy, and clear cultures are not growing or in the lag phase), in which cells cease to divide for lack of nutrients. the maximum population at the stationary phase is referred to as the carrying capacity for that environment. in the last stages of the stationary phase, cell death may occur as a result of the medium's inability to support growth. (if bacteria are grown in a medium with glucose as the main source of energy, when will the glycolytic pathway be more active: during the lag phase or during the stationary phase? - the bacteria will use glucose during the lag phase to produce atp and cellular machinery. during this period, glucose is abundant, and the cell is actively performing biosynthesis, so glycolysis is very active. during the stationary phase, however, the glucose will be depleted, and the rate of metabolism will have slowed dramatically, so the rate of glycolysis will decrease as well)

restriction endonucleases

bacterial enzymes that recognize specific sequences of dna and cut the double-stranded molecule in 2 pieces. used to create recombinant dna

DNA more stable than RNA

bc of 2' deoxy structure and also due to the fact that it spontaneously forms a compact double-stranded helix

thyroid hormone

behaves like steroid hormone, receptor found within cells

dermis

beneath epidermis. consists of various cell-types embedded in a connective tissue matrix. it contains blood vessels that nourish both the dermis and the epidermis (the epidermis has no blood vessels of its own). the dermis also has sensory receptors, which convey info about touch, pressure, pain, and temp to the cns. also found in the dermis are sudoriferous (sweat) glands, sebaceous (oil) glands, and hair follicles. hairs consist of dead epithelial cells bound tightly together. some specialized regions of skin contain ceruminous (wax) glands (eg the external ear canal).

enzyme-linked immuno-sorbent assay (Elisa)

biochemical technique that utilizes antigen-antibody interactions to determine the presence of either antigens (like proteins or cytokines), or specific immunoglobulins (antibodies) in a sample (such as cells recovered from a tumor biopsy or a patients serum). when testing for the presence of a specific antigen, the wells are coated w an antibody specific for that antigen. then the sample is added, and if the antigen is present it will bind to the antibodies. the wells are washed and a secondary antibody (specific for the antigen) is added; the secondary antibody is linked to a detection enzyme. when testing for the presence of a specific antibody in a sample, the antigen (for which the antibody is specific) is first allowed to adhere directly to the wells. the sample is added and then mixed w enzyme-linked antibodies. Elisa can be used to screen patients for viral infections. for ex serum from a pt suspected to be infected w his is loaded into wells that are coated w hiv coat proteins. if the serum contains anti-hip antibodies (indicating infection), the antibodies will adhere to the proteins on the wells, bind enzyme-linked antibodies, and effect a color change.

passive transport

biochemical term that means diffusion. it refers to any thermodynamically favorable movement of solute across a membrane. another way to phrase this is to say that passive transport is any movement of solute down a gradient. no energy is required since the concentration gradient drives movement of the solute. there are 2 types of passive transport: simple diffusion and facilitated diffusion

o Glomerular filtration

blood from renal artery flows into afferent arterial which branches into a ball of capillaries known as glomerulus. from there the blood flows into an efferent arteriole. constriction of the efferent arteriole results in high pressure in the glomerulus, which causes fluid (essentially blood plasma) to leak out of the glomerular capillaries. the fluid passes through a filter known as glomerular basement membrane and enters Bowmans capsule. lumen of Bowmans capsule is continuous w lumen of rest of the tubule. substances which are too large to pass through glomerular basement membrane aren't filtered; they remain in the blood in the glomerular capillaries and drain into the efferent arteriole. (the glomerular basement membrane is actually a layer lining each capillary of the glomerulus.) examples are blood cells and plasma proteins. (ex glucose and sodium are present in filtrate in Bowmans capsule in concentrations similar to those seen in blood and can be reclaimed)

connective tissue (skeletal system)

bone is an example of connective tissue. connective tissue consists of cells and the materials they secrete. all connective tissue cells are derived from a single progenitor, the fibroblast. this name derives from its ability to secrete fibrous material like collagen, a strong fibrous protein. another important fibrous extracellular protein is elastin which gives tissue the ability to stretch and regain its shape. fibroblast derived cells include adipocytes (fat cells), chondrocytes (cartilage cells), and osteocytes (bone cells). connective tissue differs from other tissue types in body like epithelial muscle and nervous, bc it is primarily extracellular material w a few cells scattered in it (the other 3 tissue types are the opposite, mostly cellular w little extracellular material). the extracellular material is known as the matrix and consists of the fibers described above and ground substance, a thick, viscous material. the main ingredients of the ground substance are proteoglycans; these are large macropolymers consisting of a protein core w many attached carbohydrate chains. the carbohydrate chains are called glycosaminoglycans (GAGs) and like all carbohydrates, they are very hydrophilic. hence in the body they are always surrounded by a large amount of water ("water of solvation"). this gives tissues their characteristic thickness and firmness. for ex, dehydration results in saggy skin bc of decreased hydration of the ground substance in the extracellular matrix. there are 2 types of connective tissue: loose and dense. loose connective tissues are basically packing tissues, and include areolar tissue (the soft material located btwn most cells throughout the body) and adipose tissue (fat). dense connective tissue refers to tissues that contain large amounts of fibers (especially collagen), such as tendons, ligaments, cartilage, and bone. cartilage and bone are sometime classified as supportive connective tissues, bc of the role they play in physical support of body structures.

dispersive replication

both copies of the genomes were composed of scattered pieces of new and old dna

For each type of mutation, does it involve a change in genotype, phenotype, or both?

by definition, all mutations involve a change in the genotype. most mutations also cause a change in the phenotype, but in the case of conservative mutations it is a very subtle change that would be hard to detect

biological agents

can also cause mutations. for ex, although DNA polymerase has proofreading and correction abilities, it can still make a mistake. an incorrect base pair may be repaired, but if not, it will be passed onto all daughter cells. in this case, there is no mutagen. the mistake is spontaneous. viruses can also affect dna. lysogenic viruses insert into the genome of the host cell and this can cause mutations and disrupt genetic function. some viruses can cause cancer bc of this function. and finally, transposons can induce mutations.

rules of probability

can be a shortcut to using a punnet square to determine the probability of an outcome in a cross.

endothelial cell dysfunction

can lead to a number of pathogenic conditions, such as hypercholesterolemia, hypertension, inappropriate clot formation, and coronary artery disease and atherosclerosis. in fact, this dysfunction is key fo the development of atherosclerosis and predates any clinical vascular signs by several years

kidneys

can only eliminate small hydrophils dissolved in plasma. substances that must be excreted in the urine include urea, sodium, bicarbonate, and water. sodium bicarbonate and water aren't usually wastes but are when they are present at abnormally high concentrations. you begin to see that the kidney is not like the colon, a passive container for wastes waiting to be excreted. it is a sensitive regulatory that must keep concentrations at optimum levels, as opposed to simply dumping things. this is the homeostatic role of the kidneys. homeostasis refers to constancy of physiological variables.

colon (large intestine) ■ Large Intestine o Absorption of water o Bacterial flora o Structure (gross)

cecum appendix rectum anus anal sphincter colonic bacteria important for 2 reasons 1 presence keeps dangerous bacteria from proliferating due to competition for space and nutrients. 2 colonic bacteria supply us w vitamin K which is essential for blood clotting. no digestion takes place

local autoregulation

certain metabolic wastes have direct effect on arteriolar smooth muscle, causing it to relax. hence, when a tissue is underperfused wastes build up, and vasodilation occurs automatically. autoregulation is the principal determinant of coronary blood flow (blood supply to the heart); it generally overrides nervous input

liver

chemically modify wastes and releasing them into bile. deals w hydrophobic or large waste products which cannot be filtered out by the kidney. synthesizes urea and releases it into the bloodstream. urea is a carrier of excess nitrogen resulting from protein breakdwon. excess N must be converted to urea bc free NH3 is toxic. urea excreted in urine.

eukaryotic cilia and flagella

cilia are small hairs on the cell surface which move fluids past the cell surface. ex mucociliary escalator moves mucus toward mouth. a flagellum is a large tail which moves the cell by wiggling. the only human cell which has a flagellum is the sperm. cilia are small and flagella are long, but they have the same structure, w a "9+2" arrangement of microtubules. nine pairs of microtubules form a ring around 2 long microtubules in the center. each microtubules is bound to its neighbor by a contractile protein called dynein which causes movement of the filaments past one another. the cilium of flagellum is anchored to the plasma membrane by a basal body, which as the same structure as a centriole (a ring of nine triplets of microtubules). remember that the prokaryotic flagellum is different in structure, and its motion is driven by a different mechanism. see pg 206/phone for pic

RER

clocation of synthesis/modification of secretory, membrane-bound, and organelle proteins. 1 membrane surround

chi-square test

compare observed and expected data

polygenism

complex traits that are influenced by many different genes. ex height, weight

sudoriferous gland

composed of a tube like structure that originates in the dermis and leads through the epidermis to a pore on the surface of the skin. the purpose of sweat is to allow loss of excess heat by evaporation. sweat contains water, electrolytes, and urea. sweat glands are responsive to aldosterone. ppl living in hot climates sweat a lot, in order to conserve sodium, they have a high lvl of aldosterone, and thus their sweat does not waste salt.

intergenic regions

composed of noncoding dna; they may direct the assembly of specific chromatin structures and can contribute to the regulation of nearby genes, but many have no known function. tandem repeats and transposons are major components of intergenic regions

epidermis

composed of stratified (many layers) squamous epithelial cells. these cells are constantly sloughed off and then replenished by mitosis of cells at the deepest part of the epidermis, the stratum basale. a cell in this layer divides, and one of the resulting daughter cells moves outward. soon this cell will die and be pushed farther and farther outward by continued mitosis below, until it flakes away from the surface of the body. the significance of many layers of epithelial cells is that they provide a strong protective structure. another important facet of the stratified squamous cells of the epidermis is that they are keratinized. this means that as they die, they become filled w a thick coating of the tough, hydrophobic protein keratin. keratin helps make the skin waterproof. epidermal epithelial cells also contain melanin. this is a brown pigment, produced by specialized cells in the epidermis termed melanocytes, that helps absorb uv light of the sun to prevent damage to underlying tissues.

molality (m)

concentration in terms of moles of solute per mass (in kilograms) of solvent: Molality (m) = # moles of solute / # kg of solvent molality is particularly useful when measuring properties that involve temperature bc, unlike molarity, molality doesn't change w temperature. and since a liter of water has a mass of one kilogram, the molar and molal concentrations of dilute aqueous solutions are nearly the same. this is particularly true in biological systems, where the volume (essentially a cell) is very small and the solvent is always water.

molarity (M)

concentration of a solution in terms of moles of solute per volume (in liters) of solution: Molarity (M) = # moles of solute / # liters of solution concentration is denoted by enclosing the solute in brackets. for ex, [Na+] = 1.0 M indicates a solution whose concentration is equivalent to 1 mole of sodium ions per liter of solution

viroids

consist of a short piece of circular, single stranded rna (200-400 bases long) with extensive self-complementarity (ie it can base pair with itself to create some regions that are double stranded). generally they don't code for proteins and they lack capsids. some viroids are catalytic ribozymes, while others, when replicated, produce siRNAs that can silence normal gene expression. see pg 146/phone replication of some viroids shares similarity to the replication of rna viruses. a viroid rna-dependent rna polymerase synthesizes a (-) strand, which is circularized by an rna ligase derived from the host; this is then used as the round, rolling template to make more (+) copies that match the original RNA viroid sequence. an alternative to this mechanism leaves the (-) strand in a more linear state where it can still act as a template for (+) strand creation and the become circularized. in other cases, viroids somehow hijack the cell's dna dependent rna polymerase and direct it to read rna templates. this mechanism is not well understood most of the diseases caused by viroids are found in plants. the only human disease linked to viroids is hepatitis d. the hepatitis d viroid can only enter hepatocytes (liver cells) if it is contained in a capsid with a binding protein; since viroids don't have capsids, successful hepatitis d infection required coinfection with hepatitis b from which it derives its capsid

population

consists of members of a species that mate and reproduce with each other. they dont have to live together

constriction or dilation of smooth muscle in veins results in increased cardiac output?

constriction check answer**

lysosomes

contain acid hydrolase that digest various substances. 1 membrane surrounding lyse means cut. the lysosome is a membrane bound orgnalle that is responsible for the degradation of biological macromolecules by hydrolysis. lysosome proteins are made in the RER, modified in the golgi, and released in their final form from the trans face of the golgi. organelles such as mitochondria that have been damaged or are no longer functional may be degraded in lysosomes in a process termed autophagy (self-eating). lysosomes also degrade large particulate matter engulfed by the cell by phagocytosis (cell eating). for ex, macrophages of the immune system engulf bacteria and viruses. the particle or microorganism ends up in a phagocytic vesicle, which will fuse with a lysosome. finally, crinophagy refers to lysosomal digestion of unneeded (excess) secretory products. after hydrolsysi, the lysosome will release molecular building blocks into the cytoplasm for reuse. the enzymes responsible for degradation in lysosomes are called acid hydrolases. this name reflects the fact that these enzymes only hydrolyze substrates when they are in an acidic environment. this is a safety mechanism. the pH of the lysosome is around 5, so the acid hydrolases are active. but the pH of the cytoplasm if 7.4. if a lysosome ruptures, its enzymes will not damage the cell bc the acidic fluid will be diluted and the acid hydrolases will be inactivated. however if many lysosomes rupture at once, the cell may be destroyed.

nucleus

contain and protect dna; transcription; partial assembly of ribosomes. 2 membranes surroundng it one of the primary features of eukaryotic cells distinguishing them from prokaryotic cells is the nucleus. the nucleus contains the genome surrounded by the nuclear envelope that separates the contents of the nucleus into a distinc compartment, isolated from other organelles and from the cytoplasm. in prokaryotes the genome may be localized in the cell but without a nuclear envelope to form a separate compartment the genome remains accessible to the cytoplasm. in prokaryotes, replication, transcription and translation, and everything else all happens in the same compartment (they cytoplasm). in eukaryotes, replication, transcription, and splicing occurs in the nucleus, while translation occurs in the cytoplasm

copy number variation

copy-number variations CNVs are structural variations in the genome that lead to different copies of dna sections. large regions of the genome (10^3 to 10^6 base pairs) can be duplicated (increasing copy number) or deleted (decreasing copy number). the specific mechanism by which this occurs is not clear, but it may be due to misalignment of repetitive DNA sequences during synapsis of homologous chromosomes in meiosis. these changes therefore apply to much larger regions of the genome compared to snps. they are a normal part of our genome (0.4% of the genome can have CNV), but have also been associated with cancer and other diseases. genes involved in immune system function, as well as brain development and activity, are often enriched in CNVs

■ Kidney structure o Cortex o Medulla

cortex is outer region, inner region is medulla. medullary pyramids are pyramid shaped striations within medulla. this is from many collecting ducts. urine empties from collecting ducts and leaves medulla at tip of a pyramid known as a papilla (plural: papillae). each papilla empties into a space called a calyx (plural calyces). the calyces converge to form the renal pelvis, which is a large space where urine collects. renal pelvis empties into ureter.

speciation

creation of a new species

vagus nerve

dec heart rate and increase GI activity; part of the parasympathetic division of the autonomic nervous system. bundle of axons that end in ganglia on the surface of the heart, stomach, and other visceral organs. the many axons constituting this nerve are preganglionic and come from cell bodies located in the cns. on the surface of the heart and stomach they synapse w postganglionic neurons

ohms law

delta p = q x r pressure gradient from arterial system to venous system, Q is blood flow (cardiac output) R resistance pressure can be varied by inc the force (thus changing stroke volume) or rate (beats per minute) of cardiac contraction. what about resistance? the principal determinant of resistance is the degree of constriction of arteriolar smooth muscle, aka precapillary sphincters. if artiorlar smooth muscles contract, it becomes mroe difficult for blood to flow from arteries into capillaries; that is the resistnce goes up. the resistance of the entire systemic circuit is easily calculated using above equation in the form R = delta P/Q. we can measure delta P and Q, and then solve for R. this is peripheral resistance sympathetic nervous system controls peripheral resistance. basal lvl of pressure, which is good, is provided by constant lvl of norepinephrine released by millions of sympathetic postganglionic axons innervating precapillary sphincters. this constnat nervous input is adrenergic tone sympathetic system can inc overall peripheral resistance inc bp. can also divery blood from one tissue to another for fight or flight (to skeletal msucle from gut, etc)

pulmonary circulation

deoxygenated blood carried to lungs by pulmonary artery which has left and right branches. these large arteries branch many times eventually giving rise to a huge network of pulmonary capillaries, aka alveolar capillaries. each alveolus is surrounded by a few tiny capillaries which are just wide enough to permit the passage of rbcs and have extremely thin walls to permit diffusion of gases btwn blood and alveolus. the capillaries drain into venules, which drain into pulmonary veins. the lungs are supplied w lymphatic vessels as well. small increases in left atrial pressure have very little effect on the pulmonary circulation bc pulmonary veins can dilate, accommodating excess blood. however if the pressure in the left atrium inc above a certain lvl, the pressure will increase in pulmonary capillaries, and fluid (essentially blood plasma) will be forced out of the capillaries and into the surrounding lung tissue. fluid in the lungs resulting from increased blood pressure is pulmonary edema. normally the lymphatic system prevents pulmonary edema from developing by carrying interstitial fluid out of the lungs. CO2 is mosty carried in the blood as HCO3 - + H+, some is bound nonspecifically to Hb, a little can dissolve in plasma. the contribution of each individual gas to the total pressure is the partial pressure. the partial pressure of Gas X is Px. the total pressure is the sum of all partial pressures.

colligative properties

depend on the number of solute particles in the solution rather than the type of particle. for ex, when any solute is dissolved into a solvent, the building point, freezing point, and vapor pressure of the solution will be different from those of the pure solvent. for colligative properties, the identity of the particle is not important. that is, for a 1 M solution of any solute, the change in a colligative property will be the same no matter what the size, type, or charge of the solute particles. remember to consider the van't Hoff factor when accounting for particles: one mole of sucrose (i=1) will have the same number of particles in solution as 0.5 mol of NaCl (i=2) and therefore will have the same effect on a colligative property. thus we can consider the effective concentration to be the product iM (or im); this is the concentration of particles present. the 4 colligative properties well study are vapor-pressure depression, boiling point elevation, freezing point depression, and osmotic pressure

steroid hormones

derived from cholesterol, bind to receptors in the cytoplasm or nucleus, and bind to dna to alter transcription. effects tend to occur more slowly and are more permanent

o Counter-current multiplier mechanism (loop of Henle)

descending limb permeable to water but not to ions. water exits descending limb flowing into high osmolarity medullary interstitium. filtrate becomes concentrated. thin ascending limb is not permeable to water but passively loses ions from high osmolarity filtrate into renal medullary interstitium. additionally thick ascending limb actively transports salt out of filtrate into medullary interstitium, and the medullary interstitium becomes very salty. this is important bc medulla will suck water out of collecting duct by osmosis whenever collecting duct is permeable to water (presence of ADH.) *loop of henle is counterurrent multiplier that makes medulla v salty and that this facilitates water reabsorption from collecting duct. this is how kidney is capable of making urine w a much higher osmolarity than plasma. descending limb of loop of henle is permeable to water but not to ions; water leaves the filtrate thereby concentrating it. the ascending limb is permeable to ions but not to water. Na+ K+ and Cl- are actively transported out of the filtrate and K+ is passively transported, concentrating the renal medulla. vasa recta: vasa recta form loop that helps maintain high conc of salt in medulla. ascending portions of vasa recta are near descending limb of loop of henle and thus carry off the water that leaves the descending limb. also vasa recta are branches of efferent arterioles. the vasa recta are "eager" to reabsorb water bc blood they contain is like coffee grinds which have been drained. the important thing to remember is vasa recta return to bloodstream any water that is reabsorbed from filtrate. bc blood in vasa recta moves opposite direction of filtrate in the nephron, vasa recta perform countercurrent exchange.

SER

detoxification and glycogen breakdown in liver; steroid synthesis in gonads. 1 membrane surrounding lipid synthesis

karyotype

display of an organism's genome. cell frozen during metaphase, chromosomes stained, photograph taken. homologues paired, entire genome examined. see pg 210/phone

excretion

disposal of waste products

Concentration of urine (concentration and dilution)

distal nephron includes DCT and collecting duct. controlled by 2 hormones, ADH and aldosterone 1 ADH: dehydrated, volume of fluid low and solute concentration in blood is high. so need to make small amounts of highly concentrated urine. under conditions of low blood volume and high blood osmolarity, antidiuretic hormone ADH or vasopressin is released by posterior pituitary. it prevents diuresis which is water loss in the urine by inc water reabsorption in distal nephron. this is accomplished by making the distal nephron (primarily the collecting duct) permeable to water. without adh its impermeable to water. water flows into kidney picked up by peritubular capillaries and thus returned to the blood. a drop in bp also cause ADH release. drinking a lot of water, no ADH secreted. collecting duct not permeable to water. any water in the filtrate remains in the tubule and is lost in the urine, or diuresed. alcohol inhibits ADH secretion by posterior pituitary. 2 aldosterone: bp low, aldosterone released by adrenal cortex. it causes increased reabsorption of Na+ by the distal nephron. the result is inc plasma osmolarity, leads to inc thirst and water retention, which raises the blood pressure. the fact that inc serum [Na+] inc bp is the reason ppl w high bp have to avoid salty foods.] when the blood pressure is high, aldosterone is not released. so sodium is lost in the urine. plasma osmolarity and eventually bp fall. other triggers for release of aldosterone are low blood osmolarity low blood volume and angiotensin II. ADH and aldosterone work together to inc bp. first aldosterone causes sodium reabsorption which results in increased plasma osmolarity. this causes ADH to be secreted which results in inc water reabsorption and thus increased plasma volume.

double-strand break repair

dna double-strand breaks DSBs can be caused by reactive oxygen species, ionizing radiation, uv light or chemical agents. cells have 2 pathways to help in dab repair: homologous recombination and non homologous end-joining. the goal of both is to reattach and fuse chromosomes that have come apart bc of DSB. if done incorrectly, this can lead to deletions (where genetic information is lost) or translocations (where chromosome segments move to other chromosomes)

the role of dna

dna encodes and transmits the genetic information passed down from parents to offspring. before 1944 it was believed that protein rather than dna carried genetic info since proteins have an alphabet of 20 letters (amino acids) while dna's alphabet has only 4 letters (the 4 nucleotides). but in that year, Oswald Avery showed that dna was the active agent in bacterial transformation. in short this means he proved that pure dna from one type of e coli bacteria could transform e coli of another type, causing it to acquire the genetic nature of the first type. later Hershey and chase proved that dna was the active chemical in the infection of e coli bacteria by bacteria T2

controlling gene expression at the dna lvl

dna methylation and chromatin remodeling gene dose imprinting X chromosome inactivation

desmosomes

do not form a seal, but merely hold cells together; they are also known as spot desmosomes bc they are concise points, not bands all the way around the cell. composed of fibers that span the plasma membranes of 2 cells. inside each cell, the desmosome is anchored to the plasma membrane by a plaque formed by the protein keratin. intermediate filaments of the cytoplasm attach to the inside of the desmosome. desmosomes don't freely diffuse in the plane of the plasma membrane, as suggested by the fluid mosaic model, bc they are anchored in place by intermediate filaments of the cytoskeleton. the fluid mosaic model is an idealization describing plasma membrane in pure form. in the real cell membrane, things are highly organized.

G-protein-linked receptor

does not directly transduce its signal, but transmits it into the cell w the aid of a second messenger. this is a chemical signal that relays instructions from cell surface to enzymes in cytoplasm. most important second messenger is cyclic amp cAMP. it is known as a universal hunger signal bc it is the second messenger of the hormones epinephrine and glucagon, which cause energy mobilization (glycogen and fat breakdown). second messengers such as cAMP allow a much greater signal than receptor alone produces. an epinephrine molecule activates one gpl receptor which activates many G proteins, each G protein activates many adenylyl cyclase enzymes, each adenylyl cyclase makes lots of cAMP from atp, each cAMP activates many cAMP-dPK, and each cAMP-dPK phosphorylates many enzymes. some of these enzymes will be activated, and others inactivated by phosphorylation, w the end result that the entire cell harmoniously works toward the same goal: energy mobilization. see pg 203/phone for pic 1. epinephrine arrives at the cell surface and binds to a specific g-protein-linked receptor 2. the cytoplasmic portion of the receptor activates g-proteins, caursing gdp to dissociate and gtp to bind in its place 3. the activated g-proteins diffuse through the membrane and activate adenylyl cyclase 4. adenylyl cyclase makes cAMP from ATP 5. cAMP activates cAMP-dependent protein kinases (cAMP-dPK) in the cytoplasm 6. cAMP-dPK phosphorylates certain enzymes, w the end result being mobilization of energy. for ex, enzymes necessary for glycogen breakdown will be activated, while enzymes necessary for glycogen synthesis will be inactivated, by cAMP-dPK phosphorylation. there are differnt types of g protein linked receptors. the one depicted above (steps and pic) is a stimulatory one. its g protein would be denoted Gs. inhibitory g protein linked receptors activate inhibitory g proteins Gi which serve to inactivate adenylyl cyclase instead of activating it. in this way different hormones can modulate each other's effects. there are also g protein linked receptors which have nothing to do w cAMP. instead their G proteins activate an enzyme called phospholipase C, initiating a different second messenger cascade, which results in an increase in cytoplasmic Ca2+ lvls. the common theme shared by all g protein based signal transduction systems: is their reliance on a g protein, which is a signaling molecule that binds GTP. some gpcrs activate adenylyl cyclase (enzyme) and others inhibit it. this depends on the cell, the ligand, and many other factors. **understand these key notions: cAMP as a second messenger, signal transduction, and signal amplification. the remaining details arent important for the mcat

cancer (mutations)

driven by mutation accumulation. these mutations can either be inherited, or can be caused by carcinogen exposure. a carcinogen is a mutagen that is directly involved in causing cancer. tumors typically have hundreds of mutations, ranging from point mutations to massive chromosomal changes. these mutations are often in oncogenes and tumor suppressors. an oncogene is a gene that can cause cancer when it is mutated or expressed at high lvls. tumor suppressors are the opposite in that their deletion (or expression at decreased lvls) can cause cancer. some mutations will drive tumor growth and are highly selected for. these mutations are the most promising target for developing cancer treatments, as the cancer cells rely on these mutations for growth

at what stage during meiosis are different alleles of a gene separated?

during meiosis I, at the time when homologous chromosomes separate

Hormonal changes during pregnancy

during pregnancy ovulation should be prevented. the way ovulation is prevented is for the constant high lvls of estrogen and progesterone seen during pregnancy to inhibit secretion of lh by the pituitary; no LH surge, no ovulation. constant high lvls of estrogen inhibit lh release. the result is pregnancy without continued ovulation. the secondary result is: when the corpus luteum secretes a lot of estrogen and progesterone during the menstrual cycle, lh lvls drop, causing the corpus luteum to deg\enerate. the point is that the corpus luteum degenerates unless fertilization has occurred. how can pregnancy occur? if pregnancy is to occur, the endometrium must be maintained bc it is the site of gestation (ie where the embryo lives and is nourished). if fertilization takes place within a few days a developing embryo becomes implanted in the endometrium and a placenta begins to develop. the chorion is the portion of the placenta that is derived from the zygote. it secretes human chorionic gonadotropin hCG, which can take the place of LH in maintaining the corpus luteum. in the presence of hCG, the corpus luteum doesn't degenerate the estrogen and progesterone lvls stay elevated, and menstruation doesn't occur. hCG is the hormone tested for in pregnancy tests bc its presence absolutely confirms presence of an embryo. release of oxytocin from posterior pituitary combined w pressure of fetal head inc uterine contractility to expel baby from uterus, make a pos feedback loop progesterone released early in pregnancy to dec uterine contractility

conduction system

each heartbeat begins as action potential in sa node, then spreads throughout atria, causing them to contract and fill the ventricles with blood. the action potential also spreads down the special conduction pathway which transmits action potentials very rapidly without contracting. the pathways connects the sa node to the atrioventricular node. since this pathway connects the 2 nodes, its the internodal tract. note that while the impulse travels to the AV node almost instantaneously, it spreads through the atria more slowly, bc contracting heart muscle cells pass the impulse more slowly than specialized conduction fibers. at the AV node, the impulse is delayed slightly, then passes from the node to the ventricles via conduction pathway again. this part of the conduction pathway is known as the AV bundle (bundle of His). av bundle divides into right and left bundle branches, and then into purkinje fibers, which allow the impulse to spread rapidly and evenly over both ventricles. note that the purkinje fibers spread over the inferior portion of the ventricles (apex of the heart). result is that this region of the ventricles contracts first, and blood is pushed toward the superior region of the heart (the base) where the valves and arteries are.

pleural space and lung elasticity

each lung is surrounded by 2 membranes, or pleura: the parietal pleura, which lines the inside of the chest cavity, and the visceral pleura, which lines the surface of the lungs. btwn the 2 pleura is a very narrow space called the pleural space. the pressure in the pleural space (the pleural pressure) is negative, meaning that the 2 pleural membranes are drawn tightly together by a vacuum. this negative pressure keeps the outer surface of the lungs drawn up against the inside of the chest wall. additionally a thin layer of fluid btwn the 2 pleura helps hold them together through surface tension inspiration is caused by muscular expansion of chest wall which draws lungs outward, air enters. lungs expand along w chest due to negative pressure in pleural space. the expansion of the chest during inspiration is driven primarily by contraction of the diaphragm, a large skeletal muscle that is stretched belwo the ribs btwn the abdomen and chest cavity. when resting the diaphragm is shaped like a dome bulding upward into the chest cavity. when it contracts, diaphragm flattens and draws chest cavity downward, forcing it and the lungs to expand. the external intercostal muscles btwn the ribs also contract during inspiration, pulling the ribs upward and further expanding the chest cavity. inspiration is an active process, requiring contraction of muscles to occur. resting expiration, is a passive process where no muscle contraction is required. when the diaphragm and rib muscles relax, the elastic recoil of the lungs draws the chest cavity inward, reducing the volume of the lungs and pushing air out of the system into the atmosphere. during exertion (or at other times when a more forcible exhalation is required) contraction of abdominal muscles helps the expiration process by pressing upward on the diaphragm further shrinking the size of the lungs and forcing more air out. this is forced expiration and is an active process.

islets of langerhans

endocrine cells of the pancreas

endotoxins vs exotoxins

endotoxins are normal components of the outer membrane of gram-negative bacteria that aren't inherently poisonous. however they cause our immune system to have such an extreme reaction that we may die as a result. endotoxins cause the most trouble when many bacteria die and they disintegrated outer membranes are released into the circulation. when this occurs, cells of the immune system release so many chemicals that the patient goes into septic shock, in which much of the aqueous portion of the blood is leaked into the tissues causing a drop in blood pressure, and other problems, which may be fatal. endotoxins can have various chemical structures, including lipopolysaccharide, which contains sugars bound to lipids. exotoxins are very toxic substances secreted by both gram-negative and gram-positive bacteria into the surrounding medium. exotoxins hep the bacterium compete with other bacterial species, such as normal inhabitants of the mammalian gut. some diseases that are caused by exotoxins are botulism, diphtheria, tetanus, and toxic shock syndrome

functions of parathyroid hormone

enhancing breakdown of bone by osteoclasts and the release of calcium into the bloodstream enhancing the reabsorption of calcium in the nephrons of the kidneys enhancing the absorption of calcium in the small intestine

pepsin

enzyme

renin

enzyme released by juxtaglomerular cells in kidney

■ Pancreas o Production of enzymes o Transport of enzymes to small intestine

enzymes released into duodenum for digestion. pancreatic amylase hydrolyzes polysaccharides to disaccharides. pancreatic lipase hydrolyzes triglycerides at surface of a micelle. nucleases hydrolyze dietary DNA and RNA. several different pancreatic proteases are responsible for hydrolyzing polypeptides to di and tripeptides. pancreatic proteases are secreted in their inactive zymogen forms. trypsinogen is a zymogen converted to active form trypsin by enterokinase, an intestinal enzyme. other pancreatic enzymes are then activated by trypsin. these include chymotrypsinogen (active form chymotrypsin), procarboxypeptidase (active form carboxypeptidase), and procollagenase (active form collagenase) hormones control pancreatic secretion of enzymes cholecystokinin secreted by duodenum causes pancreas to secrete. secretin, also released by duodenum, causes pancreas to secrete water and bicarbonate (high pH). parasympathetic nervous system activation increases pancreatic secretion; sympathetic activation reduces it.

