lehninger principles of biochemistry test bank 6e ch03

7/25/2019 Lehninger Principles Of Biochemistry Test Bank 6e Ch03

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Chapter 3 Amino Acids, Peptides, and Proteins


Multiple Choice Questions

1. Amino acids

Page: 72 Difficulty: 1 Ans: C

The chirality of an amino acid results from the fact that its carbon:

A) has no net charge.

B) is a carboxylic acid.

C) is bonded to four different chemical groups.

D) is in the Labsolute configuration in naturally occurring proteins.

E) is symmetric.

2. Amino acids

Page: 72 Difficulty: 2 Ans: f the !" standard amino acids# only $$$$$$$$$$$ is not optically acti%e. The reason is that its side

chain $$$$$$$$$$$.

A) alanine& is a simple methyl group

B) glycine& is a hydrogen atom

C) glycine& is unbranched

D) lysine& contains only nitrogen

E) proline& forms a co%alent bond 'ith the amino group

3. Amino acids

Page: 72 Difficulty: 1 Ans: C

T'o amino acids of the standard !" contain sulfur atoms. They are:

A) cysteine and serine.

B) cysteine and threonine.

C) methionine and cysteine

D) methionine and serine

E) threonine and serine.

4. Amino acids

Page: 7! Difficulty: 1 Ans: A

All of the amino acids that are found in proteins# except for proline# contain a(n):

A) amino group.B) carbonyl group.C) carboxyl group.

D) ester group.

E) thiol group.

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5. Amino acids

Pages: 7!"7# Difficulty: 3 Ans: C

hich of the follo'ing statements about aromatic amino acids is correct*

A) All are strongly hydrophilic.

B) +istidine,s ring structure results in its being categori-ed as aromatic or basic# depending on p+.

C) n a molar basis# tryptophan absorbs more ultra%iolet light than tyrosine.D) The maor contribution to the characteristic absorption of light at !/" nm by proteins is the

phenylalanine 0 group.

E) The presence of a ring structure in its 0 group determines 'hether or not an amino acid is

aromatic.

6. Amino acids

Page: 77 Difficulty: 2 Ans: A

hich of the follo'ing statements about cystineis correct*

A) Cystine forms 'hen the 1C+!12+ 0 group is oxidi-ed to form a 1C+!12121C+!1

disulfide bridge bet'een t'o cysteines.

B) Cystine is an example of a nonstandard amino acid# deri%ed by lin3ing t'o standard amino acids.C) Cystine is formed by the oxidation of the carboxylic acid group on cysteine.

D) Cystine is formed through a peptide lin3age bet'een t'o cysteines.

E) T'o cystines are released 'hen a 1C+!12121C+!1 disulfide bridge is reduced to 1C+!1

2+.

7. Amino acids

Page: 77 Difficulty: 2 Ans: A

The uncommon amino acid selenocysteine has an 0 group 'ith the structure 1C+!12e+ (pKa4).

5n an a6ueous solution# p+ 7 8."# selenocysteine 'ould:

A) be a fully ioni-ed -'itterion 'ith no net charge.

B) be found in proteins as D9selenocysteine.C) ne%er be found in a protein.

D) be nonionic.

E) not be optically acti%e.

8. Amino acids

Page: 7$ Difficulty: 2 Ans: %

hich t'o amino acids differ from each other by only one atom*

A) 2er and Thr

B) Leu and 5le

C) Ala and 2er

D) Asp and AsnE) 2er and Cys

9. Amino acids

Pages: 7$"7& Difficulty: 1 Ans: A

Amino acids are ampholytes because they can function as either a(n):

A) acid or a base.

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B) neutral molecule or an ion.

C) polar or a nonpolar molecule.

D) standard or a nonstandard monomer in proteins.

E) transparent or a light9absorbing compound.

10. Amino acids

Pages: 7&"$' Difficulty: 2 Ans: DTitration of %aline by a strong base# for example a+# re%eals t'o pK,s. The titration reaction

occurring at pK!(pK!7 ;.

A) 1C+ = +" 1C"= +!.

B) 1C+ = 1+! 1C"= 1+!=.

C) 1C"= 1+!= 1C+ = 1+!.

D) 1+>== +" 1+!= +!.

E) 1+!= +" 1+"= +!.

11. Amino acids

Pages: 7&"$' Difficulty: 1 Ans: C5n a highly basic solution# p+ 7 ?># the dominant form of glycine is:

A) +!1C+!1C+.

B) +!1C+!1C".

C) +!1C+>=1C".

D) +>=1C+!1C+.

E) +>=1C+!1C

".

12. Amino acids

Pages: $'"$1 Difficulty: 2 Ans:

@or amino acids 'ith neutral 0 groups# at any p+ belo' the p5 of the amino acid# the population of

amino acids in solution 'ill ha%e:

A) a net negati%e charge.

B) a net positi%e charge.

C) no charged groups.

D) no net charge.

E) positi%e and negati%e charges in e6ual concentration.

13. Amino acids

Pages: $'"$1 Difficulty: 2 Ans: A

At p+ 8."# con%erting a glutamic acid to 9carboxyglutamate# 'ill ha%e 'hat effect on the o%erall

charge of the protein containing it*

A) 5t 'ill become more negati%e

B) 5t 'ill become more positi%e.

C) 5t 'ill stay the same.

D) There is not enough information to ans'er the 6uestion.

E) The ans'er depends on the salt concentration.

