biochem 270 anki convert

#separator:tab #html:true #tags column:3 Acetyl CoA OutcomesThis compound can only go through the TCA Cycle or make fatty acids once formedMetabolite pentose locationRNApentosepathway Oxidative Pentose Pathway ProductsNADPH, pentosespentosepathway NonOxidative Pentose Pathway Productsregenerate hexoses from pentosespentosepathway Where does Pentose Pathway occur?cytoplasmpentosepathway where does NADH go in ETC?complex 1etc nadh where does NADH come from for ETC?glucose/pyruvate directly (glycolysis), or TCAetc nadh where does FADH2 go in ETC?complex 2 (succinate dehydrogrenase), direct attach to tcaetc fadh2 which ETC complexes move protons to the intermembrane space?complex 1,3, and 4etc coenzyme Q recieves electrons from where?complex 1 and 2 seperatelyetc cytochrome c contains what important feature?Hemeetc what occurs in complex 4?O2 recieves electrons to generate water, proton crosses to inner membraneetc what metal cofactors are in ETC?Iron-Sulfur, Iron-Copper, Heme (cytC), Flavincofactors etc Complex 4 structure elements?four cyrotchrome c molecules oxidize, O2 is reduced. no electrons leak out! energy pumps four protons from matric to IMS.etc What technically regulates ETC?ADP concentration! leads to increase in oxygen consumptionadp etc what is the relationship between atp synthesis and etc?They're coupled! you cannot have one without theother w/o wack circumstancesetc Give examples of inhibitors of the ETC?Antimycin A:  Amytal, Rotenone Oligomycin: (make a card for how they do it)etc etc_inhibitors Give examplesof uncouplers of ETC.UCP-1: Animal hibernation! activated by fatty acid breakdown,destroys proton gradient DNP, FCCP, Gramicidin Aetc etc_inhibitors how much of NADPH is produced in pentose pathway?60%etc etc_inhibitors What does NADPH do?reducing power during fatty acid generation, reducing power to deal with oxidative stress!!pentosepathway What is Glutathione?A tripeptide with cysteine residue, provides reducing power including reducing NADPHpentosepathway An example of Glutathione?Prevents Fe3+ from degrading red blood cells by reducing it back to Fe2+pentosepathway how are glutathione and NADPH related?Glutathione (GSH) can reduce NADPHto NADP+ but then NADPH also helps regenerate functional GSH.pentosepathway when are ribolose-5-P and NADPH made?at the same timepentosepathway how do we deal with excess ribose5P when producing it with NADPH?non oxidative phase remakes G6P from R5P, but you use 6 riboloses to make 5 glucoses (30 carbon slosh)pentosepathway What controls the oxidative phase of the pentose pathway?G6P dehydrogenasepentosepathway what organ is pentose oxidative phase most prominent?liverpentosepathway what enzyme converts 2GSH + H2O2 -> GS-SG + 2H2O?glutathione peroxidasepentosepathway what enzyme prompts GS-SG + NADPH -> 2GSH + NADP+glutathione reducatsepentosepathway What's an important pentose pathway intermediate that can be use for AAs?erythrose-4-phosphate can help synthesize aromatic amino acidspentosepathway Which TCA enzymes involve releasing a CO2 molecule?Pyruvate Dehydrogenase, Isocitrate Dehydrogenase, Alpha ketoglutarate dehydrogenase (irreversible)tca TCA enzymes using NAD+ as coenzyme?Pyruvate Dehdro, Isocitrate Dehydro, Alpha KetoDehydro, malate dehydrotca TCA enzymes using lipoic acid?pyruvate dehydro, alpha ketoglutarate dehydro.tca Which TCA enzyme generates a GTP molecule?succinyl-coa synthetasetca which tca enzyme is not in the mitochondrial matrix?succinate dehydrogenasetca Products of total pyruvate oxidation?4 NADH, 1 FADH2, 1 GTPtca What controls the TCA cycle?E1 in PDH is either phosphorylated and dephosphporylation starvation will activate PD kinase, innactivating PDH (conserve 3 carbon) pH can control Insulin activates PDHtca sources of acetyl-coaglucose/pyruvate, lipids, degraded AAs, orther 2 carbon compounds like acetatetca TCA CoenzymesOAA, NAD+, FADH, CoA, Co-SHtca What toxins affect the tca cycle?Mercury and Arsenitetca What is the Glyoxylate Cycle?go from isocitrate to malate through glyoxylatetca How does F0 operate in ATP Synthase?Like a dial, the A subunit has channels pointed up and down with aspartic acid residues, the one facing the proton rich area gets protonated and triggers the rotation. Protons flowing from high conc to low conc creates this ccw rotationatpsynthase etc How does F1 generate ATP?The beta subunit goes through 3 conformations: Loose (ADP binds),Tight (ATP synthesized) and Open (ATP released) these changes are run by the rotationfrom F0atpsynthase etc Why is the efficiency of oxidative phosphorylation of glucose 40.6%?huge energy drops at irreversible steps to ensure they're irreversible! forces reactions to the right to ensure energy porduction/prevent equilibrium issues. etc tca How many ATP are produced from NADH?3etc tca How many ATP are produced from FADH2?2etc tca How many ATP are produced from GTP?1etc tca What is a mitochondria apoptotic activator molecule?cytochrome cetc tca How does cytochrome c trigger cell death?Released to cytosol, binds to Apaf-1 leading to apoptosomes assemblyetc tca What is a Passive Diffusion example?fatty acidsetc tca how does alpha amylase workin digestion?endoenzyme, hydrolyzes links before or 2 links after branch points (starch)carb_digestion What is limit dextrin?What is leftover after alpha amylase go snipping, short chain. needs different enzyme to digestcarb_digestion what enzyme cuts the alpha 1,6 branch?alpha dextrinase (isomaltose)carb_digestion What further digests dissacharides?sucrase, maltase, Beta galactosidase(lactase) on intestinecarb_digestion Which transport type take monosacharides into the body from intestines?Active Transport: Glucose, galactose Facilitated diffusion: fructosecarb_digestion What element helps glucose transport out of the lumen?Sodium! like a vacuum helping to pull glucose in with itcarb_digestion