Introd Biochemistry, Lectures
Introd Biochemistry, Lectures BIOL 600
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This 8 page Class Notes was uploaded by Kadin Bartoletti DVM on Monday September 7, 2015. The Class Notes belongs to BIOL 600 at Kansas taught by Staff in Fall. Since its upload, it has received 18 views. For similar materials see /class/182428/biol-600-kansas in Biology at Kansas.
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Date Created: 09/07/15
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 J general base at a single pH under the l l l 39 39 39 not 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 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 4 Give an example of the quotInduced Fitquot model of substrate binding 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 P a The attacking nucleophile is S b The 1 quot 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 increase the rate constant for reachin equilibrium between substrate and product in 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 Pronto0 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 ll 53 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 the transition stat 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 I 1 quot in covalent catalysis c Act as a general acid catalyst ltlt Since the sidechain is DEprotonated it can39t be an acid P Act as a general base catalyst 11 Lysozyme is able to bind one residue of its substrate in a strained conformation because a This I 39 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 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 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 o P 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 definitionsuggestion for a good way to think about quotkineticsquot h 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 b An individual enzyme molecule has only two reaction rates IOO when substrate is bound and 0 when substrate is not bound c The reaction can be examined at a very early time when the substrate concentration is effectively constant 16 What are the 39 g of the enzyme kinetic cons quotkmquot and quotmequot a kw 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 ll 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 39 d the product release step e the active site Biol 600 Intro Biochemistry Practice Questions for Quiz 3 H P L 4 U1 Q Which one of the following groups is suf cient to make a phosphoglyceride two fatty acids glycerol and ascorbate E doesn39t have phosphate or an amino acid head group 53 glyceroliliphosphate serine and two molecules ofpalmitate just what we need to make a phosphatidate and add an amino acid to it sphingosine myelin and sarcosine E If you don39t recognize these you can bet they39re not right ea glyceroliliphosphate 2 molecules ofoleate and sarcosine E has everything but the amino acid Which statement about the CaATPase is false 3 it can diffuse laterally in the plane ofthe membrane true lateral or sidetoside diffusion is an explicit feature of the Fluid Mosaic Model which we discussed 5 its transmembrane domain consists of 7 alpha helices with hydrophobic residues facing the lipid bilayer and hydrophilic residues facing the interior of the ion channel IZl The helices m have hydrophobic residues on the outside in order to be soluble in the membrane ie to interact favorably with the hydrophobic membrane lipids This is not a soluble protein in which the helices would be hydrophilic polar on the outside Which one of the following statements is false 3 glucose and mannose are epimers ofeach other whereas ociDiglucose and iDiglucose are anomers ofeach other EThis is true ribulo se is a keto se related structurally to dihydroxyacetone whereas ribose is an aldose related to glyceraldehyde E This is true you know that glyceraldehyde is the minimal aldose and you know ribose is one of the few aldoses I asked you to learn 5 c Difructose adopts the furanose ring conformation whereas Diglucose is a pyranose E Also true You learned these structures d Polysaccharides can be formed only Via 0L7 14 glycosidic bonds E False You know that there are several important di and polysaccharides which are l4 linkages you should also remember that there are 2 and 6 bonds As a result of which structural difference between glucose and fructose can phosphorylated glucose or phosphofructose but not both do the following in glycolysis a glucose adopts a cyclic structure in solution whereas fructose remains an open linear chain E No you know these are both ring structures b the structural symmetry of fructose allows it to be doubly phosphorylated and then split into two triose phosphates during glycolysis IZl Yes The hexose must be symmetrical in order for it to be cleaved into two similar trioses GA3P and DHAP c they are anomers at C1 of each other E This isn39t possible they don39t both have the same ring structure Under anaerobic or oxygen deficit conditions in glycolysis a ATP and NADJr molecules used up in the quotpreparationquot stage ofglycolysis are always regenerated in the quotpayoffquot phase Z No NAD is regenerated only under aerobic conditions b NADJr is regenerated when NADH reduces pyruVate in the lactate dehydrogenase reaction IZl Exactly Anaerobic glycolysis can produce lactate reversibly Other products are possible such as ethanol formed irreversibly c All cellular metabolism comes to a halt Z You know this cannot be possible in the shortterm conditions we discussed In fact the liver continues to convert lactate into glucose d Glycolysis is inhibited but gluconeogenesis proceeds E LOW energy levels a low energy charge Will stimulate glycolysis in order to increase the cell39s energy charge Gluconeogenesis will be inhibited because it consumes ATP and