Biochemistry Flashcards
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| 10399381378 | exergonic/endergonic | energy exits/enters the system, negative/positive dG | 0 | |
| 10399381379 | exothermic/endothermic | heat exits/enters the system, negative/positive dH | 1 | |
| 10399381380 | entropy | dS is always positive, disorder of universe tends to increase | 2 | |
| 10399381381 | enthalpy | dH = dE + PdV, heat | 3 | |
| 10399381382 | Gibbs free energy | dG = dH - TdS, negative dG means reaction is spontaneous and favorable, this is determined by both Keq and Q dG' = - RTlnK'eq dG = dG' + RTlnQ, Q = Keq but not at any given time ATP -> ADP + P, dG = -12 | 4 | |
| 10399381383 | activation energy | energy required to produce the transition state, catalyst/enzyme stabilize the transition state and reduce Ea without changing dG higher Ea means slower reaction rate drawing a reaction coordinate graph | 5 | |
| 10399381384 | enzymes | physiological catalysts increase reaction rate so it happens in a biologically relevant time-frame, not used up in reaction, specific to a reaction (important for regulation) interact with substrate at active site, always stereospecific and can form specific stereoisomers from non-chiral molecules can interact with different substrates that have similar chemical linkages induced-fit model vs. lock-key model dimers have two similar proteins connected by hydrophobic amino acids or by *disulfide bonds* heterodimer- two different proteins homodimer- two identical proteins common types: 1. kinases takes phosphate group from donor (ATP) 2. phosphatases removes phosphate group 3. phosphorylases adds phosphate group 3. ligases combine two molecules 4. lyases break apart a molecule, form double bond 5. isomerases convert between isomers 6. transferases transfer functional groups from one molecule to another (sometimes includes kinases and phosphatases) | 6 | |
| 10399381385 | activating enzymes | *zymogen* is an inactive enzyme that needs to be cleaved *apoenzyme* is an inactive enzyme that needs a cofactor phosphorylation can activate/deactivate allosteric interactions can regulate | 7 | |
| 10399381386 | hydrolyzing enzymes | hydrolysis breaks bonds lipase- hydrolysis of lipids (triacylglycerol breaks apart into glycerol and 3 fatty acids) protease- hydrolysis of proteins (proteins are cleaved to activate subunits) endonuclease- hydrolysis of nucleotides in middle of a strand (restriction enzymes cut at palindromes) exonuclease- hydrolysis of nucleotides at the ends of a strand ribonuclease- hydrolysis of RNA (protected from my 5'-caps and 3'-poly A tails) amylase, glycosidase- hydrolysis of carbohydrates | 8 | |
| 10399381387 | enzyme regulation | 1. regulated at allosteric site 2. regulated by modifications like phosphorylation on vs. off states negative feedback- product inhibits enzyme positive feedback- product activates enzyme oxytocin is example of positive feedback, needs external regulator to eventually stop process | 9 | |
| 10399381388 | oxidation/reduction | loss/gain of hydrogen atoms, gain/loss of charge | 10 | |
| 10399381389 | Bronsted-Lowry acid/base | proton donor/acceptor | 11 | |
| 10399381390 | Lewis acid/base | electron pair acceptor/donor, usually in coordinate covalent bonds | 12 | |
| 10399381391 | acid/base-dissociation constant | large Ka/Kb means stronger acid/base Ka = [H3O+][A-]/[HA] Kb = [HB+][OH-]/[B] | 13 | |
| 10399381392 | amphoteric | can act as either acid or base, amino acids conjugate base of a weak polyprotic acid is always amphoteric each time a polyprotic acid donates another proton, it becomes a weaker acid | 14 | |
| 10399381393 | pH | pH = -log[H+], water at 25C has pH = 7 pH + pOH = 14 | 15 | |
| 10399381394 | pKa | pKa = -logKa lower pKa/pKb is the stronger the acid/base | 16 | |
| 10399381395 | buffer | weak acid and its conjugate base bicarbonate buffer system, carbonic acid and bicarbonate | 17 | |