What is SGLUT 1?active transport, sodium and glucoseactive_transport carb_digestion What is GLUT 2?Only in liver/pancreas cells, glucose transport, fructoseactive_transport carb_digestion Where is lactose synthesized?mammary gland, only late pregnancy and lactation periodsynthesis What enzyme builds lactose?lactose synthasesynthesis What breakdowns lactose?lactase, no lactase=lactose intolerantcarb_digestion What are lipids?substances from living things that dissolve in nonpolar solventslipids What can lipids be used for?energy storage, membrane structure, chemical signals, vitamins, or pigmentslipids what are the 6 lipid classes?fatty acids triacylglycerol wax esters phospholipids sphingolipids isoprenoidslipids What is the fatty acid structure?monocarboxylic acid that contain hydrocarbon chains of 12-20+carbonslipids what is the terminal carbon named in fatty acids?omega carbonlipids What are saturated fatty acids?only single carbon-carbon bondslipids what are unsaturated fatty acids?contain one or more double bonds between carbons,cis or translipids What can plants and bacteria do with acetyl-coa?make all the fatty acids they needlipids what fatty acids do animals need from their diet?Omega-3, Omega-6 (alpha linolenic acid and linoleic acid)lipids What do omega 3 and omega 6 FAs do?6-precursor of prostaglandins, thromboxanes, leukotrienes 3-cardioprotective, anti-inflammatory, anticarcinogeniclipids What are Eicosanoids?powerful, hormone like molecules including prostaglandins, thromboxanes, and leukotrieneslipids what do elicosanoids do?mediate smooth muscle contraction, inflammation, pain perception, blood flow regulationlipids Prostaglandins functionsvasodilation, inflammatory mediators, smooth muscle contractionlipids thromboxanes functionsplatelet aggregationlipids leukotrienes functioninflammatory mediatorslipids what is the major site for dietary fat digestion?liverlipids What enzyme hydrolyzes triglycerol into FA, monoacylglycerol, diacylglycerol, and glycerol?pancreatic lipaselipids What does pancreatic lipase do?hydrolyze triacylglycerol into a mix of FA, monoacylglycerol, diaglycerol, and glycerollipids Where are bile salts derived from?cholesterollipids where are bile salts produced?liverlipids where are bile salts stored?gallbladderlipids Where do triacylglycerols go?pair with chylomicrons and merge into lymph systemlipids classify chylomicronsapolipoproteinslipids what are lipoproteins?apolipoproteins (peptides) + lipidlipids what are the lipoprotein classes?Chylomicron, VLDL, IDL, LDL, HDLlipids What is the good cholesterol?HDL bc it modulates membrane fluidity, makes hormones and bile saltslipids what lowers LDL?statins, PCSK-9 inhibitorslipids what hormones mobilizes fat?epinephrine and glucagonlipids What adipose tissue enzymes help catabolize FAT into FAs and glycerols?triacylglycerol lipase, diacylglycerol lipase, and monoacylglycerol lipaselipids What enzyme catalyzes Fatty Acids entering mitochondrial matrix?Carnitine Acyltransferase 1 which FAs are gluconeogenic?odd number chains what allostericly activates G6P dehydrogenase (and pentose pathway)NADP+ what allosterically inhibits G6P dehydrogenase (pentose pathway)?NADPH what are the ketone bodiesacetoacetate, D-3-Hydroxy-butrate, acetone When are ketone bodies generated?too much acetyl-coA + too few OAA What human conditions cause ketone body generation?fasting, diabetes where in the body are ketone bodies made?Mitochondrial matrix of liver What enzyme catalyzes acetoacetate -> Acetoacetyl CoACoA transferase Where does the CoA group come from when acetoacetate becomes acetoacetyl CoA?Succinyl CoA -> Succinate what enzyme catalyzes Acetoacetyl CoA -> 2 Acetyl CoAThiolase + CoA In Ketogenesis what does 3 Acetyl CoA form?beta hydroxy beta methylglutaryl CoA HMG-CoA why does ketogenesis occur in the liver?high levels of HMG-CoA synthase What does HMG-CoA do in the cytosol?make cholesterol What happens to acetone?converted to pyruvate or excreted via urine or exhaling What tissues can use ketone bodies as fuel?skeletal and cardiac muscles, brain (starvation but at absolute minimum of glucose) NOT LIVER what is the cholesterol structurefour rings, 27 carbons What are the functions of cholesterol?major component of animal cell membrane (fluidity) precursors to bile salts, steroid hormones, vitamin D sources of cholesterol?Diet Biosynthesis (Liver>Intestinal Mucosal cells) What is the source for cholesterol biosynthesis?acetate (acetyl CoA, 2 carbons) what is the first stage of cholesterol synthesis?form Mevalonate (6 C) What is the major regulating enzyme for cholsterol synthesis?HMG-CoA reductase what enzyme catalyzes HMG-CoA -> MevalonateHMG-CoA reductase What is the second stage of cholesterol synthesis?form Squalene from Mevalonate how many carbons is Squalene?30 what is the third stage of cholesterol synthesis?cyclization of squalene what is the rate limiting enzyme for bile salt synthesis?cholesterol 7a-hydroxylase What regulates HMG-CoA reductase?transcriptionally and phosphorylation how do sterols affect HMG-CoA reductase?inhibits transcription what is mevalonate also a precursor for?dolichol and ubiquinone (co-Q) how does dolichol and ubiquinone affect HMG-reductasefeedback effect inhibiton What does the LDL receptor do?mediate endocytosis of IDL and LDL from plasma What happens without the LDL receptor?high circulating cholesterol levels what does progestin do?regulates events during pregnancy, are precursors to all other steroid hormones what do glucocorticoids do?promote gluconeogenesis and supress inflamation What do mineralocorticoids do?regulate ion balance in kidney What are the steroid hormones?progestin, glucocorticoids, mineralocorticoids, androgens, and estrogens Progestin exampleprogesterone give an example of glucocorticoids?cortisol and corticosterone give an example of mineralocorticoids?aldosterone