o Erythrocyte production and destruction; spleen, bone marrow

erythropoietin - hormone made in kidney. stimulates abc production in bone marrow. aged abcs are eaten by phagocytes in spleen and liver. erythrocyte is a cell but has not nucleus or organelles. does require energy of atp for processes like ion pumping and maintenance of cell structure during 120 day lifetime in bloodstream relies on glycolysis for atp synthesis bc no mitochondria. high surface area achieved by flat biconcave shape (like a delated basketball). able to carry oxygen bc contains hemoglobin

plasma membrane

evolution of life most likely began with a separation of inside from outside. once this had occurred, processes in the cell could increase their orderliness despite the entropic chaos of the surroundings. an alternate hypothesis is that life began w self-replicating rna floating free in the ocean. as it grew more complex, this early genome would require protection. in any case, the separation of the cytoplasm from the extracellular environment was a major milestone in evolution. bacteria, plants and fungi accomplish this by forming a cell membrane and a cell wall (made of peptidoglycan, cellulose, and chitin, respectively). eukaryotic animal cells have no cell wall and thus rely on the cell membrane as the only boundary btwn nside and outside. and they must devise another means of structural support: just as chordates have a bony endoskeleton instead of the primitive exoskeleton arthropods have, animal cells rely on an internal cytoskeleton instead of an external cell wall. further problems arise in multicellular eukaryotes. not only must each cell maintain its structural integrity, but it must also interact with its neighbors in an organized fashion.

water-soluble vitamins

excess excreted in urine by kidneys B1 B2 B3 B6 B12 C Biotin Folate

respiration

exchange of gases between the lungs and the blood or the blood and the other tissues of the body

exocrine vs endocrine secretion

exocrine glands secrete their products (digestive enzymes, etc) into ducts that drain into GI lumen. endocrine glands are ductless glands; their secretions (hormones) are picked up by capillaries and thus enter the bloodstream

exonuclease vs endonuclease

exonuclease means cutting a nucleic acid chain at the end. an endonuclease will cut a polynucleotide acid chain in the middle of the chain, usually at a particular sequence. two important types of endonucleases are: repair enzymes that remove chemically damaged dna from the chain, and restriction enzymes, which are endonucleases found in bacteria. their role is to destroy the dna of infecting viruses, thus restricting the host range of the virus.

mole fraction

expresses the fraction of moles of a given substance (which we'll denote here by S) relative to the total moles in a solution: mole fraction of S = Xs = # moles of substance S / total # moles in solution mole fraction is a useful way to express concentration when more than one solute is present.

nondisjunction

failure of chromosomes to separate correctly during meiosis. gametes resulting from it will have 2 copies or no copies of a given chromosome. such a gamete can fuse w a normal gamete to create a zygote w either 3 copies of a chromosome (trisomy) or one copy of a chromosome (monosomy)

linkage

failure of genes to display independent assortment. genes that are located on the same chromosome may not display independent assortment see pg 245/phone w genes that are found on the same chromosome, the design of a Punnett square is slightly different. the possible gametes are limited since they cannot assort independently. consider a cross btwn a homozygous ttgg pea plant and a double-heterozygous plant w both dominant alleles on one chromosome and both recessive alleles located together on another chromosome. they can only make a limited number of different gametes, not the 4 possible combinations of alleles that would be found if the genes were on different chromosomes. a Punnett square will help to illustrate linkage in this example. see pg 246/phone recombination is the exception to linkage see pg 247/phone

t or f, recombination btwn sister chromatids during gametogenesis increases genetic diversity of offspring

false, sister chromatids don't recombine, homologous chromosomes do. they're identical!!**

voltage gated ion channels in cardiac muscle

fast sodium channels slow calcium channels open in response to change in membrane potential to threshold voltage and when open allow passage of calcium down its gradient. these channels also stay open longer than the fast sodium channels do, causing membrane depolarization to last longer in cardiac muscle than in neurons, producing a plateau phase. action potentials travel down along t tubules, allow entry of calcium from the extracellular environment, and also induce the sarcoplasmic reticulum to release calcium. the combo of intracellular and extracellular calcium causes contraction of actin-myosin fibers. cardiac have longer absolute refractory period than skeletal or neuronal strength of contraction by cardiac muscle is affected by extracellular concentration of calcium ions as a significant potion of the calcium that stimulates contraction comes from the extracellular pool and enters the cell as part of the action potential

X chromosome inactivation

female mammals have 2 X chromosomes, one of which is active (called Xa) and one of which is silenced, or inactive (and is called Xi). in humans, X-inactivation occurs early in development at the blastocyst stage. each cell in the inner cell mass randomly inactivates an X chromosome, and this decision is irreversible. this means every cell derived from each cell makes its own decision, an adult can have different X chromosomes inactivated in different tissues and cells. bc of X-inactivation, all humans have the same number of gene products for the X chromosome; males have only one X chromosomes and females have only one active X chromosome. not all animals behave the same when it comes to X-inactivation. some animals (such as marsupials) consistently silence one X chromosome; in the case of marsupials, the paternally derived X chromosome is inactivated and the maternal X chromosome is active. Xi is very condensed, and packaged in heterochromatin. it has high lvls of dna methylation

o Secretion and reabsorption of solutes (selective reabsorption)

filtrate in the tubule consists of water and small hydrophilic molecules like sugars, amino acids, and urea. some of these substances must be returned to the bloodstream. they are extracted from the tubule often via active transport and picked up by peritubular capillaries, which drain into venues that lead to renal vein. for ex glucose is actively transported out of filtrate and returned to bloodstream by a cotransported identical to one involved in glucose absorption in small intestine. most of the reabsorption occurs in the part of the tubule nearest to the Bowmans capsule called the proximal convoluted tubule PCT. all solute movement in the pct is accompanied by water movement. as a result a lot of water reabsorption occurs in this region also; roughly 70% of the volume of the filtrate is reabsorbed here. the final volume of urine we make is determined by much smaller fluxes taking place in the distal nephron. this makes sense if you think about it: about 5% of our circulating blood is continuously being filtered out of the glomerulus; most of this must be taken back. note that reabsorption in the pct is selective in that it choose what to reabsorb, but it is not overly regulated, since it reabsorbs as much as possible, not a certain amount. selective reabsorption takes place further along nephron as well in distal convoluted tubule DCT. reabsorption in this location is more regulated than in PCT usually via hormones. Secretion: secretion is the movement of substances into filtrate (usually via active transport) thus inc the rate at which they are removed from the plasma. not everything that needs to be removed from blood gets filtered out at glomeruls; secretion is a backup method that ensures what needs to be eliminated does. as w reabsorotion, secretion occurs all along tubule, however unlike reabsorption, most secretion takes place in DCT and the collecting duct. note also that this is the primary way that many drugs and toxins are deposited in the urine

protein folding

first, the newly synthesized nascent protein is folded into its correct 3-dimensional shape. this is accomplished by a family of proteins called chaperones. if folded correctly, the protein is said to be in its native conformation. if the protein is unfolded or misfolded, its said to be in its non native state. chaperone proteins are found across all types of organisms (from bacteria to plants to mammals), and also function in assembly or folding of other macromolecular structures. for ex, chaperone proteins assist in nucleosome assembly from folded histones and dna. in eukaryotic cells, chaperones are found in many subcellular compartments

directional selection

form of natural selection. polygenic traits often follow a bell-shaped curve of expression, with most individuals clustered around the average and some members of a population trailing off in either direction away from the average. if natural selection removes those at one extreme, the population average over time will move in the other direction. ex giraffes get taller as all short giraffes die for lack of food

divergent selection

form of natural selection. rather than removing the extreme members in the distribution of a trait in a population, natural selection removes the members near the average, leaving those at either end. over time divergent selection will split the population in two and perhaps lead to a new species. ex: small deer are selected for bc they can hide, and large deer are selected bc they can fight, but midsized deer are too big to hide and too small to fight

gap junctions

form pore-like connections btwn adjacent cells, allowing the 2 cells' cytoplasms to mix. the connection is large enough to permit the exchange of solutes such as ions, amino acids, and carbohydrates, but not polypeptides and organelles. gap junctions in smooth muscle and cardiac muscle allow the membrane depolarization of an action potential to pass directly from one cell to another.

■ Nephron structure o Glomerulus o Bowman's capsule o Proximal tubule o Loop of Henle o Distal tubule o Collecting duct

functional unit of kidney is nephron. consists of 2 components 1 rounded region surrounding capillaries where filtration takes place known as capsule and 2. coiled tube known as renal tubule. tubule receives filtrate from capillaries in the capsule at one end and empties into collecting duct at the other end. the collecting duct dumps urine into the renal pelvis many blood vessels surround the nephron. they carry arterial blood toward the capillaries of the capsule for filtration, then surround the tubule to carry filtered blood and reabsorbed substances away from the tubule. bowman's capsule empties into first part of tubule, proximal convoluted tubule. proximal to glomerulus. both bowmans capsule and pct are located in renal cortex, the outer layer of kidney. pct empties into loop of henle. this is a loong loop that dips down into renal medulla the inner part of kidney. the part that heads into the medulla is called descending limb of loop of henle, and part that heads back out toward cortex is ascending limb. descending limb is thin walled but part of ascending limb is thin and other part is thick. these are the thin ascending limb and thick ascending limb of the loop of henle. thin portions of tubule are made of squamous flat epithelial cells whicha re not very metabolically active. thick portions composed of cuboidal epithelial cells which are large thick cells busily performing active transport. as we continue down the tubule loop of henle becomes distal convolute tubule. dct dumps into collecting duct. many collecting ducts merge to form larger tributaries which empty into renal calyces.

henry's law

gases in the air equilibrate with gases in liquids. if you place a beaker of water in a room, after a time the gases in the room will diffuse into the water. therefore partial pressures are also used to describe the amount of gases carried in the bloodstream. in order to diffuse into a cell, gas molecules from the air must dissolve into a liquid (eq extracellular fluid). according to henrys law, amount of gas that will dissolve into liquid is dependent on partial pressure of that gas as well as solubility of that gas in the liquid. using oxygen as ex: [O2] = PO2 x SO2 where [O2] is the concentration of dissolved oxygen, PO2 is the partial pressure of oxygen in the air above the fluid, and SO2 is the solubility of oxygen in that liquid. thus an increase in pressure increases the amount of gas dissolved in a liquid. note that gases become less soluble in liquids as temperatures inc; this is why a soda goes flat faster on a hot day, why goldfish gulp air when water too warm. in the lungs, oxygen and carbon dioxide diffuse btwn the alveolar air and blood in the alveolar capillaries. the driving force for the exchange of gases in the lungs is the difference in partial pressures btwn the alveolar air and the blood. for diffusion to occur (from the air to the blood) gases must first pass across the alveolar epithelium, and then through the interstitial liquid and finally across the capillary endothelium. these 3 barriers to diffusion together form the respiratory membrane (the pathway is obviously reversed for diffusion from blood to the air).

excretory system

generally refers to kidneys but includs liver large intestine and skin

imprinting (controlling gene expression)

genomic imprinting is when only one allele of a gene is expressed. in some situations, the maternal alley is expressed, and in others the paternal alley is expressed. imprinted genes tend to be clustered together on chromosomes. imprinting is a dynamic process and can change from generation to generation. in other words, a gene that is imprinted in an adult may be "unimprinted" and expressed in that adult's offspring. this observation led to the notion that imprinting is an epigenetic process. silencing of a certain gene involves dna methylation, histone modification, and binding of long ncrnas. these epigenetic marks are established in the germline and are maintained throughout life and mitotic divisions

regulation of transcription in eukaryotes (control of gene expression at rna lvl)

given the complexity of eukaryotes compared to prokaryotes, it's not surprising that the regulation of eukaryotic transcription is also more complex. most of the regulation happens at initiation. for protein-coding genes, there are upstream control elements (UCEs), usually about 200 bases upstream of the initiation site, a core promoter containing binding sites for the basal transcription complex and rna pol II (about 50 bases upstream of the transcription start site), and a TATA box at -25. the TATA box is a highly conserved dna recognition sequence for the TATA box binding protein (TBP). binding of tbp to the Tata box initiates transcription complex assembly at the promoter enhancer sequences in dna are bound by activator proteins, and this is another kind of transcriptional regulation. the enhancer may be located many thousands of base pairs away from a promoter (either upstream or downstream) and still regulate transcription. this is likely done by dna looping so enhancers and their activator proteins can get close to transcriptional machinery eukaryotes also have gene repressor proteins, which inhibit transcription; this can also be done by modifying chromatin structure. transcription factors have dna binding domains and are crucial in transcription regulation. they can bind promoters or other regulatory sequences. in fact, in many cases, transcription lvls in eukaryotes are controlled by huge committees of proteins. this produces a combinatorial effect, where each protein contributes to regulation, and can itself be regulated. these complex networks help link transcription to cell signaling and status. the binding of transcriptional machinery to dna is often regulated by extracellular signals. for ex, steroid hormones bind to receptors in the cell, and this sends the receptor to the nucleus. the complex binds dna to regulate transcription. beyond regulating the initiation of transcription, eukaryotes employ several other methods of transcriptional regulation, including: rna translocation: mRNA transcripts must be exported from the nucleus to the cytoplasm and can also be transported to different areas of the cell. they are translationally silent while this is happening. this system is especially important in cells that have a high level of polarity, where one area or end of the cell is distinctly different from the other. for ex, neurons have polarity, and some transcripts are transported to the dendrites, while others stay in the soma. this is a way of controlling gene expression: mRNA transcripts aren't translated into proteins until they are localized properly in the cell. mRNA surveillance: cells closely monitor mrna molecules to ensure that only high quality mrna transcripts are read by the ribosome. defective transcripts (such as those with premature stop codons, or those without stop codons at all) and stalled transcripts (where the ribosome is stalled in translation) are degraded rna interference: rna interference (RNAi) is a way to silence gene expression after a transcript has been made. it is mediated by miRNA and siRNA. molecular biology labs often use the RNAi system experimentally, as a way to decrease protein expression. generally speaking, the siRNAs bind complementary sequences on mRNAs, and this ds-RNA is then degraded. the amount of transcript in the cell decreases, and gene expression is thus negatively regulated

a researcher injects tiny gold beads into a cell and waits an hour. then she examines the cell and finds gold beads in the cytoplasm and in the nucleus. when she injects larger gold beads, they are not found in the nucleus. however, when she binds the larger beads to a nuclear localization sequence, she finds that they end up in the nucleus. one can conclude that: A. the nuclear localization sequence is lysine-rich B. goal beads have an inherent import signal C. the nuclear localization mechanism is nonspecific enough to confer nuclear import on gold beads D. nuclear import relies primarily on simple diffusion

gold beads are not normally found in cells, so there can't be an existing mechanism for moving them. however since the cell is capable of moving them when the localization signal is attached, the localization signal must be somewhat nonspecific (choice C is correct). it is true that the nuclear localization signal is lysine rich but this can't be concluded based on the given information (true, but it doesn't answer the question; choice A is wrong). if gold beads had an inherent import signal, then they would be transported into the nucleus on their own, without the researchers having to bind them to the localization sequence (choice B is wrong). if simple diffusion were the primary means of moving things into the nucleus, no import signal would be needed (choice D is wrong)

gray vs white matter

gray- unmyelinated white- myelinated

nucleus (psych)

grey matter deep in the brain

ganglion

grey matter in pns

horn

grey matter in the spinal cord

cortex

grey matter on the surface of the brain

catalytic receptors

have enzymatic active site on the cytoplasmic side of the membrane. enzyme activity is initiated by ligand binding at the extracellular surface. generally the catalytic role is that of a protein kinase, which is an enzyme that covalently attaches phosphate groups to proteins. proteins can be modified w phosphate on the side chain hydroxyl of serine, threonine, or tyrosine. the insulin receptor is an example of a tyrosine kinase. modification of proteins w phosphates regulates their activity

microtubules

hollow rod composed of 2 globular proteins: alpha-tubulin and beta-tubulin, polymerized noncovalently. first, alpha-tubulin and beta-tubulin form an alphabeta-tubulin dimer. then many dimers stick to one another noncovalently to form a sheet, which rolls into a tube. once formed the microtubule can elongate by adding alphabeta-tubulin dimers to one end. the other end cannot elongate, bc it is anchored to the microtubule organizing center (MTOC), located near the nucleus. microtubules are dynamic and can get longer or shorter by adding or removing tubular monomers from the end. within the MTOC is a pair of centrioles. each centriole is composed of a ring of nine microtubule triplets. when cell division occurs, the centrioles duplicate themselves, and then one pair moves to each end of the cell. during mitosis, microtubules radiating out from the centrioles attach to the replicated chromosomes and pull them apart so that one copy of each chromosome (one chromatid) moves to each end of the cell. the resulting daughter cells each get a full copy of the genome plus a centriole pair. the microtubules that radiate out from the centrioles during mitosis are called the aster, bc they are star shaped. the microtubules connecting the chromosomes to the aster are polar fibers. the whole assembly is called the mitotic spindle. the centromere of each chromosome contains a kinetochore which is attached to the spindly by tiny microtubules called kinetochore fibers. see pg 205/phone for pic in mitosis, the MTOC is essential, but the centrioles are not. microtubules also mediate transport of substances within the cell. in nerve cells, materials are transported from cell body to axon terminus on a microtubule railroad. the transport process is driven by proteins that hydrolyze atp and act as molecular motors along the microtubule.

temperature regulation by the skin

humans are homeotherms, meaning their body temp is relatively constant. heat is generated by metabolic processes and muscle contraction. some homeotherms (eg bears) can maintain their temperature by burning special fat called brown adipose tissue; this process is called chemical thermogenesis or non shivering thermogenesis. but this is not an important mechanism of temperature regulation in adult humans. also while it is true that an increased level of thyroid hormone can increase the metabolic rate and thus increase body temperature, this mechanism takes several weeks to kick in and is not thought to be important in day to day temperature regulation. so practically only 4 strategies are available to cope w cold weather: 1 contraction of skeletal muscle produces heat, whether it is involuntary (shivering) or voluntary (jumping up and down) 2 the skin insulates us so that we conserve heat generated by metabolism. subcutaneous (beneath the skin) tissue contains a layer of insulating fat, which helps 3 heat loss by conduction is minimized by constriction of blood vessels in the dermis (cutaneous vasoconstriction). cutaneous vasoconstriction occurs in response to cold weather or upon activation of the symapthetic nervous system. this is why the skin becomes cold and pale when frightened. 4 obviously, contrivances such as clothing and blankets help us conserve heat mechanism for dissipation of excess heat. 2 mechanisms: 1 sweating, which allows heat loss by evaporation 2 dilation of blood vessels in the dermis (cutaneous vasodilation) which results in heat loss by conduction or convection, when air blows past the skin (as with fan or breeze)

adaptive (specific) immunity humoral immunity antibodies, and B cells

humoral immunity refers to specific protection by proteins in the plasma called antibodies (Ab) or immunoglobulins (Ig). antibodies specifically recognize and bind to microorganisms (or other foreign particles) leading to their destruction and removal from the body. each antibody molecule is composed of 2 copies of 2 different polypeptides, the light chains and heavy chains, joined by disulfide bonds. in addition each antibody molecule has 2 regions, the constant region and the variable (antigen binding) region. there are several different classes of immunoglobulins, differentiated by constant regions. the classes have different functions with most of the antibody circulating in plasma in the IgG class. the variable regions are responsible for the specificity of antibodies in recognizing foreign particles each antibody forms a unique variable region that has a different binding specificity. the moelcule that an antibody binds to is known as the antigen (Ag). examples are viral capsid proteins, bacterial surface proteins, and toxins in the bloodstream (such as tetanus toxin). (antibodies are solube in the plasma, an antibody against a cytoplasmic protein wouldnt help immune system bc they can only recognize anteigens on surfaces that are accessible to them. a protein in the cytoplasm of a bacteria would never be accessible to antibodies in the plasma and therefore couldnt be recognized) the specificity of antigen binding is determined by the fit of antigen in a small 3D cleft formed by the vaiable region of the antiody moelcule. antigens are oftne large molecules which have many differnet recognition sites for different antibodies. the small site that an antibody recognizes within a larger molecule is an epitope. very small molecules often dont elicity the production of antibodies on their own but will when bound to an antigenic large molecule like a protein. the protein in this case is called a carrier, and the small moelcule that becomes antigenic is known as a hapten. antibody binds to antigen and: 1 binding of antibody may directly inactivate the antigen. for ex binding of antibody to a viral coat protein may prevent the virus from bidnign to cells. 2 binding of antibody can induce phagocytosis of a particle by macrophages and neutrophils 3 presence of antibodies on the surface of a cell can activate the complement system to form holes in the cell membrane and lyse the cell

proteolysis

hydrolysis of a protein by another protein. aka proteolytic cleavage. specific means of cleaving peptide bonds

2 portal systems you need to know

hypothalamic pituitary and hepatic (gastrointestinal tract to the liver)

eukaryotic chromosomes generally have only one of which of the following? A. reading frame B. origins of replication C. promoter D. centromere

if a chromosome had more than one centromere, it could be pulled toward different ends of the cell simultaneously and be torn (choice D is correct). each eukaryotic gene has only one reading frame, but since there are many genes per chromosome there are different reading frames too. note that the total number of possible reading frames is only 3, since a codon is only 3 nucleotides long (choice A is wrong). eukaryotic chromosomes are so large that they must have more than one origin of replication to finish replication of the genome in a reasonable time period (choice B is wrong), and each gene has its own promoter, and there are many genes per chromosome (choice C is wrong).

In normal eukaryotic cells, mitosis will not begin until the entire genome is replicated. If this inhibition is removed so that mitosis begins during S-phase, which one of the following would occur? A. the cells would grow more quickly B. The genome would become fragmented and incomplete C. The cells would display unregulated, cancerous growth D. The genome would be temporarily incomplete in each daughter cell, but DNA repair will fill in the missing gaps

if the genome is not completely replicated and condensed prior to mitosis, it will be torn during cell division. each daughter cell will receive only pieces of the genome rather than the complete genome and will not be able to survive (choice B is correct and A and C are wrong.) dna repair systems can only repair sequence errors or minor structural problems; this problem would be too large to fix (choice D is wrong).

regulation of HR and BP

in any regulatory system 3 components are required - input (afferent info), integration (function of the ins), and output (efferent info -generally the para and sympathetic control discussed above). the input in this regulatory system is complex but we can highly one key element- in the aortic arch and in carotid arteries there are special receptors known as baroreceptors which monitor pressure (barometer). when they notify cns that pressure is too high, cns sends out info to correct problem, increased vagal tone and decreased sympathetic input. when pressure too low, opposite happens. ppl w high bp have a poorly functioning regulatory system and must take meds.

cytoskeleton

in eukaryotes. provides structural support. also allows movement of cell and its appendages (cilia and flagella) (cilia and flagella are both made up of microtubules) and transport of substances within the cell. animal cells have an internal cytoskeleton composed of 3 types of proteins: microtubules, intermediate filaments, and microfilaments. microtubules are the thickest, microfilaments the thinnest. all 3 are composed of noncovalently polymerized proteins; in other words, they are a massive example of quaternary protein structure. see pg 204/phone for pic

fitness

in evolutionary terms, how successful an animal is in passing on its alleles to future generations

skin

in excretory system makes sweat, which has water ions and urea. sweat is similar to urine. although skin is an excretory organ sweating is not primarily controlled by the amount of waste that needs to be excreted but rather by temperature and level of sympathetic nervous system activity. therefore the excretory role of the skin is secondary

ischemia vs hypoxia

in hypoxia, wastes are adquately removed, but in ischemia they build up. ischemia is worse

which one of the following pairs of processes may occur simultaneously on the same rna molecule in a eukaryotic cell? A translation and transcription B transcription and splicing C splicing and translation D messenger rna degradation and transcription

in order for processes in eukaryotes to occur simultaneously, they must occur in the same compartment. transcription and splicing both occur in the nucleus and could therefore occur simultaneously (choice B is correct). translation occurs in the cytoplasm while transcription and splicing occur in the nucleus, thus translation cannot occur at the same time as either of these processes (choices a and c are wrong). mrna degradation and transcription cannot occur at the same time; if this were true, no mrna molecules would survive to be translated (choice D is wrong)

rna polymerase

in prokaryotes, all rna is made by the α2ββ'σ rna polymerase complex. in eukaryotes, there are many different rna polymerases: rna pol I transcribes most rRNA rna pol II transcribes hnRNA (so ultimately mRNA), most snRNA, and some miRNA RNA pol III transcribes tRNA, long ncRNA, siRNA, some miRNA, and a subset of rRNA **NOTE: in replication, we listed many prokaryotic dna polymerases. here, many eukaryotic rna polymerases.**

in a cross, does recombination occur in the parent or progeny

in the parents, where the recombinant chromosomes' genotypes affect the genotypes of their progeny?

prokaryotic translation

in prokaryotes, translation occurs in the same compartment and at the same time as transcription. in other words, while the mRNA is being made ribosomes attach and begin translating it. this means that the first end of the mrna to be translated is 5', since the mrna is made 5' end first. transcription and translation go in the same direction on mrna. note that we said ribosomeS. several ribosomes attach to the mrna and translate it simultaneously. you may hear the term polyribosome used to describe this arrangement; polyribosomes are seen in both prokaryotes and eukaryotes. translation doesn't always begin at the very end, you can deduce this from the fact that mrna is polycistronic. if there are more than one translation start site on the mrna, they can't all be at the 5' end. see pg 108/phone for pic bc prokaryotes often have polycistronic mrnas, their ribosomes can also start translation in the middle of the chain. this means termination and initiation sequences are found btwn each ORF. even for the first open reading frame on a transcript, translation doesn't begin right at the 5' end. an upstream regulatory sequence is essential for initiation, just as in transcription. here instead of a promoter, we have a ribosome binding site, aka Shine-Dalgarno sequence, located at -10 (ten ribonucleotides upstream, or on the 5' side of the start codon). the shine-dalgarno sequence is complementary to a pyrimidine-rich region on the small subunit, and thus helps position the initiation machinery on the transcript. like transcription, translation has 3 distinct stages: initiation, elongation, and termination. many antibiotics function by inhibiting a particular stage. initiation starts w the small ribosomal subunit (30S) binding 2 initiation proteins called IF1 and IF3. this complex then binds the mrna transcript. next the first aminoacyl-trna joins, along with a 3rd initiation factor called IF2, which is also bound to on gtp. finally the 50s subunit completes the complex. this process is powered by the hydrolysis of one gap molecule. the first aminoacyl-trna is special; its called the initiator trna, abbreviated fmet-trnafmet. the "fMet" stands for formylmethionine, which is a modified methionine used as the first amino acid in all prokaryotic proteins. the initiator trna sits in the p site of the 70s ribosome, hydrogen-bonded with the start codon. (the start codon only initiates translation when it is preceded by a shine-dalgarno sequence (prokaryotes)) before elongation, all initiation factors dissociate from the complex elongation, a 3 step cycle, may now begin. in the first step, the 2nd aminoacyl-trna enters the A site and hydrogen bonds with the second codon. this process requires the hydrolysis of one phosphate from gtp. this is done by an elongation factor protein called Tu (EF-Tu), which is a GTPase. a second elongation factor called EF-Ts removes the remaining gdp from EF-Tu, thus helping it reset. in the second step, the peptide transferase activity of the large ribosomal subunit (the 23S rRNA) catalyzes the formation of a peptide bond btwn fMet and the second amino acid.the amino group of amino acid #2 acts as a nucleophile, and tRNAfMet is the leaving group; it dissociates from the ribosome. a new dipeptide is now attached to trna #2. now you can figure out the direction of translation from the point of view of the polypeptide; you won't have to memorize it (the direction of synthesis is N->C since the N of amino acid #2 binds to the C of #1. as the polypeptide elongates, its N terminus will come snaking out of the ribosome). the third step is translocation, in which trna #1 (now empty) moves into the E site, tRNA #2 (holding the growing peptide) moves into the P site, and the next codon to be translated moves into the A site. elongation factor G (EF-G) helps with translocation, and this process costs one gtp. EF-G is sometimes called a translocase bc of its function in this step. the new dipeptide is still attached to trna #2 and tRNA #2 is still H bonded to codon #2. the presence of trna #1 in the E site (still Hbonded to codon #1), is thought to help maintain the reading frame of the mrna (disruption of tRNA binding to the E site results in an increase in the number of frameshift mutations in the resulting protein). EF-Tu eventually helps remove this tRNA from the E site. (does the ribosome move relative to the mrna during translocation? - it must, if the trna remains H-bonded to the mrna while moving to another spot in the ribosome) these 3 steps repeat over and over again, connecting amino acids in the order their codons appear along the mrna strand (and thus appear in the A site) termination occurs when a stop codon appears in the A site. instead of a tRNA, a release factor now enters the A site. this causes the peptide transferase to hydrolyze the bond btwn the last trna and the completed polypeptide. prokaryotes have 3 release factor proteins, which mediate translation termination by recognizing stop codons. RF1 recognizes termination codons UAA and UAG, and RF2 recognizes UAA and UGA. RF3 is a gtp-binding protein that doesn't recognize a stop codon, but instead leads to the dissociation of RF1/RF2 after peptide release. finally the ribosome separates into its subunits and releases both mrna and polypeptide. see pg 110/phone for pic why doesn't peptide bond formation require gtp hydrolysis, like the other steps in translation? - bc the bond btwn each amino acid and its trna is a high-energy bond whose hydrolysis drives peptide bond formation. remember that the aminoacyl-trna bond was formed using the energy of 2 phosphate bonds from atp. you should be able to answer questions like this: how many high-energy phosphate bonds are required to make a 50 amino acid polypeptide chain, including the energy used to activate amino acids to aminoacyl-trnas? - there are 2 phosphate bonds hydrolyzed per amino acid to make the aminoacyl-trnas, or 100 for the 50 amino acid polypeptide. 2 phosphate bonds are required for each elongation step, one for the entrance of each new aminoacyl-trna into the ribosomal A site and the other for translocation. since there are 49 elongation steps for a 50 amino acid protein, 98 high energy bonds are hydrolyzed during elongation. finally, one gtp is hydrolyzed during initiation to position the first trna and mrna on the ribosome, and one gtp is hydrolyzed in termination. thus, a total of 200 high-energy bonds are required for the translation of a 50 amino acid protein. in other words, it costs 4n high-energy bonds to make a peptide chain, where n is the number of amino acids in the chain

how are neurons and muscle tissue unique

in using the resting membrane potential to generate action potentials, although all cells have the resting membrane potential

subviral particles

infectious agents that are even smaller and simpler than viruses. include prions and viroids

hemizygosity

individual has only one copy of a chromosome in a diploid organism. examples: mitochondrial traits, y-linked traits, x-linked traits in human males

anatomy of conduction zone

inhaled air follows the pathway: nose, nasal cavity, pharynx, larynx, trachea, bronchi, terminal bronchioles, respiratory bronchioles, alveolar ducts, alveoli (respiratory bronchioles, alveolar ducts, alveoli are in respiratory zone) nose is for warming humidifying and filtering inhaled air, nasal hairs and mucus act as filters pharynx is throat larynx has 3 functions 1 made entirely of cartilage and thus keeps airway open 2 it contains the epiglottis which seals the trachea during swallowing to prevent entry of food 3 it contains vocal cords which are folds of tissue positions to partially block the flow of air and vibrate producing sound the trachea must remain open to permit air flow; rings of cartilage prevent its collapse. 2 primary bronchi, each of which supplies one lung each bronchus branches repeatedly to supply the entire lung collapse of bronchi is prevented by small plates of cartilage very small bronchi are called bronchioles. they are about 1 mm wide and have no cartilage. their walls are made of smooth muscle which allows their diameters to be regulated to adjust airflow into the system the smallest and final branches of the conduction zone are the terminal bronchioles the smooth muscle of the walls of the terminal bronchioles is too thick to allow adequate diffusion of gases; this is why no gas exchange occurs in this region. the conduction zone is strictly for ventilation.

