INTRODUCT BIOCHEM BCMB 3100
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Date Created: 09/12/15
EV E 13 Pquot 0 BIOCHEMISTRY TEST ONE REVIEW a Functional i Primary basis of organization Cell a Eukaryotes membrane another organizational basis bound organelles notdiffusion based b Prokaryotes Another organizational factor Water content a Characteristics electronegativity difference is crucial i Produces H bonds which makes water cohesive molecules uctuate positions ii Polar subsmnces are solvated quot lonic substance are hydrated Noncovalent Interactions a Electrostatic interactions attractive or repulsive Salt bonds influenced by the dielectric consmnt aka chargercharge ii H bonds weaker influenced by composition with water iii Van der Waals no effect occur between any two atoms universal and low energy iv Hydrophobic Weakest produces quot micelles L b Thermodynamic Depends on the H20 being high Hydrophobic Weakest produces detergent iii Association of quotamphipathicquot subsmnces which have both polar hydrophilic and nonpolar hydrophobic components Ionization of water slight but produces variable aciditybasicity a quotbufferingquot of cellular contents is crucia b HendersonrHasselbalch Equation comes into play Conjugate base acceptar pH pK 10910 canjugate acid donor Proteins essential feature is ligand binding functional basis a mino acids measure of hydrophobicity A dnramann quot micelles L quot ex HYD ROPHOBIC I I FVLM LESS HYDROPHOBIC IWAGCYPTS HYDROPHILIC IHENQDKR and pK approximates i Fibrous strong insoluble in water ii Globular most proteins compact and water soluble have hydrophilic residues and surfaces iii Membrane proteins hydrophilic surfaces and dry interiors d Determination of folding partly from steric effects ofside chains double bond character ofthe peptide bond is due to the electronegativity differences ofthe atoms e Levels ofstructure i Primary simple amino acid sequence disulfide bonds ii Secondary regularly repeating structure on helixes andB sheets that make motifs 1 Supersecondary domains coded by exons iii Tertiary overall 3D structure iv Quaternary final structure v Anfisen Experiment Protein structure is most favorable thermodynamically disulfides form AFTER folding Purification and Analysis a Analysis size and amphoteric character ligand binding i Requires specific identifyingproperty assay and good starting material ii Types ofanalysis 1 Reversephase llPLC also called filtration hydrophobic interactions peptide separation procedure larger units move through the column faster 2 SDSgel electrophoresis and PAGE separationby effective size subunit molecular weight used to obtain subunit molecular weight criterion ofpurity PAGE is more common b Sequencing Chemical slower must produce fragments specific ii DNA sequence need some sequence information to start gain amino acid composition 1 Edman degredation cleaves terminal acid with PITll forms PTll can39t have more than 5060 mino acids c nzymatic Cleavage 51 1 Tryp n ii Chymotrypsin serine protease FWY LIV lower rate iii V8 protease D E d Uses ofsequencing comparisons i Evolutionary basis 1 Proteins families Taxonomic analysis different sequences for different families ii Structure globular proteins are tightly packe 1 Can use Xray electron density or NMRwith concentrated solutions quaternary Structu re quaterna ry structu re of O 1 CD and 23 BPG a group i Fezt in heme must be kept reduced one function ofproteins quotglobinsquot 9 1 Globins are a family of proteins n 39 bond b Subunits L M a structure ii Hemoglobin m identically out a ociate packing ofpepetide chains 2 Binding om 39 39 u 39 7 RPG co 1 3 Hemoglobin assists in ca transport backto the lungs nzym a Classification 39 Xidoreduc 0 tases catalyze electron tmns e Transferases chemical gr r r oups from one substrate to another 1 Hydrolases add water breaking bonds iv Lyases make double bonds v lsomerases vi Ligases join two substrates b Measurement reactio c Kinetics rate of change in concentration Versus time i ES9EP ii Start substrate concentration dependence 1 Get Michaelierenten pammeters u 3 5 030 2 025 E 020 5 r g 015 010 o as 000 I t t a mob 2000 3000 4000 Substrate concentration a 39 39 b Vmax how fast reaction can go enzyme c d Km What substrate concentration