| 10399381396 | amino acids | memorize their structure, names, letters, properties, physiological pH Nonpolar: PI GALVY MWF "my PI goes to Galveston on mon/wed/fri" Acidic: DE (negative at physiological pH) Basic: HRK (positive at physiological pH) alanine - ala - A glycine - gly - G valine - val - V leucine - leu - L isoleucine - ile - I proline - pro - P phenylalanine - phe - F tryptophan - trp - W tyrosine - tyr - Y (10.1) serine - ser - S threonine - thr - T cysteine - cys - C (8) methionine - met - M lysine - lys - K (10.5) arginine - arg - R (12.5) histidine - his - H (6.1) aspartic acid - asp - D (3.9) glutamic acid - glu - E (4.1) asparagine - asn - N glutamine - gln - Q amino group (10) carboxyl group (2) | 18 | |
| 10399381397 | conservative substitution | binding affinity is not affected by the substitution, indicates that the original amino acid is not involved in binding or does not change conformation of enzyme if binding affinity goes up or down, it is not conservative | 19 | |
| 10399381398 | average weight of amino acid | 110 Da (g/mol) | 20 | |
| 10399381399 | Henderson-Hasselbalch equation | pH < pKa, will be protonated pH > pKa, will be deprotonated | 21 | |
| 10399381400 | isoelectric point | pH of amino acid where net charge is 0, zwitterion pI = average of the pKas of the two functional groups | 22 | |
| 10399381401 | peptide bond | amino group attacks the carboxyl group during synthesis proteolytic cleavage breaks peptide bonds by hydrolysis N-C synthesis, N-terminus is synthesized first and written first | 23 | |
| 10399381402 | disulfide bridge | cysteines are oxidized to cystine in a disulfide bridge join together multiple subunits of proteins reducing conditions in a gel will break apart disulfide bridges and thus the subunits | 24 | |
| 10399381403 | pi stacking | tryptophan and other aromatic compounds can undergo pi stacking interactions with each other | 25 | |
| 10399381404 | protein primary structure | order of amino acids, sequence, N-C synthesis, defined by peptide bonds nonpolar sequences prefer to be on the inside of a protein or in the transmembrane region | 26 | |
| 10399381405 | protein secondary structure | alpha-helix is right-handed, 3.6 aa per turn, no prolines, favorable for transmembrane proteins, defined by hydrogen bonds between backbone components beta-sheet is parallel or antiparallel, hydrogen bond prolines and glycines are used for turns in protein structure | 27 | |
| 10399381406 | protein tertiary structure | interactions between residues in the chain covalent: disulfide bonds non-covalent: hydrophobic interactions- hydrophobic residues fold in the interior of the protein polar interactions- van der Waals ionic interactions- acid/base side groups | 28 | |
| 10399381407 | protein quarternary structure | interactions between residues between different polypeptides, allows connection of subunits to form protein | 29 | |
| 10399381408 | hydrophobic force | hydrophobic collapse- proteins fold to push hydrophilic sections to the exterior and hydrophobic sections to the interior solvation shell- water molecules interact unfavorably with hydrophobic sections, so water molecules forced to lock their orientation and form shells around the protein this low entropy and high free energy state is relieved by protein folding | 30 | |
| 10399381409 | protein unfolding | sigmoidal since its a cooperative process determines thermodynamic stability | 31 | |
| 10399381410 | drugs | IC50 is concentration of drug that inhibits 50% of cells Kd is dissociation constant between drug and target, with a lower value indicating higher affinity drugs are metabolized by the body for excretion | 32 | |
| 10399381411 | vmax | all active sites on enzymes are occupied, vmax constant kinetic measurement depends on: 1. type of enzyme 2. concentration of enzyme when there is high concentration of substrate. vmax is more important than Km | 33 | |
