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THE MCAT-BIO 1
MOLECULAR BIOLOGY, CELLULAR RESPIRATION
| Question | Answer |
|---|---|
| Phase contrast microscope | view live organisms but can't focus on certain structures |
| electron microscope | use beam of electrons to focus on dead organism in detail |
| In centrifugation, what types of organelles will be on top / bottom? | mitochondria & lysosomes on top ribosomes on bottom |
| What do prokaryotes have instead of nucleus? | nucleoid |
| What is plasmid? | -small circular pieces of DNA that carry genetic info -replicate independently and can be passed from one prok to another |
| Do prokaryotes have cell membrane? | yes |
| What is the benefit of membrane-bound organelles? | separates bio. reactions and functions into separate compartments |
| What do transport proteins do? | allow polar molecule and ions to move in and out of cell |
| What is nuclear membrane? | double membrane to separate nucleus from cytoplasm? |
| What is nucleolus and where is it located? | -rRNA synthesized here -located inside nucleus |
| How is genetic material organized? | DNA --> genes --> wound around histone proteins --> chromatid --> chromosome |
| What do free ribosomes make? | make proteins in cytosol |
| What do bound ribosomes make? | -proteins that directly insert into the ER -px are used within plasma mem or expelled from cx |
| What does smooth ER do? | -lipid & steroid synthesis -detox drugs and poison |
| What does rough ER do? | involved in producing transmem px or secreted px |
| What do lysosomes do? | use hydro |
| Where are the proteins used in peroxisomes produced? | cytosol --> mature polypeptide made and then attaches to peroxisomes through a signal |
| Where do peroxisomes come from? | ER |
| Where do lysosomes come from? | golgi |
| What do lysosomes do? | -breakdown cellular waste -apoptosis -digest macromolecules from phagocytosis |
| What do peroxisomes do? | -beta-oxidation -lipid biosynthesis -catalase to convert H2O2 to water -detox rxns. in liver |
| What is beta-oxidation? | process where fatty acids are broken down in mito to make acetyl coA |
| How are mito. semiautonomous? | have their own genes and replicate independently of nucleus via binary fission |
| Where are the enzymes for cellular respiration located? | mito. matrix |
| What are microfilaments used for and what are they made of? | -muscular contraction and cytokinesis -actin |
| What are microtubules used for? | -chromosomal separation during meiosis and mitosis -cilia and flagella -intracx transport of organelles and vesicles |
| What are lysosomal storage diseases? | accumulation of carbs, lipids, and proteins from failure of production of an enzyme within lysosome to break down |
| hypotonic | -conc. of solutes inside cell is higher --> gain water |
| hypertonic | -conc. of solutes outside cell is higher --> lose water |
| isotonic | -conc. of solutes is equal --> no net movement |
| What are viruses? | nucleic acid surrounded by protein coat |
| Difference between the way bacteria and virus attack cells? | Bacteria never enter cell while viruses always enter cell to replicate |
| What are lipids made of? | -carboxylic acid + alcohol --> ester link (even number of carbons and max # is 24 in humans) |
| Saturated vs. unsaturated | saturated has single / unsaturated has double bond |
| amphipathic | polar and nonpolar end (that's why phospholipids are good for cell membrane) |
| What is glycerol? | 3-carbon backbone found in lipids |
| Where are glucolipids found? | membrane of myelinated cells in human nervous system |
| Formation of lipids requires what kind of bond? | ester linkage |
| Steroids | 4-ringed structures |
| Terpenes | Vitamin A |
| Eicosanoids | -signaling molecules involved in inflammation and immunity -include prostaglandins and leukotrienes |
| What does aspirin inhibit? | synthesis of prostaglandins |
| How are lipids transported in the body? | lipoproteins |