inspiration and expiration

inspiration is an active process driven by contraction of the diaphragm, which enlarges the chest cavity and the lungs along with it drawing air in. passive expiration is driven by the elastic recoil of the lungs and doesn't require active muscle contraction

■ Capillary beds o Mechanisms of gas and solute exchange o Mechanism of heat exchange o Source of peripheral resistance

intercellular clefts are spaces btwn endothelial cells that make up the capillary wall. 3 substances might be able to pass through clefts: nutrients, wastes, WBCs. its not necessary for O2 or CO2 to pass through the clefts bc they can pass straight through any cell by simple diffusion 3 main types of nutrients: amino acids, glucose, lipids. amino acids and glucose are absorbed from digestive tract and carried by hepatic portal vein to the liver. the liver stores amino acids and glucose and releases them into the bloodstream as needed. from the bloodstream they can pas through capillary clefts into tissues. lipids: fats are absorbed from instant and packaged into chylomicrons, which are a type of lipoprotein. the chylomicrons enter tiny lymphatic vessels in the intestinal wall called lacteals. lacteals empty into larger lymphatics which eventually drain into a large vein near the neck. hence dietary fats bypass the hepatic vein. the result is that after eating a fatty meal a persons blood will appear milky. this is called lipemia, or lipids flowing in the blood. the chylomicrons are taken up by the liver and converted into another type of lipoprotein, which is released into the bloodstream. this lipoprotein carries fats to adipocytes (fat cells) for storage. when fats are to be used for energy, adipocyte triglycerides are hydrolyzed and free fatty acids are released into bloodstream. they can pass easily through capillary pores and thus can be picked up by cells of various tissues. wastes diffuse through capillary walls into bloodstream. liver removes many wastes and converts them into forms which can be excreted in feces. such compounds passed into gut as bile. other wastes excreted directly by the kidneys. white blood cells must be able to pass out of capillaries in order to patrol the tissues for invading microorganisms. 2 of the 6 types of white blood cell can squeeze through the clefts: the macrophages and neutrophils, even though they are larger than RBCs, bc they are capable of amoeboid motility. RBCs aren't capable of independent motility. plasma proteins like albumin keep water in the plasma instead of going into cells. but some water does flow out of capillaries. osmotic pressure provided by plasma proteins is called oncotic pressure. cycle: 1 beginning of capillary, hyrdostatic pressure high. result is that water squeezes out into the tissues. 2 as water continues to leave the capillary, the relative concentration of plasma proteins increases. 3 at the end of the capillary the hydrostatic pressure is quite low, but since the blood is now very concentrated, the oncotic pressure is very high. as a result, water flows back into the capillary from the tissues. during inflammation, capillaries dilate, increasing size of intercellular cleft. this allows more space for white blood cells to migrate into tissues. side effect of plasma proteins and a lot of water are lost into the tissues. the result is water in the tissues, edema - swelling. fluids proteins and white blood cells in tissues returned to bloodstream via lymphatic system

would a protoplast moved from salt water to fresh water shrivel or burst?

it would burst, since water would flow into the cell by osmosis

reproductive isolation

keeps existing species separate. 2 types. prezygotic and postzygotic

skin function and structure

largest organ by size and weight. role to protect from pathogens, prevent excessive evaporation of water and regulate body temp. outermost layer of skin is epidermis; lies upon deeper dermis, which rests on subcutaneous tissue or hypodermis. the hypodermis is protective insulating layer of fat (adipose tissue).

human life cycle

life begins w a diploid cell, the zygote. diploid organisms (or cells) have 2 copies of the genome in each cell, while haploid cells have one copy of the genome. in sexual reproduction, the diploid zygote is produced by fusion of 2 haploid gametes: a haploid ovum from the mother and a haploid spermatozoon from the father. the zygote then goes through many mitotic divisions to develop into an adult, with half of the genetic material in each cell from each parent. the adult, male or female, produces haploid gametes by meiotic cell division to repeat the life cycle once again.

ligaments, tendons, and joints

ligaments and tendons are strong tissues composed of dense connective tissue. ligaments connect bones to other bones and tendons connect bones to muscles. the point where one bone meets another is a joint. synarthroses are immovable joints, are points where 2 bones are basically fused together. for ex the skull is formed from many fused bones. amphiarthroses - slightly movable joints, provide both movability and a great deal of support (amphi - both). vertebral joints are an ex. freely moveable joints are diarthroses. there are several types like ball and socket and hinge. all movable joints are supported by ligaments. movable joints are lubricated by synovial fluid, which is kept within the joint by the synovial capsule. the surfaces of the 2 bones that contact each other are perfectly smooth bc they are lined by special articular cartilage (composed of hyaline cartilage). like all cartilage, articular cartilage lacks blood vessels. hence it is easily damaged by overuse or infection. inflammation of joints (arthritis) leads to destruction of the articular cartilage which causes pain and stiffness.

penetrance

likelihood that a person w a given genotype will express the expected phenotype. several things can affect it for an allele, like age-related penetrance, environment and lifestyle modifiers, and many alleles have genetic modifiers that affect penetrance; since several human traits are polygenic, alleles at different loci can affect penetrance

oligodendrocytes

located in cns, forms myelin

Schwann cells

located in pns, forms myelin

lub dup

lub: closure of the AV valves at the beginning of systole dup: the sound of semilunar valves closing at the end of systole diastole is longer since it occupies the space btwn lub dub and lub dub. systole is shorter, since it occupies the space btwn lub and dup

■ Structure of lymphatic system ■ Major functions o Equalization of fluid distribution o Transport of proteins and large glycerides o Production of lymphocytes involved in immune reactions o Return of materials to the blood

lymphatic system is a one way flow system which begins w tiny lymphatic capillaries in all the tissues of the body that merge to form larger lymphatic vessels. these merge to form large lymphatic ducts. lymphatic vessels have valves, and the larger lymphatic ducts have smooth muscles in their walls. as a result, the lymphatic systems acts like a suction pump to retrieve water, proteins, and white blood cells from the tissues. the fluid in lymphatic vessels is called lymph. lymph is filtered by numerous lymph nodes. lymph nodes are an important part of immune system bc they contain millions of WBCs that can initiate immune response against anything foreign that may have been picked up in the lymph. the large lymphatic ducts merge to form the thoracic duct which is the largest lymphatic vessel located in the chest. thoracic duct empties into a large vein near the neck. also lymphatic vessels from the intestines dump dietary fats in form of chylomicrons into thoracic duct.

which bacteria would be more susceptible to lysis when treated with lysozyme: gram-positive or gram-negative?

lysozyme hydrolyzes linkages in peptidoglycan to weaken the cell wall. the peptidoglycan in gram-positive cells is more accessible since these cells don't possess an additional outer layer; therefore, gram-positive cells will lyse more easily when treated with lysozyme

peptide hormones

made from amino acids, bind to receptors on the cell surface, typically affect target cells via second messenger pathways. effects tend to be rapid and temporary.

depolarizing

making it more likely to fire. increasing membrane potential

female reproductive system

male and female genitalia derived from a common undifferentiated precursor. bc of this the structures of the female external genitalia are homologous to those of the male. in the female the XX genotype leads to formation of ovaries capable of secreting female sex hormones (estrogens) instead of testes that secrete androgens. in the male, testosterone causes a pair of skin folds known as labioscrotal swellings to grow and fuse forming the scrotum. in the female, without the influence of testosterone, the labioscrotal swellings form the labia majora of the vagina (labia = lips, majora = larger). the structure that gave rise to penis in the male embryo becomes the clitoris in the female, located within the labia majora in the uppermost part of the vulva. just beneath the clitoris is the urethral opening where urine exits the body. surrounding the urethral opening is another pair of skin folds called labia minora. opening of the vagina is also found btwn the labia minora. the female internal genitalia (vagina, uterine tubes, uterus) are derived from the mullerian ducts so there are no homologous structures in the male. the vagina is a tube which would end in the pelvic cavity except that another hollow organ the uterus opens into its upper portion. the part of the uterus which opens into the vagina is called the cervix (neck as in cervical). innermost lining of uterus (closest to lumen) is endometrium. responsible for nourishing a developing embryo and in absence of pregnancy it is shed each month producing emnstrual bleeding. surrounding the endometrium is the myometrium which is a thick layer of smooth muscle comprising the wall of the uterus. the uterus ends in 2 uterine tubes Fallopian tubes which extend into the pelvis on either side. each uterine tube ends in a bunch of finger like structures called fimbriae. the fimbriae brush up against the ovary, which is the female gonna. at ovulation, the oocyte comes from ovary and must be swept into uterine tube by constant flow of fluid into uterine tube caused by cilia.

viral genomes

many factors determine the uniqueness of each virus. the type of genome, possession of lack of an envelope, nature of cell-surface proteins, and type of life cycle are examples. all of these parameters are used in the classification of viruses, and all are potential targets for therapeutic intervention. the nature of the genome is perhaps the most important of these and has important consequences for how infection by each virus proceeds. in the following discussion we will look at a few viral genomes with an eye to what proteins the virus must encode or actually carry in its capsid based on its genome type. our purpose is not to provide new information, but rather to demonstrate what conclusions can be drawn from what you already know (typical mcat passage material). don't memorize but read for comprehension. we won't discuss ds-RNA or ss-DNA genomes, but by the end you should be able to imagine components they might require.

electrophoresis

means of separating things by size (for ex nucleic acids or proteins) or by charge (for ex proteins or individual amino acids). a gel is made out of either acrylamide or agarose, by solubilizing the acrylamide or agarose, pouring it into a rectangular mold, and then allowing it to cool and solidify. acrylamide and agarose form "nets" as they solidify; the more acrylamide or agarose used in the initial solution, the smaller the pores in the nets. the mold used to pour the gel creates wells in the gel into which samples can be loaded. an electrical current is applied such that the end of the gel with the wells is negatively charged and the opposite end is positively charged. this causes the samples to migrate toward the positive pole, according to size; smaller things migrate faster (bc they fit more easily through the pores of the gel) and larger things migrate more slowly. in addition to determining their sizes, fragments of dna (or rna) in an electrophoreses gel can be transferred to a more solid and stable membrane in a process called blotting. there are several types of blots used.

ejection fraction

measurement, expressed as a percentage, of how much blood the left ventricle pumps out with each contraction. only about 2/3 of the blood is normally ejected from the ventricle

population vs species

members of a species can mate and produce fit offspring. members of a population do. remember it this way: a population is a subset of a species

Hyperpolarization

membrane potential of the cell is more negative, relative to the normal resting potential. less likely to fire (neurons)

peroxisomes

metabolize lipids and toxins using H2O2. 1 membrane surrounding small organelles that perform a variety of metabolic tasks. the peroxisome contains enzymes that produce hydrogen peroxide as a byproduct. they are essential for lipid breakdown in many cell types. in the liver they assist in detoxification of drugs and chemicals. h2o2 is a dangerous chemical but peroxisomes contain an enzyme called catalase which converts it to H2O+O2. separating these activities into the peroxisomes protects the rest of the cell from damage by peroxides or oxygen radicals.

location (prokaryotic vs eukaryotic transcription)

meukaryotic means "true-kernelled." prokaryotic means "before the kernel." the karyon (kernel) is the nucleus. the fact that prokaryotes have no nucleus means transcription occurs free in the cytoplasm in the same compartment where translation occurs, and transcription and translation can occur simultaneously. eukaryotes must transcribe their mrna in the nucleus, modify it, and then transport it across the nuclear membrane to the cytoplasm where it can be translated. transcription and translation in eukaryotes don't occur simultaneously. another important difference btwn prokaryotic and eukaryotic gene expression is that the primary transcript in prokaryotes is mrna. in other words, the product of transcription by prokaryotic rna polymerase is ready to be translated. in fact translation of prokaryotic mrna begins before transcription is completed in contrast the eukaryotic primary transcript (hnRNA made by RNA pol II) is modified extensively before translation. the most important example is splicing. eukaryotic dna has noncoding sequences intervening btwn the segments that actually code for proteins. sometimes these intervening sequences contain enhancers or other regulatory sequences and they can be quite long. the avg size of a mammalian intron, for ex, is about 2000 nucleotides. INTervening sequences in the rna are called INTrons. note that introns are intragenic regions (and not intergenic space). protein coding regions of the rna are termed EXons bc they actually get EXpressed. before the rna can be translated, introns must be removed and exons joined together; this is accomplished via splicing splicing is mediated by the spliceosome, a complex that contains over 100 proteins and 5 small nuclear rna (snRNA) molecules. about half the proteins stably bind snRNAs, and these form three small nuclear ribonucleic particles snRNPs. each snRNP is therefore made of proteins and snRNAs. the spliceosome is not a preassembled complex, but rather assembles around each intron that needs to be removed. this happens in a series of steps, where different snRNP components are recruited and released as the rxn proceeds. the complex undergoes many conformational changes to attain catalytic activity. to catalyze the splicing reaction, snRNPs recognize and hydrogen bond to conserved nucleotides in the intron: typically GU at the 5' end, AG at the 3' end, and an adenine 15-45 bases upstream of the 3' splice site. this aligns the hnRNA such that the splicing mechanism can take place. two splicing rxns are catalyzed by the spliceosome. the first rxn attaches one end of the intron to the conserved adenine. this causes the intron to form a looped structure, then the second reaction joins the two exons and releases the loop. the 5 conserved nucleotides necessary for this rxn (GU, A and AG) are found in all genes and across all eukaryotic species. see pg 100/ phone for pic for a given gene, there are often differnt options or patterns of splicing, a phenomenon called alternative splicing. there are many different common patterns. one gene could have different promoters in the 5' region, which can change where/how the rna begins. there can be alternative 5' exons or 3' exons which can affect either end of the rna. in the middle, too, some exons can be included or skipped. finally, there could be mutually exclusive exons, where sometimes one is included and sometimes the other is kept. all these patterns lead to different mrnas being made from one dna gene sequence; the mrnas can be different in length and sequence. shuffling exons in this way is one way to inc the complexity of gene expression. see pg 101/phone for pic alternative splicing is mediated by introns and exons, as well as by the proteins that can bind to these sequences. there are almost 200,000 introns in the human genome, with an average of about 7 per gene. it was initially thought that introns were unimportant and had no function. while its true that a lot of intron sequences are probably junk, the current picture of introns is a little more complicated than first believed eukaryotic hnRNA must be modified in 2 other ways before translation can occur. a tag is added to each end of the molecule: a 5' cap and a 3' poly-A tail. the 5' cap is a methylated guanine nucleotide stuck on the 5' end (5' end is made first). the polyA tail is a string of several hundred adenine nucleotides. the cap is essential for translation, while both the cap and the polyA tail are important in preventing digestion of the mRNA by exonucleases that are free in the cell. (why would active exonucleases be floating free in the cell? - two conceivable reasons 1. mrna has a v short lifespan; it is degraded rapidly, and more must be made if the protein is still needed. note that this is consistent with the idea that regulation of gene expression occurs primarily at the transcipritonal lvl since this is more efficient. 2. viruses may inject rna into the cell. if it doesn't have the correct cap and tail modifications, exonucleases will destroy it.) see pg 102/phone for pic

Do spermatogonia divide by mitosis or meiosis?

mitosis. spermatogonia undergo meiotic s phase (replicate genome) but the stages which undergo actual meiotic divisions are called spermatocytes. all gamete precursors with "cyte" in their name undergo a meiotic division

meiosis

mitotic cell division produces 2 daughter cells that are identical to the parent. however, the production of haploid cells such as gametes from a diploid cell requires a type of cell division that reduces the number of copies of each chromosome from 2 to 1; this method of cell division is meiosis. in males, meiosis occurs in the testes w haploid spermatozoa as the end result; in females, meiosis in the ovaries produces ova. (note: this is not always the case, and while meiosis begins in the ovaries, it is completed only after fertilization). specialized cells termed spermatogonia in males and oogonia in females undergo meiosis. spermatogenesis and oogenesis share the same basic features of meiosis but differ in many of the specific features of gamete production. mitosis and meiosis are similar in many respects. mitosis and meiosis are both preceded by one round of replication of the genome (S phase), leaving a diploid cell w 4 copies of the genome. the different phases in cell division are referred to by the same names (prophase, metaphase, anaphase, and telophase) in both meiosis and mitosis and are mechanistically very similar. the primary difference btwn meiosis and mitosis is that replication of the genome is followed by one round of cell division in mitosis and 2 rounds of cell division in meiosis, meiosis I and meiosis II. another important difference is that in meiosis, recombination occurs btwn homologous chromosomes. see pg 231/phone for pics the first step in meiosis is prophase I. as in mitotic prophase, chromosomes condense in meiotic prophase I, and then the nuclear envelop breaks down. unlike mitosis, however, homologous chromosomes pair w each other during meiotic prophase I in synapsis. homologous chromosomes align themselves very precisely with each other in synapsis, w the 2 copies of each gene on 2 different chromosomes brought closely together. the paired homologous chromosomes are called a bivalent or tetrad. when the dna is aligned properly, it can then be cut precisely at the same location on homologous chromosomes. genes are then swapped btwn the pair, and the chromosomes are relegated. this process is known as crossing over or recombination. due to the extreme complexity of crossing over, meiotic prophase takes the most time in meiosis, days sometimes. recombination during meiosis is an important source of genetic variation during sexual reproduction. see pg 232/phone for pic see pg 233/phone for pic since precision is crucial in chromosome swapping, formation of the tetrad is highly regulated. synapsis is mediated by a protein structure called the synaptonemal complex (SC). this structure starts to form early in meiotic prophase I. first, proteins names SYCP2 and SYCP3 attach to each of the 2 homologous chromatin structures that are to be paired. this makes up the lateral elements of the SC. the lateral regions then align and attach via a central region (made of SYCP1 and many other proteins). both the lateral and central regions together form the SC, and essentially work like a zipper to connect homologous chromosomes. see pg 233/phone for pic while no physical connection has yet been shown btwn the synaptonemal complex and recombination machinery, its been demonstrated that SC formation and recombination are interdependent. both happen around the same time of meiosis, and work on mice w defective synaptonemal complex formation or recombination shows that these 2 processes rely on one another. when synaptonemal complex formation is inhibited, recombination is disturbed, and vice versa. after prophase I is metaphase I. in meiotic metaphase I, alignment along the metaphase plate occurs, as in mitosis. the difference is that in meiotic metaphase I, the tetrads are aligned at the center of the cell (the metaphase plate), whereas in mitosis, sister chromatids are aligned on the metaphase plate. in anaphase I, homologous chromosomes separate, and sister chromatids remain together. the cell then divides into 2 cells during telophase I. it is important to note that at this point the cells are considered to be haploid**. each cell has a single set of chromosomes. the chromosomes, however, are still replicated (still exist as a pair of sister chromatids). the whole point to the second set of meiotic divisions is to separate the sister chromatids so that each cell has a single set of unreplicated chromosomes. see pg 234/phone for pic in some species, meiosis II begins immediately after telophase I, while in other species, there is a period of time before meiosis II begins. in either case, there is no further replication of the dna before the second set of divisions. the movements of the chromosomes during meiosis II are identical to the movements in mitosis, with the sole difference being that in meiosis II there is a haploid number of chromosomes, while in mitosis there is a diploid number, the sister chromatids are separated during anaphase II, and after telophase II is complete, four haploid cells have been produced from a single diploid parent cell. see pg 234/phone for pic

Golgi apparatus

modification and sorting of protein, some synthesis. 1 membrane surrounding the Golgi apparatus is a group of membranous sacs stacked together like collapsed basketballs. it has the following functions: 1. modification of proteins made in the RER; especially important is the modification of oligosaccharide chains. 2. sorting and sending proteins to their correct destinations. 3. the golgi also synthesizes certain macromolecules, such as polysaccharides to be secreted. the vesicle traffic to and from the golgi apparatus is mostly unidirectional; the membrane-bound or secreted proteins which are to be sorted and modifed enter at one defined region and exit at another. (traffic is said to be mostly unidirectional bc on occasion, proteins that are supposed to reside in the ER accidentally escape, and must be returned to the ER from the Golgi. this is called "retrograde traffic.") each region of the Golgi has different enzymes and a different microscopic appearance. the portion of the Golgi nearest the RER is called the cis stack, and the part farthest from the RER is the trans stack. the medial stack is in the middle. (note cis means near, as in cis double bond. trans means far. medial means in the middle. also note the order is alphabetical: cis-medial-trans) vesicles from the ER fuse with the cis stack. the proteins in these vesicles are then modified and transferred to the medial stack where they are further modified before passing to the trans stack. proteins leave the golgi at the trans face in transport vesicles. (if vesicle fusion w the cis Golgi was inhibited, could plasma membrane proteins still reach the cell surface? - no. secretory proteins must proceed via a specific path: from the ER to the cis Golgi to the medial and trans Golgi and from there to the cell surface.) the route taken by a protein is determined by signals within the protein that determines which vesicle a protein is sorted into in the trans Golgi. when a vesicle moves from the trans golgi toward the cell surface, it fuses w the cell membrane. as a result, the contents of the vesicle are released into the extracellular environment in a process termed exocytosis. alternatively, if the vesicle contains proteins anchored to its membrane, these proteins will remain attached to the cell as cell-surface proteins. some proteins are sent in vesicles from the golgi immediately to the cell surface, in the constitutive secretory pathway. constitutive connotes continuous or unregulated. in contrast, specialized secretory cells )like pancreatic cells, b-cells of the immune system, etc) store secrtory proteins in secretory vesicles and release them only at certain times, usually in respone to a change in (or signal from) the extracellular environment. this is a regulated secretory pathway.

■ Innate immune system cells o Macrophages

monocytes: macrophage - phagocytose debris and microorganisms; amoeboid motility; chemotaxis

bone growth and cells

most bone growth occurs by endochondral ossification, in which hyaline cartilage is produced and then replaced by bone. intramembranous ossification refers to synthesis of bone from an embryonic tissue called mesenchyme. this tissue is found in layers, thus intramembranous ossification results in flat bones (like bones of the skull). growth of long bones: in childhood, epiphyseal plate btwn diaphysis and epiphysis. epiphyseal plate is a disk of hyaline cartilage that is actively being produced by chondrocytes. as the chondrocytes divide, the epiphysis and diaphysis are forced apart. then the cartilage is replaced by bone (ossified). this process is stimulated by growth hormones and rate of ossification is slightly faster than rate of chondrocyte cell division (cartilage growth). at 18 the diaphysis and epiphysis meet and fuse together and lengthening can no longer occur. this fusion of epiphyses is seen in X-rays and used to notify adolescents when they have stopped growing taller. epiphyseal line is the fusion point in adults. during adulthood, bones don't elongate. however bone is continually degraded and remade in a process termed remodeling. the cells which make bone by laying down collagen and hydroxyapatite are called osteoblasts. the osteoblast synthesizes bone until it is surrounded by bone. the space it is left in is now called a lacuna, and the osteoblast is now called an osteocyte. cells called osteoclasts continually destroy bone by dissolving hydroxyapatite crystals. the osteoclast is a large phagocytic cousin of the macrophage. bone destroyed by osteoclasts must be replaced by osteoblasts. an increased ratio of osteoclast to osteoblast activity results in liberation of calcium and phosphate into blood stream (and a decreased ratio has the opposite effect). thus activity of these cells is important not only for bone structure but also for maintenance of proper blood levels of calcium and phosphate. the hormones PTH (parathyroid hormone), calcitonin, and calcitriol (derived by the kidney from vitamin D) regulate their activity and thus blood calcium levels. PTH and calcitriol inc blood calcium, and calcitonin reduces it. PTH cause bone resorption by stimulating osteoclasts. calcitonin inhibit osteoclasts, preventing bone resorption. excessive vit d result inc calcium absorption in small intestine and more likely subsequent bone formation. thyroxine is not involved in calcium regulation.

effectors

motor neurons carry info from nervous system to organs which can act upon that information, known as this. 2 types are muscles and glands

efferent neurons

motor neurons. efferents go to effectors

ventilation

movement of air in and out of the lungs

mrna in transcription

mrna doesn't stay bound to the dna template strand for any length of time, regardless of half-life. as mrna is transcribed, the dna helix reforms immediately behind it, releasing the mrna from the transcription bubble as it is synthesized.

repeated sequences: tandem repeats

much of our genome is single copy, meaning there is one copy of the gene in a haploid set of the genome. this is true for most eukaryotic genes that code for proteins. however, genomes also have regions of tandem repeats, where short sequences of nucleotides are repeated one right after the other, from as little as 3 to over 100 times. the human genome has over a thousand regions of tandem repeats. repeats can be unstable, when the repeating unit is short (such as di- or trinucleotides) or when the repeat itself is very long. unstable tandem repeats can lead to chromosome breaks and some have been implicated in disease. tandem repeats often show variations in length btwn individuals, which can be useful in dna fingerprinting. heterochromatin, centromeres, and telomeres are all rich in repeats

movement of joints (skeletal muscle)

muscles attached to bones by tendons, connective tissue formed of collagen. muscle cannot expand by force it can only contract to cause force on bones and movement. skeletal muscles can move a joint by flexing (reducing the angle of the joint), extending (increasing the angle of the joint), by abducting (moving away from the body's midline) or adducting (moving toward midline). one of the 2 bones joined by a skeletal muscle is generally closer to the center of the body and tends to stay in place when the muscle contracts. the point on this bone where the muscle attaches is called the origin of that skeletal muscle and the point where the muscle attaches on the bone more distant from the center of the body is the insertion. insertion is brought to origin during contraction. antagonistic - muscles that are responsible for movement in opposite directions synergistic- muscles that move a joint in the same direction connective tissue holds contractile tissue together in bundles called fascicles to allow flexibility within the muscle. myofibers, muscle fibers, skeletal muscle cell. skeletal muscle cells are multinucleate syncytial formed by the fusion of individual cells during development. innervated by a single nerve ending and stretch entire length of the muscle. cell membrane is the sarcolemma made of plasma membrane and layer of polysaccharide and collagen for the cell to fuse w tendon fibers. within each myofiber there are many myofibrils. its like a specialized organelle. responsible for striated appearance and generates contractile force. proteins in myofibril that generate contraction are polymerized actin and myosin. actin polymerizes to form thin filaments visible under the microscope, and myosin forms thick filaments. striated appearance of skeletal muscle is due to overlapping arrangement of bands of thick and thin filaments in sarcomeres. a myofibril is composed of many sarcomeres aligned end to end. each sarcomere is bound by 2 Z lines. thin filaments which is actin attach to each z line and overlap w thick filaments myosin in the middle of each sarcomere; the thick filaments aren't attached to z lines. the regions of the sarcomere composed only of thin filaments are I bands. full length of thick filament represents A band within each sarcomere; this includes both overlapping regions of thick and thin filaments (where contraction is generated), as well as region composed of only thick filaments (seen in resting sarcomeres only and is the H zone).

(-) rna viruses

must carry rna dependent rna pol (and of course, encode it too) the genome of a (-) RNA virus is complementary to the piece of rna that encodes viral proteins. in other words, the genome of a (-) RNA virus is the template for viral mrna production. if host ribosomes translate (-) rna, useless polypeptides will be made. hence the virus must not only encode an rna dependent rna polymerase, it must actually carry one with it in the capsid. when the virus enters the host cell, this enzyme will create a (+) strand from the (-) genome. then the viral life cycle can proceed. (-) rna viruses causes rabies, measles, mumps, and influenza. do (-) strand rna viruses use host enzymes to catalyze rna production in transcription or in replication of the genome? - neither. viral rna dependent rna polymerase first makes (+) strand as mrna and then uses the (+) strand as the template to replicate new (-) strand genomes

(+) RNA viruses

must encode RNA dependent rna pol (and don't have to carry it) a (+) RNA virus, with a single stranded rna genome, is the simplest imaginable type of viral genome. (a piece of single stranded viral rna which serves as mrna is called (+) rna.) as soon as the (+) rna genome is in the host cell, host ribosomes begin to translate it, creating viral proteins. the viral genome acts directly as mrna. the technical way to describe this scenario is to say the genome is infective, meaning injecting an isolated genome into the host cell will result in virus production. in order for the virus to replicate itself, one of the proteins it encodes must be an rna-dependent rna polymerase, the role of which is to copy the rna genome for viral replication; the host never makes rna from rna. (+)rna viruses causes the common cold, polio, and rubella.

retroviruses

must encode reverse transcriptase hiv, the virus that causes aids, and htlv (human T-cell leukemia virus) are examples of retroviruses. these are (+) rna viruses that undergo lysogeny. in other words, they integrate into the host genome as proviruses. in order to integrate into our double-stranded dna genome, a viral genome must also be composed of double-stranded dna. since these viral genomes enter the cell in an rna form, they must undergo reverse transcription to make dna from an rna template. this snubbing of the central dogma is accomplished by an rna dependent DNA polymerase (reverse transcriptase) encoded by the viral genome. retroviruses are theoretically not required to carry this enzyme, only to encode it. (why? - bc the viral rna genome can be translated by host ribosomes; thus reverse transcriptase may be made after the viral genome enters the host. it just so happens that HIV does carry its reverse transcriptase within its capsid. you should understand why this isn't a theoretical necessity.) the 3 main retroviral genes are gag (codes for viral capsid proteins), pol (polymerase codes for reverse transcriptase) and env (envelope codes for viral envelope proteins.)

oncogenes

mutated genes that induce cancer. normally these genes are required for proper growth of the cell and regulation of the cell cycle. oncogenes then are genes that can convert normal cells into cancerous cells. sometimes these are abnormal versions of standard cellular growth genes. sometimes the genes enter the cell bc of a viral infection. (teratomas are tumors w formed tissues from multiple germ layers. what steps might lead to their formation? - teratomas form when oncogenes cause certain tissues to dedifferentiate (lose their specific function and regress), and then dedifferentiate to become something different. this is why teratomas can contain tissues such as teeth and hair.)

frameshift mutation

mutations that cause a change in the reading frame. generally speaking, they are very serious. note that a frameshift can lead to premature termination of translation (yielding an incomplete polypeptide) if it results in the presence of an abnormal stop codon. not all insertions or deletions are frameshift mutations; if you insert or delete one whole codon or several whole codons, you add or remove amino acids to the polypeptide without changing the reading frame

intermediate filaments

named for their thickness, which is btwn that of microtubules and microfilaments. unlike microtubules and microfilaments, intermediate filaments are heterogeneous, composed of a wide range of polypeptides. another difference is that intermediate filaments are more permanent, whereas microfilaments and microtubules are often disassembled and reassembled as needed by the cell. intermediate filaments appear to be involved in providing strong cell structure, such as in resisting mechanical stress.

which is larger, the cardiac output of the right ventricle or of the left ventricle?