| 10399381412 | Km | concentration of substrate to reach 1/2 vmax thermodynamic measurement essentially the affinity of E for S, high affinity means low Km, depends on the properties of the binding site always assume reversibility if vmax is lowered than Km is lowered too when there is low concentration of substrate, Km is more important than vmax | 34 | |
| 10399381413 | competitive inhibition | same vmax, increased km inhibitor binds at active site can always be out competed by additional substrate, so vmax doesn't change |  | 35 |
| 10399381414 | noncompetitive inhibition | decreased vmax, same km inhibitor binds at allosteric site alters shape of active site, so vmax decreases binds to enzyme and enzyme-substrate substrate with same affinity | | 36 |
| 10399381415 | uncompetitive inhibition | decreased vmax, decreased Km inhibitors binds to ES complex, mixed inhibition type I increased substrate increases inhibitor effectiveness locks S in active site, so decreases vmax and km |  | 37 |
| 10399381416 | mixed inhibition | decreased vmax, increased/decreased km binds at allosteric site, better affinity than substrate type I: prefers to bind ES complex, so decreased Km type II: prefers to bind E alone, so increased Km |  | 38 |
| 10399381417 | Michaelis-Menten equation | v = vmax[S]/(Km+[S]) vmax = k_cat*[E] *catalytic efficiency = k_cat/Km* |  | 39 |
| 10399381418 | Lineweaver-Burke plot | inverse of rxn speed is y inverse of substrate conc. is x 1/Vmax is y-intercept 1/Km is x-intercept useful for testing inhibitor's effect on vmax and Km, plot two lines with and without inhibitor *slope is Km/vmax* |  | 40 |
| 10399381419 | ternary complex mechanisms | both substrates occupy active site at same time: 1. ordered mechanism- one substrate must bind first 2. random order mechanism- doesn't matter which is first | 41 | |
| 10399381420 | specific activity | units of enzyme per total protein mg use specific activity to calculate purity use just the units of enzyme (specific activity times total protein) to calculate yield | 42 | |
| 10399381421 | cellular respiration | NAD (nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide) accept electrons by getting reduced, later get oxidized on delivery to ETC glucose is oxidized to CO2, O2 is reduced to H2O 1. glycolysis occurs in the cytosol 2. PDC and TCA cycle occurs in mitocondrial matrix, except in prokaryotes where it occurs in cytosol 3. ETC and oxidative phosphoylation occurs on inner mitochondrial membrane, except in prokaryotes where it occurs on cell membrane |  | 43 |
| 10399381422 | electron carriers | NADH -> NAD+ + H+ + 2e- FADH2 -> FAD+ + H+ + 2e- NADH and FADH2 carry 2 electrons CoQ carries 1 or 2 electrons cytochrome C carries 1 electron | 44 | |
| 10399381423 | glycolysis | all cells possess this pathway, occurs in cytoplasm glucose is oxidized and split into two pyruvates, produced net 2 ATP, 2 NADH 3 key steps: 1. hexokinase- converts glucose to glucose-6-P, uses ATP 2. phosphofructokinase (PFK) - converts fructose-6-P to fructose-1,6-P2, committed step of glycolysis, allosterically inhibited by high ATP 3. pyruvate kinase- converts PEP to pyruvate, produces 2 ATP "goodness gracious, father franklin did go buy phat pumpkins (to) prepare pies" *"GG, final fantasy did get boring playing people punching people"* |  | 45 |
| 10399381424 | steps in glycolysis that create/require energy | require ATP (2 ATP investment for 1 glucose): 1. hexokinase- glucose to glucose-6-P 2. PFK- fructose-6-P to fructose-1,6-P2 create ATP (4 ATP total, 2 ATP net for 1 glucose): 1. phosphoglycerate kinase- 1,3-bisphosphoglycerate to 3-phosphoglycerate 2. pyruvate kinase- PEP to pyruvate create NADH (2 total for 1 glucose): 1. GAP DH- glyceraldehyde-3-P to 1,3-bisphosphoglycerate | 46 | |
| 10399381425 | fermentation | aerobic conditions- pyruvate enters Krebs cycle, NADH from glycolysis is oxidized in ETC anaerobic conditions- 2 ATP produced, 2 NADH must go back to regenerate NAD+ to continue glycolysis to regenerate NAD+, pyruvate reduced to ethanol (yeast) or lactate (muscle), toxic when building up |  | 47 |