| Which lipoprotein has the highest lipid percentage? | chylomicrons |
| Name all parts of an amino acid | amino (NH2), carbonyl (COOH), hydrogen, R group |
| Can a single protein have both alpha helix and beta pleated sheet? | yes! |
| Tertiary structure | secondary structure folds upon itself |
| How does proline affect peptide structure? | creates turns that disrupt helix and beta sheet |
| quaternary structure | two or more polypeptides |
| What structures does denaturing proteins affect? | secondary, tertiary, quaternary |
| What are 5 forces that create tertiary structure? | -H-bonds -hydrophobic side chains (pushed to center) -electrostatic interactions btwn acidic and basic side chains -van der Waals -covalent disulfide bonds |
| cytochrome | membrane bound hemopx that have a heme and carry out ETC |
| proteoglycans | proteins that are heavily glycosylated |
| glycoproteins | carbs covalently attached to proteins |
| Basic amino acids (3) | histidine, lysine, arginine |
| acidic amino acids (2) | glutamic acid and aspartic acid |
| How are alpha and beta glucose different? | -alpha glucose has -OH on axial and equatorial -beta glucose has -OH on both axial / equatorial |
| If cell as enough ATP, what happens to glucose? | becomes glycogen |
| Where is glycogen found? | muscle and liver cells |
| How does the liver regulate blood glucose? | glucose --> glycogen --> glucose |
| How is glucose absorbed into bloodstream? | 1.) against a concentration gradient with secondary active transport with sodium 2.) facilitated diffusion (increases with insulin) |
| What has beta / alpha links | cellulose / everything else |
| 3 components of nucleotides | -5-carbon sugar -nitrogenous base -phosphate group |
| Phosphodiester bond | phosphate of one nucleotide and 3rd carbon of pentose of other nucleotide |
| What do minerals do? | transport substances entering and exiting the cell through electrochemical gradient |
| activation energy | energy required to break bonds before new bonds can form |
| Are enzymatic reactions reversible? | yes |
| What do enzymes do? | -lower Ea for forward and reverse rxns -increase rate of reaction (increase rate constant k) -select which reactions will occur |
| What don't enzymes do? | -not consumed in a rxn or altered -do not start rxns that wouldn't normally occur |
| Induced Fit Model | Enzyme and substrate change shape --> increases specificity and helps rxn proceed |
| Substrate squeezing in / release is endothermic / exothermic? | endothermic / exothermic |
| Most enzymes function around which pH | 7.4 |
| Do enzymes affect Keq or delta G? | NOOO --> no thermodynamics only kinetics! |
| Enzymes can be protein and...? | RNA --> ribosome |
| transition state analog | -resemble transition state and can act as competitive inhibitor |
| turnover number | -when enzyme is completely saturated with substrate, number of substrate molecules converted to product |
| When substrate conc is small and enzyme conc is constant, velocity is proportional to substrate conc. as ______ order? | first |
| When substrate conc. is large and velocity is independent of substrate conc as ____ order? | zero |
| What is Km? | point where 1/2 enzyme's active sites are full and rxn rate is 1/2 max value --> enzyme affinity for substrate |
| lysozyme | -enzyme that hydrolyzes glycosidic bonds in bacterial cell walls |
| ribonuclease | -catalyzes hydrolysis of phosphodiester in RNA |
| carboxypeptidase | -digestive pancreatic enzyme to cleave carboxy terminal peptide bond |
| chymotrypsin | -hydrolysis of ester and peptide bonds |
| peptide --> | amine and acid |
| ester | alcohol and acid |
| What is Vmax proportional to? | enzyme concentration |
| What does low Km mean? | high affinity for substrate |
| What does high Km mean? | low affinity for substrate |
| When substrate concentration is less than Km, changes in [s] will greatly affect rxn rate T / F? | True |