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

2 sources of genetic variation in a population

new alleles and new combinations of existing alleles. new alleles are the result of mutations in the genome. new combinations of alleles are generated during sexual reproduction as a result of independent assortment, recombination and segregation during meiosis

can a neuron change the neurotransmitter it releases

no

a disease agent that is isolated from a human cannot reproduce on its own in cell-free broth but can reproduce in a culture of human cells. in its pure form it possesses both RNA and DNA. is it possible that the disease agent is a virus?

no it can't be a virus. viruses posses only one kind of nucleic acid. the disease agent is another kind of obligate intracellular parasite (certain bacteria can only reproduce inside host cells, eg Chlamydia)

after integration of a retrovirus into the cellular genome, a reverse transcriptase inhibitor is added to the cell. will the production of new viruses be blocked?

no it will not. reverse transcriptase is required for only one phase of the retrovirus life cycle: the copying of the viral rna genome into dna so that it can integrate into the host genome and be transcribed. once the viral genome has integrated, transcription to produce viral mrna and new viral rna genomes doesn't involve reverse transcriptase. it can proceed with the normal host-cell enzymes

is epinephrine secreted by a duct into the bloodstream?

no. endocrine hormones are not secreted through ducts

can mrna coding for a protein destined to be embedded in the plasma membrane associate with rough er prior to the initiation or translation?

no. it is the signal peptide in the nascent polypeptide that is recognized and bound by SRP and talent o receptors in the surface of the RER. the signal is an amino acid sequence on the nascent polypeptide, not a nucleotide sequence on mrna.

if a mutation occurs in a muscle cell of an individual who then has many progeny, does this mutation increase genetic variation in the population?

no. mutation must occur in the germ line to introduce a new allele into a population. a mutation in a somatic cell cannot be passed on to the next generation.

will an infectious virus be produced if the genome of an enveloped (+) strand RNA virus is added to an extract prepared from the cytoplasm of eukaryotic cells that retains translational activity but lacks dna replication or transcription of host genes?

no. the (+) strand RNA virus will be able to produce viral genome and proteins, but progeny will not be able to acquire the envelope they need to be infectious

is it likely that the 3 nucleotides of the anticodon contribute to the tertiary structure of trna by base-pairing with other nucleotides in the chain?

no. they must be available for base pairing with the codon

Would thyroid hormone affect isolated mitochondria directly?

no. thyroid hormone affects mitochondria indirectly, through the regulation of nuclear genes

can viruses move viral flagellular propulsion to find host cells?

no. viruses lack any means of energy production on their own and any means of active movement. they rely on diffusion to find host cells

which one of the following can create new alleles in a population? A non-random mating B random drift C recombination D deletion

nonrandom mating and random drift will alter allele frequencies but do not create new alleles (A and B are incorrect). recombination will not alter allele frequencies or create new alleles, but create new combinations of alleles (C is wrong). the correct answer is D. only mutation of the genome can create new alleles. a deletion can create a new allele, even if the new allele is a truncated gene product or doesn't express any gene product at all

protooncogenes

normal versions of the genes that allow for regular growth patterns, but can be converted into oncogenes under the right circumstances. conversion may be due to mutation or bc of exposure to a mutagen. uv radiation (sunlight or tanning booth) and various chemicals (benzene) are examples of common mutagens.

If the hypothalamic-hypophysial portal circulation is severed, how does this affect the function of the pituitary?

normally the pituitary receives hormones directly from the hypothalamus. if the portal system is severed, hormones must take a longer route and will be diluted and degraded before they reach the pituitary. as a result, secretion by the pituitary will not be effectively regulated by the hypothalamus

how might a dec in temp inc bacterial growth rate

normally you expect dec temp to dec the rate of all chemical, biochemical, and biological processes, since reactions accelerate when kinetic energy increases. however bacteria that have evolved to live at low temperature (psychrophiles) possess enzymes that may be optimally active at low temperature, leading to better growth)

good and bad mutations

not all mutations are bad. some are beneficial. many are neutral, and have no effect. mutations can also be disease causing. in some cases, one mutation is sufficient to induce a diseased state. in other cases, many mutations have to cooperate and occur together to cause a disease

frequency of recombination

number of recombinant phenotypes resulting from a cross divided by the total number of progeny. RF = recombination frequency = number of recombinants / total number of offspring the farther apart two genes are on a chromosome, the more likely recombination will occur btwn the genes during meiosis. if the genes are located far enough apart, recombination will occur so frequently btwn the genes that they will no longer display linkage and will assort as independently as if they were on separate chromosomes. since the frequency of recombination is proportional to the physical distance of genes from each other, it can be used as a tool to map genes in relation to each other on chromosomes. max freq of recombination is the calculation of when there is no linkage and genes assort independently

vitamins

nutrients which must be included in the diet bc they can't be synthesized in the body

x-linked traits

observed quite frequently and can be x-linked recessive or x-linked dominant. there are several well-studied examples of x-linked recessive traits that are common in the human population; hemophilia is an example. women are often carriers of x-linked recessive alleles but will only express x-linked traits when they are homozygous. men are homozygous for x-linked traits; they have only one copy of genes on the X chromosome. as a result, males always express recessive x-linked alleles. these traits tend to affect males more than females

oxidative stress

occurs when the lvl of production of reactive oxygen species outstrips the cell's ability to detoxify them. this can include increased lvls of peroxides or free oxygen, which then generates radicals. while reactive oxygen species are normally produced as part of metabolism, at high untreated lvls they can damage dna, cellular proteins, and even lipid bilayers. as such, oxidative stress is linked to cancer, since the damage it can cause sets up conditions in the cell to allow oncogenes to become active and cell growth to be impacted. though the potential for damage exists, creating oxidative stress is also a component of the immune system. activated phagocytes may produce nitric oxide or superoxide (O2 -) in order to broadly kill pathogens. the effect on foreign cells needs to be balanced against the damage being caused to host tissues.

double-stranded dna viruses

often encode enzymes required for dNTP synthesis and dna replication these viruses often have large genomes that include genes for enzymes involved in deoxyribonucleotide synthesis (which we do whenever we make dna) and dna replication. (given the limited information that viruses may contain in their genomes, why carry around genes for an enzyme possessed by the host? - the host cell will only make dNTPs in preparation for replication. if the virus wants to reproduce without waiting for the host to do so, it must encode its own enzymes for the synthesis of dna building blocks why don't rna viruses do this? - transcription is always occurring in all cells, so NTPs (not dNTPs) are always present what is a factor likely to limit the size of rna genomes? - the error rate in rna synthesis is much higher than in dna synthesis, in part bc there are mechanisms to proofread and correct errors in dna synthesis (but not in rna synthesis). if an rna genome were too large, every copy of the viral genome synthesized would suffer from so many errors that no infectious virus would be produced. some dna viruses induce infected host cells to enter mitosis and may even override cellular inhibition of cell division so strongly that the cell becomes cancerous; what is the advantage to the virus of inducing host-cell division? - to replicate, the DNA virus must either provide all of the necessary components (such as dNTPs) itself, infect a cell that is already dividing, or induce the cell it infects to enter mitosis and produce the ingredients for dna synthesis)

testcross

one individual of unknown genotype crossed to another individual that has a homozygous (or purebreeding) recessive genotype. the presence of all recessive alleles in one parent allows alleles from the other parent to be displayed phenotypically. the progeny are called the F1 generation

spermatogenesis

only one process in a human involves meiosis; gametogenesis. process where diploid germ cells undergo meiotic division to produce haploid gametes. meiotic cell division fosters genetic diversity in the population (by independent assortment of genes and by recombination). the gametes produced by the male are spermatozoa, sperm. females produce ova, eggs. the role of the sperm is to swim through the female genital tract to reach the egg and fuse with it. this fusion is known as syngamy, and results in a zygote. the gametes produced by males and females differ dramatically in structure but contribute equally to the genome of the zygote (except in the special case of the 2 different sex chromosomes, X and Y given to male offspring). although both gametes contribute equally to the genome the egg provides every other part of the zygote, since the only part of the sperm which enters the egg is a haploid genome. this is maternal inheritance. for ex mitochondrial inherited maternally. sperm synthesis is called spermatogenesis. it begins at puberty and occurs in the testes throughout adult life. the seminiferous tubule is the site of spermatogenesis. the entire process of spermatogenesis occurs w the aid of the specialized sustentacular cells found in the wall of the seminiferous tubule. immature sperm precursors are found in the outer wall of the tubule, and nearly mature spermatozoa are deposited into the lumen; from there they are transported to the epididymis. the cells that give rise to spermatogonia (and to their female counterparts, oogonia) are germ cells; under the right conditions, they germinate, and give rise to a complete organism. final stages of sperm maturation occur in epididymis. when they first enter epididymis, spermatozoa are incapable of motility. many days later, when they reach the ductus deferens, they are fully capable of motility. but they remain inactive due to the presence of inhibitory substances secreted by the ductus deferens. this inactivity causes sperm to have a very low metabolic rate, which allows them to conserve energy and thus remain fertile during storage in the ductus deferens for as long as a month. spermatids develop into spermatozoa in the seminiferous tubules with the aid of sustenacular cells. the dna condenses, the cytoplasm shrinks, and the cell shape changes so that there is a head, containing the haploid nucleus and the acrosome, and a flagellum which forms the tail. theres is also a neck region at the base of the tail, which contains many mitochondria. these mitochondria get their energy from the fructose which the seminal vesicles contribute to the semen and from vaginal secretions. the acrosome is a compartment on the head of the sperm that contains hydrolytic enyzmes required for penetration of the ovum's protective layers. bindin is a protein on the sperm's surface that attaches to receptors on the zona pellucida surrounding the ovum.

oogenesis and ovulation

oogenesis begins prenatally. in the ovary of a female fetus, germ cells divide mitotically to produce large numbers of oogonia. oogonia not only undergo mitosis in utero but they also enter the first phase of meiosis and are arrested in prophase I (as primary oocytes). the number of oogonia peaks at about 7 million at mid gestation (20 weeks into fetal life). at this time mitosis ceases, conversion to primary oocytes begins, and there is a progressive loss of cells. only about 400 oocytes are every actually ovulated (released) in the average woman and the remaining 99.9% will simply degenerate. primary oocytes formed in a female fetus can be frozen in prophase I of meiosis for decades, until they reenter the meiotic cycle. beginning at puberty and continuing on a monthly basis hormonal changes in the woman's body stimulate completion of the first meiotic division and ovulation. this meiotic division yields a large secondary oocyte (containing all of the cytoplasm and organelles) and a small polar body (containing half the dna but no cytoplasm or organelles). polar body (called the first polar body) remains in close proximity to the oocyte. the second mitotic division (ie completion of oogenesis) occurs only if the secondary oocyte is fertilized by a sperm; this division is also unequal, producing a large ovum and the second polar body. note that if fertilization does occur the nuclei from the sperm and egg don't fuse immediately. they must wait for the secondary oocyte to release the second polar body and finish maturing to an ootid and then an ovum. finally the 2 nuclei fuse and a diploid (2n) zygote is formed. the primary oocyte is not an isolated cell. it is found in a clump of supporting cells called granulosa cells, and the entire structure (oocyte plus granulosa cells) is a follicle. the granulosa cells assist in maturation. an immature primary oocyte is surrounded by a single layer of granulosa cells, forming a primordial follicle. as the primordial follicle matures, the granulosa cells proliferate to form several layers around the oocyte, and the oocyte itself forms a protective layer of mucopolysaccharides termed the zona pellucida. there may be several follicles in the ovary, they are surrounded and separated by cells termed thecae cells. stimulated by leutinizing hormone. of the several maturing follicles only one progresses to the point of ovulation each month; all other degernate. the mature follicle is known as a Graafian follicle. during ovulation the Graafian follicle bursts, releasing the secondary oocyte w its zona pellucida and protective granulosa cells into Fallopian tube. at this point the layer of granulosa cells surrounding the ovum is known as corona radiata. follicular cells remaining in ovary after ovulation form a new structure called corpus luteum. estrogen is made and secreted by the granulosa cells (w help from the thecal cells) during the first half of the menstrual cycle. both estrogen and progesterone are secreted by the corpus luteum during the second half of the cycle. estrogen is a steroid hormone that plays an important role in the development of female secondary sexual characteristics in the menstrual cycle and during pregnancy. estrogen exerts its effects on a cell by: a cytoplasmic receptor binds estrogen and binds to specific dna elements in promoters and enhancers to regulate transcription. progesterone is also a steroid hormone involved in the hormonal regulation of the menstrual cycle and pregnancy, but with different effects than estrogen.

ligand-gated ion channels

open an ion channel upon binding a particular neurotransmitter

divergent evolution

opposite of convergent evolution. divergent selection causes cladogenesis, which is branching speciation, where one species diversifies and becomes 2 or more new species.

eukaryotic genome

organized into linear molecules of double-stranded dna, while the genome of prokaryotes is a single circular dna molecule. the large size of the typical eukaryotic genome appears to make it necessary to split the genome into pieces, each a separate linear dna molecule, termed a chromosome. yeast have 4 different chromosomes, while there are 23 different human chromosomes. since humans and most adult animals are diploid they have 2 copies of each chromosome (except for the sex chromosomes). chromosomes have a centromere near the middle to ensure that newly replicated chromosomes are sorted properly during cell division, one copy to each daughter cell (mitosis and meiosis). each eukaryotic chromosome also has special structures at both ends termed telomeres. telomeres have large numbers of repeats of a specific DNA sequence and, with the help of a special DNA polymerase termed telomerase, maintain the ends of the linear chromosomes during dna replication. [what special problems are there in replicating the 5' ends of linear DNA chromosomes? - dna pol cannot synthesize dna without an rna primer and can't synthesize dna in a 3' to 5' direction. it will replciate dna from an rna primer at (or very near to) the end of the chromosome, but the rna primer cannot be replaced w dna. w each round of replication, the chromosome grows shorter and shorter bc of the inability to synthesize dna at its very ends. bc of the large number of repeated sequences at the ends (the telomeres), the loss of a little bit of dna is usually not critical. however, eventually all the telomere sequences are lost, and gene sequences start to be lost. if the lost gene sequence is critical for cell function, the cell will die at this point. telomerase helps prevent this problem. this unique enzyme contains an rna sequence and acts as a reverse transcriptase, utilizing this rna sequence as a template to extend the dna at the end of the chromosome. this provides a location where a normal primer can be synthesized and dna replication can proceed along the very end of the chromosome, preserving it. note that telomerase is turned off in most cells, and its inactivity is implicated in cell aging and death] within each chromosome is also a portion of the many thousands of genes in the genome as a whole. genes can be mapped genetically and physically to the chromosome they reside on and to a specific location on that chromosome, a locus. the expression of eukaryotic genes is regulated by specific promoter and enhancer elements of that gene, but can also be affected by the position of the gene on the chromosome. some regions of a chromosome are folded into densely packed chromatin, termed heterochromatin, within which genes tend to be inaccessible and turned off. other regions known as euchromatin are more loosely packed (although still packaged into chromatin) and allow genes to be activated). [if a retrovirus inserts its genome into regions of heterochromatin and nowhere else, how is this likely to affect the infection process? - the retroviral genes will not be expressed very frequently, and the virus will tend to remain as a provirus unless a change in the surrounding heterochromatin allows viral genes to be expressed] finally, the nucleus is not a loose membrane bag with dna floating inside. if nuclei are treated with DNase and with detergent, an insoluble mesh of protein, known as the nuclear matrix or nuclear scaffold, is left behind. the role of the nuclear matrix may be in part analogous to the role of the cytoskeleton in the cytoplasm: to support and provide overall structure. the matrix may also play a role in regulating gene expression. the dna in chromosomes is attached to the matrix at specific sites, and these (in some cases) appear to be involved in regulating gene expression or in limiting the effects of promoters and enhancers to discrete chromosomal regions known as domains. the role of the nuclear matrix is an area of ongoing research

osmotic pressure

osmosis describes the net movement of water across a semipermeable membrane from a region of low solute concentration to a region of higher solute concentration in an effort to dilute the high concentration solution. the semipermeable membrane prohibits the transfer of solutes, but allows water to transverse through it. see pg 194/phone for pic osmotic pressure (Π) can be defined as the pressure it would take to stop osmosis from occurring. if a pressure gauge were added to the same system (in pic), osmotic pressure could be measured. the osmotic pressure of a solution is given by the van't Hoff equation: Π=MiRT where Π is osmotic pressure in atm, M is the molarity of the solution, i is the van't Hoff factor, R is the universal gas constant (0.0821 L-atm/K-mol), and T is the temperature in kelvins again, changes in osmotic pressure are affected only by the number of particles in solution (taking into account the van't Hoff factor), not by the identity of those particles

oxygen utilization and tolerance of bacteria

oxygen metabolism is aerobic metabolism. bacteria which require oxygen are called obligate aerobes. bacteria which do not require oxygen are called anaerobes. there are 3 subcategories: facultative anaerobes will use oxygen when it's around, but they don't need it. (how much more atp can they make per glucose molecule when O2 is present? - 16 times as much.) tolerant anaerobes can grow in the presence or absence of oxygen but don't use it in their metabolism. obligate anaerobes are poisoned by oxygen. this is bc they lack certain enzymes necessary for the detoxification of free radicals which form spontaneously whenever oxygen is around. (the enzymes include superoxide dismutase (converts O2 - to H2O2) and catalase (converts H2O2 to H2O + O2). an example of a harmful O2 by product is superoxide anion, O2 -.) obligate anaerobes commonly infect wounds

■ Oxygen transport by blood o Hemoglobin, hematocrit o Oxygen content o Oxygen affinity

oxygen too hydrophobic to dissolve in plasma in significant quantities so RBCs used to bind and carry it. hemoglobin complex protein composed of 4 polypeptide subunits. each subunit has one molecule of heme which is a large multiring structure that has a single iron atom mount at its center. the role of heme with its iron atom is to bind O2. since each hemoglobin has 4 subunits and each subunit has one heme, each molecule of hemoglobin can carry 4 molecules of oxygen. hemoglobin has some important properties which make it an excellent oxygen carrier. tense conformation has relatively low affinity for oxygen, when none of the subunits have oxygen bound. relaxed state - higher affinity than tense. when one of the subunits binds oxygen. ? hemoglobin binds oxygen cooperatively** (subunits affinity connected?) important for ability to transport oxygen efficiently. high affinity in lungs, low affinity in tissues, so pick up a lot in lungs and release a lot for tissues that need it. certain factors stabilize the tense configuration (which has a low O2 affinity). these factors are: 1 decreased pH 2 increased PCO2 (lvl of CO2 in the blood) and 3 increased temperature the fact that these factors stabilize tense hemoglobin and thus reduce its oxygen affinity is the Bohr effect. these factors characterize environment within active tissues (whwer oxygen is most needed!) sigmoidal shape of % sat vs PO2 curve resembles behavior of cooperative enzymes

insulin

peptide hormone

glucagon

peptide hromone

all hypothalamic and pituitary hormones are

peptides

why might a bacteriaphage inject its dna, while animal viruses don't?

phage must puncture the bacterial cell wall, while animal viruses can be internalized whole into animal cells (since they do not have a cell wall)

homologous structures

physical features shared by 2 different species as a result of a common ancestor

pili

pili are long projections on the bacterial surface involved in attaching to different surfaces. the sex plus is a special pilus attaching F+ (male) and F- (female) bacteria which facilitates the formation of conjugation bridges. fimbriae are smaller structures that aren't involved in locomotion or conjugation but are involved in adhering to surfaces. (what other bacterial structure is involved in adhering to surfaces? is it possible that the fimbriae play a role in infection by pathogenic organisms? - the capsule, or glycocalyx is also involved in adherence. and yes, fimbriae do play a role in infection, by facilitating adhesion to cells so that the bacteria can colonize a tissue)

■ Composition of blood o Plasma, chemicals, blood cells o Regulation of plasma volume

plasma - liquid portion formed elements - cellular elements of blood plasma accounts for 55% of volume of blood and consists of items dissolved in water: electrolytes, buffers, sugars, blood proteins, lipoproteins, CO2, O2, and metabolic waste products. electrolytes refer to Na+ K+ Cl- Ca2+ and Mg2+ ions. buffers in the blood maintain constant pH of 7.4; principal blood buffer is bicarbonate (HCO3-) principal sugar in the blood is glucose. a constant concentration must be maintained so that all the cells of the body receive adequate nutrition. blood proteins, most of which are made by the liver, include albumin, immunoglobulins (antibodies), fibrinogen, and lipoproteins. albumin is essential for maintenance of oncotic pressure (osmotic pressure in capillaries due only to plasma proteins). the immunoglobulins are a key part of the immune system. fibrinogen is essential for blood clotting (hemostasis). lipoproteins are large particles consisting of fats, cholesterol, and carrier proteins. their role is to transport lipids in the blood stream. CO2 and O2 involved in respiration. Co2 important for role in buffering the blood (Co2 + H2O <> H2CO3 <> HCO3- + H+.) the principal metabolic waste product is urea, a breakdown product of amino acids. urea is basically a carrier of excess nitrogen. there are other important waste products too like bilirubin, a breakdown product of heme hematocrit - volume of blood occupied by red blood cells leukocytes white blood cells and platelets account for a small volume all the formed elements in the blood develop from special cells in the bone marrow known as bone marrow stem cells. serum is similar to plasma but lacks all the proteins involved in clotting

renal regulation ph

plasma ph too high, HCO3 - excreted in urine. plasma ph too low, H+ excreted carbonic anhydrase is involved. involved in epithelial cells in neprhon, excepts squamous flat cells of thin parts of loop of hence. carbonic anhydrase catalyzes conversion of co2 into carbonic acid H2CO3 which dissociates into bicarbonate plus a proton. once this takes place kidney can reabsorb or secrete a bicarbonate or protons as needed. generally protons secreted and bicarbonate reabsorbed, the amounts are adjusted to adjust ph lungs exhal CO2 removing H2CO3 raising ph. hyperventilation rases plasma ph.

■ Coagulation, clotting mechanisms

platelets have no nuclei and limited liefspan. aggregate at site of damage to a blood vessel wall forming a platelet plug. this immediately helps stop bleeding. hemostasis is a term for the bodys mehcanism of preventing bleeding. other component of hemostatic response is fibrin. this is a threadlike protein wich forms a mesh that holds the platelet plug together. fibrin mesh dries, it becomes a scab, which seals and protects the wound. the plasma protein fibrinogen is converted into fibrin by a protein called thrombin when blleding occurs. a blood clot or thrombus is a scab ciruclaitng in the blood stream. calcium as well as many accessory proteins are necessary for activaiton of thrombin and fibrinogen. several of the proteins depend on vitamin K for thier funciton. defects in these proteins result in hemophilia an X linked recessive group of diseases.

prezygotic barriers

prevent formation of a hybrid zygote. such barriers may be: ecological- individuals who could otherwise mate live in different habitats, and thus cannot access each other temporal - individuals mate at different times of the day, season, or year behavioral- some species require special rituals or courtship behaviors before mating can occur mechanical - reproductive structures or genital organs of 2 individuals are not compatible (even if they court and attempt copulation) gametic- sperm from one species cannot fertilize the egg of a different species due to incompatibilities in the sperm-egg recognition system

postzygotic barriers to hybrization

prevent the development, survival, or reproduction of hybrid individuals and thus prevent gene flow if fertilization btwn 2 different species does occur. 3 types: hybrid inviability: hybrid offspring do not develop or mature normally, and normally die in the embryonic stage hybrid sterility: a hybrid individual is born and develops normally but doesn't produce normal gametes and thus is incapable of breeding (eg a mule is sterile) hybrid breakdown: when 2 hybrids mate successfully to produce a hybrid offspring, but this second generation hybrid is somehow biologically defective

rule of multiplication

probability of both of 2 independent events happening can be found by multiplying the odds of either event alone.

senescence

process of biological aging which occurs at both the cellular and organismal lvl. for eukaryotic cells, the length of the telomeres on the ends of chromosomes are a measure of cellular age; the longer the telomeres, the younger the cell. these sequences are meant to be maintained by the enzyme telomerase. research is being pursued as to whether the biological age of a cell can be reset if telomerases are manipulated to maintain the length of the telomeres. additionally, as cells age they become prone to apoptosis. though stressors can induce apoptosis earlier than expected, this mechanism of programmed cell death is also how organisms destroy and disassemble cells that need to be removed due to age. the cumulative effects of cellular senescence lead to the aging of the entire organism. the functioning of organs is affected to the point where the body stops working and death occurs. these effects can be hastened based on environmental exposures and beahviroal factors, but even without additonal stressors, senescence is inevitable for organisms.

mitochondria

produce atp via the Krebs cycle and oxidative phosphorylation. 2 membranes surrounding it mitochondria are the site of oxidative phosphorylation. the interior of mitochondira, the matrix, is bounded by the inner and outer mitochondrial membranes. the matrix contains pyruvate dehydrogenase and the enzymes of the Krebs cycle. the inner membrane is the location of the electron transport chain and ATP synthase and is the site of the proton gradient used to drive ATP synthesis by atp synthase. the inner membrane is impermeable to the free diffusion of polar substances, like protons, and is folded into the matrix in projections called cristae. the outer membrane is smooth and contains large pores that allow free passage of small molecules. the space btwn the membranes is called the intermembrane space. ATP produced within mitochondria is transported out into the cytoplasm to drive a great variety of cellular processes. [why is the inner membrane folded into cristae? - the folding of the membrane increases its surface area and allows for increased electron transport and ATP synthesis per mitochondrion. (folding is used elsewhere to inc surface area, such as in the kidney tubules and the lining of the small intestine).] [are the enzymes of glycolysis found in the matrix? - no, in the cytoplasm.] [if the inner membrane is impermeable, how does pyruvate get into the matrix where pyruvate dehydrogenase is located? - pyruvate is transported through the inner mitochondrial membrane by a specific protein in the membrane]. see pg 179/phone for pic mitochondria possess their own genome which is far smaller than the cellular genome and consists of a single circular dna molecule. (sound familiar?) it encodes rrna, trna, and several proteisn, including some components of the electron transport chain and parts of the atp synthase complex although most mitochondrial proteins are encoded by nuclear genes. even more curious, mitohcondira use a different system of transcription and translation than nuclear genes do. this includes a unique genetic code and unique rna polymerases, dna replication machinery, ribosomes, and aminoacyl-trna synthetases. in order to explain the fact that mitochondria possess a second system of inheritance, investigators have postulated that mitochondria originated as independent unicellular organisms living within larger cells. this is the endosymbiotic theory of mitochondrial evolution (endo = within; symbiotic = living together). in fact, if you compare a mitochondrion to a gram-negative bacterium, youll note that they look pretty similar. pay attention to where the enzymes of electron transport are located and the genome shape. (remember that bacterial electron transport depends on a proton gradient across the cell membrane. in a gram-negative bacterium, this membrane would correspond to the mitochondrial inner membrane) bc many unique mitochondrial polypeptides are encoded by the cellular genome and not the mitochondrial genome, it has been suggested that the genes coding for these proteins may have been transferred to the nuclear genome over time. [what difficulty may be encountered in translation of a mitochondrial gene moved to the nucleus? - the coding system of the cellular genome is different from that of the mitochondrial genome. one might wonder how our transcription and translation machinery could sensibly produce mitochondrial gene products.) mitochondria exhibit maternal inheritance. this means that mitochondria are inherited only from the mother, since the cytoplasm of the egg becomes the cytoplasm of the zygote. (the sperm contributes only genomic [nuclear] dna.) maternal inheritance departs from the rules of mendelian genetics, which state that traits are inherited from both parents. if a woman has a disease caused by an abnormal mality in her mitochondrial genome, what are the chances that her children will have the disease (assuming her mate does not have the disease)? - all of her children will have it, since they will inherit mitochondria exclusively from her. for a maternally inherited trait, it doesnt matter whether the father has it or not.

tumor suppressor genes

produce proteins that are the inherent defense system to prevent the conversion of cells into cancer cells. the 2 primary means of cancer prevention are to (a) detect damage to the genome and halt cell growth and division until the damage can be repaired, or (b) to trigger programmed cell death if the damage is too severe to be repaired. p53 is an example of a product of a common tumor suppressor gene. though normally at low lvls in cells, its production is scaled up when genetic damage or oncogene activity is detected, and if sufficient repair is not possible, p53 will cause the cell to die in a process referred to as apoptosis. see pg 212/phone

apoptosis

programmed cell death. allows a cell to shrink and die while simultaneously minimizing damage to neighboring cells and limiting the exposure of other cells to its cytosolic contents. the death of a cell is triggered by a stressor which may be external (such as nitric oxide, a toxin, or cytokines) or internal (such as when the level of the p53 tumor suppressor protein reaches a critical level). a family of proteases, referred to as caspases, is responsible for carrying out the events of apoptosis. they have a cysteine in their active site and they cleave their target proteins at aspartic acid sites, hence their name (c asp ases). caspases, like all potentially damaging enzymes, are produced in their inactive form as procaspases. 12 different caspases have been identified in humans and they are generally grouped into 2 categories, initiators and effectors. initiator caspases respond to extra or intracellular death signals by clustering together; this clustering allows them to activate each other. the activation of the initators leads to the activation of the effector caspases in a cascade of activation. effector caspases then cleave a variety of cellular proteins to trigger apoptosis. see pg 213/phone for pic

the first cells, prokaryotic or eukaryotic

prokaryotic

flagella (bacteria)

prokaryotic flagella are the predominant means of bacterial locomotion another item only some bacteria have are long, whip-like filaments known as flagella, which are involved in bacterial motility. a bacterium which possesses one or more flagella is said to be motile, bc flagella are the only means of bacterial locomotion. bacteria may be monotrichous (meaning they have a flagellum located at only one end), amphitrichous (meaning they have a flagellum located at both ends), or peritrichous (meaning that they have multiple flagella). the structure of the flagellum is fairly complicated, with components encoded by over 35 genes, but it can be broken down into a few major components: the filament, the hook, and the basal structure. the basal structure contains a number of rings that anchor the flagellum to the inner and outer membrane (for a gram-negative bacterium) and to serve to rotate the rod and the rest of the attached flagellum in either a clockwise or counterclockwise manner. the most important thing to remember about the prokaryotic flagellum is that its structure is different from the eukaryotic one (which contains a "9+2" arrangement of microtubules) see pg 152/phone for pic the rotation of the rod is powered by the diffusion of H+ down the proton gradient generated across the inner membrane by electron transport. bacterial motion can be directed toward attactants, such as food, or away from toxins, such as acid, in a process called chemotaxis. the connection btwn chemotaxis and flagellar propulsion is dependent upon chemoreceptors on the cell surface that bind attractants or repellents and transmit a signal that influences the direction of flagellar rotation. a good analogy would be the blind man's bluff game played by children, in which a person is blindfolded and moves randomly but selects among favorable or unfavorable movements toward the goal based on the responses "warmer" or "colder" (like chemoreceptors binding attractant or repellent and sending a signal to the bacteria to tumble or not to tumble). the response of flagellar rotation to chemical attractants (or repellents) is not dependent on an absolute concentration, but to a change in the concentration over time. thus as the bacterium moves throuogh the solution it is able to detect whether it is moving toward or away from the highest concentration and respond accordingly

saltatory conduction

rapid jumping conduction in myelinated axons

controlling gene expression at the rna lvl

regulation of transcription in prokaryotes regulation of transcription in eukaryotes

cell-surface receptors

receptors form an important class of integral membrane proteins that transmit signals from the extracellular space into the cytoplasm. each receptor binds a particular molecule in a highly specific lock-and-key interaction. the molecule that serves as the key for a given receptor is termed the ligand. the ligand is generally a hormone or a neurotransmitter. the binding of a ligand to its receptor on the extracellular surface of the plasma membrane triggers a response within the cell, a process termed signal transduction. many cancers result from mutant cell-surface receptors which constitutively relay their signal to the cytoplasm, whether ligand is present or absent. for ex, a growth factor exerts its effect by binding to a cell-surface receptor and constitutive activity of a receptor for the growth factor causes uncontrolled growth of the cell. there are 3 main types of signal-transducing cell-surface receptors: ligand-gated ion channels, catalytic receptors, and G-protein-linked receptors