NADPH hence reducing the energy charge If a muscle cell has a low energy charge the glycolytic pathway will be i a activated because the low concentration of ATP relieves inhibition of PyruVate Kinase and Phosphofructokinase Yes A low energy charge stimulates energyproducing pathways and a high energy charge inhibits them Here both PK and PFK are inhibited by ATP Biol 600 Intro Biochemistry Practice Questions for Quiz 3 g m D H b inhibited because the low concentration of ATP inhibits Pyruvate Kinase and Phosphofructokinase E No this is the opposite of what happens c inhibited by fructoseil67bisphosphate and by fru7267bisphosphate Both these compounds stimulate glycolysis frul6P2 at PK and fruZ6P2 at PFK d activated by high concentrations of citrate E No this activates gluconeogenesis and inhibits glycolysis Which of the following is the correct relationship between anabolic and catabolic processes a anabolism stores potential energy chemical potential and reducing potential in reduced carbon compounds whereas catabolism releases energy in the form ofheat from reduced carbon compounds E Unfortunately this isn39t correct The description of anabolism is OK but the description of catabolism suggests that all the energy from oxidation of food is wasted given off as heat rather than conserved as ATP and NADPH b catabolism is an oxidative process that extracts energy from reduced carbon compounds and stores it in ATP and NADH anabolism transfers the potential energy ofATP and NADPH to reduced carbon compounds IZl Good Glycolysis proceeds in the direction of pyruvate formation because each step by itself is energetically favorable E Some ofthe steps are unfavorable 1 1 1 53 the unfavorable energy ofconverting l L 1 1 the negative AGO 39 for hydrolysis of PEP lZl Exactly so the pathway is quotpushed forwardquot by the energyiyielding step of glucose767P formation M This step is also one which puts energy into the pathway However see the reservation in l 0 a below 91 11 to 1 1 is more than compensated by Q d most of the reaction steps are phosphoryl transfers E Although many steps are ptransfers only a few are transfers from ATP which are strongly exergonic energyyielding or essentially irreversible and can drive the pathway The others are intramolecular transfers which have a very low free energy change ATP is said to be a quothigh energyquot compound because a it releases energy when combusted in a bomb calorimeter E True but irrelevant so does glucose This energy comes from total combustion of the entire molecule The useful quotenergyquot stored in ATP is different b the terminal phosphoryl group of ATP is in an excited state E Not true c the terminal phosphoryl group is highly reactive E No the terminal P isn39t very reactive unless acted on by a catalyst d it possesses a very negative free energy for transfer ofthe terminal phosphoryl group to another acceptor M Yes the phosphoryl is readily transferred to an acceptor Transfer to alcoholic or acidic oXygens or to certain amines relieves the unfavorable interactions between adjacent phosphates in ATP In a multistep biochemical pathway such as glycolysis which one of the following would not be a likely regulatory step a triose phosphate isomerase M This reaction is relatively reversible and it controls an input to glycolysis if you blocked TPI glycolysis would still continue at V2 the normal rate so it39s not a good candidate for regulation b hexokinase E Hexokinase is relatively irreversible and in muscle cells it traps glucose within the cell thus committing it to one of several metabolic fates Because it39s not a a step exclusively of glycolysis it isn39t a speci c regulatory step of glycolysis c pyruvate kinase E This is an essentially irreversible step so it39s a good point for control d glyceraldehyde 37pho sphate dehydrogenase IZlAlso a step with a low free energy change hence relatively and not a good choice for regulation Biol 600 lntro Biochemistry Sample test with Answers for Quiz 1 KUID 1234567 7 l 7 Please answer the following questions You will nut need a calculator You may assume that 90 ionization is equivalent to full charge Note 1 Mg ark Jame quextzb x r whitUm tannat wake yer mxuwptzb A CHEMICAL BONDS IONIZATION AMINO ACID FUNCTIONAL GROUPS 1 P L CocaCola contains phosphoric acid syrup as a stomach soother Suppose Coke is 10 mM phosphoric acid and 100 leI monobasic sodium phosphate If the pILs of phosphoric acid are 2 7 and 12 what is the pH of Coke You should be able to gure out that the ionization sequence is H3P04 HZPOAquot HPOAZquot POA3 You can do the math in your head a 175 b 20 c 30 gtgt The pKa for the ionization of phosphoric acid quotAHquot to monobasic singlydeprotonated phosphate quotAquot is given as 20 The ratio of AH to A is 000 Using the rule of thumb the phosphoric acid is 0000 1 IO protonated We know that if protonation is less than 50 pH must be higher than pKa Since a IOfold change in protonation means a pH change of IO the pH of Coke must be 2 3 Check Using the HendersonHasselbalch equation pHpKa log AIAH so pH20 log I00I0 20 IogIO 20 IO 30 d 44 Apair of amino acids that could interact by electrostatic bonding is a Leu 77 He c Asp Asn d Lys 77 Gln At pH 9 which of the following amino acid side chains will have a net negative charge a Tyr pH is about below pKa so will be 90 protonated Charge 0 b Cys pH is above pKa hence 90 deprotonated Charge 09 2 Best answer c His pH is 3 above pKa hence 999 deprotonated Charge z 0 d Lys pH is 35 below pKa so will be gt999 o protonated Charge 0 The amino acid shown at the right is NHa a Leu b lle 000 K Me i d Ala Me The amino acid containing a single imidazole ring is Biol 600 lntro Biochemistry Sample test with Answers for Quiz 1 KUID 1234567 7 2 7 Q g m Which amino acid sidechains