Androgen exampleandrostenedoine and testosterone Androgen functionpromote and maintain male sexual characteristics estrogens example?esterone and estradiol estrogens function?support female sexual characteristics? Progestagens are the precursors to:glucocorticoids, mineralocorticoids, androgens androgens are the precursor to:estrogens What two compounds combine to make amino acids?alpha keto acid and NH3 Where does the NH3 come from?nitrogen fixation (reducing nitrogren gas to ammonia) How do bacteria make ammonia?reduce nitrate or nitrite What catalyzes alpha ketoglutarate + NH3 +NAD(P)H <-> Glutamate + NAD(P)glutamate dehydrogrenase What is the general reaction for AA synthesis?glutamate + alpha keto acid <-> alpha ketoglutarate + alpha amino acid what enzymes catalyzes AA synthesis?transaminases/aminotransferases Which aminotransferase catalyzes glutamate + OAA <-> alpha keto. + aspartateSerum Glutamate-OAA Transaminase Which aminotransferase catalyzes glutamate + pyruvate <-> alpha keto. + alanineSerum Glutamate-Pyruvate Transaminase Where are the SGOT and SGPT enzymes abundant?liver and heart Do humans use proteins as a reservoir for glucoses?no How do we get rid of ammonia in the body?urea or uric acid Does Urea or Uric Acid require a lot of water?Urea What are the four major compounds in the urea cycle?Arginine, Ornithine, Citrulline, Argininosuccinate Whats the most important enzyme in the urea cycle?carbamoyl phosphate synthetase classify ornithineamino acid classify argininosuccinateamino acid What are additional functions of Aspartate and Glutamate?donate amine groups What are the essential amino acids?phe, val, trp, thr, ile, met, his, arg, leu, lys. What does transamination of an alpha keto acid do?make amino acids! What do proteolytic enzymes break proteins into?Amino Acids and Oligopeptides in the Lumen What enzyme catalyzes oligopeptides enetering the cell?Aminopeptidase What enzyme transports AA and tri/dipeptides to the blood?Peptidases What do proteins have to be broken into before absorption?Amino Acids and di/tripeptides What aspect of the stomach denatures proteins?low pH Where are proteolytica enzymes secreted?pancreas What are inactive protelotyc enzymes called?zymogens What are the three zymogens?pepsinogen, trypsinogen, and chymotrysinogen What are the activated zymogens?pepsin, chymotrypsin, and trypsin What activates Pepsin?stomach low pH What activates trypsin?enteropeptidase What activates Chymotrypsin?Trypsin What kind of transport do AAs use?active transport What percent of our proteins can we recycle?75% What is the N-Terminal rule?the first amino acid in a chain determines the half life of a protein What four amino acid arrangement results in a shorter lifespan?PEST: Proline, Glutamate, Serine, Threonine What is Ubiquitin?highly conserved small (76AA) peptide that tags proteins for degradation  What enzymes are part of the Ubiquitin tagging system?E1, E2, and E3 What is another name for the Ubiquitin E3 enzyme?ubiquitin protein ligase Why is E3 so important for tagging?catalyzes transfer of ubiquitin to target protein What is a unique property of E3?It encompasses a large group of different variations that target different proteins What are the nucleic acids?nuceotides, nucleosides, ribose, deoxyribose, and nucleobases, purine rings, and pyrimidine rings How many types of Purine rings?four Examples of purine rings?Uric Acid, caffeine What purine rings are involved with nucleotide catabolism?Inosine, guanine, hypoxanthine, and xanthine What is the final product of nucleotide catabolism?uric acid What are the three eznymes that digest nucleic acids?pancreatic nucleases, phosphatases, and nucleosidases What are the final products of nucleic acid digestion?phosphate, ribose, and nucleobases What type of transport do the phosphates, riboses, and nucleobases use?faciliated What are the two pathways of Nucleotide MetabolismSalvage and De Novo Pathway Whats the salvage pathway?utilization of preformed purine and pyrimidines (nucleobases) from diet What does the de Novo pathway do?synthesize nucleotides from small molecules Which enzyme converts bases back to nucleotides? (Purine salvage)HGPRT (purine phosphoribosyltransferase) What molecules do salvage pathways collect and combine to form nucleotides?hypoxanthine, guanine, and PRPP What enzyme handle the adenosine salvage pathway?APRTase WHAT ARE THE SMALL MOLECULE SOURCES FOR PURINES?Aspartate, CO2, Glycine, Glutamine, and 10-Formyl-THF What is the purine ring sugar foundation?ribose-5-P What is the limiting substance for purine synthesis?PRPP synthetase Where do most of our riboses come from?pentose pathway myoglobinfound in muscle tissue, responsible for storage of oxygen and intracellular transport hemoglobinfound in red blood cells, transports oxygen from the lungs to the tissues hemeprosthetic group that specifically binds to myoglobin and hemoglobin into a hydrophobic crevice, is not covalenelty bound prostheitc groupcofactor that covalently binds very tightly to a protein  function of hemecontains iron, which readily binds to oxygen and other gases since Hb and Mb cannot bind to oxygen by themselves protoporyphyrin IXbinds iron to an amino acid or peptide through four N atoms. When it is bound to iron, the complex is called heme proximal histidinethe 8th histidine residue, the N of the imidazole side chain binds directly to iron  how many ligands does iron like to be bound to 6 binding groups in octahedral geometry ( four are from poryphyrin, one is from imidazole side chain) 6th coordination site of deoxyhemoglobin vs oxyomyoglobindeoxy- the 6th site is left open, iron does not bind to anything. In oxy, the 6th side is occupied by oxygen how does the distal histidine help stabalize oxygen binding the distal histidine H bonds to O2. It thus increases the binding specficigy for binding to O2 over other