| what pH does pepsin function / pancreatic enzymes | 2 and 8.5 |
| Co-factors | 1.) bind substrate to enzyme 2.) stabilize enzyme in active conformation |
| Apoenzyme / holoenzyme | enzyme w/o cofactor & enzyme with co-factor |
| What are 2 types of co-factors? | co-enzymes and metal ions |
| What are coenzymes? | prosthetic groups or cosubstrates (reversibly bind to enzyme - ATP) |
| Irreversible inhibitors | -covalently bind and permanently disrupt function at active site |
| Competitive Inhibitors and how to overcome? | -bind reversibly with noncovalent bonds -increase conc. of substrate (Km increases) |
| Noncompetitive Inhibitors and how to overcome? | -bind noncovalently to site other than active site -change conformation of enzyme -increase enzyme conc. |
| How are noncompetitive different than competitive? | -do not prevent substrate from binding -do not resemble substrate so can act on more than one enzyme -bound far or near active site |
| What do Vmax and Km depend on? | Vmax - enzyme conc Km - substrate conc |
| What do competitive vs. noncompetitive inhibitors do? | competitive - raise Km, do not change Vmax noncompetitive - lower Vmax, do not change Km |
| Do noncompetitive inhibitors affect substrate binding and enzyme affinity for substrate? | NO --> that's why Km stays the same |
| Can enzyme catalyze reaction as long as noncompetitive inhibitor is bound? | NO --> substrate can still active site though |
| Vmax vs. Km graph: competitive shift right | apparent Km increases, Vmax no effect |
| Vmax vs. Km graph: competitive shift left | apparent Km decreases, Vmax no effect |
| Allosteric enzyme | one active and one regulatory site where inhibitors and activators can bind |
| How do allosteric inhibitors / activators act? | change quaternary structure |
| Are allosteric regulators noncompetitive inhibitors? | not necessarily |
| Negative / positive feedback inhibition? | allosteric inhibitor / activator act on reaction |
| Irreversible covalent modification example | zymogens are irreversibly activated |
| Reversible covalent modification example | phosphorylation |
| kinase vs. phosphatase | enzyme that phosphorylates vs. enzyme that dephosphorylates |
| hexokinase | phosphorylates glucose |
| Antitrypsin | inhibits trypsin and prevents digestive enzymes from digestinb doy |
| Humans can synthesize NAD as long as there is what amino acid in diet? | Trp |
| What is FAD derived from? | Vitamin B2 |
| Where does ATP energy come from? | loose and covalent bonds of phosphate groups |
| NAD, NADPH, FAD are _____ agent and are ____ during ____ reactions | oxidizing / reduced / catabolic |
| NADH, NADPH, FADH are _______ and are ______ during _____ reactions. | reducing / oxidized / anabolic |
| Where does glycolysis occur and what does it produce? | -cytosol -2 pyruvate and 2 NADH |
| substrate-level phosphorylation | formation of ATP without intervention of ETC |
| What is the main importance for fermentation and how much ATP? | -regenerate NAD+ to continue glycolysis anaerobically (aerobically, NAD+ regenerated through ETC) -2 ATP |
| What can pyruvate turn into with fermentation? | 1.) ethanol/CO2 & 2 NAD+ 2.) lactic acid & 2NAD+ |
| Where does pyruvate decarboxylation take place and what does it produce? | -mito matrix -2 acetyl coA, 2 CO2, 2 NADH |
| How do pyruvate and NADH pass into mito? | -pyruvate and NADH can pass through outer mem via facilitated diffusion through porin px -inner mem, pyruvate can move in but NADH may need hydrolysis of ATP |
| What does TCA produce for each turn of cycle? | 1 ATP, 3 NADH, 1 FADH2, 2 CO2 |
| How to begin TCA cycle? | transfer 2C from acetyl coA combines with oxaloacetate (4C) to create citrate (6C) |
| When are ketone bodies produced? | levels of acetyl coA exceed TCA capacity |
| Where is ETC located and what is it | series of 4 large metallopx bound to inner membrane |
| Where is ETC and OP located for prokaryotes? | Proks don't have mito so ETC and OP occurs in inner plasma mem |