gives half that Value e K3 is oftenthe slowest step k a k E S E S a E P k 2 Km k2 k3 overal rate ofloss ofsubstrate E complex kJ overall rate of gain o k ETutnl N LineweaverrBurk plots 3 slgnl cance a J product per second per mole ofenzyme b Km otten near the Kn 39 I l 4 l c ata saturated substrate level 1 my Tme specl cactwlty e 392 I Hm r the rate n l 39 L r l m 21m a graph th 2 leS kzk3 f 127 51 311de e k showthe relatlonshlp to Km 12 V ls rst order and llnear dependable d Inhlbltlon L I I u Reversableb dllutlon T e Bindsm vmx competltlve I E I lncrease I none I noncom etrtlye EorES none I reduced uncDmEetmve ES reduced reduced lu ineweaverrBurkplots are very dlstlnctlye Panel A Panel B Plus mmDEDLlVE lnhlblmr IN MI Unlnhlllli d Enzyme WM unmmmlen enzyme 13931 Wis Panel 0 plus mntompellm lnmnllu Panel D vlux untampautlva lnmhlmr unlnnlolreu ermme Ul llrlhlbltE enzyme 13 IS Control of Enz mes l Concentratlon control covalent bonds are involved 1 Exam 1e 2 ogens secreted enzymes secreted aslnactlve 2 syntheSlsdegredatlon Vla genetlc control modlflcatlon covalent u Kigicontrol l Feedbackllke mmpetltlve lnhlbltlon 2 quotmodulatorsquot enzyme 3 Isozymes 4 39 Enzyme mechanrsms mnree ten r e i Transition states 1 Substitutions a Nucleophilic substitution 7 sxarnng maxenms r acumen complexi r producxs 7 339 539 i Nut 7gt C L 7 Nur39VCVVVL lt7 Nuic 7 L l l b Direct displacement CHJI CHJ I s 2 Cleavage Carbanion formed RaCY 9 RaC39 Y b Carbonium ion RaCX 9 R3C x c Free radicals produced very reactive products ROOR9RO39 OR 3 OxidationReduction a Re uctant donates e39 and becomes oxidized b Oxidant accepts e39and becomes reduced remember when it becomes reduced that the oxidation number DECREASES ii Types 1 Polar residues in active sites involved in H transferbonding hydrophobichydrophilic environment can strongly affect ionic 2 Acidbase catalysis ll both acid andbase 3 Covalent catalysis Possible to isolate intermediate b About 20 ofenzymes use this 4 pH effects a Interactions between groups can affect pKvalues b Lysozyme charge separation disfavored bylaw dielectric constant 02m 1m Huang micw 10 Diffusion controlled reactions a K1 is limiting not K3 unable to see the saturation effect i Therefore since you can39t saturate there is no Vmax and you cannot show the MichaelisMenten kinetics 11 Modes of catalysis quantitative enzymology Chemical provides a rate enhancement but not a great increase 101 orZfold i Acid base ii Covalent b Binding i Proximity effect increases the effective reactant concentrations ES effect Brewer Test 2 Study Guide Questions from Previous Exams March 2010 1 FAD stand for a Flavin adenine dinucleotide Composed of 2 nucleotides joined each having an organic base connected to a sugar ribose and a phosphate 2 Matching a FADubiquinone semiquinone readily forms free radical one electrontwo electron junction b Ribo avin adenine dinucleotide one e2 e rxns c Pyridoxal phosphate transamination Schiff base d Vitamin a Schiff base e Thiamin pyrophosphate thiamine oxidative decarboxlyase two carbon ketose transfer active aldehyde beriberi f Vitamin e antioxidant alpha tocopherol g Niacin NAD hydride transfer 2 electron transfer pellagra h Biotin 1 carbon transfer carboxyl group transfer carboxylation avidin i Vitamin k 1 carbon transfer carboxylation phylloquinone gamma carboxyglutamate synthesis j 812 1 carbon transfer methyl transfer methionine biosynthesis k Folic acid 1 carbon transfer Lipoic acid acyl group transfer CoA thiol containing high energy bond 4 U1 Ch 1 9 For the reactions occurring at constant changes in are equal to changes in a Pressure enthalpy heat content The gibbs free energy is considered a state function what does this mean a Value depends only on the initial state the final state is independent ofthe path What is the effect on the following phenomena accompanying the reaction a Increased electron localization or products i Lower delta G b Increaded hydration of products i Increased delta G c Greater or more extensive resonance in products i Increased delta G What structural feature of cellobiose makes it undigestible by humans a The beta 14 link cannot be hydrolyzed by human enzymes Write the names of the substrates and products of the reactions of glycolysis that are regulated