gases, because the distal histidine cannot hydrogen bond to other gases liek CO what color does a spectrum display when hemobglobin binds to oxygenas more oxygen binds, the visible spectrum shifts from blue to red  how can UV/vis be used to determine the fraction of Mb or Hb that is bound to oxygen?absorbance is prop to amount of O2 bound, so as more O2 is bound, a visible change from blue to red/purple occurs looking at a binding curve: what is Yo2?the fraction of O2 binding sites that rae occupied with O2 looking at a binding curve: what is P50?the [O2] at which 50% of myoglobin molecules are bound to oxygen  (same as Kd but in units of pressure)- O2 binding affinity of myoglobin!! what does lower P50 indicate?higher binding affinity, and higher means lower binding affinity  what does it mean that myglobin has a low P50 and why does it have this?means high binding affinity for oxygen, bc its function is to store oxygen in muslce cells where  Po2 is low Po2 levels in the msuclesat normal resting, the Po2 in msucle is low, but when Po2drops due to msucle acitivy, oxygen is released why is myglobin inefficent in transport from the lungs to the muscles it is a hyperbolic binding curve, so high binding affinity, low P50 means that not enough oxygen would be released into the muslces. with low binding affinity, high P50, the protein would not satruate with O2 in the lungs what does the curve look like for an optimal transport protein (of oxygen from the lungs to the muscles)high binding affinity in the lungs, but low binding affinity in the tissues so oxygen can be released  how many oxygen binding sites does hemoglobin contain4 total what are the two types of subunits in hemoglobin, and what type of interactions bind them together/ how do we know?there are two alpha units and two beta units. When placed in mild detergent hemoglobin seperates into two alpha-beta dimers, which suggests that there are strong noncovalent interactions btwn alpha and beta subunits  cooperative binding since hemoglobin has 4 binding sites, binding of oxygen at one subunit increases the binding affinity at remaining sites  what is evidence for cooperative binding sigmoidal binding curves- starts out with a low slope, and then the slope rapidly increases before leveling off  why is the binding curve for hemoglobin sigmoidal?at low Po2, hemoglobin binds to oxygen with low affinity, but as more oxygen binds, the affinity for O2 increases, Hemoglobin can also shift btwn confomrations that either have high or low binding affinity for oxygen  hill coefficent number of binding sites (n) and how strongly they interact  When does the value of h approach n as the interactionbetween sites increases what happens when h=1there is no interaction between binding sites what happens when h is between 1 and npositive cooperativity, binding of one ligand makes binding of additional ligands more favorable (observed in hemoglobin!!) when h<1negative cooperativty, thus binding of one ligand makes binding of the others less favorable  allosteric effectligand binding alters the strucutre of a protein, and thus its functional properties  what are the two models for allosteric transitions that promote oxygen binding and release in hemoglobinsequential (KNF) model, and symmetry (MWC) model  sequential KNF model each hemoglobin subunit can changes its conformation from a low affintity state to high affinity state independently of the other subnitis. However, oxygen binding at one subunit favors transition to higher affinity state in adjacent subunits  the symmetry model the entire hemoglobin tetrameter exists in low affintiy (T state) or affinity (R state) conformation. (so lies between equilibirum between the two) Binding of oxygen favors the R state/ high affinity state. shift from Tense to relaxed is concered what model for allosteric transitions is favored and whysymmetry model bc there is a lot of evidence that supports it, such as x ray crystallography  according to x ray crystallography, what is the difference btwn T and R states O2 binding (R state)causes rotation of alpha-beta dimer relative to each other, bringing beta subunits much closer together and closing the central cavity btwn subunits  why would hemoglobin ever change conformation?one form is more stable than the other depending on if oxygen is bound  when is hb T state from stabalized vs R state formT is stablized in deoxy form while R is more stable once oxygen binds  what are the strong non covalent interactions that stabalize the deoxyy t state -inter subunit salt bridge btwn his146 carboxylate and a lys side chain of the alpha sub unit (and also btwn his and asp side chain) - at the alpha subunit c terminus the terminal arg forms two sallt bridges with the other alpha subunit and an h bond with the beta subunit (and makes a bridging interaction through a chloride ion) how doe hb transition from T to Rintreactions must be broken to transition to R, unfavorable energy cost is paid by favorable oxygen binding  what does the iron atom look like in the deoxy state of hbit is pulled slightly out of the plane of the proyphorin and the proximial his is not peripinduclar to the plane of heme what does the subunit look like once oxygen is boundiron atom is pulled onto the plane of heme and the proximal his rotates to tbe peripindicualr, this pulls down the F helix, producing a larger confromational shift in the protein strucutre placing all subunits in the R state what favors oxygen release at low Po2R state is stabalixed with increasing O2 saturation, the T state is more stable without full saturation so it favors oxygen release perutz mechanism for T to R transition strcutural reorganization at the heme binding site upon oxygen binding produces the larger conformational shift from T to R tetsed peurtz model wild type hemoglbin characterisitcs oxygen binding pulls on F-helix, hemoglobin transtiions from T to R tetsed peurtz mode proximal his to G mutatnat + free imidazole hemoglbin characterisitcs oxygen binding is unlinked from the F felix so hemoglobin is stuck in the T state  """Unlinking the F helix from heme abolishes cooperativity""  true or false"true how does a mutation of H146D in the beta subunit of hemoglobin affect the ability of hemoglobin to deliver oxygen to tissues the mutation increaes oxygen binding affinity and thus decreases oxygen delivery to tissues, because H146  is invovled in a salt bridge interaction that stabalizes the hemoglobin T state. If this charge interaction cannot occur, hB is unresponsive to the Bohr effect and stability of T state is decreased.  