Innate (non-specific) immunity

refers to general nonspecific protection the body provides against various invaders. simplest example is barrier of skin. principal components of innate immunity 1 skin is excellent barrier against entry of microorganisms 2 tears, saliva, blood contain lysozyme, an enzyme that kills some bacteria by destroying their cell walls 3 the extreme acidity of the stomach destroys many pathogens which are ingested with food or swallowed after being passed out of the respiratory tract 4 macrophages and neutrophils indiscriminately phagocytize microorganisms (not cell mediated immunity) 5 complement system is a group of about 20 blood proteins that can nonspecifically bind to surface of foreign cells, leading to their destruction

deletion (mutation)

removal of nucleotides from the sequence. can cause a shift in the reading frame. can involve thousands of bases. can be caused by transposons

key info about eukaryotes

replication bubbles, genome is several linear pieces of dna, one DNA polymerase, three rna polymerases, capping, tailing, and splicing of mrna prior to translation, monocistronic mrna, transcription in nucleus, translation in cytosol, larger ribosomes

fat-soluble vitamin

require bile acids for solubilization and absorption A D E K excess are stored in adipose tissue

propagation of action potential in cardiac muscle

requires voltage gated ion channels

fermentation vs respiration (bacteria)

respiration is glucose catabolism with use of an inorganic electron acceptor such as oxygen. in contrast, fermentation is glucose catabolism which doesn't use an electron acceptor such as O2; instead a reduced byproduct of glucose catabolism such as lactate or ethanol is given off as waste. why is fermentation necessary whenever an external electron acceptor is not used? - bc NAD+ must be regenerated from NADH for glycolysis to continue. in fermentation, the electrons are passed from NADH to a molecule other than O2, such as pyruvic acid

regulation of ventilation rate

respiratory control center in medulla of brain stem. increased PCO2, dec pH, dec PO2 (CO2 and pH primary regulatory and O2 secondary) chemical stimuli that affect ventilation rate. these variables are monitored by special autonomic sensory receptors. peripheral chemoreceptors are located in the aorta and the carotid arteries and monitor the PCO2, pH, and PO2 of the blood, while central chemoreceptors are found in the medullar respiratory control center, and monitor PCO2 and pH of the cerebrospinal fluid. recall that pH and PCO2 are connected through carbonic acid buffer system of blood CO2 <> H2CO3 <> H+ + HCO3 - respiration eliminates CO2 from the body. thus changes in ventilation rate can have rapid effects on pH due to the dec or inc in PCO2 and the resulting shift to maintain the above equilibrium. for ex a person hyperventilating during anxiety attack can have elevated pH. give them a paper bag to breathe into, forces them to rebreathe their exhaled CO2. this pushes equilibrium of equation to right and brings pH back down to normal. a person whose ventilation rate has been reduced due to extreme alcohol intoxication can become acidotic. similarly changes in pH can be compensated for by inc or dec ventilation rate. for ex, diabetics who are acidotic due to the metabolism of proteins and fats instead of glucose will have an increased ventilation rate to remove CO2 and increase pH. mechanical stimuli that affect ventilation rate include physical stretching of lungs and irritants. mehcanical stretching of lung tissue stimulates stretch receptors that inhibit further excitatory signals from the respiratory center to the muscles involved in inspiration. walls of bronchi and larger bronchioles contain smooth muscle. contraction of this smooth muscle is bronchioconstriction. irritation of inner lining of lung stimulates irritant receptors, and reflexive contraction of bronchial smooth muscle prevents irritants from continuing to enter. this contractile response is determined by parasympathetic nerves that release ach. during allergy attack, mast cells release histamine, which also causes bronchoconstriction. epinephrine opposes this; it increases ventilation by causing airway smooth muscles to relax (bronchodilation). irritant receptors in lung that trigger coughing and/or bronchoconstriction when an irritating chemical (smoke) is detected

cardiac muscle cells

resting membrane potential -90mv (very close to K+ equilibrium potential) phase 0 (depolarization) is again the upstroke of the action potential and is caused by the transient increase in Na+ conductance (just like in neurons). action potentials propagating through the intercalated discs stimulate myocytes to reach threshold for voltage-gated Na+ channels. once threshold is reached, the Na+ channels open and Na+ rushes into the cell Phase 1 (initial repolarization) the Na+ channels inactivate and K+ channels open. this leads to an efflux of K+ and a slight drop in cell potential. furthermore, the inc potential due to the initial Na+ influx causes the opening of voltage gated Ca2+ channels; this leads to phase 2, plateau pahse. during platuea, influx of Ca2+ ions balance K+ efflux from phase one, leading to a transient equilibrium in cell potential phase 3 (repolarization) occurs when Ca2+ channels close and K+ channels continue to allow K+ to leave the cell (again this is just like in nueonrs). phase 4 (resting membrane potential) is the period during which inward and outward current are equal. remember this is dictated by action of the Na+/K+ ATPase and slow K+ leak channels

translocation

result when recombination occurs btwn non homologous chromosomes. this can create a gene fusions, where a new gene product is made from parts of 2 genes that were not previously connected. this is a common occurrence in many types of cancer. translocations can be balanced (where no genetic information is lost), or unbalanced (where genetic information is lost or gained). see pg 87/phone for pic

■ Pulmonary and systemic circulation

right side of the heart pumps blood to the lungs and left side pumps blood to rest of the body. flow of blood from heart to the lungs and back to the heart is the pulmonary circulation, and the flow of blood from the heart to the rest of the body and back again is the systemic circulation.

microfilaments

rods formed in the in the cytoplasm from polymerization of the globular protein actin. actin monomers form a chain, and then 2 chains wrap around each other to form an actin filament. microfilaments are dynamic and are responsible for gross movements of the entire cell, such as pinching the dividing parent cell into 2 daughters during cell division, and amoeboid movement. amoeboid movement involves changes in the cytoplasmic structure which cause cytoplasm and the rest of the cell to flow in one direction.

leukocytes

role is to fight infection and dispose of debris. all are large complex cells w all the normal eukaryotic cell structures (nucleus, mitochondria, etc). some (macrophages and neutrophils) move by amoeboid motility (crawling). this is important bc they are able to squeeze out of capillary intercellular junctions (spaces btwn capillary endothelial cells) and can therefore roam free in the tissues, hunting for forming particles and pathogens. some wbcs exhibit chemotaxis, which is movement directed by chemical stimuli. the chemical stimuli can be toxins and waste products released by pathogens or can be chemical signals released from other white blood cells. there are 6 types of white blood cells

sinoatrial node

sa node initiation of each action potential that starts each cardiac cycle occurs automatically. in right atrium its cells act as pacemaker of the heart its action potential is commonly divided into 3 separate phases; phase 0, phase 3, phase 4 (other cardiac myocytes (muscle cells) additionally have phases 1 and 2, but the SA node doesn't) has an unstable resting potential. this is phase 4 (automatic slow depolarization) and is caused by special sodium leak channels that are repsonsible for its rhythmic, automatic excitation. thhis inward sodium leak brinds cell potential to threshold for voltage gated calcium channels; when they open they cause phase 0, the upstroke of the pacemaker potential. it is caused mianly by an inward flow of Ca2+. (note skeletal muscle cells and other myocytes depolarize bc of a Na+ influx, not the Ca2+ like the SA node.) this Ca2+ drives the membrane potential of the SA nodal cells towrad the positive Ca2+ equilibrium potential. note also that the Ca2+ channels operate more slowly than the Na+ channels, leading to a more gradual upsweepin the action potential. phase 3 is repolarization. it is caused by closure of the Ca2+ channels and opening of the K+ channels, leading to an outward flow of K+ from the cell. this loss of postiively charged K+ ions drives the membrane potential back down towrad the negative K+ equilibrium potential ...(didnt write)

saliva

salivary amylase (ptyalin) hydrolyzes starch, smallest fragment it breaks it into being disaccharide lingual lipase for fat digestion no digestion of proteins lysozyme which attacks bacterial cell walls (lytic phages also make lysozyme) so mouth also participates in innate immunity

pulmonary and aortic semilunar valves

set of valves btwn the large arteries and the ventricles. together these 2 valves are known simply as the semilunar valves

male reproductive system

scrotum - contains male gonads, which are testes (testicles). the scrotum is important for temperature regulation. sperm synthesis in the testes must occur at a few degrees below normal body temp. this is why the testes are located outside the body. relaxation of the scrotum facilitates cooling of the testes. when the environment is cold, the scrotum contracts, pulling the testes up against the body, warming them. the testes have 2 roles: 1 synthesis of sperm (spermatogenesis), and 2 secretion of male sex hormones (androgens, eg testosterone) into the bloodstream. site of spermatogenesis within the testes are the seminiferous tubules. the walls of the seminiferous tubules are formed by cells called sustentacular cells (Sertoli cells). sustentacular cells protect and nurture the developing sperm, both physically and chemically. the tissue btwn the seminiferous tubules is simply referred to as testicular interstitial. important cells found in the testicular interstitial are the interstitial cells (aka leydig cells). they are responsible for androgen (testosterone) synthesis. the seminiferous tubules empty into epididymis, a long coiled tube located on posterior of each testicle. the epididymis from each testicle empties into a ductus deferens (vas deferens) which in turn leads to the urethra. to get to the urethra, the ductus deferens leaves the scrotum and follows a path: enters inguinal canal, a tunnel that travels along the body wall toward the crest of the hip bone. (there are 2 inguinal canals, left and right). from the inguinal canal, the ductus deferens enters the pelvic cavity. near the back of the urinary bladder, it joins the duct of the seminal vesicle to form the ejaculatory duct. the ejaculatory ducts from both sides of the body then join the urethra. a pair of glands known as seminal vesicles is located on posterior surface of bladder. they secrete about 60% of total volume of semen into ejaculatory duct. semen is highly nourishing fluid for sperm and is produced by 3 seperate glands: the seminal vesicles, the prostate, and the bulbourethral glands. these are the accessory glands. the ejaculatory ducts empties into the urethra as it passes through the prostate gland. one final set of glands, the bulborethral glands, contributes to the semen near the beginning of the urethra. specialized erectile tissue in the penis allows erection. it is composed of modified veins and capillaries surrounded by a connective tissue sheath. erection occurs when blood accumulates at high pressure in the erectile tissue. 3 compartments contain erectile tissue: the corpora cavernosa (there are 2 of these) and the corpus spongiosum (only one).

dna replication, transcription, and translation similarities and differences

see pg 124/phone for chart

eukaryotic cell; each item that you should be able to explain the function of

see pg 173/phone for pic

6 inheritance patterns

see pg 252/phone for chart

taxonomic characteristics

see pg 262/phone for chart

bilateral symmetry and anatomical axes

see pg 263/phone

summary of brain functions

see pg 293/phone

summary of hormones

see pg 317/phone

■ Structure of antibody molecule

see pg 353/phone (and above) variable region, constant region, light chain, heavy chain

rods

sensitive to dim light and motion, more concentrated in periphery

analogous structures

serve the same function in 2 different species, but not due to the common ancestry

radioimmunoassay (RIA)

similar to ELISAs but use radiolabeled antigen and antibodies rather than enzyme linked antibodies. thus the presence of target proteins or antibodies is assayed by measuring the amount of radioactivity instead of a color change. RIAs are more extensively used in the medical field to measure the relative amounts of hormones or drugs in patients' sera. a known amount of radiolabeled antigen is mixed w a known amount of antibody and the total amount of radioactivity is measured. then unlabeled antigen is added in increasing amounts; the unlabeled antigen displaces the radiolabeled antigen so that less radioactivity is measured. this data is used to formulate a standard curve, and the steps are repeated using the patient's serum instead of the unlabeled antigen. the radioactivity is measured and compared to the standard curve to determine the amount of antigen.

cardiac vs skeletal muscle

similarities 1 thick and thin filaments organized into sarcomeres. (striations) 2 t tubules serve same function 3 troponin tropomyosin regulates contraction in same way 4 length tension relationship works same way and more significant in cardiac muscle. differences in cardiac muslce 1 not structurally syncytial. intercaliated disks. functional syncytium 2 cardiac muscle cells each connected to several neighbords by intercalated disks 3 some of calcium required for contraction comes from extracellular enviornemnt through voltage gated calcium channels while in skeletal muscle all calcium for contraciton comes from sarcoplasmic reticulum which is inside the cell. 4 cardiac muscle contraction doesnt depend on stimulation by motor neurons. in fact the most important nerve releasing ach at chemical synapses w the heart is inhibitory. this is the vagus nerve a parasympathetic nerve. it synapses w the sinoatrial node where it releases ach to inhibit spontaneous depolarization w the result being a slower heart rate. contrast w skeletal muscle innervation in which neurons release ach to stimulate contraction. pacing by the siinoatrial node instead triggers cardiac contraction. 5 action potential in cardiac mucscle depends not only on voltage gated sodium channesl (fast sodium channels as in skeletal muscle) but also on voltage gated calcium channels. these are slow channels bc they respond more slowly to threshold dpeolarization opening later than fast channels and taking longer to close. the voltage gated calcium channels cause the cardiac action potential to have the distinctive plateau in ap graph. significance of plateau phase: 1 a longer duration of contraction faciliates ventricular emptying (better ejection fraction), and 2 a longer refractory period helps prevent disorganized transmission of impulses throughout the heart, and makes summation and tetanus impossible. this is advantageous bc the heart must relax after each contraction. so remember: skeletal muscle cells and neurons ahve the same steeply spiking action potential while cardiac muscle cells have a spike and a plateau**.

smooth muscle vs skeletal

similarities of smooth contraction accomplished by sliding of actin and myosin filaments; the 4 step contractile cycle is the same. contraction is triggered by an increase in cytoplasmic [Ca2+]. smooth muscle cells don't branch. differences of smooth muscle 1 much narrower and shorter 2 t tubules not present. cell so small they're unnecessary; a depolarization of the surface can depolarize the entire cell 3 each smooth muscle cell has only one nucleus and is connected to its neighbors by gap junctions like cardiac muscle cells. which allow impulses to spread from cell to cell. thus both smooth and cardiac are functional syncytia. 4 thick and thin filaments are not organized into sarcomeres in smooth muscle. instead they are dispersed in the cytoplasm. this is why the cell appears smooth instead of striated (no regular A band, H zone, etc). they have sarcomeres by nonlinear aligned? 5 troponin-tropomyosin complex not present. instead contraction is regulated by calmodulin and myosin light-chain kinase. in brief, calmodulin binds Ca2+ and then activates myosin light chain kinase. myosin light chain kinase phosphorylates a portion of the myosin molecule thus activating its enzymatic/mechanical activity 6 while skeletal muscles rely heavily on Ca2+ from sarcoplasmic reticulum, the sarcoplasmic reticulum in smooth muscles is poorly developed. it stores some Ca2+ that can be released upon depolarization but the cell also relies heavily on extracellular stores of calcium for contraction 7 smooth muscle cell action potential varies depending on location of smooth muscle cell. most smooth muscle cells can elicit action potentials (spike potentials) similar to skeletal muscle action potentials, but since smooth muscle cells have almost no sodium fast channels and their action potential is determined by slow channels only, it takes 10-20 times as long as a skeletal muscle action potential 8 some smooth muscle that must sustain prolonged contractions (such as the uterus or vascular smooth muscle) has action potentials similar to those of cardiac muscle, although with a less sharp spike 9 smooth muscles have constantly fluctuating resting potential. ions pass through gap junctions causing changes in resting potential to propagate like waves through the connected smooth muscle cells. these fluctuations in resting potential are called slow waves. slow waves aren't spike potentials and do NOT elicit muscle contractions but they are necessary to help coordinate the action potentials. in response to local stimuli (eg stretching of smooth muscle in the gut wall due to a food bolus), neurotransmitter from parasympathetic neurons is released. the neurotransmitter binds to receptors on smooth muscle cells and primes them for an action potential by pushing their electrical potential closer to threshold. slow waves then pass through these "primed" smooth muscle cells, they reach threshold and undergo an action (spike) potential. the amplitude of these slow waves is increased by ACh and decreased by NE (eg stimulating gut during parasympathetic response and slowing it down during a sympathetic one) 10 like skeletal muscle, smooth are innervated by motor neurons, but in the case of smooth muscle they are autonomic motor neurons instead of somatic motor neurons. individual neurons do activate smooth muscle cells (as in skeletal muscle) but as mentioned the action potential then spreads from cell to cell. recall that in skeletal muscle each action potential is limited to one large myofiber while the heart is one large functional syncytium in which each action potential spreads to every cell. therefore regarding innervation and spread of impulses, smooth muscle shares features of both skeletal and cardiac)

kinetic concerns of passive transport types

simple diffusion can be distinguished from all forms of facilitated diffusion by the kinetics of the process. the rate of simple diffusion is limited only by the surface area of the membrane and the size of the driving force (gradient). facilitated diffusion, however, depends on a finite number of integral membrane proteins. hence it exhibits saturation kinetics. increasing the driving force for facilitated diffusion increases the rate of diffusion (the flux) but only to a point. then all the transport proteins become saturated, and no further increase in flux is possible. see pg 197/phone for pic

a sample of bacteria is evenly mixed into a cool liquid agar nutrient mix in the absence of oxygen and then poured into a glass walled tube that is open to the atmosphere on top. when the agar mix cools, it solidifies, and bacterial growth is observed as shown below. how would you classify the bacteria in terms of oxygen utilization and tolerance? (note: agar is practically impermeable to oxygen.)

since the bacteria grew only at the bottom of the tube, farthest away from any oxygen, this indicates that they could only grow in the absence of oxygen. thus they are obligate anaerobes

a bacterium that causes an infection in the bloodstream of humans is most likely to be classified as which of the following? A chemoautotroph B photoautotroph C chemoheterotroph D photoheterotroph

since there's no sunlight in the bloodstream, B and D are out. if its a parasite, it most likely uses some of our chemicals, so it must be a heterotroph, which eliminates A. the answer is C

bacteriophage life cycles

since viruses lack the ability to produce energy and replicate on their own, they use the machinery of the cell they infect to carry out these processes. the viral genome contains genes that redirect the infected cell to produce viral products. the first step is binding to the exterior of a bacterial cell in a process termed attachment or adsorption. the next step is injection of the viral genome into the host cell in a process termed penetration or eclipse. it is called "eclipse" bc the capsid remains on the outer surface of the bacterium while the genome disappears into the cell, removing infectious virus from the media. from this point forward a phage follows one of 2 different paths: it enters either the lytic cycle or the lysogenic cycle

Structure of three basic muscle types: striated, smooth, cardiac

skeletal muscle - voluntary. cardiac skeletal and cardiac are striated smooth - walls of all hollow organs such as GI tract, urinary system, uterus, etc. no conscious control over cardiac or smooth bc innervated only by autonomic nervous system

muscle fiber types

slow twitch fibers and fast twitch fibers. slow and fast refer to contractile speeds. type 1 slow twitch fibers red slow twitch or red oxidative fibers bc high myoglobin content. much better blood supply than fast twitch due to extensive surrounding capillary network. combo of good oxygen delivery from the blood stream and ability to store oxygen on their myoglobin allows these fibers to maintain contraction for extended periods of time without fatigue. these are the fibers that allow marathoners and long distance cyclists to run or bike for hours at a time. type II fast twitch fibers fall into 2 subcategories according to ability to resist fatigue. both fiber types contract quickly but type IIA fast twitch fibers have more mitochondria than type IIB fast twitch and thus more fatigue resistant. type IIA - fast twitch oxidative fibers, somewhat resistant to fatigue. cannot maintain activity for as long as slow twitch fibers can (only around 30 mins or so) but far exceed duration of use of type IIB fibers type IIB - aka white fast twitch fibers due to their lack of mitochondria, these fibers contract very quickly with great force. however they fatigue just as quickly, maxing out at around one minute of use. these are the fibers that provide the explosive force needed for jump shots and pole vaults.

surfactant

soapy substance that coats alveoli that reduces surfaces tension. mix of phospholipids, proteins, and ions secreted by cells in the alveolar wall

recessive lethal alleles

some mutant alleles can cause death of an organism when present in a homozygous manner. these typically code for essential gene products. in diploid organisms, these alleles can be studied by maintaining heterozygous stocks, which are then mated together to form a homozygous recessive offspring. embryonic development studies can shed light on when this organism dies and possibly why. studying recessive lethal alleles in haploid organisms is much harder. here, a conditional system is usually used where the allele is normal (or permissive) under certain conditions, allowing survival of the organism. the mutant allele can be induced under different conditions (such as different temp), to study effects of the allele

endospore formation

some types of gram-positive bacteria, such as the bacteria responsible for botulism, form endospores under unfavorable growth conditions. endospores have tough, thick external shells comprised of peptidoglycan. within the endospore are found the genome, ribosomes, and rna which are required for the spore to become metabolically active when conditions become favorable. endospores are able to survive temperatures above 100 degrees C, which is why autoclaves or pressure cookers are required to completely sterilize liquids and substances that cannot be heated sufficiently in a dry oven. the metabolic reactivation of an endospore is termed germination. a single bacterium is able to form only one spore per cell. thus bacteria cannot increase their population through spore formation. (when are bacteria most likely to form endospores: during lag phase, log phase, or stationary phase? is endospore formation a means for bacteria to reproduce? - stationary. forming an endospore is like hibernating, not reproducing. bacteria do it in order to sleep through the bad times.)

glial cell

specialized non neuronal cells that typically provide structural and metabolic support to neurons. glia maintain a resting membrane potential but do not generate action potentials

origin of replication

specific sequence of nucleotides that can be recognized by special enzymes necessary for the formation of the open complex

pulmonary ventilation: volumes and capacities

spirometry is measurement of volume of air entering or exiting lungs at various stages of ventilation.

Mendel's second law, law of independent assortment

states that the alleles of one gene will separate into gametes independently of alleles for another gene.

aldosterone

steroid hormone

cortisol

steroid hormone

cartilage

strong but flexible extracellular tissue secreted by chondrocytes (cells). 3 types of cartilage: hyaline, elastic, and fibrous. hyaline cartilage is strong and somewhat flexible. the larynx and trachea are reinforced by hyaline cartilage and joints are lined by hyaline cartilage known as articular cartilage. elastic cartilage is found in structures (such as the outer ear and the epiglottis) that require support and more flexibility than hyaline cartilage can provide; it contains elastin. fibrous cartilage is very rigid and is found in places where very strong support is needed, such as pubic symphysis (anterior connection of pelvis) and intervertebral disks of spinal column. cartilage is not innervated and doesn't contain blood vessels (it is avascular). it receives nutrition and immune protection from the surrounding fluid.

5 roles of skeletal system

support body provide framework for movement protect vital organs (brain, heart, etc) store calcium synthesize formed elements of the blood (red blood cells, white blood cells, platelets). this occurs in the marrow of flat bones and is called hematopoiesis

nuclear envelope

surrounding the nucleus and separating it from the cytoplasm is the nuclear envelope, composed of 2 lipids bilayer membranes. the inner nuclear membrane is the surface of the envelope facing the nuclear interior, and the outer nuclear membrane faces the cytoplasm. the membrane of the endoplasmic reticulum is at points continuous with the outer nuclear membrane, making the interior of the ER (the lumen of the ER) contiguous with the space btwn the 2 nuclear membranes. [is the space btwn the inner and outer membranes contiguous w the cytoplasm? - no it is not. the space btwn the nuclear membranes is contiguous w the er lumen, which is isolated from the cytoplasm] the nuclear envelope is punctuated w large nuclear pores that allow the passage of material into and out of the nucleus. molecules that are smaller than 60 kilodaltons, including small proteins, can freely diffuse from the cytoplasm into the nucleus through the nuclear pores. larger proteins cannot pass freely through nuclear pores and are excluded from the nuclear interior unless they contain a sequence of basic amino acids called a nuclear localization sequence. proteins w a nuclear localization sequence are translated on cytoplasmic ribosomes and then imported into the nucleus by specific transport mechanisms. it also appears likely that rna is transported out of the nucleus by a specific transport system rather than freely diffusing into the cytoplasm. [if a 15 kD protein has a nuclear localization sequence that is then deleted from its gene, will the mutated protein still be found in the nucleus? - yes. the protein is small enough that it can still pass through the nuclear pores by diffusion even without a nuclear localization sequence] see pg 177/phone for pic

translation

synthesis of polypeptides according to the amino acid sequence dictated by the sequence of codons in mrna. during translation, an mrna molecule attaches to a ribosome at a specific codon, and the appropriate amino acid is delivered by a trna molecule. then the second amino acid is delivered by another trna. then the ribosome binds the 2 amino acids together, creating a dipeptide. this process is repeated until the polypeptide is complete, at which point the ribosome drops the mrna and the new polypeptide departs

ribosomes

synthesize proteins. 0 membranes surrounding it

systolic and diastolic pressure

systolic, highest pressure that ever occurs in the circulatory system of this particular patient during the time the bp is being measured. this lvl is attained as the ventricles contract (during systole). diastolic is as low as the [arterial] pressure gets btwn heartbeats (during diastole) during the measurement. pulse pressure is the difference btwn systolic and diastolic pressures highest pressure is in the left ventricle, aorta, and other large arteries diastolic - pressure btwn heartbeats systolic - pressure during heartbeats

bacterial growth requirements

temperature, nutrition, growth media, oxygen utilization and tolerance

diffusion

tendency for liquids and gases to fully occupy the available volume. particles in the liquid or gas phase are in constant motion, depending on temp. if all particles are concentrated in one portion of a container, we have an orderly situation, which is unfavorable according to the second law of thermodynamics (law of entropy). the constant thermal motion of particles in the cell leads to their spreading out to occupy all available space, which maximizes entropy (remember, ΔG = ΔH-TΔS, so increasing ΔS decreases ΔG, indicating a thermodynamically favorable process). a solute will always diffuse down its concentration gradient, which means from high to low concentration. diffusion continues until the solute is evenly distributed throughout the available volume. at this point, movement of solute back and forth continues, but no net movement occurs.

hormonal control of spermatogenesis

testosterone plays essential role of stimulating division of spermatogonia. luteinizing hormone (LH) stimulates the interstitial cells to secrete testosterone. follicle stimulating hormone (FSH) stimulates the sustenacular cells. the hormone inhibin is secreted by sustenacular cells; its role is to inhibit FSH release. fsh and lh are gonadotropins secreted by the anterior pituitary. the reason this occurs is to provide negative feedback. testosterone, estrogen, progesterone, and inhibin are all hormones that exert feedback inhibition upon the anterior pituitary and hypothalamus.

bacteria cultured in the presence of 35S-labeled cysteine and 32P-labeled phosphates are infected with phage T4. when phage from this culture are used to infect a new nonradiolabeled bacterial culture, which of the isotopes will be found in the interior of the newly infected bacteria?

the 35S cysteine will be incorporated into viral coat proteins and the 32P phosphate will be incorporated into the viral nucleic acid genome in newly released viral particles. (proteins contain no P and nucleic acids contain no S.) when these viruses infect bacteria, their nucleic acids are injected into the bacteria while the capsid proteins remain on the exterior, which means that only the 32P will be found in the interior of the newly infected cells

endoplasmic reticulum

the ER is a large system of folded membrane accounting for over half of the membrane of some cells. there are 2 types of ER: rough ER and smooth ER, each with distinct functions. the rough ER is called rough due to the large number of ribosomes bound to its surface; it is the site of protein synthesis for proteins targeted to enter the secretory pathway. the smooth er is not actively involved in protein processing but can contain enzymes involved in steroid hormone biosynthesis (gonads) or in the degradation of environmental toxins (liver). the membrane of the endoplasmic reticulum is joined with the outer nuclear membrane in places, meaning that the space within the nuclear membranes is continuous with the interior of the ER (the ER lumen). the rough ER plays a key role directing protein traffic to different parts of the cell. see pg 180/phone

Na+/K+ ATPase and the resting membrane potential

the Na+/K+ ATPase is a transmembrane protein in the plasma membrane of all cells in the body. the activity provided by this protein is to pump 3 Na+ out of the cell, 2 K+ into the cell, and to hydrolyze one ATP to drive the pumping of these ions against their gradients. (the pumping of sodium and potassium by the Na+/K+ ATPase is an example of what form of transport? - the pumping of ions against a gradient which is coupled to ATP hydrolysis is primary active transport) the sodium that is pumped out of the cell stays outside, since the plasma membrane is impermeable to sodium ions. some of the potassium ions which are pumped into the cell are able to leak back out, however, through potassium leak channels. potassium flows down its concentration gradient out of the cell through leak channels. the movement of ions out of the cell helps the cell to maintain osmotic balance with its surroundings. as potassium leaves the cell through the leak channels, the movement of positive charge out of the cell creates an electric potential across the plasma membrane w a net negative charge on the interior of the cell. this potential created by the Na+/K+ ATPase is known as the resting membrane potential. the concentration gradient of high sodium outside of the cell established by the Na+/K+ ATPase is the driving force behind secondary active transport of many different molecules, including sugars and amino acids. to summarize, the activity of the Na+/K+ ATPase is important in 3 ways: 1. to maintain osmotic balance between the cellular interior and exterior 2. to establish the resting membrane potential 3. to provide the sodium concentration gradient used to drive secondary active transport see pg 199/phone for pic of Na+/K+ ATPase (what would happen if there were much more adp + pi than ATP, as well as very high extracellular Na+ conc and v high intracellular K+ conc in the artificial cell? - the pump would run backward. remember: all active transporters are reversible.) Na+ - intracellular conc - 10 mM, extra 142 K+ - 140 mM, 4mM Cl- - 4mM, 110mM Ca2+ - .0001 mM, 2.4mM (why is chloride so concentrated outside the cell? - the cell contains millions of negative charges on macromolecules (eg nucleic acids). for the charge to be "approximately" balanced on both sides of the membrane, some negatively charged substance must be more concentrated outside. chloride serves this role. why "approximately" balanced? remember: the cell is a bit more negative on the inside; that's the resting membrane potential.) a useful mnemonic is to remember that life evolved in the ocean, which has very high concentrations of NaCl; thus the concentrations of Na+ and Cl- are high outside the cell and low inside.

regenerative capacity

the ability to restore damaged tissues is an important survival strategy, and depends on how stem cells are maintained in the body of an organism. planarians (simple flatworms) have collections of stem cells throughout their bodies that can migrate to areas of damage and rebuild necessary tissues. newts or lizards that lose a limb have cells that dedifferentiate and then dedifferentiate to grow back all the components of that limb. within mammals, however, the regenerative capacity is considerably more limited. the multipotent stem cells within the bone marrow are constantly regenerating the cellular components of the blood and immune system. hepatocytes in the liver divide to produce more cells, but this process is much slower; these cells are described as being unipotent. some cells, like neurons, do not regenerate, though inducing them to do so is an active area of research so as to better address injuries and damage caused by neurological degrading illnesses. since regnerative capacity invovles cell growth, dedifferentiation and redifferentiation, the possibility exists for the process to go awry and for cancerous growht to then be stimulated. regeneration needs to be tightly regulated in order for it to proceed correctly.

which one of the following categories best describes an organism which uses sunlight to drive atp production but cannot incorporate carbon dioxide into sugars? A chemoautotroph B photoautotroph C chemoheterotroph D photoheterotroph

the ability to use sunlight indicates that the organism is a phototroph, and the inability to use carbon dioxide as a carbon source indicates that it is a heterotroph - it must use organic molecules as a carbon source. the answer is D

if you analyzed a thousand trna molecules, which region would you expect to vary the most

the anticodon is different for each of the different trna molecules. part of the rest of the molecule varies from one trna to the next, but about 60% is constant. the amino acid binding site is always the same: CCA (at the 3' end of the trna molecule)

the cell membrane and cell wall (bacteria)

the bacterial cytoplasm is bounded by a lipid bilayer which is similar to our own plasma membrane. outside the lipid bilayer is a rigid cell wall. it provides the support for the cell, preventing lysis due to osmotic pressure. (animal cells lack a cell wall. they deal with the problem of osmotic pressure by continuously pumping ions across the cell membrane) the bacterial cell wall is composed of peptidoglycan, a complex polymer unique to prokaryotes. it contains cross-linked chains made of sugars and amino acids, including d-alanine, which is not found in animal cells (our amino acids have the L configuration). the bacterial cell wall is the target of many antibiotics such as penicillin. the enzyme lysozyme, which is found in tears and saliva and made by lytic viruses, destroys the peptidoglycan in the bacterial cell wall, resulting in an osmotically fragile structure called a protoplast.

if a bacterium cannot use oxygen as an electron acceptor is it an obligate anaerobe, a tolerant anaerobe, or a facultative anaerobe, or is it not possible to distinguish based on the information given?

the bacterium cannot be a facultative anaerobe since the question states it cannot use O2. it could be either an obligate or a tolerant anaerobe depending on its ability to neutralize harmful oxygen free radicals

transmembrane transport

the cell requires membranes to act as barriers to diffusion but also requires the transport of many different substances across membranes. integral membrane proteins transport material through membranes that cannot diffuse on their own across membranes. transport across a membrane can be either passive (doesn't require cellular energy) or active (requires cellular energy).