| How are protons from inner membrane pumped to intermem? | energy from ETC pumps protons through peremases |
| oxidative phosphorylation | creation of ATP through ETC |
| How many ATP does NADH and FADH2 create? Why does FADH2 create less? | -3 ATP / 2 ATP -electrons from FADH2 travel shorter distance |
| What is final electron acceptor and what is it reduced to? | O2 and water |
| Is ATP synthase reversible T/F? | TRUE - can make NADH |
| Is inner membrane permeable to protons? | NO |
| Uncoupling protein | -mito inner mem px that dissipates H+ gradient to block OP -energy used to generate heat instead of ATP -increase permeability of inner mito mem so protons pumped out return |
| Pentose phosphate pathway | 1. generates NADPH --> f. a. synthesis 2. produces ribose --> nucleotide synthesis |
| Difference between NADP and NAD? | NAD is used in catabolism while NADP is used in anabolism |
| What is largest class of human mutations? | sex-linked deficiency in glucose-6-phosphate dehydrogenase -don't make NADPH / reduced glutathione (mosquitoes need to survive) |
| Gluconeogenesis | lactate goes to liver and converted to glucose to return to muscle -net loss of ATP to make this happen |
| What are 3 steps for f.a. oxidation? | transport to mito, beta oxidation, ETC |
| How do free fatty acids travel? | bound to albumin |
| What activates lipases for beta oxidation? | glucagon and epi |
| What creates ammonia? | deamination of a.a. |
| What is chief/second nitrogenous waste of mammals and how is it excreted? | urea/uric acid and kidneys |
| What causes kidney stones? | uric acid |
| What is glyceraldehyde 3-P also known as? | PGAL |
| Can glycerol backbone of fats enter glycolysis? | YES --> becomes PGAL |
| How can amino acids be converted to TCA cycle substrate? | -deaminated in liver -converted to acetyl coA |
| How can glycogen be converted to glycolysis intermediate? | glycogen --> glucose 6-P for glycolysis |
| Do muscles have glucose-6-phosphatase? | NO --> glycogen stored is for muscle use only |
| Does liver have glucose-6-phosphatase? | YES --> glucose can be shared with other cells |
| Final products of aerobic respiration? | -36-38 ATP -2 FADH2 -10 NADH |
| What are the irreversible reactions of glycolysis? | -creation of glucose 6-P, creation of fructose 1,6-bisP, creation of pyruvate |
| What reaction does phosphofructokinase catalyze? | fructose 6-P --> fructose 1,6-bisP |
| What inhibits phosphofructokinase for glycolysis regulation? | -high ATP, high H+, high citrate |
| What promotes phosphorfructokinase activity? | -low ATP, high AMP |
| What do prokaryotes lack? | true nucleus |
| Why don't enzymes change the Keq of a reaction? | lowers activation energy for both forward and reverse reactions |
| Enzymes affect the _______ of a reaction, NOT the ________. | kinetics / thermodynamics |
| Enzymes can be specific enough to distinguish between steroisomers. True or False? | True |
| Enzymes in the body can be _____ or ______. | protein or RNA (ribosome) |
| Non-competitive inhibition decreases? | Vmax |
| Does non-competitive inhibition change the amount of substrate needed for Vmax? | NO |
| Can you overcome non-competitive inhibition by adding more substrate? | NO |
| Where does the oxygen from the water produced in aerobic respiration come from? | oxygen you breathe in |
| Where does carbon in glucose end up in? | carbon dioxide |
| Where doe soxygen in glucose end up in? | carbon dioxide |
| When electrons are passed from NADH to O2 in ETC, what is released? | energy |
| What does FADH2 skip in the ETC which creates its lower energy? | skips FMN and passes to Coenzyme Q |
| Energy released from ETC generates what? | proton gradient which drives ATP synthesis |
| What inhibits ETC? | antibiotics, cyanide, carbon monoxide |
| Where does beta oxidation occur? | matrix of mitochondria |
| Where does ester hydrolysis occur and waht does it become? | -cytosol -free fatty acids and glycerol |