allosteric effectorsmolecules that bind to a protein to regulate function active sitelocatin on a protein where a small molecule must bind to carry out its primary function substratesmolecules that bind a the active site  what is the active site for heme and whythe heme pocket bc this is where oxygen is bound  allosteric siteslocations distant from the active site that bind to small molecules and regulate function at the active site positive vs negative effectors increase protein activity upon binding vs decrease protein activity upon binding  homotropic vs heterotropic effectors bind at active site and affect their own binding, bind at allosteric sites distant from the active site  what are the four heterotropic effectors that negatviely regulate hemoglobin and what do they do H+, CO2, Chloride, and BPG  which decrease oxygen binding affinity bohr effectresponse to a drop in pH, rbc's adapt to changes by maximizing hemoglobin oxygen binding capacity in the lungs while also optimizing oxygen delivery to tissues with the greatest demand  what drops the pH in tissues and bloodcarbonic anhydrse catalyzes conversion of CO2 into bicarbonate and H+, lactic acid is also produced by vigorous activity which causes a combined dropi n pH is there a salt bridge present in the r state of hbno how to dyou increase the release of oxygen stabalize the T state of hb, which is stabalized by a salt bridge froming between his and asp near the c terminus of the beta subunit  in the R state is his mostly unprotenated or protenated at physiolocial pH and whymostly unprotenated bc it has a pka of 6.4 Is H146 protenated or deprotenated at phsyicolgical temp in the T state nd what affect does this haveit is protenated, allowing the salt bridge to form, as pH drops, a larger fraction of H146 is protenated which favors transition to the T state and release of oxygen  how does Co2 help regulate oxygen binding affinitydissolved carbon dioxide generates bicarbonate and H+, the bicarbonate can react w the N terminus of hemoglobin to form carbamate which contributes to bohr effect what does carbamate formation allowhemoglobn to transport some co2 into the lungs  example of CO2 regulationhyperventilatoin (breathe too fast, Co2 levels will drop and oxygen will not be efficently deliverd to the tissues  how does chloride impact favored hb state and co2 concentrationwhen bicarbonate is transferred out of the cell, chloride is transferred into the cell. (so higher Co2, higher cl). chlordie ions also stabalize the N terminus of the alpha subunit so higher [cl] therefore facors deoxy hb and weaker oxygen binding affinity BPGallosteric regulator that is very negative, it binds in the central cavity of the hb the higher BPG concentration, which state is favoredthe T/ deoxy state is stabalized bc the cavity is opened and BPG can bind so there will be lower oxygen binding affinity. (R state is not large enough to fit BPG) carbamate when bicarbonate reats with the N terminus of hb this is what is formed  what is the equation for formation of carbamate"<img src=""Screen Shot 2024-05-11 at 10.45.13 AM.png"">" higher [BPG]...lowers Hb affinity for oxygen and promotes its release into tissues , also how we acclimate to high altitudes fetal hemoglobinfetus relies on mother for oxygen so must have higher affinity for oxygen than the mothers, has a mutation to bind 2,3-BPG with lower affinity thus favoring the R state more strongly and having a higher affintiy for O2 bidnig than the mother catalystincreases the rate of rxn without being changed in the process enzymebiological catlayst, most enzymes r proteins but some are made of ribosomes  what are the 6 major classes of enzymesoxidoreductates, transferases, hyrodlases, lysases, isomerases, ligases oxidoreductasecatalyzes oxidation and reduction reactions transferasescatalyzes transfer of functional groups from one molecule to another hydrolasescatalyzes hydrolytic cleavage, could be considred a sub class of transferases lysasescatalyze addtion or elimination rxns isomerasescatalyze intramolecular rearragnmenets  ligasescatalyze rxns that join two molecules coenzymescofactors that particpate in the reaction mechansim  what can be used as enzymes for cofactorsmetals, derivatives of vitamin b such as thiamine pyrophosphate, coenzyme A, folate, etc rate of the forward rxn is given bychange in product or substrate concentrations over time  reaction rate is prop to...reactant concentration (rate law!!) what is k and what does it tell youhow fast the rxn is  n: what does it depend on and what are the diff units?depends on reactin order, must be experimentally determined for first order: units are 1/s for second order: units are 1/Ms what values do enzymes effect and what values do they not effectthey effect [p]/[s] and K1/K-1 but do not effect Keq enzymes function and what they do not do they increase the rate of chemical reactions, do not affect the thermodynamic favoribility of the rxn, or the equilibirum distributions of reactants and products  transition statestrcuture in which molecules are colliding in the proper orientation to permit a reaction. Covalent bonds are half broken, formed, or