| 10399381426 | pyruvate dehydrogenase complex | oxidative decarboxylation, pyruvate oxidized to acetyl-CoA (loses a carbon) uses up CoA, NAD+ reduced to NADH, releases CO2 TPP- prosthetic group which is a covalently bound cofactor that helps with decarboxylation, derived from thiamine (vitamin B) thiamine deficiency would increase rate of anaerobic glycolysis allosteric regulation- ATP and fatty acids inhibit, since acetyl-CoA goes to fatty acid synthesis and ATP synthesis |  | 48 |
| 10399381427 | cofactors of pyruvate dehydrogenase complex | 1. TPP- thiamine derived 2. lipoic acid 3. FAD+ 4. NAD+ (converted to NADH, so technically not cofactor) 5. CoASH (attached to pyruvate to form acetyl-CoA) | 49 | |
| 10399381428 | TCA cycle | acetyl-CoA converted to citric acid, OAA from previous cycle also converted to citric acid each turn produces *2 CO2, 3 NADH, 1 GTP, 1 FADH2* each glucose does two turns aconitase- only enzyme name that doesn't match product "can I keep selling sex for money, officer?" |  | 50 |
| 10399381429 | regulation of TCA cycle | substrate availability- amino acids can be converted to alpha-ketoglutarate to speed up TCA cycle substrates inhibit their own enzyme- citrate inhibits citrate synthase, succinyl-CoA inhibits aKG DH allosteric regulation- ATP, NADH inhibit TCA cycle | 51 | |
| 10399381430 | steps in TCA cycle that create energy | create NADH (3 total for 1 turn, 6 total for 1 glucose): 1. pyruvate DH complex- pyruvate to acetyl-CoA (technically not part of TCA cycle) 2 isocitrate DH- isocitrate to alpha-ketoglutarate 3. aKG DH- alpha-ketoglutarate to succinyl-CoA 4. malate DH- malate to OAA create GTP (1 total for 1 turn, 2 total for 1 glucose): 1. succinyl-CoA synthetase- succinyl-CoA to succinate create FADH2 (1 total for 1 turn, 2 total for 1 glucose): 1. succinate DH- succinate to fumarate | 52 | |
| 10399381431 | oxidative phosphorylation | two steps: 1. ETC- empty the electron carriers 2. chemiosmosis- make ATP 3 complexes pump H+ to intermembrane space: 1. NADH dehydrogenase- converts NADH to NAD+, CoQ carries electrons to complex 3 2. converts FADH2 to FAD+, CoQ carries electrons to complex 3 3. cytC reductase- cytC carries electrons to complex 4 4. cytC oxidase- O2 accepts electrons, converts to H2O ATP synthase- H+ flows allowed to flow from intermembrane space to matrix, converts ADP to ATP NADH produces 3 (2.5) ATP, moves 10 H+ FADH2 produces 2 (1.5) ATP, moves 6 H+ |  | 53 |
| 10399381432 | energetics of glucose catabolism (ATP count) | 1. glycolysis- 2 ATP, 2 NADH (5 - 2 to bring NADH into mitochondria = ~3 ATP) 2. PDC- 2 NADH (~5 ATP) 3. 2 GTP (2 ATP), 6 NADH (~15 ATP), 2 FADH2 (~3 ATP) ideal total: *38 ATP per glucose* (actual: 30 ATP) prokaryotes ideal total: 38 ATP anaerobic glycolysis: 2 ATP | 54 | |
| 10399381433 | gluconeogenesis | activated by low glucose, high ATP requires 6 ATP, 2 NADH to convert pyruvate to glucose slightly different from glycolysis because pyruvate kinase is irreversible, so instead pyruvate is converted to OAA, then to PEP bypasses acetyl-CoA, which means fatty acids cannot be converted to glucose first step by pyruvate carboxylase happens in mitochondria, then transported out to cytosol formation of glucose, fructose-6-P, and PEP are irreversible steps that push equilibrium to favor gluconeogenesis glycogen- stored in liver, converted to glucose |  | 55 |
| 10399381434 | steps in gluconeogenesis that require energy | require ATP (6 total for 1 glucose): pyruvate carboxylase- pyruvate to OAA PEP carboxykinase- OAA to PEP phosphoglycerate kinase- 3-phosphoglycerate to 1,3-bisphosphoglycerate require NADH (2 total for 1 glucose): GAPDH- 1,3-bisphosphoglycerate to glyceraldehyde-3-P adding phosphate to glucose and fructose at the end does not require ATP | 56 | |
| 10399381435 | starting materials of gluconeogenesis | lactate, pyruvate, glycerol (enters through DHAP), amino acids (enter through pyruvate), any TCA cycle intermediates (enter through OAA) | 57 | |
