Review Sheet for BIOL 600 at KU 2
Popular in Course
Popular in Department
This 3 page Class Notes was uploaded by an elite notetaker on Friday February 6, 2015. The Class Notes belongs to a course at Kansas taught by a professor in Fall. Since its upload, it has received 18 views.
Reviews for Review Sheet for BIOL 600 at KU 2
Report this Material
What is Karma?
Karma is the currency of StudySoup.
Date Created: 02/06/15
Biol 600 Intro Biochemistry Sample test with Answers for Quiz 1 KUID 1234567 7 1 7 Please answer the following questions You will nut need a calculator You may assume that 90 ionization is equivalent to full charge Note I wry ark Jame quextzb x r whitUm tannat wake yer mxuwptzb A CHEMICAL BONDS IONIZATION AMINO ACID FUNCTIONAL GROUPS 1 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 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 0 the pH of Coke must be 2 3 Check Using the HendersonHasselbalch equation pHpKa log AIAH so pH20 log I00I0 20 IogIO 20 0 30 d 44 2 Apair of amino acids that could interact by electrostatic bonding is a Leu 77 Ile b Arg Asp c Asp Asn d Lys 77 Gln 3 At pH 9 which of the following amino acid side chains will have a net negative charge Tyr pH is about below pKa so will be 90 protonated Charge 0 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 4 The amino acid shown at the right is Ms a Leu b Ile 000 K Me i d Ala Me 5 The amino acid containing a single imidazole ring is a Pro b Phe d Trp e Tyr Biol 6001ntro Biochemistry Sample test with Answers for Quiz 1 KUID 1234567 7 2 7 6 Which amino acid sidechains would you expect to be leist common on the surface ofa soluble protein and st common in the interior a Cys Thr Cys is mixed polarity Thr is moderately polar b Asp Arg Polar and charged Ala Val gtgt Hydrophobic amino acids tend to pack together within the interior of a folded polypeptide Hydrophilc or chareged side chains are most common near the exterior d Gln Asn Fairly polar 7 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 of polypeptides a bind cell membranes 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 shorterange interactions instead ofa few longerange ones 8 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 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 esheet requires at least two adjacent chains 9 Addition of 1 to 2 M ammonium sulfate NH4ZSO4 giving 2 to 4 M amInonium 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 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 intoll 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 increasedl 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 ECHECHENHE b Thr c Trp gtgt It39s the only AA with this double ring structure l H d Tyr REVIEW For these topics you must know 0 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 sheet is not d The OL heliX is formed from a single chain whereas the B sheet requires at least two adjacent chains 2 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 0 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