growth media for bacteria

the environment in which bacteria grow is the medium. in the lab, the most common solid medium is agar, a firm transparent gel made from seaweed. bacteria live in the agar but don't metabolize it. the agar is usually kept in a clear plastic plate called a Petri dish, and the process of putting bacteria on such a plate is called plating. when one bacterium is plated onto a dish, if it grows it will eventually give rise to many progeny in an isolated spot called a colony. minimal medium contains nothing but glucose (in addition to the agar). more key terms: a wild-type bacterium (or a wild-type strain) is one which possesses all the characteristics normal to that particular species. the dense growth of bacteria seen in laboratory Petri dishes is known as a bacterial lawn. a plaque is a clear area in the lawn. plaques result from death of bacteria and are caused by lytic viruses or toxins. bacteria can reproduce very rapidly, provided that the conditions of their environment are favorable and nutrients are abundant. the doubling time is the amount of time required for a population of bacteria to double its number. it ranges from a mime of 20 minutes for e coli to a day or more for slow growers, such as the bacteria responsible for tuberculosis and leprosy. the doubling time of a bacterial species will vary, depending upon the availability of nutrients and other environmental factors. one other important term in bacterial nutrition is auxotroph (don't confuse this with autotroph). this is a bacterium which cannot survive on minimal medium because it can't synthesize a molecule it needs to live. therefore, it requires an auxiliary trophic substance to live. for instance, a bacterium which is auxotrophic for arginine won't form a colony when plated onto minimal medium, but if the medium is supplemented with arginine, a colony will form. this arginine autotrophy is denoted arg-. autotrophy results from a mutation in a gene coding for an enzyme in a synthetic pathway bacteria can be differentiated not only by what substances they require, but also by what substances they are capable of metabolizing for energy. for instance, a strain of bacteria may be capable of surviving on final medium that has the disaccharide lactose as the only carbon source (no glucose). this would be denoted lac+. mutation in a gene for the enzyme lactase would impair the bacterium's ability to survive on lactose-only medium. a bacterial strain incapable of growing with lactose as its only carbon source would be denoted lac-. genetic exchange between bacteria by means of conjugation, transduction, or transformation can remedy these disabilities.

dna replication

the dna genome is the control center of the cell. when mitosis produces two identical daughter cells from one parental cell, each daughter must have the same genome as the parent. therefore, cell division requires duplication of the dna, known as replication. this is an enzymatic process, just as the Krebs cycle and glycolysis are enzymatic processes. it occurs during S (synthesis) phase in interphase of the cell cycle. there is only one logical way to make a new piece of dna that is identical to the old one: copy it. the old dna is called parental dna, and the new is called daughter dna. what is the relationship btwn parental and daughter dna after replication? there are several possibilities. in other words, where do the atoms from the parent go when the daughters are made? experiments done by meselson and stahl in 1958 aimed to determine if dna replication is semiconservative, conservative, or dispersive. they showed that its semiconservative; after replication, one strand of the new double helix is parental (old) and one strand is newly synthesized daughter dna see pg 76/phone for pics of replication replication at the molecular lvl. when its not being replciated, dna is tightly coiled. the replication process cannot begin unless the double heliz is uncoiled and separated into two single strands. the enzyme that unwinds the double heliz and separates the strands is called helicase, which uses the energy of atp hydrolysis bc separating the strands requires the breaking of many h-bonds. the place where the helicase begins to unwind is not random. its a specific location (sequence of nucleotides) on the chromosome called the origin of replication (ORI). this sequence is found by proteins with tertiary structures to specifically recognize a particular pattern of nucleotides. they scan along the chromosome (like a train on a track) until they find the right spot; then they call in helicase and other enzymes to initiate dna replication. in prokaryotes, a protein called DnaA finds the ORI to initiate DNA replication. in eukaryotes, three proteins cooperate to find the ORI, two of which are synthesized during M and G1 phases of the cell cycle but rapidly destroyed once the S phase begins. (dna replication occurs in the s phase? and is semiconservative in nature)this means these 2 proteins link dna replication to the cell cycle, ensuring dna replication doesn't initiate during other phases of the cell cycle. when helicase unwinds the helix at the origin of replication, the helix gets wound more tightly upstream and downstream from this point. the chromosome would get tangled and eventually break, except that enzymes called topoisomerases cut one or both of the strands and unwrap the helix, releasing the excess tension created by the helicases. another potential problem is that single-stranded dna is much less stable than ds-dna. single-strand binding proteins SSBPs protect dna that has been unpackaged in preparation for replication and help keep the strands separated. the separated strands are referred to as an open complex. replication may now begin. see pg 77/phone for pic a rna primer must be synthesized for each template strand. this is accomplished by a set of proteins called the primosome, of which the central component is an rna polymerase called primase. primer synthesis is important bc the next enzyme, dna polymerase, cannot start a new dna chain from scratch. it can only add nucleotides to an existing nucleotide chain. the rna primer is usually 8-12 nucleotides long, and is later replaced by dna daughter dna is created as a growing polymer. dna polymerase catalyzes the elongation of the daughter strand using the parental template, and elongates the primer by adding dNTPs to its 3' end. in fact, the 3' hydroxyl group acts as a nucleophile in the polymerization reaction to displace 5' pyrophosphate from the dNTP to be added. (if the daughter is made 5' to 3', and the 2 strands have to end up antiparallel, the template must be read 3' to 5'). dna pol is part of a large complex of proteins called the replisome. other accessory proteins in this complex help dna polymerase and allow it to polymerize dna quickly. the prokaryotic replisome contains 13 components, and the eukaryotic replisomes contain 27 proteins; additional complexity in the eukaryotic system is required bc replication machinery must also unwind dna from histone proteins rapid elongation of the daughter strands follows. since the two template strands are antiparallel, the two primers will elongate toward opposite ends of the chromosome. after a while it looks like this: see pg 78/phone dna polymerase checks each new nucleotide to make sure it forms a correct base-pair before it is incorporated in the growing polymer. the thermodynamic driving force for the polymerization rxn is the removal and hydrolysis of pyrophosphate (P2O7 4-) from each dNTP added to the chain replication proceeds along in both directions away from the origin of replication. both template strands are read 3' to 5' while daughter strands are elongated 5' to 3'. the areas where the parental double helix continues to unwind are called the replication forks. see pg 79/ phone for pic problem: it seems like only half of each template strand will be replicated. the problem is that chain elongation can only proceed in one direction, 5' to 3', but in order to replicate the right half of the top chain and the left half of the bottom one (pg 78) continuously, we would have to go in the opposite direction. heres the solution: see pg 79/phone the solution to this problem involves building strands of dna on opposite sides of the ORI using different methods. as the bottom chain on the right is elongated continuously, the replication fork widens. after a good bit of the top template chain becomes exposed, primase comes in and lays down a primer, which dna pol can elongate. then, when the replication fork widens again and more of the top template becomes exposed, these events are repeated. the bottom daughter on the right side, and the top daughter on the left side are called the leading strands bc they elongate continuously right into the widening replication fork. the top daughter on the right, and the bottom daughter on the left are called the lagging strands bc they must wait until the replication fork widens before beginning to polymerize. the small chunks of dna comprising the laggin strand are called okazaki fragments. as the replication forks grow, helicase has to continue to unwind the double helix and separate the strands

hardy-weinberg law

the frequencies of alleles in the gene pool of a population will not change over time, provided that a number of assumptions are true: 1. there is no mutation. 2. there is no migration. 3. there is no natural selection. 4. there is random mating. 5. the population is sufficiently large to prevent random drift in allele frequencies. what hard-weinberg means at the molecular lvl is that segregation of alleles, independent assortment, and recombination during meiosis can alter the combinations of alleles in gametes but cannot increase or decrease the frequency of an allele in the gametes of one individual or the gametes of the population as a whole. the hardy-weinberg law has also been translated into mathematical terms. assuming that there are 2 alleles of a gene in a population, the letter p is used to represent the frequency of the dominant allele, and the letter q is used to represent the frequency of the recessive allele. since there are only 2 alleles, the following fundamental equation must be true: p+q=1 based on allele frequency, it is possible to calculate the proportion of genotypes in a population. take a situation where the frequency of a dominant allele, G, equals p and the frequency of a recessive allele, g, equals q. if the equation above is squared on both sides, it becomes: (p+q)^2=1 p^2+2pq+q^2=1 where p^2=the frequency of the GG genotype 2pq = the frequency of the Gg genotype q^2 the frequency of the gg genotype

genome structure and genomic variations

the human genome contains 24 diff chromosomes (22 autosomes, plus 2 different sex chromosomes), 3.2 billion base pairs, and codes for about 21,000 genes. the sequence of the human genome was reported by 2 independent groups in 2001 the human genome has numerous regions with high transcription rates, separated by long stretches of intergenic space genomic regions with high transcription rates are rich in genes. a gene is a dna sequence that encodes a gene product. it includes both regulatory regions (such as promoters and transcription stop sites), and a region that codes for either a protein or a noncoding rna

human genome

the human genome is split into 24 different chromosomes: 22 autosomes (non sex chromosomes) and 2 are sex chromosomes (allosomes, X and Y). each human has 23 pairs of chromosomes (22 autosomes and a sex chromosome), for a total of 46 chromosomes. one chromosome of each pair is from the mother and one is from the father. the 2 nonidentical copies of a chromosome are called homologous chromosomes. although these 2 copies look the same when examined at the crudest lvl under a microscope, and although they contain the same genes, the copies of the genes in the 2 homologous chromosomes may differ in their DNA sequence. different versions of a gene, alleles, may carry out the gene's function differently. since a person carries 2 copies of every gene, one on each homologous chromosome, a person could potentially carry 2 different alleles. individuals carrying different alleles of a gene will often have traits that allow the inheritance of alleles to be followed.

when phage are first added to a bacterial culture, the number of infective viruses initially decreases before it later increases. why does this occur?

the initial decrease is due to the simple fact that many phage have injected their genomes into hosts and are no longer infectious

■ Endothelial cells

the inner lining of all blood vessels is formed by a thin layer of these cells; the walls of capillaries are formed from a single layer of such cells. these cells have important roles in a number of vascular functions such as: vasodilation and vasoconstriction - the secretion of substances like nitric oxide and endothelia can regulate vessel diameter. this is important in maintaining bp, tissue oxygenation, and thermoregulation. inflammation - the release of inflammatory chemicals from injured tissues stimulate endothelial cells to inc their expression of adhesion molecules. these molecules allow white blood cells to adhere to the endothelial cells and ultimately enter the injured tissue angiogenesis (formation of new blood vessels) - angiogenic growth factors stimulate endothelial cells to break free from existing vessel and proliferate in surrounding tissues, ultimately forming new vessels altogether. this property has important implications for cancer treatments, as many tumors secrete angiogenic growth factors. the resulting vascular increase supplies oxygen and nutrients to a developing tumor to help sustain its extraordinary cell division and growth. angiogenesis inhibitors are drugs that can be used to restrict blood flow to tumors and help reduce or halt their growth. thrombosis (blood clotting) - undamaged endothelial cells secrete substances that inhibit the coagulation cascade, thus preventing the formation of potentially life-threatening clots inside undamaged or unbroken vessels

when an enzyme that degrades dna (DNase) is incubated with intact dna isolated from an organism, the dna is degraded. but when DNase is injected into the cytoplasm of cells from the same organism, no effect on the genome is observed. which of the following is the best explanation for this? A. the cell is a prokaryote; therefore, the genome is inaccessible to cytoplasmic enzymes B. the cell is a prokaryote; therefore, the circular genome is resistant to DNase C. the cell is a eukaryote; therefore, the genome is inaccessible to cytoplasmic enzymes D. the cell is a eukaryote; therefore, the linear genome is resistant to DNase

the isolated genome and the genome in the cell respond differently, so the key is not the circular or linear nature of the genome (B and D are wrong). the key is that in prokaryotes the injected cytoplasmic DNase will have access to the genome to degrade since they are in the same compartment, while in eukaryotes the DNase will not have access to the genome unless it enters the nucleus (C is the best choice)

the lysogenic cycle of phages

the lytic cycle is an efficient way for a virus to rapidly increase its numbers. it presents a problem though: all host cells are destroyed. this is an evolutionary disadvantage. some viruses are cleverer: they enter the lysogenic cycle. upon infection, the phage genome is incorporated into the bacterial genome and is now referred to as a prophage; the host is now called a lysogen. the prophage is silent; its genes are not expressed, and viral progeny are not produced. this dormancy is due to the fact that transcription of phase genes is blocked by a phage-encoded repressor protein that binds to specific dna elements in phage promoters (operators). the cleverness of the lysogenic cycle lies in the fact that every time the host cell reproduces itself, the prophage is reproduced too. eventually the prophage becomes activated. it now removes itself from the host genome (in a process called excision) and enters the lytic cycle one potential consequence of the lysogenic cycle is that when the viral genome activates, excising itself from the host genome, it may take part of the host genome along with it. when the virus replicates, the small piece of host genome will be replicated and packaged with the viral genome. in subsequent infections, the virus will integrate the "stolen" host dna along with its own genome into the new host's genome. the presence of the new dna will become evident if it codes for a trait that the newly infected host did not previously possess, such as the ability to metabolize galactose. this process is called transduction. (why would a bacterial gene, carried with a virus and integrated with viral genes into a new bacterial genome, not be repressed along with the viral genes during lysogeny? - prophage latency results from a viral repressor protein binding to viral dna in a sequence-specific manner. the specific DNA sequence to which the repressor binds is present in the viral genes but not in the bacterial genes, so the bacterial gene can be expressed while the viral genes are repressed) see pg 141/phone for lysogenic cycle

active transport

the movement of molecules through the plasma membrane against a gradient. active transport requires energy input, since it is working against a gradient, and always involves a protein. another way of saying that active transport requires energy input is to say that the transport process is coupled to a process which is thermodynamically favorable (ΔG<0). the gradient being pumped against is not necessarily just a concentration gradient, but for charged molecules, like ions, it can also involve electric potentials that form a combined electrochemical gradient that must be pumped against. the form of energy input used to drive movement of molecules against an electrochemical gradient varies. in primary active transport, the transport of a molecule is coupled to atp hydrolysis. in secondary active transport, the transport process is not coupled directly to atp hydrolysis. instead, atp is first used to create a gradient, then the potential energy in that gradient is used to drive the transport of some other molecule across the membrane. since atp is not used in the actual transport of the "other" molecule, the atp use is described as indirect. for ex, the transport of glucose into some cells is driven against the glucose concentration gradient by the cotransport of sodium ions down the sodium electrochemical gradient, previously established by an ATPase pump. a common mechanism driving secondary active transport of many different molecules involves coupling transport to the flow of sodium ions down a gradient.

conduction zone

the parts of the respiratory system that participate only in ventilation

steps of inspiration

the pressure of air in the alveoli and the pleural pressure vary during inspiration and expiration. during inspiration the following steps occur: 1 the diaphragm contracts and flattens (moves downward) 2 volume of chest cavity expands 3 pleural pressure decreases, becoming more negative 4 lungs expand outward 5 pressure in alveoli becomes negative 6 air enters the lungs and the alveoli

respiratory epithelium: protection from disease and particulate matter

the respiratory tract from nose to bronchioles is epithelial cells that are tall columnar cells. they are too thick to assist in gas exchange. some of these secrete mucuse and are goblet cells. columnar epithelial cells of upper respiratory tract have cilia on their apical surfaces which constantly sweep the layer of mucus toward the pharynx where mucus containing pathogens can be swallowed or coughed out. this is mucociliary escalator. gas exchanging surfaces are lined w a single layer of thin, delicate squamous epithelial cells (squamous means flat). a single layer of squamous epithelial cells is simple squamous epithelium. mucus would get in the way, so macrophages are there instead in alveoli engulfing foreign particles

viral structure and function

the structure of viruses reflects their life cycle. in general all viruses possess a nucleic acid genome packaged in a protein shell. the exterior protein packaging helps to convey the genome from one cell to infect other cells. once in a cell, the viral genome directs the production of new copies of the genome and of the protein packaging needed to produce more virus. however the nature of the genome, the protein packaging, and the viral life cycle vary tremendously btwn different viruses a viral genome may consist of either dna or rna that is either single or double-stranded and is either linear or circular. viruses utilize virtually every conceivable form of nucleic acid as their genome. however, a given type of virus can have only one type of nucleic acid as its genome, and a mature virus does not contain nucleic acid other than its genome (there are exceptions. for ex, it has been recently discovered that hep b virus has a circular dna genome which is part single-stranded and part double-stranded. the take-home point here is that when a virus isn't inside a host cell, it contains only its genome, which is always the same (except in special situations such as when a piece of host genome accidentally becomes incorporated in the viral genome). in contrast, a true cell contains not only its genome, but also mrna, rRNA, and trna.) a factor that influences all viral genomes, regardless of the form of the nucleic acid used as genome, is size as a limiting factor. viruses are much smaller than the hosts they infect, both prokaryotic and eukaryotic. figure 1 depicts the relative size of a bacteriophage (a virus that infects bacteria) and its host (see pg 136/phone) not only are viruses small, but the exterior protein shell of a virus is typically a rigid structure of fixed size that cannot expand to accommodate a larger genome. to adapt to this size constraint, viral genomes have evolved to be extremely economical. one adaptation is for the viral genome to carry very few genes and for the virus to rely on host-encoded proteins for transcription, translation, and replication. (they use host ribosomes) another adaptation found in viral genomes is the ability to encode more than one protein in a given length of genome. a virus can accomplish this feat by utilizing more than one reading frame within a piece of dna so that genes may overlap with each other. surrounding the viral nucleic acid genome is a protein coat called the capsid. the capsid provides the external morphology that is used to classify viruses. it is made from a repeating pattern of only a few protein building blocks. helical capsids are rod-shaped, while polyhedral capsids are multiple-sided geometric figures with regular surfaces. complex viruses may contain a mixture of shapes. for ex, the T4 bacteriophage has a helical sheath and a polyhedral head. this virus is commonly used in reserach; its host is the bacterium e coli. the genome is located within the capsid head. other parts of the capsid are used during infection of the host. the tail fibers attach to the surface of the host cell, as does the base plate. the sheath contracts using the energy of stored atp, injecting the genome into the host. see pg 137/phone for pic the most important thing to understand is that the entire viral capsid is composed of protein, while the viral genome is composed of nucleic acid (DNA or RNA). most viruses are not as structurally complex as the bacteriophage shown on pg 137. see pg 138/phone for more examples many animal viruses also possess an envelope that surrounds the capsid. this is a membrane on the exterior of the virus derived from the membrane of the host cell. it contains phospholipids, proteins, and carbohydrates from the host membrane, in addition to proteins encoded by the viral genome. enveloped viruses acquire this covering by budding through the host cell membrane. to infect a new host, some enveloped viruses fuse their envelope with the host's plasma membrane, which leaves the de-enveloped capsid inside the host cell. viruses which dont have envelopes are called naked viruses. all phages and plant viruses are naked. (why? - remember: viruses acquire envelopes by budding through host membranes. phages and plant viruses infect hosts that possess cell walls. when viruses begin to exit the cell, the cell wall is destroyed, and host membranes rupture. thus there is no membrane through which the remaining viruses must bud; they simply escape in a lytic explosion) (t or f, viruses that infect human cells must have an envelope? - although viruses w an envelope (lipid bilayer coating) are restricted to infecting animal cells, the outer membrane is not required. not true) whether enveloped or naked, the surface of a virus determines what host cells it can infect. viral infection is not a random process, but highly specific. a virus binds to a specific receptor on the cell surface as the first step in infection. after binding, the virus will be internalized, either by fusion with the plasma membrane or by receptor-mediated endocytosis. only cells with a receptor that matches the virus will become infected, explaining why only specific species or specific cell types are susceptible to infection. the viral surface is also important for recognition by our immune system

comparing prokaryotic and eukaryotic transcription

they are similar but 4 major differences, in location, rna polymerases, primary transcripts, and regulation of transcription

refractory period

the time following an action potential during which a new action potential cannot be initiated. based on characteristics of the voltage-gated sodium and potassium channels.

a virus possessing an rna genome relies on rna polymerase rather than DNA polymerase to replicate its genome. will this virus have a higher or lower rate of spontaneous mutation than organisms with ds-DNA genomes?

the virus will have a v high rate of mutation. its a general law that most mutations are harmful. hence, individual viruses will be far less likely to survive than organisms with dna genomes. however the high mutation rate will allow the entire species of virus to evolve very rapidly, making it very successful as a parasite (since it will evade host defense systems)

RER and secretory pathway

there are 2 sites of protein synthesis in eukaryotic cell: either on ribosomes free in the cytoplasm or on ribosomes bound to the surface of the RER. proteins translated on free cytoplasmic ribosomes are headed toward peroxisomes, mitochondria, the nucleus, or will remain in the cytoplasm. proteins synthesized on RER will end up either 1 secreted into extracellular environment 2 as integral plasma membrane proteins, or 3 in the membrane or interior of the ER, Golgi apparatus, or lysosomes. membrane bound vesicles pass btwn these cellular compartments. since the membranes of these organelles communicate through the traffic of vesicles, the interior of the er, the Golgi apparatus, lysosomes, and the extracellular environment are in a sense contiguous. proteins synthesized on the RER are transported in vesicles that bud from the er to the Golgi app then to the plasma membrane or lysosome. a secreted protein that enters the er lumen is separated by a membrane from the cytoplasm until the protein leaves the cell. whether a protein is translated on the RER is determined by the sequence of the protein itself. all proteins start translation in the cytoplasm; however some proteins (secreted proteins and lysosomal proteins) have an amino acid sequence at their N-terminus called a signal sequence. the signal sequence of a nascent polypeptide is recognized by the signal recognition particle SRP, which binds to the ribosome. the RER has SRP receptors that dock the ribosome SRP complex on the cytoplasmic surface (along with the nascent polypeptide and mrna). translation then pushes the polypeptide, signal peptide first, into the er lumen. after translation is complete, the signal peptide is removed from the polypeptide by a signal peptidase in the er lumen. for secreted proteins, once the signal sequence is removed the protein is transported in the interior of vesicles through the Golgi apparatus to the plasma membrane where it is released by exocytosis into the extracellular environment. integral membrane proteins are processed slightly differently. integral membrane proteins have sections of hydrophobic amino acid residues called transmembrane domains that pass through lipid bilayer membranes. the transmembrane domains are essentially signal seqeunces that are found in the interior of the protein (that is, not at the N-terminus). they are not removed after translation. a single polypeptide can have several transmembrane domains passing back and forth through a membrane. during translation, the transmembrane domains are threaded through the ER membrane. the protein is then transported in vesicles to the Golgi apparatus and plasma membrane in the same manner as a secreted protein. (for a protein in the plasma membrane, does the portion of the protein in the ER lumen end up facing the cytoplasm or the cellular exterior? - the cellular exterior) additional functions of the rough er include the initial post translational modification of proteins. although glycosylation (the addition of saccharides to proteins) is usually associated w the Golgi apparatus, some glycosylation occurs in the lumen of the er. disulfide bond formation also occurs in the er lumen. 2 last notes about protein traffic throughout the cell: first, the defat target for proteins that go through the secretory path is the plasma membrane. targeting signals are needed if a protein going through that path needs to end up elsewhere (eg the Golgi, ER, lysosome). second, proteins that are made in the cytoplasm but need to be sent to an organelle that is not part of the secretory path (eg the nucleus, mitochondria, or peroxisomes) require sequences called localization signals. see pg 182/phone for chart of cellular protein traffic see pg 182/phone for secretory pathway

replication of animal viruses

there are a number of differences btwn phages and viruses which infect animal cells. (animal viruses don't have a special name like "phage") the general outline of the viral life cycle, however, remains the same. the virus must specifically bind to a proper host cell, release its genetic material into the host, take over host machinery, replicate its genome, synthesize capsid components, assemble itself, and finally escape to infect a new cell. animal cells have proteins on the surface of their plasma membranes that serve as specific receptors for viruses. these receptors play a role in normal cellular function; they dont exist simply for the benefit of the virus. part of the tissue-specificity of animal viruses is due to the distribution of receptors necessary for adsorption. for ex, the binding of the hiv virus protein gp120 to a T cell membrane protein termed CD4 is one of the first steps in HIV infection (would treatment of an hiv-infected person with a soluble form of cd4 protein affect the infectivity of the virus? - yes it would. the soluble cd4 protein would bind to the virus's CD4 receptor (gp120) and block attachment of the virus to the T cells) (mutation of the cell-surface receptor that viruses attach to would be a means for an organism to become resistant to viral infection. why is this mechanism not common? - 2 reasons 1. the receptor has a specific role in the normal physiology of the host, which a mutation might compromise. 2. viruses generally evolve so rapidly that they can keep up with any changes in the host, but this is not an absolute rule. cells of our immune system keep us alive by keeping up with most microorganisms' tricks) (treatment of an enveloped animal virus with a mild detergent solubilizes several proteins from the virus, although the genome doesnt become accessible. which one of the following is consistent with this scenario? A. some of the proteins that are released by detergent may be encoded by the genome of the infected cell B. the infectivity of the virus is not affected by detergent treatment C. the proteins released by detergent are capsid proteins D. all the proteins released by the detergent are encoded by the viral genome - the detergent solubilized the viral envelope (choice C is wrong). as stated in the text, some envelop proteins are encoded by the virus and some are derived from the host's membranes during budding (choice A is correct, and choice D is wrong). removal of envelope proteins will impair viral adsorption and reduce infectivity (choice B is wrong)) the next step in the infection of an animal cell is penetration into the cell, just as in bacterial infection by a phage. many animal viruses enter cells by endocytosis (a process whereby the host cell engulfs the virus and internalizes it). (why don't phages enter their hosts by endocytosis? - bacteria don't perform endocytosis, in part bc they have a rigid cell wall that doesn't permit them to) once inside the host, the viral genome is uncoated, meaning it is released from the capsid. alternatively, some viruses fuse with the plasma membrane to release the virus into the cytoplasm. from this point, an animal virus may enter either a lytic cycle, a lytic-like cycle called the productive cycle, or a lysogenic cycle the lytic cycle in animal viruses is the same as in phages. the productive cycle is similar to the lytic cycle but doesnt destroy the host cell. its possible bc enveloped viruses exit the host cell by budding through the host's cell membrane, becoming coated with this membrane in the process. budding doesnt necessarily destroy a cell since the lipid bilayer membrane can reseal as the virus leaves. (productive cycle cant occur in hosts w cell walls like bacteria) finally, in the animal virus lysogenic cycle the dormant form of the viral genome is called a provirus (analogous to a prophage). for ex, herpes simplex I is the virus that causes oral herpes. after infection, it may remain dormant as a provirus for an indefinite period of time. then one day, usually when the host encounters stress (eg lack of sleep, upcoming professional school entrance exams), the virus reactivates

causes of genetic mutation

there are many causes of mutation. most are induced by an environmental factor or chemical; however, they can also occur spontaneously. ex physical mutagens, reactive chemicals, biological agents

key info about prokaryotes

theta replication, genome is a single circular piece of dna, three different dna polymerases, one rna polymerase, no mrna processing, polycistronic mrna, simultaneous transcription/translation, smaller ribosomes

are the terms polypeptide enzyme and gene product synonymous? or are there gene products that aren't polypeptide enzymes? are there polypeptides which aren't enzymes?

they aren't synonymous. all polypeptides are gene products, but some gene products aren't polypeptides and some polypeptides aren't enzymes. transfer rna and rRNA are gene products, but not polypeptides. microfilaments and other elements of the cytoskeleton, as well as collagen and many other polypeptides, aren't enzymes

anaerobic respiration (bacteria)

this is not a contradiction in terms! it refers to glucose metabolism with electron transport and oxidative phosphorylation relying on an external electron acceptor other than O2. for ex, instead of reducing O2 to H2O, some anaerobic bacteria reduce SO4 2- to H2S or CO2 to CH4. nitrate (NO3 -) is another possible electron acceptor

domain archaea

though all bacteria are prokaryotes, not all prokaryotes are equal. certain prokaryotes belong to the domain Archaea, to be distinguished from the more "typical" bacteria (or eubacteria) which we have just discussed. the archaea are the organisms that live in the world's most extreme environments, including hot springs, thermal vents, and hypersaline environments (although they can also be found in less extreme environments, such as soil, water, the human colon, etc). structurally, they differ from other bacteria bc their cell wall lacks peptidoglycan. genetically, they share traits with eukaryotes including the presence of introns and the use of many similar mrna sequences. however, since they are single celled, they do reproduce via fission or budding. [what does this mean for their ability to increase their genetic diversity? - archaea would need to use separate strategies to increase their genetic diversity, just like eubacteria. the ability to become more genetically diverse would not be built into reproduction as it is in humans, in part bc meiosis isn't occurring] since archaea have to produce enzymes that can function in extreme environments, they are of great use in industrial applications, such as food processing and sewage treatment. the development of applications for products from these cells is an ongoing area of research

if a viral genome is (+) strand rna, what is used as a template by the rna-dependent rna polymerase?

to make (+) strand copies of the genome, the virus needs the complementary strand as a template: the (-) strand rna. thus the rna-dependent rna polymerase produces a (-) strand intermediate before generating new (+) strand genomes

■ Recognition of self vs. non-self, autoimmune diseases

tolerance - immune system not activated against all normal proteins and cell structures (elimination of self reactive lymphocytes) production of trillions of different B cells and T cells w different receptors is random and as a result many of them will be specific for normal molecules found in the human body, or self antigens. B and T cells must go through selection process to eliminate any self reactive cells. for B cells, this generally occurs in bone marrow, but can also occur in lymph nodes. an immature B cell whose surface receptor binds to normal cell surface proteins (for ex, MHCs or other proteins on a macrophage or other bone marrow cell) is induced to die through apoptosis. those whose surface receptors bind to normal soluble proteins (for ex hemoglobin or lipoproteins) don't go through apoptosis but become unresponsive or anergia. only those B cells whose surface receptors bind to no normal proteins during maturation are released into the circulation. for T cells, the process is similar, but occurs in the thymus or in the lymph nodes. immature T cells whose antigen receptors bind normal proteins in the thymus undergo apoptosis, and (bc not all proteins are expressed in the thymus), some T cells are released that may bind surface proteins in the periphery; these cells become anergic. the result of this is that billions of B and T cells survive but billions of others don't. the ones that survive go on to proliferate if stimulated by antigen in the proper context each producing a group of identical B or T cells, all specific for a particular antigen. such a group is known as a B cell or T cell clone. clonal selection in response to antigen recognition is similar in B and T cells. important to get rid of all cells specific for self-antigen bc such cells can cause an autoimmune rxn. treated w immunosuppressant drugs or steroids to reduce inflammatory response

y-linked traits

traits encoded by genes on the Y chromosome, would only be passed from male parents to male children. y-linked traits are quite rare, bc the Y chromosome is small and contains a relatively small number of genes. many of the genes on the Y chromosome function in sex determination.

mitochondrial inheritance

traits inherited via the mitochondrial genome (genes should be given the prefix mt). a small, haploid dna genome inside the mitochondria and humans inherit this genome from their mothers. affected females have all affected offspring (sons and daughters). affected individuals must have an infected mother, and affected males cannot have any affected offspring. an individual cannot inherit mitochondrial traits from their father

sex-linked traits

traits that are determined by genes located on the X or Y chromosome

return to gene structure: a summary

transcription begins at a start site, but needs a promoter upstream of this. it ends at a termination signal. the rna transcript contains the open reading frame (which goes from start codon to stop codon), as well as both 5' and 3' regulatory regions see pg 123/phone for pic