| 10399381436 | glycogenolysis | glycogen is converted to glucose-6P glycogen phosphorylase- just add phosphate group, no ATP required regulation: allosteric- ATP and glucose inhibit glycogenolysis hormonal- epinephrine and glucagon activates glycogenolysis, insulin inhibits, all done through cAMP/pkA signalling 3 endpoints: 1. glycolysis- energy source for muscles 2. gluconeogenesis- glucose-6-phosphatase is only in live, converts to glucose and releases to blood 3. pentose phosphate pathway | 58 | |
| 10399381437 | regulation of cellular respiration | high ATP and citrate indicate Kreb's cycle activity, both inhibit PFK allosterically, activate fructose-1,6-P2ase (FBP) substrate availability- glucose influx activate glycolysis, OAA influx activates gluconeogenesis insulin- released with high glucose, activate PFK, promotes glycolysis, also recruits glucose transporters to plasma membrane, *increases storage in glycogen and lipids* glucagon- released with low glucose, inhibit PFK, activate FBP, promotes gluconeogenesis, *breaks down stored glycogen and lipids* |  | 59 |
| 10399381438 | pentose-phosphate pathway | starts with glucose-6-P getting converted by GAPDH *releases 2 NADPHs total* oxidative phase- glucose-6-P converted to ribulose-5-P, 2 NADPHs and CO2 produced non-oxidative phase- ribulose-5-P converted to ribose-5-P and glycolysis intermediates (2 GAP, 2 fructose-6-P) it takes *3 glucose-6-P* to make it through both phases 3 goals: 1. NADPH for reducing power in fatty acid synthesis 2. NADPH for eliminating free radicals 3. ribose-5-P for producing nucleotides |  | 60 |
| 10399381439 | fatty acid oxidation (beta oxidation) | saturated fatty acids- dehydrogenase to create double bond (produce FADH2), then produce NADH to create ketone, breaks off acetyl-CoA, repeat unsaturated fatty acids- isomerase to move double bond, then produce NADH to create ketone, break off acetyl-CoA, repeat in mitochondrial matrix needs *2 ATP* to initially activate fatty acid need 1 FAD, 1 NAD+ for each 2 C removed produces *1 FADH2, 1 NADH* |  | 61 |
| 10399381440 | fatty acid metabolism | energy stored as triglycerides, glycerol, fatty acids lipase is enzyme that breaks down triglycerides 1. in cytosol, fatty acid activated by addition of S-CoA to carboxylic end 2. in matrix, fatty acid undergoes beta oxidation to acetyl-CoA 3. goes to TCA cycle | 62 | |
| 10399381441 | fatty acid ketogenesis | during starvation, glucose level fall and fatty acids are oxidized to supplement TCA cycle in liver cells, remaining acetyl-CoA produced react together to form ketone bodies, enter brain or other organs to be reconverted to acetyl-CoA 2 acetyl-CoAs combined to form acetoacetate, which can split to beta-hydroxybutyrate and acetone |  | 63 |
| 10399381442 | fatty acid synthesis | starts with acetyl-CoA and malonyl-CoA (from acetyl-CoA, using bicarbonate), activated to acetyl-ACP and malonyl-ACP acetyl-ACP to acetyl-FAS (with fatty acid synthase attached) fatty acid synthase helps combine malonyl-ACP with acetyl (release CO2), NADPH to remove ketone, then NADPH to remove double bond in cytosol need *2 NADPH* for each 2 carbons added |  | 64 |
| 10399381443 | protein catabolism | protein broken down to amino acids by proteases 3 endpoints: 1. can be used to construct other proteins 2. amino end can be used for nucleotides or urea (excretion) 3. remaining carbon skeleton can be converted to acetyl-CoA or glucose |  | 65 |
| 10399381444 | metabolic rate | how quickly an organism uses up stored energy reserves (protein, lipids, sugars) | 66 | |
| 10399381445 | metabolic states | absorptive state- glucose storage as glycogen in liver, fatty acid storage as triglycerides in adipose tissue, brain and muscle still using up glucose post-absorptive state- glycogen broken down to glucose in liver, triglycerides broken down to acetyl-CoA to power TCA cycle and ketogenesis (which can enter brain) | 67 |