Review Sheet for BIOL 600 at KU
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Date Created: 02/06/15
Biol 600 Intro Biochemistry Fall 2005 Practice Questions and Answers for Quiz 2 7 1 7 1 Which amino acids can be a general acid OR a general base between pH 6 to 7 a His is the most obvious Since it has a pKa in this range it can reversiny donate and accept protons 2 Which amino acid functional groups can not function either as a general acid and a general base at a single pH under the appropriate conditions not simultaneously a Any of the non ionizable sidechains b In fact any sidechain which acts as a general acid or base must also regenerate itself by acting as a general base or acid The carboxylates Asp amp Glu can function as proton donors or acceptors at different steps of the same reaction as they do in the ysozyme reaction You know that His displays this ability in the chymotrpsin reaction 3 Which types of amino acids could NOT stabilize the oxyanion transition state of chymotrypsin a Those which are neither positively charged nor H bond donors all but Lys Arg Asn Gln His Ser and THr and most likely Tyr 4 Give an example of the quotInduced Fitquot model of substrate binding a The only protein we39ve mentioned which operates like this is adenylate kinase in which part of the enzyme a quot apquot region folds to cover the active sites after binding the substrate ATP 5 The catalytic mechanism of Lysozyme provides evidence for is an example of which model of enzyme action a Lysozyme39s mechanism provides a good example of the quotLock and Keyquot model Variations on this model are referred to as quotsteric guidance orbital steeringquot and quotentropic constraintquot 6 In the mechanism of a thiol protease a peptide bondhydrolyzing enzyme whose reactive amino acid is cysteine rather than serine which of the following are true can ha en a The attacking nucleophile is S b The nucleophile will attack a carbonyl oxygen ltltNO but The nucleophile will attack a carbonyl carbon c There cannot be a covalent enzymeeproduct intermediate lt Sure there can just like serine proteases esterases d The carbonyl group will be the leaving group lt No the amine or alcohol group R2 leaves e The thiol group must be deprotonated by a general acid ltSay what Acids give not receive protons 7 Which of the following is Impossible when an enzyme catalyzes a biochemical reaction a increase the rate constant for reaching equilibrium between substrate and product b shift the reaction equilibrium to favor product rather than substrate lt Yes even in Kansas we have so far no violations of the laws of thermodynamics use a chemical mechanism not found in the uncatalyzed reaction lower the free energy of the transition state reduce the rate constant for reaching equilibrium between substrate and product destabilize the transition state This would make the reaction more difficult not less raise the free energy of the ground state the conformation of the free substrate before it binds to the enzyme lt Same as f above Wong 0 Biol 6001ntro Biochemistry Fall 2005 Practice Questions and Answers for Quiz 2 7 2 7 8 A serine protease such as chymottypsin uses an activesite serine residue as the attacking nucleophile The serine is activated a when an adjacent His residue accepts a proton from the serine hydroxyl group b when the adjacent His sidechain is deprotonated by an Asp residue c by transferring its proton to an aspartate via the adjacent histidine d because the aliphatic alcohol moiety of serine is readily deprotonated at neutral pH 9 Some hydrolytic enzymes like lysozyme apparently bind their substrate in a quotstrainedquot conformation that increases the rate of bond breakage at the correct place in the substrate This confonnation is called a the conversion stage b the round state c the transition state l d the product release step 10 The glutamate sidechain CH2CH2COO if present in an enzyme39s active site can readily do all but which of the following a Stabilize a positivelyecharged transition state b Act as an attacking nucleophile in covalent catalysis c Act as a general acid catalyst ltlt Since the sidechain is DEprotonated it can39t be an acid I d Act as a general base catalyst 11 Lysozyme is able to bind one residue of its substrate in a strained conformation because a This conformation is more unstable so it has a lower free energy than the unstrained substrate b The energetic quotcostquot of forcing one residue to bind in an high energy conformation is more than made up by the decrease in free energy when adjacent residues bind snugly to the enzyme39s active site c The multiple hydrogenebond and Van der Waal39s interactions between enzyme and substrate are thermodynamically unfavorable lt They reduce the free energy of the enzymesubstrate system so they are favorable d The strained conformation is more stable so it has more time to bind to the active site 12 Understand how the pKa of a catalytic amino acid sidechain can be altered by the properties of neighboring amino acids ie the quotlocal microenvironmentquot a Consider deprotonation of an acid COOH gt COOquot H An environment with many polar groups offers many opportunities for bonding hence stabilizing the charged species that result from deprotonation This makes it quoteasierquot for the acid to deprotonate it will release its proton at a lower pH that it would have otherwise In other words the acids pKa will be lowered Conversely a binding pocket or active site with mostly hydrophobic sidechains will have few groups able to make ionic or H bonds with the dissociated COOquot and HT This makes it energetically unfavorable for the acid COOH to dissociate a higher pH will be required to pull the proton off In other words the acids pKa will increase 13 Understand the role of an enzyme39s active site in creating an anhydrous environment for watersensitive chemical reactions a If the reaction intermediates are labile or readily attacked by water the enzyme can eliminate competing side reactions by excluding water from the active site As in the adenylate kinase reaction the enzyme s active site can rearrange after binding substrates to a quotclosedquot conformation which blocks the entry of water Biol 600 Intro Biochemistry Fall 2005 Practice Questions and Answers for Quiz 2 7 3 7 14 Understand the meaning of enzyme quotkineticsquot It39s not just how fast the enzyme catalyzes a reaction it refers to the dependence of reaction rate Q substrate concentration and hence the way reaction rate changes over time a This is just a defin onsuggestion for a good way to think about quotkineticsquot 15 What three assumptions are suf cient to establish the MichaelisMenton model of enzyme kinetics a Substrate must bind to the enzyme in order for the reaction to occur Binding is simple and follows the law of mass action resulting in a saturable binding isotherm An individual enzyme molecule has only two reaction rates IOO when substrate is bound and 0 when substrate is not bound The reaction can be examined at a very early time when the substrate concentration is effectively constant 16 What are the meanings of the enzyme kinetic constants quotkmquot and quotmequot a kcat is the apparent first order rate constant in secquot for conversion of the E S complex to free E and P This is also known as the turnover number the number of substrate molecules converted to product per unit time per individual enzyme molecule me is the rate in Msquot at which a solution of enzyme molecules performs its reaction Numerically Vmax kmE E is expressed in molar units 17 The best de nition of the Michaelis constant KM is a The binding af nity of enzyme for substrate b The dissociation constant of the E78 complex lt This is true only when the rate constant for catalysis km is much slower than the rate constant for dissociation k c The ratio of the rate at which the E S complex breaks down to the rate at which it forms d the ratio of substrate binding rate to product release rate 18 Some hydrolytic enzymes like lysozyme apparently bind their substrate in a quotstrainedquot conformation that increases the rate of bond breakage This conformation is called a the conversion stage b the ground state ltThis is the conformation of the substrate free in solution before binding to enz me c the transition state d the product release step e the active site
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