strained and it is higher in energy that the reactants and products  free energy of activationenergy diff between the reactants and the transition state, the energy barrier that must be overcome for a reaction to occur  rate constant is related to .. what equation gives this relationshipfree energy of activation, arrhenius equation what are the two ways to increase the rate of a reactionincrease temp (not ideal for cells), or lower the activation energy  how do enzymes increase the rate of biochemical rxnslower the activation energy aka stabalize the transition state of a reaction  what are the important takeawys of a free energy diagram1) free energy is the same whether the enzyme is present or not 2) enzyme lowers actiavtion energy for both the forward and reverse reactions  rate enhancement ratio of rate constants for the catalyzed divided by uncatlayzed reaction (Kcat over Knon) how do we determine how  much energetic stablization is required to acheive rate enhancements rate enhancement and arrhenius equation to get delta delta G energy of activation what is delta delta G diff in activation energy btwn the catalyzed and uncatlayzed rxns  what does an enzyme need to acheive massive rate enhancementa few stabalixing noncovalent interactions with the transition state one way to lower activation energy relative to the uncatalyzed rxn: lower delta H (enthalpy)cna do this by making favorable NC interactins with the transition state, usually the biggest contributer to lowering delta G to lower activation energy, the enzyme must bind to >>>the transition state w higher affinity than the substrate induced fit binding the enzyme has a strucutre that is complementrary to the transition state, so only the two can bind together one way to lower activation energy relative to the uncatalyzed rxn: raise delta S(entropy)aka make delta S less negative, raises this by binding substrates and constraining them into a very specfic oreintation that favors reaction, so very little change in conformational entropy is required before the molecules react  methods use to lower free energy by enzymeselectrostatic catalysis, general acid base catalysis, catalysis by approx, conformational strain and distortion, covalent catalysis  electrostatic catalysisusing charged amino acid side chains or metal ions to stabalize positive and negative charges that develop over the course of a rxn (lowers delta H) general acid base catalysisgeneral acids and bases are amino acid residues that facilitate proton transfers in the enzyme reacioton mechansim (general means acid/base besides water) ex of enzyme catalyzed rxn ester hydrolysiswater attacks at the site of the carbonyl, then both an acid and base deprotanate/ protenate at the same time to form an intermdiate that speeds up the reaction common acid/bases used by enzymesduring GABCglu, asp, lys, arg, his  catalysis by approximation bringing two reactants in very close proximity to position them favorably so the rxn can succeed, invovles the removal of both translational and rotational degrees of freedom which raises delta S conformational strain and distortionbinding substrates in a way that induces structural strain can make them much more reactive, raises the free energy of the enzyme substrate complex  covalent catalysisenzyme provides an alternate reaction pathway that invovles a covalent intermediate. The intermediate is lower in energy than the uncatalyzed transition state. the activation energies for formation and breakdown of the intermediate are lower than that of the uncatalyzed rxn  what needs to happen for covalent catalysis to work 1) steps in alternate rxn pathway must have lower delta G than uncatalyzed rxn 2) the covalent intermediate is less stable than product which amino acids form covalent intermediates in enzyme rxnsany that can act as nucs, such as cys, ser, thr or asp, gly, tyr proteasesenzymes that catalyze peptide amide bond hydrolysis ex of some proteases and their functionstrypsin, chymotrypisn, and subtilisn imp for digestion of protein and peptide nutrients. Thrombin and plasmin have roles in blood clotting, elastase is secreted by bacteria to help digest connective tissue serine proteaseuse a serine residue as a nucleophile to acheive amide bond cleavage  what is the mechanism for uncatalyzed amide hydrolysisdirect attack of water on the amide carbonyl gourp to form a tetrhaderal intermediate hartley and kilby model for chymotrypsin mechanism - chymotrypisin reacts w ester substrate PNPA to make a yellow product - rapid burst of yellow than plateu, which is called biphasic kinetics, adding more enzyme had same effect - thus chymotrypsin doesn't catalyze direct amide hydorlysis it occurs in two steps again what does the biphasic kinetic model suggestchymotrypisin amid hydrolysis mechanism is done in two steps: fast burst and slow step (slow = rate determing step) rate determining stepslowest step within a chemical reaction how was the identity of active site residue found/ what is itincubating chymotrypsin with an inhibitor, DIPF blocks enzyme activity by modifying the protein, covalently binds to only one ser residue what is the active site nucleophile in chymotrpsinand how does this make sensethe alochol side chain of serine, which is only a good nuc if deprotenated. therefore a base must be present to deprotenate it  evidence for his being invovled as a base in the chymotrupsin mechansim based on graph, enzyme is maximally active at pH 7.5-8, his has pka closest to neutral, thus it can act as a base to deproenate ser (but only at pH greater than 7) what are the three catalytic residues/ catalytic triad of serinehis (base), ser (nuc), asp  how are the catalytic triad arranged?his hydrogen bonds to the serine hydroxyl group, asp makes ser positioned within h bonding distance to his which stabalizes the postive charge that would build up on his when it is protenated.  