Include all cofactors a Glucose ATP Mg2 9 glucose 6 phosphate ADP Mg2 b Fructose 6 phosphate ATP Mg2 9 fructose 16 bisphosphate c Phosphoenolpyruvate ADP Mg2 9 pyruvate ATP Mg2 Write reactions including cofactors of the reactions of gluconeogenesis that are regulated a Pyruvate C02 HCO3 ATP Mg2 9 ADP Mg2 HPO42 H20 oxaloacetate b Oxaloacetate GDP ATP 9 C02 phosphoenolpyruvate c Fructose 16 bisphosphate H20 9 HPO42 fructose 6 phosphate d Glucose 6 phosphate H20 9 HPO42 glucose 9 Give names of enzymes controlling the ratelimiting step in glycolysis Give two substances that activate that enzyme a PFK1 b Activators AMP fructose 26 bisphosphate 10 Substance that limits the rate of the initial part of the pentose phosphate pathway a NADP 11 Describe how blood glucose concentration controls glycogen metabolism a Pg 378 12 Free energy of hydrolysis ofATP is high 3 reasons a electrostatic repulsion bw phosphoryl oxygen s b Mg2 preferentially bind to ADP c Products ADP Pi are more heavily solvated than ATP d Products have more resonance forms than ATP 13 convert sugars to glycolytic intermediates a mannose ATP 9 ADP mannose 6phosphate 9 fructose 6P b fructose ATP 9 ADP fructose 1P 9 DHAP GA3P c galactose ATP 9 ADP galactose 1P 14 four reactions that use ATP in glycolysis a glucose ATP 9 Glucose 6P ADP b fructose6P ATP 9 fructose 16bisP ADP c 13 bisphosphoglycerate ADP 9 3 bisphosphoglycerate ATP d phosphoenolpyruvate ADP 9 pyruvate ATP 15 reactions of enzymes which reduce NAD and oxidize NADH during anaerobic glycolysis in muscle a glyceraldehyde3P NAD Pi 9 NADH H 13bisphosphoglycerate b pyruvate NADH 9 Lactate NAD c acetylaldehyde NADH H 9 ethanol NAD 16 overall reaction for glycolysis aerobic and anaerobic a glucose 2ADP 2Pi 2NAD 9 2pyruvate 2ATP 2NADH 2H20 2H b glucose 2ADP 2 Pi 9 2 lactate 2ATP 2 H20 17 phosphoenolpyruvate has a very high free energy of hydrolysis why a Hydrolysis produces enolpyruvate which isomerizes to pyruvate the free energy of the isomerization is great and adds to the actual hydrolysis free energy 18 Most common cofactor a Mg2 19 Binding ofions to proteins in water solution is entropy driven a The ion and whatever charged or polar groups it binds to are hydrated and on binding some of the bound water molecules are released producing an increase in entropy 20 Hydrolysis of terminal phosphoryl of ATP is accompanied by a negative free energy change of73 give 2 reasons a Electrostatic repulsion bw negatively charged oxygen s is reduced on hydrolysis b ADP and inorganic phosphate are more solvated than ATP 2 1 Hydrolysis of acetyl CoA is also large free energy change Chemical factor a The hydrolysis produces acetic acid which at pH 7 ionizes to acetate The ionization free energy contributes to the overall free energy 22 Overall equations for the isomerase rxns in glycolysis a Glucose 6P 9 fructose 6P b Glyceraldehyde 3P 9 dihydroxyacetone phosphate 23 Complete reactions which form NADH and FADH2 in citric acid cycle a Isocitrate NAD 9 alphaketoglutarate NADH C02 H b Alphaketoglutarate CoASH NAD 9 Succinyl CoA C02 NADH H c Malate NAD 9 oxaloacetate NADH H d Succinate FAD 9 fumarate FADH2 24 Pyruvate to acetyl CoA a Pyruvate CoA NAD 9 acetyl CoA C02 NADH H 25 Compounds in citric acid from carb and protein a fed glucose i pyruvate C02 ATP 9 oxaloacetate ADP Pi b starving Protein i alanine 9 pyruvate ii glutamate 9 alphaketoglutarate iii asparase 9 oxaloacetate 26 Citric Acid cycle function a to oxidize acetyl CoA to 2C02 and generate reducing equivalents in the form of NADH and FADHZ 27 reactions catalyzed by glucose 6P dehydrogenase 6phosphogluconate dehydrogenase transketolase and transaldolase 3 functions ofpentose phosphate pathway a NADP glucose6P 9 G6P dehy NADPH H 6phosphogluconolactone b NADP 6Phosphogluconate 9 NADH H C02 ribulose5P c Xylulose5P ribose5P 9 transketolase sedoheptulose7P glyceraldehyde 3P d Xylulose5P erythrose4P 9 transketolase fructose6P glyceraldehyde 3P e Sedoheptulose7P glyceraldehyde3P 9 transaldolase fructose6P f Generate reducing equivalents such as NADPH BCMB 3100 Exam 1 Worksheet 2 Aromatic 39 39 l 39 39 39 STRUCTURE NAME full 3 letter 1 letter l AliEhatic Amino Acids CTURE STRU NAME full 3 letter 1 letter 3 Aromatic hxdrophilic STRUCTURE NAME full 3 letter 1 letter