| How is fatty acid activated for beta oxidation? | -With ATP, f.a. is "activated" by CoA (becomes thioester) |
| What happens during beta oxidation? | -breaks down fatty-coA, 2 carbons at a time, to make acetyl coA |
| What does beta oxidation produce? | acetyl coA, FADH2, and NADH |
| What is nitrogen converted to in humans? in desert animals, birds, and reptiles? | -urea -uric acid |
| For px metabolism, carbon in a.a. is converted to? | pyruvate, acetyl coA, or any other metabolic intermediate depending on a.a. |
| What is fat for carbon products from a.a. metabolism? | - go into Kreb's -starting material for gluconeogenesis |
| What do bacteria lack? | no nuclear membrane, mitotic apparatus, golgi, ER, mito, chloroplasts |
| How do prok pull replicating cells apart w/o mitotic apparatus? | prok cytoskeleton pulls replicated DNA apart |
| bacteria flagella is made of ________. eukaryotic flagella is made of ________. | flagellin / microtubules |
| What powers bacterial flagella? Eukaryotic flagella? | -proton/sodium gradient -ATP |
| What is motion of bacterial flagella? Eukaryotic flagella? | -rotation -whip like motion |
| Describe fission. | DNA replicates, DNA attaches to cx mem as cx elongates, cytokinesis |
| Defining characteristics of euks. | True nucleus, membrane-bound organelles, divide by mitosis |
| What are 3 factors of mito according to endosymbiosis theory? | self-replicate, have own DNA, have own ribosomes --> all are different than host |
| How do lysosomes work? | Wastes gets into a vacuole by endocytosis or phagocytosis -vacuole fuses with lysosome |
| What is another name for smooth ER in muscles? | sarcoplasmic reticulum --> stores calcium |
| What are the roles of smooth ER and rough ER in membrane biosynthesis? | -smooth ER - makes mem lipids -rough ER - makes transmembrane px |
| How do transmem px / secreted px produced correctly? | -have signal sequence at beginning -ribo starts to make px with signal sequence first -signal recognition particle recognizes and drags to RER |
| ER is connected to what? | nuclear membrane |
| relationship between RER and golgi? | RER makes px --> modified in Golgi --> buds off Golgi and exits by exocytosis |
| Where does glycosylation of px occur? | Golgi |
| What does glycosylation do to px? | affect's px structure, function, and protect from degradation |
| Fluid mosaic model | protein boats floating in sea of lipids |
| The resting membrane potential is positive / negative? | negative |
| gap junction | connect 2 cx and allow stuff to flow through |
| tight jxn | glues cx together to form impermeable barrier |
| desmosomes | -connects 2 cx together by linking cytoskeleton -mechanical strength, not impermeable barrier |
| Microfilaments and intermediate filaments support cx shape by bearing _________. Microtubules support cx shape by bearing __________. | -Tension -Compression |
| Where is kinetochore located? | point joining two sister chromatids |
| What is a centrosome vs. centriole? | Centrosome = centriole plus matrix and is where microtubules originate |
| Centrioles, microtubule organizing centers? | microtubules radiate out of these barrel shaped structures which are made of microtubules |
| What are the stages of interphase? | G0, G1, S, G2 |
| Formula for number of peptides that contain "n" amino acids? | n! |
| What stabilizes 3-D structure of px | covalent bonds and noncovalent interactions |
| What is endosymbiotic theory? | mito are descendents of prok engulfed by endocytosis into a vesicle lined with a euk mem. |
| Inne rmem of mito is analogous to ____ of prok. | plasma membrane (has oxidative phos. enzymes) |
| During starvation, what is broken down first, second, and last? | -carbs, lipids, body px |
| What is the major microtubule organizing center? | centrosome |
| How are the flagella in euk and prok different in structure? | -euk = 9+2 microtubules -prok = thin strand of flagellin px |