how does the presence of asp affect his pka ? how does it affect basicicity of his?stabalization of the his conjugate acid by asp is sufficent to make his basic enough to deprotenate ser  what are the three combo mechansims of chymotrypsin to achieve amide bond hydrolysis general acid base catalaysis, covalent catalysis, electrostatic catalysis what is the first step of the chymotrypsin mechanism called"the ""acylation"" step" step 1 of chymotrypsin mechanism a peptide substrate binds, the catalytic triad activates ser as a nuc, his acts as general base to faciltiae nuc attack on the amide carbonyl  step 2 of chymotrypsin mechanism tetrahedral intermediate is formed and the negative charges are stabalized by backbone amides in the oxyanion hold. His acts as a general acid to facilitate breakdwon of the intermediate and expulsion of the amine leaving group oxyanion holepocket in the active site of an enzyme that stabalizes transition state negative charge on a deprotenated oxygen or alkoxide  step 3 of chymotrypsin mechanism the amine leaving group exits the enzyme. the acylated ser residue is left, which is calle dthe acyl enzyme intermediate. Ser is covalently bound to the substrate acyl enzyme intermediae the acylated ser residue left in step 3 the second half of the chymotrypsin mechanism is referred to as the deacylation step  step 4 of chymotrypsin mechanism a water molecule enters the active site and attacks the acyl enzyme intermediate. His again acts as a general base to help deprotenate water  step 5 of chymotrypsin mechanism a new tetrahdera; intermediate is formed and stabalized oxyanion hole. His acts as a general acid to facitliate breakdwon of intermediate and expulsion of the carboxyl LG step 6 of chymotrypsin mechanism the C terminal product leaves and the enzyme is ready for another round of catalysis  why do some serine proteases have unqiue substrate preferences when the mechanism and active site structures are nearly identical?there is a pocket near the active site reidues that accommodates the aminoa cid side chain that is c terminal to the scissile amide bond. In chymotrypsin, this pocket is hydorphobic thus only aromatic hydrophobic residues can bind.  ex of specificity within the pocket- trypsin and elastasetrypsin has an asp so the negative charged residue selects for positive substrates. elastase has two bulk residues so larger amino acids are excluded which is why it prefers to cleave at ala and gly. examples of other protease familiescysteine, metalloproteases, aspartyl proteases cysteine proteasesuse an active site cys as a nuc (ex papain, bromelain, cathespin B) metalloproteasesuse a metal ion to facilitate direct attack of water on the amide bond (ex carboxypeptidase A) aspartyl proteasesuse aspartate to facilitate direct attack by water. Often active at low pH like in the gastric fluid  lysozymean enzyme that catalyzes hydrolysis of the peptidoglycan polymer that forms the bacterial cell wall resulting in death of the bacterial cell wall where is lysozyme found and whyinvolved in antibacterial defenese so found in secreteion like tears, milk, saliva, and egg white glyocsidasescatalyzes hydrolysis of the glycosidic bonds of carb polymers (ex lysozyme) peptiglycan sugars sequencealtnerating GlcNac and MurNac sugars connected through beta1-4 linkage  where does the peptidglycan substrate bind into a deep cleft in the lysozyme structure, six sugar residues are accomadated with sites A-F where does cleavage of peptidoglycan occurat the glycosidic bond between MurNac in site D and ClcNAc in site E what type of catalysis does lysozyme use substrate strain/distrortion  describe substrate strain/distrotionsugar at site D is distroed from its most stable, chair conformation into what resembles half chair.. destabalization of a substrate can make it more reactive  what are the two catalytic residues identified for lysozyme activityE35 and D52 what is the mx pH acitivty of lysozymepH 5, E35 is buried in the binding cleft and thus an elevated pKa of 6 for this residue is expected DF2 and E35 must be protenated or deprotenatedDF2 must be deprotenated and E35 protenated  two mechanisms for lysozyme all invovleelectrostatic catlaysis, general acid base catalysis, and catalysis by strain/distortion mechanism 1 of lysozyome formationSn1 like reaction, E35 acts as a general acid to make GlcNAc a better leaving group. Forms a carbocation like intermediate called an oxocarbenium, which is stabalized by D52 which is deproteonated in an ion pair interaction oxocarbeniumhalf chair structure how is the substrate impacted upon binding to lysozyme substratedistorted when binding to lysozyme into an orientation resembling that of the transition state and oxocarbenium intermediate  Mechanism 2 of lysozome formation"SN2 liek double displacement mechanism, E35 again acts as a general acid to make ""OR"" a better leaving group, OR leaving accours with simultaneous nuc attack of D52 on the anomeric carbon leading to a covalent intermediate , covalent catalaysis " transition state of SN2oxocarbenium like species, which has a formation favored by substrate distortion  Which mechanism is favored"some ppl believe that mech #1 is stable enoguh, cannot prove a reactionmechanism " detailed kinetic measurements give- fundamental info abt the catalyst - reaction mechansims - inhibitor mechanisms  in steady state what is the relationship between ES formation and breakdwonthe rates are equal  diffusion limitedan enzyme catalyzed reaction that approaches the max of 10^8-10^9 1/Ms what does a larger Kcat/ K m ratio indicatedgreater enzyme preference for a substrate  what do mutations affecting Kcat indicatethe residue is invovled in catalaysis (lowering activation energy) Mutations affecting Km indicatethe residue is involved in substrate binding  how can Kcat and Km be determined