would you expect to be least common on the surface ofa soluble protein and most common in the interior a Cys Thr Cys is mixed polarity Thr is moderately polar b Asp Arg Polar and charged c Ala Val gtgt Hydrophobic amino acids tend to pack together within the interior of a folded Proteins start to fold up in a cell even while they are being synthesized When polypeptides are synthesized at a very rapid rate and very high concentrations they often aggregate into insoluble clumps This happens because the interior hydrophobic residues ofpolypeptides polypeptide Hydrophilc or chareged side chains are most common near the exterior d Gin Asn Fairly polar a bind cell L and aren39t released b bind the interior residues of adjacent polypeptides before they can finish folding up gtgt You know that proteins tend to fold with hydrophobic residues in the interior and that this folding is driven by the Van der Waal39s interactions between hydrophobic residues Hence you shouldn39t be surprised if two adjacent polypeptides folded up the same way You aren39t expected to know the answer in advance rather you should recognize that it makes more sense in terms of what you39ve learned so far than the others c must interact with macromolecular complexes called chaperones in order to fold properly d make many shortirange interactions instead ofa few longirange ones Which of the following statement about u heliX and isheet structures is not true a The sidechains project outwards from each structure b They are stabilized by hydrogen bonding between backbone amide and carbonyl groups c The whelix is partly stabilized by interactions between adjacent amino acid sidechains whereas the Bsheet is not gtgt In some instances adjacent sidechains in a helix might interact but this is not a general feature of the uhelix itself d The aeheljx is formed from a single chain whereas the isheet requires at least two adjacent chains Addition of 1 to 2 M ammonium sulfate NH4ZSO4 giving 2 to 4 M anunonium ion to a solution of protein often causes the protein to precipitate The most likely reason for this is that a The polarity of the solvent is increased so the proteins have stronger electrostatic attractions to each other b Water molecules must reorient to interact with the ammonium and sulfate ions leaving fewer waters available to solvate bind to the protein gtgt With fewer water molecules available to Hbond with polar groups on the protein39s surface the polar groups on one protein molecule are more likely to interact with polar groups on the surface of another protein When two proteins quotbump intoquot each other they stay associated More proteins coalesce Since these protein aggregates aren39t bonding much with water they become insoluble lnA other words the polarity of the solution is reduced so polar molecules tend to aggregate with each other just as a few water droplets in oil would merge There are several ways to alter the polarity of a solution of which salt addition is the most common in biochemistry El You are not expected to quotknowquot the answer but to recognize it as an application of a principle you39ve learned c The polarity of the solvent is increased so the proteins have stronger Van der Waals interactions with each other gtgtAddition of salt decreases the polarity of water If the polarity were increased this answer wou d be correct d The electrostatic interaction between adjacent proteins is reduced causing them to fall out of solution Biol 600 Intro Biochemistry Sample test with Answers for Quiz 1 KUID 1234567 3 10 The neurotransmitter serotonin pictured at right is derived from which amino acid a Pro b Thr ECHECHENHS c Trp gtgt It39s the only AA with this double ring structure d Tyr REVIEW For these topics you must know Structure of all normal amino acids Emphasis on the different types of side chains aliphatic aromatic etc and the different chemical properties of the side chains You must know the pKa of every ionizable sidechain to the nearest 05 pH eg 83 could be quotabout 85quot 109 would be quotabout 11quot You won39t have to do Henderson Hasselbalch pH calculations but you must know the quotrule of thumbquot I went over this in class Thursday You must be able to deduce the fractional ionization given the pKa and the actual pH and deduce the pKa given the ionization and the observed pH B PROTEIN STRUCTURE 1 When polypeptide chains start to fold up they rst form alphahelices and betasheets These structures form readily and contain many different amino acids with widelyvarying sidechain properties because a The sidechains project outwards from each structure They are stabilized by hydrogen bonding between backbone amide and carbonyl groups rather than between speci c sidechains gtgt Yes this is why they can accommodate diverse sidechains c The OL heliX is stabilized by interactions between adjacent amino acid sidechains whereas the Bsheet is not d The OL heliX is formed from a single chain whereas the B sheet requires at least two adjacent chains The pair of amino acids at the right is from left to right a Thr Met 0 gtgt b Ala Ser C gt Leu Ile e Ala Gly REVIEW Questions on protein structure will cover Primary Secondary Tertiary and Quaternary structure Be able to describe the properties of the peptide bond the important structural features of ahelices sheets and IBturns NOTE both sheets AND turns have H bonds spaced 4 residues apart not 3 as shown on the overhead Be able to predict what side chains would be on the exterior vs interior of a soluble protein or of a protein embedded in a membrane Be able to describe how tertiary structure domains are formed from secondary structural elements Know the kinds of forces which hold together tertiary and quaternary structures
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