■ Carbon dioxide transport and level in blood

transported in blood in 3 ways: 1 majority of CO2 transport accomplished by conversion of CO2 to carbonic acid which can dissociate into bicarbonate and a proton according to rxn: CO2 + H2O <> H2CO3 <> HCO3 - + H+. these compounds are extremely water-soluble and thus easily carried in the blood. conversion of CO2 into carbonic acid is catalyzed by an RBC enzyme called carbonic anhydrase. remember that this rxn is also important as principal plasma pH buffer 2 some CO2 ( ~20% ) is transported by simply being stuck onto hemoglobin. it does not bind to the oxygen binding sites, but rather to other sites on the protein. binding of CO2 to hemoglobin is important in the Bohr effect bc it stabilizes tense Hb 3 CO2 is somewhat more water soluble than O2, so a fair amount (~7%) can be dissolved in the blood and carried from the tissues to the lungs. virtually no oxygen can be dissolved in the blood

vapor-pressure depression

type of colligative property. vapor pressure is the pressure exerted by the gaseous phase of a liquid that evaporated from the exposed surface of the liquid. the weaker a substance's intermolecular forces, the higher its vapor pressure and the more easily it evaporates. for ex, if we compare diethyl ether, H5C2OC2H5, and water, we notice that while water undergoes hydrogen bonding, diethyl ether doesn't, so despite its greater moelcular mass, diethyl ether will vaporize more easily and have a higher vapor pressure than water. easily vaporized liquids, liquids w a high vapor pressure, like diethyl ether, are said to be volatile. now lets think about what happens to vapor pressure when the liquid contains a dissolved solute. the solute molecules are attached to solvent molecules and act as anchors. as a result, more energy is required to enter the gas phase since the solvent molecules need to break away from their interactions with the solute before they can enter the gas phase. in fact, the boiling point of a liquid is defined as the temperature at which the vapor pressure of the solution is equal to the atmospheric pressure over the solution. thus at sea lvl, where the atmospheric pressure is 760 torr, the solution must have a vapor pressure of 760 torr in order to boil. adding more solute to the same soln will dec its vapor pressure. boiling will still take place when vapor pressure is 760 torr, but more heat will have to be supplied to reach this vapor pressure, and thus the solution will boil at a high temp. for ex salted water (like for cooking pasta) boils at a higher temp than unsalted water.

receptor-mediated endocytosis

type of endocytosis. is very specific. the site of endocytosis is marked by pits coated with the molecule clathrin (inside the cell) and with receptors that bind to a specific molecule (outside the cell). an important example is the uptake of cholesterol from the blood. cholesterol is transported in the blood in large particles called lipoproteins. cells obtain some of the cholesterol they require by receptor mediated endocytosis of these lipoproteins. if they are not removed from the blood, cholesterol accumulates in the bloodstream, sticking to the inner walls of arteries. this results in atherosclerosis (a buildup of plaque on the walls of the arteries). (does clathrin recognize and bind to lipoproteins? - no. clathrin is a fibrous protein inside the cell that associates with the cytoplasmic portions of the cell-surface receptors that bind lipoproteins) when the receptor-lipoprotein compels internalizes, it is taken into a vesicle that is termed an endosome. lipoproteins are taken from the endosome to a lysosome where the cholesterol is released from the lipoprotein and the lipoprotein is degraded. the lipoprotein receptor is returned to the cell surface where it may again bind a lipoprotein. (how is receptor-mediated endocytosis similar to and different from active transport? - both import a particular substance. one difference is that in endocytosis the substance ends up sealed in an endosome, whereas in active transport the substance is just dumped into the cytoplasm.)

sexual selection

type of natural selection. animals often don't choose mates randomly, but have evolved elaborate rituals and physical displays that play a key role in attracting and choosing a mate. ex some birds have bright plumage to attract a mate, even at the cost of increased predation

artificial selection

type of natural selection. humans intervene in the mating of many animals and plants, using artificial selection to achieve desired traits through controlled mating. ex the pets and crop plants we have are the result of many generations of artificial selection

kin selection

type of natural selection. natural selection doesn't always act on individuals. animals that live socially often share alleles with other individuals and will sacrifice themselves for the sake of the alleles they share with another individual. ex a female lion sacrifices herself to save her sister's children

facilitated diffusion: channels

type of passive transport. channel proteins in the plasma membrane allow material that cannot pass through the membrane by simple diffusion to flow through the plasma membrane down a concentration gradient. channels do this by forming a narrow opening in the membrane surrounded by the protein. channels are very selective in what passes through the opening in the membrane. there are many kinds of ion channels, each of which allows the passage of only one type of ion through the channel down a gradient. all cells have potassium ion channels, for ex, that allow only potassium (and not sodium) to flow through the plasma membrane down a gradient. ion channels are said to be gated if the channel is open in response to specific environmental stimuli. a channel that opens in response to a change in the electrical potential across the membrane is called a voltage gated ion channel. one that opens in response to binding of a specific molecule like a neurotransmitter is called a ligand-gated ion channel. the regulation of membrane potential by gated ion channels plays a key role in the nervous system. (can ion channels move ions against an electrochemical gradient? - no. ion channels are only involved in facilitated diffusion, the movement of molecules down an electrochemical gradient with the help of a protein) see pg 195/phone for pic

simple diffusion

type of passive transport. diffusion of a solute through a membrane without help from a protein. for ex, steroid hormones are free to move back and forth across the membrane by simple diffusion as pushed by concentration gradients, thanks to their hydrophobicity. however, lipid bilayer membranes are impermeable to most solutes; that is one of the main functions of membranes. the plasma membrane is a barrier to the free movement of all large and/or hydrophilic solutes. facilitated diffusion is the movement of a solute across a membrane, down a gradient, when the membrane itself (the pure lipid bilayer) is intrinsically impermeable to that solute. specific integral membrane proteins allow material to cross the plasma membrane down a gradient in facilitated diffusion. for ex, red blood cells require glucose, which they get from the bloodstream. however glucose is a bulky hydrophilic molecule that cannot cross the RBC lipid bilayer. instead, it must be shuttled across by a particular protein in the rbc plasma membrane. there are 2 well-characterized types of proteins that serve this sort of function: channel proteins and carrier proteins. channels and carriers give the membrane its essential feature of selective permeability: permeability to some things despite impermeability to most things.

bacterial cytoplasm

unlike a eukaryotic cell, there are no membrane bound organelles in prokaryotic cells (note that ribosomes, which aren't membrane-bound, are found in bacteria). the prokaryotic genome is a single double-stranded circular dna chromosome (there are a few exceptions too this (eg bacteria with more than one chromosome and/or linear chromosomes). it is not located in a nucleus, and it is not associated with histone proteins as the eukaryotic genome is. in bacteria, transcription and translation occur in the same place at the same time. ribosomes begin to translate mrna before it is completely transcribed. many ribosomes translating a single piece of mrna form a structure known as a polyribosome remember that the bacterial ribosome is structurally different from the eukaryotic ribosome, though both function the same way. the differences allow us to prescribe various antibiotics which interfere with bacterial translation without disrupting our own. examples are streptomycin and tetracycline, which bind only to bacterial ribosomes see pg 149/phone for pic one last genetic element that can be found in prokaryotic cells is the plasmid. this is a circular piece of double-stranded dna which is much smaller than the genome. plasmids are referred to as extrachromosomal genetic elements. they often encode gene products which may confer an advantage upon a bacterium carrying the plasmid. for ex, plasmids frequently carry antiobiotic-resistance genes (genes that encode proteins which can break down antibiotics). many plasmids are capable of autonomous replication which means that a single plasmid molecule within a bacterial cell may cause itself to be replicated into many copies. plasmids are important not only bc they may encode advantageous gene products, but also bc they orchestrate bacterial exchange of genetic info, or conjugation.

urinary system anatomy

urine leaves kidney in ureter, which empties into urinary bladder. 2 sphincters internal sphincter made of smooth (involuntary) muscle and an external sphincter made of skeletal (voluntary) muscle. the internal sphincter relaxes reflexively (and bladder contracts) when bladder wall stretched. person can choose when to relax external sphincter allowing urine to flow from bladder into urethra out of body.

rule of addition

used to calculate the chances of either of 2 events happening. the chance of either A or B happening is equal to the probability of A added to the probability of B, minus the probability of A and B occurring together (their product).

t-tests

used to compare 2 data sets

systole

ventricles contract. ensuing buildup of pressure causes the av valves to slam shut. over the next few milliseconds the pressure in the ventricles increases rapidly, until the semilunar valves fly open and blood rushes into the aorta and pulmonary artery. period of time during which the ventricles are contracting, beginning at the "lub" sound and ending at the "dup." at the end of systole, the venticles are nearly empty and stop contracting. as a result the pressure inside falls rapidly, and blood begins to flow backward, from the pulmonary artery into the right ventricle, and from the aorta into the left ventricle. but very little backflow actually occurs bc the semilunar valves slam shut when the pressure in the ventricles becomes lower than the pressure in the great arteries. at this point back in diastole

diastole

ventricles relaxed, blood able to flow into them from atria. atria contract to propel blood into the ventricles.

skeletal structure

vertebrate endoskeleton divided into axial and appendicular components. axial skeleton consists of skull, vertebral column, and the rib cage. all other bones are part of the appendicular skeleton. 2 primary bone shapes: flat and long. flat bones like the scapula, ribs, bones of the skull are the location of hematopoiesis and are important for protection of organs. the bones of the limbs are long bones, important for support and movement. the main shaft of a long bone is called they diaphysis. the flared end is called the epiphysis. general structure of bone may be compact or spongy. as the names imply compact bone is hard and dense while spongy bone is porous. spongy bone is always surrounded by a layer of compact bone. the diaphysis of long bones is a tube composed only of compact bone. bone marrow is non bony material found in shafts of long bones and in the pores of spongy bones. red marrow found in spongy bone within flat bones is the site of hematopoiesis. its ativity inc in response to erythropoietin, a hormone made by kidney. yellow marrow found in shfats of long bones is filled w fat and is inactive. bone is composed of collagen and hydroxyapatite which is a solid material consisting of calcium phosphate crystals. hydroxyapatite formed around collagen to make bone. spongy bone under the microscope looks like a sponge. it has a disorganized structure in which many spikes of bone surround the marrow containign cavitities. the spikes of bone in spongy bone are spicules or trabeculae. compact bone has a specific organization. basic unit of compact bone structure is the osteon (haverisan system). in the center of the osteon is a hole called the central (haversian) canal, which contains blood, lymph vessels, and nerves. surrounding the canal are concentric rings of bone termed lamellae (which just means sheets or layers). tiny channels, or canaliculi, branch out from the central canal to spaces called lacunae (lakes). in each lacuna is an osteocyte, or mature bone cell. osteocytes have long processes which extend down the canaliculi to contact other osteocytes through gap junctions. this allows the cells to exchange nutrients and waste through an otherwise impermeable membrane. perforating (volkmann's) canals are channels that run perpendicular to central canals to connect osteons.

viruses

viruses infect all life forms on earth, including plants, animals, protists, and bacteria. a virus is an obligate intracellular parasite. as such, they are only able (obligated) to reproduce within (intra) cells. while within cells, viruses have some of the attributes of living organisms, such as the ability to reproduce; but outside cells, viruses are without activity. viruses on their own are unable to perform any of the chemical rxns characteristic of life, such as synthesis of atp and macromolecules. (note however that some viruses store some atp in their capsids. they acquired this atp from the previous host and typically use it to power penetration.) viruses are not cells or even living organisms. to reproduce, they commandeer the cellular machinery of the host they infect and use it to manufacture copies of themselves. in the final analysis, a virus is nothing more than a package of nucleic acid that says: "pick me up and reproduce me." remember this crucial definition: a virus is an obligate intracellular parasite that relies on host machinery whenever possible.

aminoacyl-trna synthetases

we have stated that incorporation of the appropriate amino acid in a growing polypeptide depends on the delivery of the correct amino acid by a specific trna. but we also noted that the amino acid acceptor sites of all trna molecules are the same. how is the attachment of the appropriate amino acid to each trna molecule accomplished? aminoacyl-trna synthetase enzymes are specific to each amino acid, and there is at least one aminoacyl-rna synthetase for every amino acid. this family of enzymes recognizes both the trna and the amino acid based on their 3d structures. they are highly specific, which is important bc joining the wrong amino acid to a trna would result in the wrong amino acid being incorporated into a polypeptide. given that some amino acids differ only by a single methyl group, this specificity is quite amazing. aminoacyl-trna synthetases also function with a very low error rate (longer proteins have a higher chance of containing errors) overall then, amino acid activation serves 2 functions. one is specific and accurate amino acid delivery, and the other is thermodynamic activation of the amino acid

control of gene expression at the protein lvl: translation initiation

we've already discussed complex process of assembling translational machinery. in both prokaryotes and eukaryotes, this is a highly regulated process that links protein synthesis with upstream signaling pathways. otherwise there is little control at the lvl of translation

freezing-point depression

what happens when we add a solute to a liquid, then try to freeze the solution? solids are held together by attractive intermolecular forces. during freezing, the molecules in a liquid will assemble into an orderly, tightly packed array. however, the presence of solute particles will interfere with efficient arrangement of the solvent molecules into a solid lattice. as a result, a liquid will be less able to achieve a solid state which a solute is present, and the freezing point of the solution will decrease. (or equivalently, the melting point of a solid containing a solute is decreased.) the good news is that the formula for freezing point depression has exactly the same form as the formula for boiling-point elevation, except that the temp is going down instead of up (that is, the equation for freezing point depression has a minus sign whereas the equation for boiling point elevation has a plus sign). freezing-point depression ΔTf=-kfim in this equation, kf is the solvent's freezing point depression constant, i is the solute's van't Hoff factor, and m is the molal concentration of the solution. for water, kf is approx equal to 1.9 degrees C / m

convergent evolution

when 2 different species come to possess many analogous structures due to similar selective pressures

boiling-point elevation

when a liquid boils, the molecules in the liquid acquire enough energy to overcome the intermolecular forces and break free into the gas phase. the liquid molecules escape as a vapor at the surface btwn the liquid and air. but what happens when a non-volatile solute is added to the liquid? as described before, the solute particles are attached to solvent molecules and act as "anchors." as a result, more energy is required since you not only have to covert the solvent into the gas phase, but you first have to break the interaction with the solute. what happens to the boiling point? in order for the molecules to escape, they need more energy than they did without the solute. this translates into an elevation of the boiling point. the increase in boiling point is directly related to the number of particles in solution and the type of solvent. for a given solvent (again, in biological systems this is always water), the more solute particles, the greater the boiling point elevation. also, you have to consider that some compounds dissociate when they dissolve, so the equation for boiling point elevation includes the van't Hoff factor, i: Boiling-point elevation ΔTb=kbim in this equation, kb is the solvent's boiling point elevation constant, i is the solutes van't Hoff factor, and m is the molal concentration of the solution. for water, kb is approx equal to .5 degrees C/m

if bacterial contain only one copy of the bacterial genome, how can recombination occur?

when an Hfr cell conjugates with an F- cell and transfers a portion of the bacterial chromosomes, the F- cell will have 2 copies of some genes, and recombination can occur btwn the 2 copies

electrolytes

when ionic substances dissolve, they dissociate into ions. free ions in a solution are called electrolytes bc the soln can conduct electricity. some salts dissociate completely into individual ions, while others only partially dissociate (that is, a certain percentage of the ions will remain paired, sticking close to each other rather than being independent and fully surrounded by solvent). solutes that dissociate completely (like ionic substances) are called strong electrolytes, and those that remain ion-paired to some extent are called weak electrolytes. (covalent compounds that don't dissociate into ions are non electrolytes). solutions of strong electrolytes are better conductors of electricity than those of weak electrolytes. different ionic compounds will dissociate into different numbers of particles. some won't dissociate at all, and others will break up into several ions. the vant Hoff (or ionizability) factor (i) tells us how many ions one unit of a substance will produce in a solution. for ex, C6H12O6 is nonionic, so it doesn't dissociate. therefore, i=1 (note: the van't Hoff factor for almost all biomolecules -- hormones, proteins, steroids, etc-- is 1) NaCl dissociates into Na+ and Cl-. therefore, i=2 HNO3 dissociates into H+ and NO3 -. therefore i=2 CaCl2 dissociates into Ca2+ and 2 Cl-. therefore, i=3

a bacteriophage with an important capsid gene deleted infects the same cell as another virus with a normal copy of the same gene. at the time of host-cell lysis: A. all released viruses will be capable of infecting new hosts, but only some of these new infections will give rise to phage capable of infecting new hosts b. no infective viruses will be released c. each individual virus that is released will produce a mixture of infective and noninfective viruses in subsequent infections d. only normal viruses will be released

when two viruses infect the same cell, its called co-infection. some normal viruses will result, and some genomes from defective viruses will get packaged into capsids made from proteins encoded by the normal virus. the latter will be capable of infecting new hosts, but when they do their progeny will not survive due to the capsid abnormality. choice A is correct, choices b and d are wrong. think about it: where did the phage with the deleted capsid gene come from?! the deficient virus must have come from a co-infection such as this. the deficient phage can only infect host cells and reproduce with the help of normal viruses. note that bc a single virus carries only a single genome, it can produce only one type of progeny (choice C is wrong)

nerve

white matter in pns

tract

white matter in the brain

tract or column

white matter in the spinal cord

a man that is homozygous for eye color, bb, is married to a woman who is heterozygous at the same gene: Bb. what are the chances that a child will have the Bb genotype and be a boy?

without drawing a punnet square, it is possible to see that all children must receive at least one b allele (from the father), and that 50% of the children will receive the B allele from the mother; thus 50% of the children will be Bb. the odds of a boy are 50%. therefore the odds a child is both a boy and has the Bb genotype are, by the rule of multiplication, .5 x .5 = .25, or 25%

sex chromosomes

women have 23 pairs of chromosomes that are homologous while men have only 22 pairs of chromosomes that match in appearance. the 2 chromosomes in men that did not match each other are the X and Y chromosomes bc of their appearance during mitosis. males have an X and a Y, while females have 2 X chromosomes. the presence of a Y chromosome in humans (genotype XY) is a key factor in the determination of the sex of an embryo, and subsequent development into a male. the absence of a Y (genotype XX) results in a female as the default developmental pathway. during meiosis, females generate gametes that contain an X chromosome; males generate gametes with either an X or Y chromosome, meaning that it is the male gamete that determines the gender of an embryo. see pg 244/phone for pic the sex chromosomes also play a key role in the inheritance of other traits that are not directly invovled in sexual development. much of what has been dicussed about inheritance was dependent on the assumption that there are 2 copies of every chromosome and therefore 2 copies of every gene in each cell. this is true for genes found on every pair of chromosomes except for one pair: the sex chromosomes. genes that lie on the x chromosome will be present in 2 copies in females but only in one copy in males. (in males, recessive alleles on the x chromosomes are always expressed since no other allele is present that can mask the recessive allele.) traits that are determined by genes on the X or Y chromosome are called sex-linked traits bc of their unique patterns of expression and inheritance.

adenoviruses have a single linear ds-dna genome, which contains a number of different promoters that are regulated during infection. although transcription is carried out by cellular rna polymerase, the viral E1A gene product is required for transcription of most viral genes. if the E1A gene is deleted from the virus or if the gene product is inactivated, viral infection is unable to proceed. adenoviruses also encode much of their own replication machinery, including DNA polymerase. if 2 different adenoviruses infect the same cell, one with a deleted E1A gene and another with a deleted DNA polymerase gene, will successful infection of the cell result?

yes, thanks to complementation. the mutant viruses will complement each other, one providing the E1A protein and the other providing DNA polymerase. note that this had to have happened before; how else could a defective virus such as these exist? one virus which complements another is called a helper virus

if the F factor in an Hfr strain integrates near a gene required for lactose metabolism, is it likely that other genes involved in lactose metabolism will be transferred during conjugation at the same time?

yes. gene for proteins of related functions are often adjacent to each other in prokaryotes (in operons) and so will transfer to an F- cell together

replication rules to memorize

1. dna replication is semiconservative individual strands of the double-stranded parent are pulled apart, and then a new daughter strand is synthesized using the parental dna as a template to copy from. each new daughter chain is perfectly complementary to its template or parent 2. polymerization occurs in the 5' to 3' direction, without exception this means the existing chain is always lengthened by the addition of a nucleotide to the 3' end of the chain. there is never 3' to 5' polymerase activity 3. dna pol requires a template it cannot make a dna chain from scratch but must copy an old chain. this makes sense bc it would be pretty useless if dna pol just made a strand of dna randomly, without copying a template 4. dna pol requires a primer it cannot start a new nucleotide chain 5. replication forks grow away from the origin in both directions each replication fork contains a leading strand and a lagging strand 6. replication of the leading strand is continuous and leads into the replication fork, while replication of the lagging strand is discontinuous, resulting in okazaki fragments 7. eventually all rna primers are replaced by dna, and the fragments are joined by an enzyme called dna ligase

replicating telomeres in eukaryotes

DNA polymerase can only build dna in one direction (5' to 3'), and requires both a template and a primer. these requirements lead to a roadblock at chromosome ends. eventually there will be no place on the lagging strand to lay down a primer, and primers close to the end of dna cannot be replaced with dna bc there is nothing on the other side (DNA polymerase usually uses a previous length of upstream dna to replace the primer, but this isn't available at the end of a chromosome). this means that dna replication machinery is unable to replicate sequences at the very ends of chromosomes, and after each round of the cell cycle and dna replication, the ends of chromosomes shorten. telomeres are disposable repeats at the end of chromosomes. they are consumed and shorten during cell division, becoming btwn 50 and 200 base pairs shorter when telomeres become too short, they reach a critical length where the chromosome can no longer replicate. as a consequence, cells can activate dna repair pathways, enter a senescent state (where they are alive but not dividing), or activate apoptosis (preprogrammed cell death). the hayflick limit is the number of times a normal human cell type can divide until telomere length stops cell division. many age-related diseases are linked to telomere shortening telomerase is an enzyme that adds repetitive nucleotide sequences to the ends of chromosomes and therefore lengthens telomeres. telomerase is a ribonucleoprotein complex, containing an RNA primer and reverse transcriptase enzyme. reverse transcritpases read rna templates and generate dna. in humans, the rna template is 3' CCCAAUCCC5', and this allows for chromosome extension, one DNA repeat (5'TTAGGG3') at a time. the telomerase complex continuously polymerizes, then translocates, allowing extension of 6-nucleotide telomere repeats. see pg 83/phone for pic in most organisms, telomerase is only expressed in the germ line, embryonic stem cells, and some white blood cells. however, cancer cells can also express telomerase, which can help the cells immortalize. telomere extension allows the cells to bypass senescence and apoptosis, and can therefore contribute to their transformation to a pre-cancerous state

non-coding rna (ncRNA)

a functional RNA that isn't translated into a protein. the human genome codes for thousands of ncRNAs, and there are several types. the 2 major types are transfer rna (tRNA) and ribosomal RNA (rRNA) tRNA is responsible for translating the genetic code. tRNA carries amino acids from the cytoplasm to the ribosome to be added to a growing protein. rRNA is the major component of the ribosome. humans have only 4 different types of rRNA molecules (18S, 5.8S, 28S, and 5S), although almost all the rna made in a given cell is rRNA. all rRNAs serve as compoenets of the ribosome, along with many polypeptide chains. one rRNA provides the catalytic function of the ribosome, which is a little odd. in most other cases, enzymes are made from polypeptides. catalytic rnas are also called ribozymes (or ribonucleic acid enzymes), since they are capable of performing specific biochemical reactions, similar to protein enzymes. there are additional examples of ribozymes, including snRNA and some introns that are self-splicing some other ncRNAs are: small nuclear rna (snRNA) molecules (150 nucleotides) associate with proteins to form snRNP (small nuclear ribonucleic particles) complexes in the spliceosome microrna (miRNA) and small interfering RNA (siRNA) function in rna interference (RNAi), a form of post-transcriptional regulation of gene expression. both can bind specific mRNA molecules to either inc or dec translation PIWI-interacting RNAs (piRNAs) are single stranded and short (typically btwn 21 and 31 nucleotides in length). they work with a class of regulatory proteins called PIWI proteins to prevent transposons from mobilizing long ncRNAs are longer than 200 nucleotides. they help control the basal transcription lvl in a cell by regulating initiation complex assembly on promoters. they also contribute to many types of post-transcriptional regulation by controlling splicing and translation, and they function in imprinting and X-chromosome inactivation

controlling gene expression

adult humans have over 220 different types of cells, all with the same genome, but with different attributes such as morphology, lifespan, function, ability to secrete, response to signaling molecules, mobility, etc. these changes are due to differences in gene expression and protein function. in each cell type, some genes are expressed and others are silenced, further, genes that are expressed can have different lvls of expression, where in one cell type the gene is expressed at a high lvl (to produce lots of ncRNA or protein), and in a different cell type the same gene is expressed at a low lvl. they can also have varying activity, stability, and half-life. these variations in gene expression can be altered using many different mechanisms. see pg 112/phone for pic ** (good pic) transcription is the principle site of the regulation of gene expression in both eukaryotes and prokaryotes. this means that the amount of each protein made in every cell is affected by the amount of mrna that gets transcribed. gene expression can also be controlled epigenetically. broadly speaking, epigenetic focuses on changes in gene expression that aren't due to changes in DNA sequences, but are either heritable or have a long-term effect. the 3 most commonly studied areas in this field are dna methylation, chromatin remodeling, and rna interference.

reference points in transcription

chromosome is referred to as the template, not parent. what about the individual strands of the chromosome? are they both templates for the same mrna? only one of the strands of the dna template encodes a particular mrna molecule. but it makes sense: paired dna strands are complementary, not identical. the strand which is actually transcribed is called the template, non-coding, transcribed, or antisense strand; its complementary to the transcript. the other dna strand is called the coding or sense strand; it has the same sequence as the transcript (except is has T in place of U). its customary to say that transcription starts at a point and proceeds downstream, which means toward the 3' end of the coding strand and transcript. upstream means toward the 5' end of the coding strand, beyond the 5' end of the transcript. upstream nucleotide sequences are referred to using negative numbers, and downstream sequences are referred to using positive numbers. the first nucleotide on the template strand which is actually transcribed is called the start site. the corresponding nucleotide on the coding strand is given the number +1. regulatory sequences on the chromosome are referred to by where they occur on the coding strand. see pg 98/phone. transcript labeled mrna on pg, is this accurate in all life forms (hint, in eukaryotes is the initial transcript mature mrna, ready to be translated?) - no, it is accurate for prokaryotes only. in eukaryotes, the rna transcript must be processed (spliced) and transported out of the nucleus before it can be translated

ribosome

composed of many polypeptides and rRNA chains held together in a massive quaternary structures. ribosomes float around in the cytoplasm, and each has a small subunit and a large subunit. the unit of measurement is the Svedberg, or S, unit. svedbergs are a sedimentation rate, that is, how quickly something will sink in a gradient during centrifugation, and the units aren't additive the prokaryotic ribosome sediments in a gradient at a rate of 70S, so its referred to as the 70S ribosome. its composed of a 30S small subunit and a 50S large subunit. the small subunit is made of a 16S rRNA and 21 peptides. 2 rRNA molecules (23S and 5S) and 31 peptides make up the large subunit eukaryotes have an 80S ribosome. it also has a small and large subunit. the large subunit has 3 rRNA molecules (5S, 5.8S, and 28S) and 46 peptides, and sediments in a gradient at a rate of 60S. the small subunit has 33 peptides and one rRNA (18S) and sediments in a gradient at a rate of 40S the 23S rRNA in prokaryotes and the 28S rRNA in eukaryotes have ribozyme function. they help link amino acids during protein synthesis via peptides transferase activity. this contributes to peptide bond formation. notice how the ribozymes activity of the ribosome is found in the large subunit of both prokaryotic and eukaryotic ribosomes. see pg 107/phone for ribosome components in both prokaryotes and eukaryotes, the complete ribosome (both subunits together) has 3 special bonding sites. the A site (aminoacyl-tRNA site) is where each new tRNA delivers its amino acid. the P site (peptidyl-tRNA site) is where the growing polypeptide chain, still attached to a tRNA, is located during translation. the E site (exit-tRNA site) is where a now-empty tRNA sits prior to its release from the ribosome. during translation, the next codon to be translated is exposed in the A site, since this is where the next amino acid to be added must bind. tRNAs move through the sites from A->P->E. see pg 108/phone for pic

transfer rna (tRNA)

each trna is composed of a single transcript produced by rna pol III. the tertiary structure of every trna molecule is similar. trnas have a stem and loop structure stabilized by hydrogen bonds btwn bases on neighboring segments of the rna chain. several modified nucleotides are found in trna (eg dihydrouridine). one end of the structure is responsible for recognizing the mRNA codon to be translated. this is the anticodon, a sequence of 3 ribonucleotides which is complementary to the mRNA codon the trna translates. a key step in translation is specific base paring btwn the trna anticodon and the mRNA codon. it is this specificity that dictates which amino acid of the 20 will be added to a growing polypeptide chain by the ribosome. the other end of the trna molecule has the amino acid acceptor site, which is where the amino acid is attached to the trna. since there is a trna for each codon, each trna is specific for one amino acid, while each amino acid may have several trnas. each trna can be named according to the amino acid its specific for. for ex, a trna for valine would be written tRNAval. when the amino acid is attached, the trna is written this way: Val-tRNAVal. see pg 103/phone for pic of tRNA trna molecules often contain nitrogenous bases in many positions that have been covalently modified. base methylation is particularly common. some specific examples are inosine (derived from adenine), pseudouridine (derived from uracil), or lysidine (derived from cytosine). inosine in particular plays an important role in wobble base pairing

genetic code

dna doesn't directly exert its influence on cells, but merely contains sequences of nucleotides known as genes that serve as templates for the production of another nucleic acid known as rna. the process of reading dna and writing the info as rna is termed transcription. this can generated either a final gene product (as in the case of all noncoding rnas, discussed below), or a messenger molecule. the messenger rna (mrna) is then read and the info is used to construct protein. the synthesis of proteins using rna as a template is termed translation and is accomplished by the ribosome, which is a massive enzyme composed of many proteins and pieces of rna (known as ribosomal rna rRNA) overall process looks like this: DNA -> RNA -> protein. this unidirectional flow equation represents the central dogma (fundamental law) of molecular biology. this is the mechanism whereby inherited information is used to created actual objects, namely enzymes and structural proteins this language used by dna and mrna to specify the building blocks of proteins is known as the Genetic Code. the alphabet of the genetic code contains only 4 letters ATGC. how can 4 letters specify the ingredients of the multitude of proteins in every cell? a number of experiments confirmed that the genetic code is written in 3-letter words, each of which codes for a particular amino acid. a nucleic acid word (3 nucleotide letters) is referred to as a codon see pg 74 for genetic code 64 codons. 61 of them specify amino acids; the remaining three are stop codons. note that most of the 20 amino acids can be coded for by more than one codon. often, all four of the codons with the same first 2 nucleotides (eg CU_) encode the same amino acid. 2 or more codons coding for the same amino acid are known as synonyms. bc it has such synonyms, the genetic code is said to be degenerate. however its very important to realize that though an amino acid may be specified by several codons, each codon specifies only a single amino acid. this means that each piece of dna can be interpreted only one way: the code has no ambiguity the code on page 74 is the standard genetic code and is used by most organisms. however some protists use an alternate genetic code, and the mitochondrial genome of many organisms (including humans and many other vertebrates) uses a slightly different code

dna pol IV and dna pol V

in prokaryotes. have similar characteristics they are error prone in 5' to 3' polymerase activity, but function to stall other polymerase enzymes at replication forks when dna repair pathways have been activated. this is an important part of the prokaryotic checkpoint pathway

dna pol II

in prokaryotes? has 5' to 3' polymerase activity, and 3' to 5' exonuclease proofreading function. it participates in dna repair pathways and is used as a backup for dna pol III

dna pol III

in prokaryotes? responsible for the super-fast, super-accurate elongation of the leading strand. in other words, it has high processivity. it has 5' to 3' polymerase activity as well as 3' to 5' exonuclease activity. this is when the enzyme moves backward to chop off the nucleotide it just added, if it was incorrect; the ability to correct mistakes in this way is known as proofreading function. it has no known function in repair, and so is considered a replicative enzyme