from datausing non linear regression analysis  michaelis menten equation"<img src=""Screen Shot 2024-05-11 at 8.15.33 PM.png"">" when [s]=Km...the reaction is at half maximal velocity when [s]<<Km...the intial rate is directly prop to [s] the curve is roughly linear at low [s] when [s]>> Km...the rxn is zero order with respect to the substrate V0=Vmax Km michaelis constantKm, units of concnetration, tells you the substrate concentration required for effective catalaysis  turnover numberaka Kcat, tells the time required for the enzyme to convert  large kcat and small Km is indicative of whatefficent catalysis bc the ratio is larger what can be used to measure product formation UV-vis spectroscopy  lineweaver burke plot measures Kcat and Km  irreversible inhibitors covalently modify the enzyme reversible inhibitors binds to an enzyme via noncovalent interactiosn, inhibition can be reveresed by removal of the inhibitor  what are the three types of reversible inbibitors competivie, uncompetitive, and mixed  competitive inhibitionbind at the same location as the enzyme substrate in the active site but do not undergo conversion to product bc substrate cannot bind.  how does chemcial equilibtirum shift when a competitive inhibitor is usedshifts to the left in the rpesence of an inhibtior (increase in Km) inhibitor disassocaition constanteq constant for the enzyme inhibitor complex, low Ki= high affinity binding to the enzyme, high Ki= low affinity binding to the enzyme  what is the apparent Kmthe observed Km in the presence of a certain concnetration of injbitor. The inhibitor increases the amount of substrate required for each rxn to reach 0.5Vmax how is Vmax affected in the presence of a chemical inhibitor since the rate of rxn only depends on the relative inhibitor and substrate []'s, at high [S], Vnot= Vmax, thus in the presence of a competitive injbitor Vmax doesn't change  why does Vmax stay the same in competitive inhibtion the inhibitor can only bind to the free enzyme active site, so if [S] is very high, S will out compete the inhbiotr for enzyme binding and reaction rate will aproach Vmax  uncompetitive inhibitionthe inhibitor binds tot he ES complex but not free E... the inhibitor binds at a location that is diff from the active site and prevents turnover to product  what does uncompetitive inhibition affectboth Km and Kcat for an enzyme  what is the factor that Vmax and Km apparent are affected by in uncompetitive inhibitionthe reduce by a factor of 1/alpha prime  why does Vmax and Km behave in that way for uncompetitive inhibitoinbc the inhibitor only binds to ES, increaseing [S] does nothing to prevent inhibitor binding. The result is that Vmax decreases in the presence of an inhibitor. At low [S] the affect of the inhibiotr is minimal, but when [S]> Km, the inhibiotr removes some ES from the equilibirum, shifting it for form more ES. Thus the presence of the inhibiotr causes an apparent decrease in Km what does the lineweaver burke plot look like for uncompetitive inhibition shows parallel lines with increasing Y intercept and decreasing x intercept as the inhibiotr concentration increases  what type of rxns do uncompeitvie inhibitors usually inhibitreactions involving two substrates  what is mixed inhibition the inhibitor can bind to both the enzyme and the enzyme substrate compelx  noncompetitive inhibitiona special type of mixed inhibition where the inhbitor binds to E and ES with equal affinity  how are Vmax and Km affected in mixed inhibitionVmax decreases by 1/alpha' like uncompetivie inhibtion, but then Km usually increases because Ki=Ki prime noncompetitve inhibitors affect on Km Km remains unchanged because Ki=Ki prime bisubstrate rection binds to two substrates and converts them to two products how does the inhibitor bind to the enzyme in a bisubstrate rxn inhibitor binds to the same site as H2F (if NADPH is held constant and H2F is varied) if NADPH is varied and H2F is held constant, how does the inhibiotr behaveas an uncompetitve inhbitor of NADPH, (inhbitor must bind to an alternate site to NADPH), NADPH can also be only bound to ES before the inhibitor can bind  substrate analogs/ transition state analogs small molecules that are reversible enzme inhibitors, it resemebles the normal enzyme substrate in structure and makes similar interactions w the enzyme  what do transition state analogs typically structrally resemble and why does this make it a good inhibitor the transition state, bc enzymes with the highest affinity to the transition state  irreversible inhibitor an inhibitor that covalently modifies an active site residue to inactive the enzyme (can be classifiyed as a substrate analog) ex of a famous irreverisble inhibiotr and how it fucntionspenicillin, inhibits crosslinking of the bacetrial cell wall by resembling the d-ala stem peptide that is attacked by a nucleophilic ser, so it is considered a substrate analog  why is acylation of the enzyme favorable in penicillin mechanism it occurs with opening of the 4 membered beta lactam ring, an ester and is resistant to hydrolysis  ex of a transition state analog that acts by irreversible inhibitionsarin gas becase it covalenelty inhibts acetylcholine esterase, phosphate group resembles the tetrahedral intermediate that forms in normal hydrolyusis of acetylcholine  mechanism based inhibitorsirreversible inhbitors that are highly specgic, unlike normal irreversible inhibitors . they unmask a reactive group during the course of the normal enzyme reaction mechanism  beta fluroalanine  and how it works a mechanism based inhibitor of alananine racemase, acts as a normal substrate in the first few steps of the rxn mechanism, and creates a resultiing elctorphilic intermediate which covalently reacts with a nucelophilic residue in the active site

biochem 270 anki convert

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