| ANtibiotics that block translation by prok ribo but NOT euk ribo also block translation by_____? | mito ribo |
| Most px used by mito are coded by ________ | nuclear DNA |
| What is most common extracx matrix px? | collagen |
| protease | enzyme involved in protein digestion |
| isozymes | enzymes that differ in a.a. sequence but catalyze same reaction |
| What is main metabolic produce of CO2? | TCA cycle |
| Primary structure of proteins | linear sequence of a.a. held together by covalent peptide bonds |
| Secondary structure of px | alpha helix or beta sheet |
| Which organelles replicate independently of the cx? | peroxisomes and mito |
| WHich is the a.a. capable of forming disulfide bonds? | cysteine |
| What are the 2 nonpolar a.a.? | valine and alanine |
| What are the 2 acidic a.a.? | glutamic acid and aspartic acid |
| WHat are 3 basic a.a.? | arginine, histidine, lysine |
| What does it mean to be membrane-bound? | -have double phospholipid membrane |
| What are membrane-bound organelles? | mito, lysosome, nuclear envelope, ER, golgi bodies |
| What do endosomes do? | intracx sorting organelles that deliver fats, px, and other materials to lysosomes fro degradation |
| Microfilaments are associated with _____ while Microtubules are associated with _____. | -amoeboid mvmt. -phagocytosis |
| What most resembles the golgi apparatus? | smooth ER |
| Is the interaction between inhibitor and enzyme permanent in competitive inhibition? | NO --> transitory |
| Do cx walls, spore coats, or capsules have lipid bilayer? | NO |
| What does microtubule paralysis cause? | nerve degeneration and muscle weakness |
| autophagy | lysosomes engulf and digest damaged/old intracx organelles |
| phagosome | phagocyte + ingested material |
| Are sodium channels open at rest? | NO --> ALWAYS CLOSED |
| What channel majorly determines resting potential? | potassium |
| What determines negative resting emmbrane potential? | closed Na/Cl channels and open leaky K channels |
| Does simple diffusion rely on channels to transport molecules? | NO |
| What determines the resting membrane potential? | leaky potassium chanels |
| body tissue | group of similar cells |
| organ | collection of several tissues |
| Where are cilia located? | trachea/bronchi of respiratory tract, lumen of small intestine, fallopian tubes |
| obligate anaerobes | absolutely unable to grow in oxygen |
| facultative anaerobes | able to grow in presence in presence or absence of oxygen |
| obligate aerobes | must have oxygen to survive |
| According to Poiseuille's Equation, what creates faster velocity conduction? | increased radius, decrease in length F = r^4 / L |
| Can ntm diffuse across cx membrane? | NO --> HYDROPHLIC |
| Why does the axon terminal have lots of mito? | ntm exocytosis is an active process that requires a lot of ATP |
| What are the non-membrane bound organelles? | microtubules, intermediate filaments, microfilaments, ribosomes |
| Are myosin and actin microfilaments or microtubules? | microfilaments |
| Is the esophagus part of the digestive or respiratory tract? | digestive |
| What px structure is a heterodimer? | quaternary |
| Does the retina require ATP to function? | YES |
| What do uncouplers do to ETC? | decrease intermembrane acidity by dirupting H gradient |
| When is BP reached? | VP is equal to atmospheric pressure |
| Higher vapor pressure... | lower boiling point |
| If OP is blocked, what will the body do instead? | increase ATP synthesis through glycolysis |
| Does hyperpolarization cause inhibition or activation? | inhibition |
| Where are muscarinic vs. nicotinic receptors found? | muscarinic - CNS nicotinic - PNS |
| What type of rx are nicotinic and muscarinic? What system are they a part of? | cholinergic / PNS |
| Where are a lot of ribosomes found in a neuron? | soma |
| prokaryotic DNA | single, circular, uncoated, double stranded DNA molecule |
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