dna pol I

in prokaryotes? starts adding nucleotides at the rna primer; this is 5' to 3' polymerase activity. bc of its poor processivity (it can only add 15-20 nucleotides per second), dna pol III usually takes over about 400 base pairs downstream from the ORI. dna pol I is also capable of 3' to 5' exonuclease activity (proofreading). dna pol I removes the rna primer via 5' to 3' exonuclease activity, while simultaneously leaving behind new dna in 5' to 3' polymerase (remember all polymerization is 5' to 3') activity. finally dna pol I is important for excision repair

prokaryotic transcription

in bacteria (prokaryotes), all types of rna are made by the same rna polymerase. prokaryotic rna polymerase is a large enzyme complex consisting of 5 subunits: 2 alphas subunits, a beta subunit, a beta' subunit, and an omega subunit (α2ββ'ω). this is the core enzyme responsible for rapid elongation of the transcript. however the core enzyme alone cannot initiate transcription. an additional subunit termed the sigma factor (σ) is required to form what is sometimes referred to as the holoenzyme (holo = complete), which is responsible for initiation transcription occurs in 3 stages: initiation, elongation, and termination. initiation occurs when rna polymerase holoenzyme binds to a promoter. the typical bacterial promoter contains 2 primary sequences: the pribnow box at -10 and the -35 sequence. holoenzyme scans along the chromosome like a train on a railroad track until it recognizes a promoter and then stops, forming a closed complex. the rna polymerase must unwind a portion of the dna double helix before it can begin to synthesize rna the rna polymerase bound at the promoter with a region of single-stranded dna is termed the open complex. once the open complex has formed, transcription can begin. the sigma factor plays 2 roles in helping the polymerase find promoters. the first is to greatly inc the ability of rna polymerase to recognize promoters. the second is to dec the nonspecific affinity of holoenzyme for dna. once the open complex and several phosphodiester bonds have been formed, the sigma factor is no longer necessary and leaves the rna polymerase complex the core enzyme elongates the rna chain processively, with one polymerase complex synthesizing an entire rna molecule. as the core enzyme elongates the rna, it moves along the dna downstream in a transcription bubble in which a region of the dna double helix is unwound to allow the polymerase to access the complementary dna template. when a termination signal is detected, in some cases with the help of a protein called rho, the polymerase falls off of the dna, releases the rna, and the transcription bubble closes

physical mutagens

ionizing radiation (like X-rays, alpha particles, and gamma rays) can cause dna breaks. if these only occur on one strand, they can be easily patched up bc the dna helix is still held together in one piece. however, if both backbones are broken close to each other on a segment of dna, a double-strand break DSB occurs. here the chromosome has been split into 2 pieces and its much more difficult to piece them back together. see pg 84/phone for pic uv light causes photochemical damage to dna. for ex, if two pyrimidines (2 Cs or 2 Ts) are beside each other on a dna backbone, uv light can cause them to become covalently linked. these pyrimidine dimers distort the dna backbone and can cause mutations during dna replication if they are not repaired. see pg 84/phone for pic

processing

many proteins require cleavage of some sort to become mature or functional. cleavage can occur at either end of a peptide chain, or in the middle. protein precursors are often used when the mature protein may be dangerous to the organism. bc the precursor is already made, it allows large quantities of mature protein to be available on short notice. enzyme precursors are called zymogens or proenzymes. a well-known example of post-translational processing is insulin. insulin is made from a prohormone; preproinsulin is the primary translational product of the human INS gene. this peptide is 110 amino acids in length. to form proinsulin, an N-terminus signal peptide is removed and disulphide bonds form, in the endoplasmic reticulum. 3 cleavage events are necessary to process proinsulin: the C peptide is removed by a family of enzymes called pro protein convertases, and a dipeptide fragment is removed from the C-terminus of the b chain peptide by a carboxypeptidase. these cleavage events occur in a secretory vesicle. the biological effects of insulin are well known, but its recently been shown that peptide C also has signaling properties. see pg 122/phone for pic

coding rna

messenger rna (mRNA), the only type of coding rna. this molecule carries genetic information to the ribosome, where it can be translated into protein; each unique polypeptide is created according to the sequence of codons on a particular piece of mrna, which was transcribed from a particular gene. to allow for this, each mrna has several regions. the 5' region is not translated into protein (so is called the 5' untranslated region, or 5'UTR), but is important in initiation and regulation. following the 5'UTR is the region that codes for a protein. this starts at a start codon and ends at a stop codon, and is called the open reading frame ORF. the 3' end of the mrna (after the stop codon) isn't translated into protein but often contains regulatory regions that influence post-transcriptional gene expression eukaryotic mrna is usually monocistronic and obeys the "one gene, one protein" principle. this means that each piece of mrna encodes only one polypeptide (and so contains one ORF). hence, there are as many different mrnas as there are proteins. bc each mrna can be read many times, each transcript can be used to make many copies of its polypeptide. there are a few exceptions to the "one gene, one protein" principle; recently, some polycistronic eukaryotic mrnas have been discovered in contrast, prokaryotic mrna often codes for more than one polypeptide and is termed polycistronic. different open reading frames on the same polycistronic mrna are generally related in function. (for ex, if 5 enzymes are necessary for the synthesis of a particular molecule, then all 5 enzymes might be encoded on a single piece of mrna) translation termination and initiation sequences are found btwn the ORFs. the termination information helps finish the previous peptide chain, and initiation information helps start translation of the next ORF on the transcript messenger rna is constantly produced and degraded, according to the cell's need for the proteins encoded by each piece of mrna. in fact, this is the principal means whereby cells regulate the amount of each particular protein they synthesize. this is an important point. note that in eukaryotes, the first rna transcribed from dna is an immature or precursor to mrna called heterogeneous nuclear rna (hnRNA). processing events (such as addition of a cap and tail, and splicing) are required for hnRNA to become mature mRNA. since prokaryotes don't process their primary transcripts, hnRNA is only found in eukaryotes

post-translational modification

newly synthesized proteins released from the ribosome are rarely able to function. they need to be correctly folded, modified or processed, and transported to where they function in the cell. these modifications are called post-translational events since they occur after protein synthesis examples: protein folding, covalent modification, and processing

if a mutation in a eukaryotic fat cell reduces the lvl of several proteins related to fat metabolism, does this mean the proteins are encoded by the same mRNA?

no, it does not. EUKARYOTIC MRNA IS MONOCISTRONIC*** a more likely explanation is that a number of different genes located throughout the genome have related regulatory sequences that bind the same sequence-specific transcription factors. this is the means used by eukaryotes to achieve coordinated expression of genes. related proteins are clumped together on the same piece of mrna in prokaryotes only

homology-dependent repair

one of the benefits of dna structure is the presence of a back-up copy; bc dna is double stranded, mutations on one strand of dna can be repaired using the undamaged, complementary information on the other strand. repair pathways that rely on this characteristic of dna are called homology-dependent repair pathways. these can be divided into repair that happens before dna replication (excision repair), or repair that happens during and after dna replication (post-replication repair)

gene does

one way to inc gene expression is to inc the copy number of a gene by amplification. increasing gene dose will allow a cell to make large quantities of the corresponding protein. similarly, gene deletion causes a dec in gene expression. both are examples of copy number variation

prokaryotic vs eukaryotic replication

prokaryotes have only one chromosome, and this one chromosome has only one origin. bc the chromosome is circular, as replication proceeds the partially duplicated genome begins to look like the greek letter theta. hence the replication of prokaryotes is said to proceed by the theta mechanism and is referred to as theta replication see pg 81/phone for pic in eukaryotic replication, each chromosome has several origins. this is necessary bc eukaryotic chromosomes are so huge that replicating them from a single origin would be too slow. as the many replication forks continue to widen, they create an appearance of bubbles along the dna strand, so they are referred to as "replication bubbles." eventually the replication forks meet, and the many daughter strands are ligated together see pg 82/phone

genetic mutation

refers to any alteration of the DNA sequence of an organism's genome. these can be inherited or acquired throughout life. mutations that can be passed onto offspring are called germline mutations, since they occur in the germ cells (which give rise to gametes). somatic mutations occur in somatic (non-gametic) cells and aren't passed onto offspring. in other words, somatic mutations can have a major effect on an individual, but will not be passed onto future individuals in that population. our cells have evolved elaborate repair pathways to help deal with mutations

insertion (mutation)

refers to the addition of one or more extra nucleotides into the DNA sequence. can cause a shift in the reading frame. can involve thousands of bases. can be caused by transposons

gene expression

refers to the process whereby the information contained in genes begins to have effects in the cell. the central dogma tells us that genetic information must be written in the form of rna (ie it must be transcribed); and then is must be expressed as protein (ie it must be translated).

characteristics of rna

rna is chemically distinct from dna in 3 important ways: 1. rna is single-stranded, except in some viruses 2. rna contains uracil instead of thymine 3. the pentose ring in rna is ribose rather than 2' deoxyribose there are several different types of rna each w a unique role

regulation of transcription in prokaryotes

regulation of transcription is the primary method of regulation of gene expression in prokaryotes. one simple mechanism of transcriptional regulation in bacteria is that some promoters are simply stronger than others. the problem with this mechanism of regulation is that it is "pre-set" and cannot respond to changing conditions within the cell. bacteria also possess far more complex regulatory mechanisms, which activate or suppress transcription depending on current needs for specific gene products. for ex, bacteria only produce the enzyme beta-galactosidase and other proteins required for lactose catabolism when lactose is present. it takes a great deal of atp to synthesize rna and protein, so its more energy-efficient to transcribe and translate only the proteins that are needed enzymes invovled in anabolism (biosynthesis) should be produced when the item they help make (their product) is scarce. enzymes involved in catabolism (degradative metabolism) should be produced when the item they help break down (their substrate) is abundant, such as food. thus there are 2 basic ways we can imagine how transcription is regulated. the transcription of enzymes involved in biosynthetic pathways sould be inhibited by their product. the transcription of enzymes involved in catabolic pathways should be automatically inhibited whenever the substrate isnt around, and activated when it is. that is in fact exactly what happens. anabolic enzymes whose transcription is inhibited in the presence of excess amounts of product are repressible. catabolic enzymes whose transcription can be stimulated by the abundance of a substrate are called inducible enzymes. (so note: the default for repressible systems is "ON"; for inducible systems the default is "OFF") there are 2 common examples of this. the lac operon is inducible, since the enzymes it codes for are part of lactose catabolism, and the trp operon is repressible, since the enzymes it codes for mediate tryptophan biosynthesis or anabolism. an operon has 2 components, a coding sequence for enzymes, and upstream regulatory sequences or control sites. operons may also include genes for regulatory proteins, such as repressors or activators, but don't have to. these genes can be located elsewhere in the genome and typically have their own promoters

point mutations

single base pair substitutions (ex a in place of G). can be transitions (substitution of a pyrimidine for another pyrimidine or substitution of a purine for another purine) or transversions (substitution of a purine for a pyrimidine or vice versa). there are 3 types of point mutations: 1 missense mutation: this causes one amino acid to be replaced with a different amino acid. this may not be serious if the amino acids are similar (like susbstituting a small hydrophobe like valine for another small hydrophobe like leucine; another way of defining conservative mutations is that they cause changes in primary structure but don't affect secondary, tertiary, or quaternary structure) 2. nonsense mutation: a stop codon replaces a regular codon and prematurely shortens the protein 3. silent mutation: a codon is changed into a new codon for the same amino acid, so there is no change in the protein's amino acid sequence

nucleotide variation

small-scale and large-scale variation across a genome is common. for ex, one person could have the sequence CCCGGG, while another has CCTGGG. its been predicted that there are single nucleotide changes once in every 1000 base pairs in the human genome. these variations are called single nucleotide polymorphisms SNPs (snips) and are essentially mutations. these snps occur most frequently in noncoding regions of the genome, however some snps can lead to specific traits and phenotypes. for ex, about 70% of ppl taste phenylthiocarbamide PTC as very bitter, and the remaining 30% don't taste PTC at all. this ability is a dominant genetic trait and is determined by a gene on chromosome 7. three SNPs in this gene determine PTC taste sensitivity

several aspects of molecular biology that aren't explicitly stated in the central dogma

some viruses (retroviruses) make dna from rna using the enzyme reverse transcriptase (a dna polymerase?) information can also be transferred in other ways. for ex, dna methylation and post-translational modification of proteins can alter gene expression and convey information, despite the fact that neither is directly included in the Central Dogma many final gene products are not proteins but are rnas instead

effects of genetic mutations

there are many mechanisms by which mutations can exert their effects on the cell. a single amino acid change can affect protein activity, localization, degradation, half-life, or interactions, or, it may have no effect at all. the outcome of a mutation on a protein depends on where the mutation occurs. mutations on sex chromosomes typically have a greater effect than mutations on autosomes since autosomes are present in double copies. males have only one X chromosomes and one Y chromosome, with no back-up copy of either. similarly, most families only express one of their X chromosomes, and so they too, often don't have a back-up copy. haploid expression in a diploid organism is hemizygosity, and this can lead to an increased effect of mutations on these chromosomes gain-of-function mutations increase the activity of a certain gene product, or change it such that it gains a new and abnormal function. loss-of-function mutations are the opposite; they result in the gene product having less or no function. in haploinsufficiency, a diploid organism has only a single functional copy of a gene, and this single copy is not enough to support a normal state. haploinsufficiency highlights the importance of gene dose: many times, just expressing a gene is not enough. you must express ENOUGH of the gene to maintain good health.

replication vs transcription

transcription is the synthesis of rna (usually mrna, tRNA, or rRNA) using dna as the template. the word transcription indicates that in the process of reading and writing information, the language doesn't change. information is transferred from one polynucleotide to another. this should lead you to expect transcription to be fairly similar to replication. and it is. both replication and transcription involve template-driven polymerization. bc of this the rna transcript produced in transcription is complementary to the dna template, just as the daughter strand produced in replication was. the driving force for both processes is the removal and subsequent hydrolysis of pyrophosphate from each nucleotide added to the chain, with the existing chain acting as nucleophile. (transcription, like replication can occur only in the 5' to 3' direction. the polymerase enzymes in both replication and transcription don't require a primer; rna pol doesn't require a primer. remember the primer in replication is a piece of rna, made by an rna polymerase) another important difference btwn transcription and dna replication is that rna polymerase hasn't been shown to possess the ability to remove mismatched nucleotides (it lacks exonuclease activity); in other words, it cannot correct its errors. thus transcription is a lower fidelity process than replication. another similarity is that transcription, like replication, begins at a specific spot on the chromosome. the name of the site where transcription starts (the start site) is different from the name of the place where replication begins, the origin. the sequence of nucleotides on a chromosome that activates rna polymerase to begin the process of transcription is called the promoter, and the point where rna polymerization actually starts is called the start site. from this point forward just about every event in transcription is given a different name from the events in replication

direct reversal

type of dna repair. ex some enzymes can repair uv-induced pyrimidine photodimers using visible light. this process is called photoreactivaiton, and directly repairs the uv damage to dna. this is commonly performed by bacteria and many plants. if pyrimidine dimers aren't directly repaired, nucleotide excision repair can be used instead. this is the main mechanism of repair in humans, but can introduce a mutation when trying to complete the repair. if left unprepared, pyrimidine dimers in humans may lead to melanoma, a type of very dangerous and malignant skin tumor

non homologous end joining

type of double-strand break repair. cells that aren't actively growing or cycling through the cell cycle don't have the option of using sister chromatids to repair DSBs in an error-free way. since dna replication isn't happening, there is no chromosome backup to use. in this case, even a poorly repaired chromosome is better than one with a DSB, since chromosome breaks can lead to rearrangements non homologous end joining is used to accomplish repair in this case. this process is common in eukaryotes but relatively uncommon in prokaryotes. first, broken ends are stabilized and processed, then DNA ligase connects the fragments. nothing about this process requires specificity; the goal is just to reconnect broken chromosomes. often this can result in base pairs being lost or chromosomes being connected in an abnormal way

excision repair

type of homology-dependent repair. involves removing defective bases or nucleotides and replacing them. if these bases aren't repaired, they can induce mutations during dna replication, since replication machinery can't pair them properly

chromosome amplification

when a segment of a chromosome is duplicated. this is similar to copy number variations

inversion

when a segment of a chromosome is reversed end to end. the chromosome undergoes breakage and rearrangement within itself. can be caused by transposons. see pg 86/phone for pic

a bacterial strain with a point mutation in the gene for hexokinase isn't able to metabolize glucose. the mutation causes a substitution of arginine for serine. these bacteria are used to test whether chemicals are mutagenic. the chemical is added to bacteria w glucose as only carbon source. any bacteria that grow must have undergone a mutation which remedied the problem (suppression of the mutation). when a particular ingredient tested, several colonies grow on the glucose only medium. which of the following might act as a suppressor of the first mutation? A a point mutation during replication of a trna gene B mutation in rna polymerase that inc the rate of promoter recognition C base pair deletion in the hexokinase gene D a point mutation during transcription of a trna molecule

a single base change in the anticodon of the trna for arginine could cause it to recognize the codon for serine. if that happened in the mutant bacteria, problems might ensue, but one good result would be that the correct amino acid would be incorporated at the mutated site in hexokinase (choice A correct). note that point mutations in trna genes are actually a common means of suppression in bacteria. inc the rate at which rna pol recognizes the promoter might inc rate of transcription but wouldn't fix a mutant enzyme (choice b is wrong), and a base pair deletion in the hexokinase gene would cause a frameshift mutation and a significant change in protein structure and function (choice C is wrong). a point mutation during transcription of a trna molecule might have a temporary effect on a single bacterium, but wouldn't be passed onto its progeny; **remember that only dna mutations have lasting effects and errors made during transcription are generally insignificant** (choice D is wrong)

the trp operon

bacteria use a 5 enzyme synthetic pathway to make the amino acid tryptophan from chorismic acid. in the presence of tryptophan, there is little point in making these enzymes, which are also co-localzied in an operon the repressor protein is coded by the trpR gene. the repressor binds tryptophan when it is present, and the two together then bind the operator, to turn off transcription of the other 5 trp genes. in the absence of tryptophan, the bacterial cell must make its own. with no tryptophan present, the repressor protein cannot bind the operator. without this block, rna polymerase transcribed the 5 genes in the trp operon, and the 5 gene products allow the cell to make tryptophan. this is an example of anabolic repressible transcription see pg 119/phone for pic

types of genetic mutations

based on structure, there are 7 kinds of mutations: 1 point mutations 2 insertions 3 deletions 4 inversions 5 amplifications 6 translocations and rearrangements 7 loss of heterozygosity

dna methylation and chromatin remodeling

both prokaryotic and eukaryotic dna can be covalently modified by adding a methyl group. bacteria methylate new dna shortly after synthesis, and the brief delay is useful in mismatch repair pathways. methylation can also control gene expression in prokaryotes, either by promoting or inhibiting transcription eukaryotic dna methylation has been found in every vertebrate genome studied so far. broadly speaking it plays an important role in controlling gene expression (especially during embryonic development), and has also been implicated in several diseases. dna methylation turns off eukaryotic gene expression 2 ways: 1. methylation physically blocks the gene from transcriptional proteins 2. certain proteins bind methylated CpG groups and recruit chromatin remodeling proteins that change the winding of dna around histones

dna polymerase

can rapidly build dna and is able to add tens of thousands of nucleotides before falling off the template. it is therefore said to be processive. eukaryotes have several different DNA polymerase enzymes, and their mechanisms of action are complex. prokaryotes on the other hand have 5 types of dna polymerases, called DNA polymerase I, II, III, IV, and V. know the functions of dna pol III and dna pol I

lac operon

contains several components: 1. P region: the promoter site on dna to which rna polymerase binds to initiate transcription of Y, Z, and A genes 2. O region: the operator site to which the Lac repressor binds 3. Z gene: codes for the enzyme beta-galactosidase, which cleaves lactose into glucose and galactose 4. Y gene: codes for permease, a protein which transports lactose into the cell 5. A gene: codes for transacetylase, an enzyme which transfers an acetyl group from acetyl-coa to beta-galactosides (note that this function is not required for lactose metabolism) additionally there are 2 genes, each with their own promoter, that code for proteins important in the regulation of the lac operon: 1. crp gene: located at a distant site, this gene codes for a catabolite activator protein (CAP) and helps couple the lac operon to glucose lvls in the cell 2. I gene: located at a distant site, this gene codes for the Lac repressor protein so overall, there are 5 protein coding genes and 2 regulatory sequences. both crp and I have their own promoters. the protein products of these 2 genes control gene expression of Z, Y and A bacterial cells preferentially use glucose as an energy source. this means that in the presence of glucose, the lac operon will be off, or expressed at low amounts. this is mediated by the CAP and repressor proteins. glucose lvls control a protein called adenylyl cyclase, which converts atp to cAMP. In high glucose conditions, adenylyl cyclase is inactivated and camp lvls are v low. in low glucose conditions, the opposite is true: adenylyl cyclase is activated and cAMP lvls are high. CAP binds cAMP and this complex binds the promoter of the lac operon. this helps activate rna polymerase at the lac operon and contributes to the operon being turned on when glucose lvls are low. the I gene codes for a repressor protein, which binds the operator of the lac operon. this prevents rna pol from binding the promoter and transcribing Z, Y, and A genes, thereby blocking transcription of the operon when lactose is absent. the repressor protein can also bind lactose, and this blocks its activity on the operator. this binding is allosteric, meaning it happens at a distant site from operator binding. it causes a conformational change in the tertiary structure of the repressor protein, such that it is no longer capable of binding to the operator. as a consequence, it falls off the dna. high transcription of Z, Y, and A genes occurs when glucose is absent and lactose is present. low glucose results in an increased amount of cAMP, which binds to CAP and helps activate rna polymerase activity at the lac operon. lactose presence means the Lac repressor protein is unable to bind the lac operator and negatively regulate transcription; thus the polycistronic mrna is transcribed at high lvls. when the supply lactose becomes very scarce, there isn't enough to bind to the repressors, and most of the repressor proteins return to their original structure. they now rebind to the operator, decreasing transcription of Z, Y, and A genes see pg 117/phone for pics see pg 118/phone for pic

if the operator is mutated so that the lac repressor can no longer bind, what effect will this have on transcription? A transcription of Gene Z will be activated, and Genes Y and A will not be affected B none of the genes will be transcribed, regardless of the presence or absence of lac repressor C transcription will still be activated by lactose D all 3 genes will be expressed constitutively, regardless of the presence of lactose

if the repressor cannot bind to the operator, nothing will prevent rna polymerase from transcribing all the genes on the operon in an unregulated, constitutive (or continuous) fashion (choice D is true, choice B is wrong). all genes on the operon are expressed or repressed together (choice A is wrong), and lactose will no longer have any effect (the expression of the genes is unregulated, so choice C is wrong)

cap-independent translation

it was long thought that all eukaryotic translation started at the 5' end of an mrna. in other words, all eukaryotic transcripts were assumed to be monocistronic, and coded for only one polypeptide chain. it is true that this mechanism is by far the major one in eukaryotic cells. bc of the important role of 5' mrna cap recognition, its called cap-dependent translation however, its recently been discovered that eukaryotes are sometimes capable of starting translation in the middle of an mrna molecule, called cap-independent translation (bc the beginning of translation doesn't require the 5' cap of the mrna). to do this, the transcript must have an internal ribosome entry site, or IRES. this is a specialized nucleotide sequence, and was first discovered in viruses. since then, IRESs have been found in a number of eukaryotic transcripts. most code for proteins that help the cell deal with stress, or help activate apoptosis. in other words, the IRESs found so far make sure the cell can make essential proteins when under sub-optimal growth conditions. cells under stress generally inhibit translation (via inhibiting translation initiation), and cap-independent translation allows the cell to make proteins when doing so is crucial for survival or programmed cell death. activation of translation using an IRES requires different proteins than normal initiation additional nucleotide sequences have been identified, which allow cap-independent translation in eukaryotes. while some of these are used in molecular biology labs, its unclear how or if they function in normal eukaryotic cells

reactive chemicals

many chemicals interact directly with dna, and many others turn into damaging agents as they're being processed by a cell. chemicals can covalently alter bases or can cause cross-linking or strand breaks. cross-links are abnormal covalent bonds btwn different parts of dna. any compound that can cause mutations is called a mutagen. compounds that look like purines and pyrimidines (with large flat aromatic ring structures) cause mutations by inserting themselves between base pairs, or intercalating, thereby causing errors in dna replication. ethidium bromide is often used to visualize nucleic acids during gel electrophoresis in molecular biology labs. this chemical is used bc it is planar (and therefore intercalates with the DNA ladder), and glows orange when exposed to uv light (meaning nucleic acids in a gel can be easily visualized). however bc it intercalates w dna, it also distorts the structure and can therefore disrupt dna replication and transcription. thus ethidium bromide is a mutagen

covalent modification

many proteins are covalently modified. some have hydrophobic groups added to facilitate membrane localization. for ex, the addition of a fatty acid can target a protein to a membrane (either the plasma membrane or an organelle membrane) smaller chemical groups can also be added. for ex, proteins can be: 1. acetylated: addition of an acetyl group (-C(O)CH3) usually at the N-terminus of a protein, or at a lysine amino acid 2. formylated: addition of a formyl group (-C(O)H) 3. alkylated: addition of an alkyl group (such as methyl, ethyl, etc). methylation is a common post-translational modification, and is usually done to lysine or arginine amino acids 4. glycosylated: addition of a glycosyl group to arginine, asparagine, cysteine, serine, threonine, tyrosine, or tryptophan amino acids. a glycosyl group is the substituent form of a cyclic mono-, di-, or oligosaccharide. this results in a glycoprotein 5. phosphorylated: addition of a phosphate group (PO4 3-) to a serine, threonine, tyrosine, or histidine amino acid 6. sulphated: addition of a sulphate group (SO4 2-) to a tyrosine amino acid proteins can also be linked to other proteins. for ex, in ubiquitination, proteins are covalently linked to ubiquitin there are many other examples of protein covalent modification. overall these modifications can have many effects on a protein and its function. they can change protein subcellular localization, target a protein for degradation, change interactions btwn proteins and other molecules, activate or inhibit enzyme activity, or change enzyme affinity for substrates. these modifications are typically studied in the lab using mass spectrometry, western blotting, or eastern blotting.

amino acid activation

peptide bond formation during protein synthesis is a process that requires a lot of energy bc the peptide bond has unfavorable thermodynamics (ΔG>0) and slow kinetics (high activation energy). reaction coupling is used to power the process: two high-energy phosphate bonds are hydrolyzed to provide the energy to attach an amino acid to its trna molecule. this process is called trna loading or amino acid activation and is useful bc breaking the aminoacyl-trna bond will drive peptide bond formation forward. amino acid activation occurs in several steps: 1. an amino acid is attached to amp to form aminoacyl amp. in this rxn, the nucleophile is the acidic oxygen of the amino acid, and the leaving group is PPi 2. the pyrophosphate leaving group is hydrolyzed to 2 orthophosphates. this rxn is highly favorable (ΔG<<0) 3. trna loading, an unfavorable rxn, is driven forward by the destruction of the high energy aminoacyl-AMP bond created in step 1 see pg 105/phone for pic overall, amino acid activation requires 2 atp equivalents bc it uses 2 high energy bonds. an atp equivalent is a single high energy phosphate bond. you can get 2 atp equivalents by hydrolyzing 2 atp to 2 amp + 2 Pi or by hydrolyzing 1 atp to amp + 2 Pi eventually, the bond btwn the amino acid and the trna molecule will be broken. this hydrolysis will power peptide bond formation: the nitrogen of another amino acid will nucleophilically attack the carbonyl carbon of this amino acid, and trna will be the leaving group

eukaryotic translation

there are several differences btwn eukaryotic and prokaryotic translation. many of these have already been mentioned: the ribosome is larger (80S) and has different components than the prokaryotic ribosome, the mrna must be processed before it can be translated (spliced, with cap and tail added), and the N-terminal amino acid is different (Met instead of fMet). also remember that eukaryotic mrna must only be spliced, capped, and tailed, but it also requires transport from nucleus to cytoplasm, thus transcription and translation CANNOT proceed simultaneously eukaryotes don't use the shine-dalgarno sequence to initiate translation. there are 5' UTR sequences in eukaryotes that function in starting translation; a common one is the Kozak sequence, which is a consensus sequence typically located a few nucleotides before the start codon eukaryotic translation begins with formation of the initiation complex. first a 43S pre-initiation complex forms, composed of the 40S small ribosomal subunit, Met-tRNAmet, and several proteins called eukaryotic initiation factors (eIFs). next this assembled complex is recruited to the 5' capped end of the transcript, by an initiation complex of proteins (including other eIF proteins). additional proteins are recruited (such as a polyA tail binding protein) and the initiation complex starts scanning the mrna from the 5' end, looking for a start codon. once the start codon has been found, the large ribosomal subunit (60S) is recruited and translation can begin some eIF proteins are essential to initiate translation and others help regulate the process. for ex, eIF3 bings the small ribosomal subunit and prevents it from prematurely associating with the 60S subunit. the amount of eIF proteins in the cell is closely controlled, and this affects the amount of translation occurring. eIF4A is a helices and unwinds mrna, eIF4E binds the 5' cap of the mrna and eIF4g is a scaffold protein. each of these 3 function in the initiation complex, and their lvls are a rate-limiting step for translation. higher amounts of these 3 proteins means the cell can perform more translation, while a lower amount dec translation. activity of eIF proteins is controlled by post translational modification, such as phosphorylation. this couples translation to upstream cell signaling pathways eukaryotes have 2 elongation factors. eEF-1 has 2 subunits, one that helps with entry of an amino-acyl tRNA into the A site and one that is a guanine nucleotide exchange factor, catalyzing the release of gdp. the eukaryotic translocase is called eEF-2. additional elongation factors are required to facilitate peptide bond formation the order in which the initiation complex is formed is different in eukaryotes. (are the nascent (newly formed) polypeptide chains emerging from a polyribosome in a eukaryote all the same? - in eukaryotes, the answer is: yes, always, bc eukaryotic mrna is monocistronic. in prokaryotes, however, different polypeptides may be translated from a single piece of mrna, since prokaryotic mrna is polycistronic) eukaryotic translation termination involves 2 release factors. eRF1 recognizes all 3 termination codons, and eRF3 is a ribosome-dependent GTPase that helps eRF1 release the completed polypeptide

post-replication repair

type of homology-dependent repair. mismatch repair pathway (MMR) targets mismatched Watson-crick base pairs that weren't repaired by DNA polymerase proofreading during replication. to do this, mispaired bases must be identified and fixed, but the crucial question is: which base is the correct one and which is the mistake? some bacteria use genome methylation to help differentiate btwn the older dna template strand and the newly synthesized daughter strand. methylation take a while to complete, which means that shortly after dna synthesis, the parental template strand will be labeled with methylated bases and the new daughter strand will not. bacterial machinery can read these methyl tags and know which base is the correct one (the one on the older strand) and which needs to be replaced (the newer one) other prokaryotes and most eukaryotes use a different system, where the newly syntehsized strand is recognized by the free 3' terminus on the leading strand, or by the presence of gaps btwn okazaki fragments on the lagging strand

the wobble hypothesis

using the standard genetic code, you would guess that organisms have 61 distinct trna molecules to recognize the 61 amino acid-coding codons possible in mrna. in actual fact, most organisms have fewer than 45 different types of trnas, meaning some anticodons must pair with more than one codon. Francis crick's wobble hypothesis explains this and states that the first 2 codon-anticodon pairs obey normal base pairing rules, but the 3rd position is more flexible. this allows for nontraditional pairing and explains why a smaller number of trnas are possible. see pg 104/phone for pic a modified inosine base (I) at the 5' end of the anticodon is particularly wobbly, as it can bond to 3 different codon bases (A, U or C). some common wobble pairing combinations are shown pg 104/phone in other words, the most common wobble base pairs are guanine-uracil, inosine-uracil, inosine-adenine, and inosine-cytosine (GU IU IA and IC). both the wobble base pair and the normal Watson-crick base pair have similar thermodynamic stabilities