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14. Amino acids

Pages: $'"$1 Difficulty: 2 Ans: C

At p+ 8."# con%erting a proline to hydroxyproline# 'ill ha%e 'hat effect on the o%erall charge of theprotein containing it*

A) 5t 'ill become more negati%e

B) 5t 'ill become more positi%e.C) 5t 'ill stay the same.

D) There is not enough information to ans'er the 6uestion.

E) The ans'er depends on the salt concentration.

15. Amino acids

Pages: $'"$1 Difficulty: 3 Ans:

hat is the approximate charge difference bet'een glutamic acid and 93etoglutarate at p+ ;.4*

A) "

B)

C) ?

D) ?E) !

16. Peptides and proteins

Page: $2 Difficulty: 1 Ans:

The formation of a peptide bond bet'een t'o amino acids is an example of a(n) $$$$$$$$$$$$$$

reaction.

A) clea%age

B) condensation

C) group transfer

D) isomeri-ation

E) oxidation reduction


Page: $2 Difficulty: 1 Ans: C

The peptide alanylglutamylglycylalanylleucine has:

A) a disulfide bridge.

B) fi%e peptide bonds.

C) four peptide bonds.

D) no free carboxyl group.

E) t'o free amino groups.

18. Peptides and proteinsPages: $2"$3 Difficulty: 1 Ans: C

An octapeptide composed of four repeating glycylalanyl units has:

A) one free amino group on an alanyl residue.B) one free amino group on an alanyl residue and one free carboxyl group on a glycyl residue.

C) one free amino group on a glycyl residue and one free carboxyl group on an alanyl residue.

D) t'o free amino and t'o free carboxyl groups.

E) t'o free carboxyl groups# both on glycyl residues.

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Page: $2"$3 Difficulty: 1 Ans: C

At the isoelectric p+ of a tetrapeptide:

A) only the amino and carboxyl termini contribute charge.

B) the amino and carboxyl termini are not charged.C) the total net charge is -ero.

D) there are four ionic charges.

E) t'o internal amino acids of the tetrapeptide cannot ha%e ioni-able 0 groups.


Pages: $3"$( Difficulty: 2 Ans: C

hich of the follo'ing is correct 'ith respect to the amino acid composition of proteins*

A) Larger proteins ha%e a more uniform distribution of amino acids than smaller proteins.

B) roteins contain at least one each of the !" different standard amino acids.

C) roteins 'ith different functions usually differ significantly in their amino acid composition.

D) roteins 'ith the same molecular 'eight ha%e the same amino acid composition.E) The a%erage molecular 'eight of an amino acid in a protein increases 'ith the si-e of the protein.



The a%erage molecular 'eight of the !" standard amino acids is ?>/# but biochemists use ??" 'hen

estimating the number of amino acids in a protein of 3no'n molecular 'eight. hy*

A) The number ??" is based on the fact that the a%erage molecular 'eight of a protein is ??"#"""

'ith an a%erage of ?""" amino acids.

B) The number ??" reflects the higher proportion of small amino acids in proteins# as 'ell as the

loss of 'ater 'hen the peptide bond forms.

C) The number ??" reflects the number of amino acids found in the typical small protein# and onlysmall proteins ha%e their molecular 'eight estimated this 'ay.

D) The number ??" ta3es into account the relati%ely small si-e of nonstandard amino acids.

E) The number ?>/ represents the molecular 'eight of conugated amino acids.


Page: $( Difficulty: 1 Ans: C

5n a conugated protein# a prosthetic group is:

A) a fibrous region of a globular protein.B) a nonidentical subunit of a protein 'ith many identical subunits.

C) a part of the protein that is not composed of amino acids.

D) a subunit of an oligomeric protein.E) synonymous 'ith protomer.

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Pages: $("$! Difficulty: 1 Ans: A

rosthetic groups in the class of proteins 3no'n as glycoproteins are composed of:

A) carbohydrates.

B) fla%in nucleotides.

C) lipids.D) metals .

E) phosphates.

24. )or*ing +ith proteins

Page: $! Difficulty: 1 Ans: %

@or the study of a protein in detail# an effort is usually made to first:

A) conugate the protein to a 3no'n molecule.

B) determine its amino acid composition.

C) determine its amino acid se6uence.

D) determine its molecular 'eight.

E) purify the protein.



5n a mixture of the fi%e proteins listed belo'# 'hich should elute second in si-e9exclusion (gel9

filtration) chromatography*

A) cytochrome c Mr7 ?>#"""B) immunoglobulin Mr7 ?F4#"""C) ribonuclease A Mr7 ?>#8""D) 0A polymerase Mr7 F4"#"""E) serum albumin Mr7


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Pages: &'"&1 Difficulty: 3 Ans: A

The first step in t'o9dimensional gel electrophoresis generates a series of protein bands by isoelectric

focusing. 5n a second step# a strip of this gel is turned ;" degrees# placed on another gel containing

2D2# and electric current is again applied. 5n this second step:

A) proteins 'ith similar isoelectric points become further separated according to their molecular

'eights.

B) the indi%idual bands become stained so that the isoelectric focus pattern can be %isuali-ed.

C) the indi%idual bands become %isuali-ed by interacting 'ith protein9specific antibodies in thesecond gel.

D) the indi%idual bands undergo a second# more intense isoelectric focusing.

E) the proteins in the bands separate more completely because the second electric current is in the

opposite polarity to the first current.


Page: &1 Difficulty: 1 Ans:

The term specificactivitydiffers from the term activityin that specific acti%ity:

A) is measured only under optimal conditions.

B) is the acti%ity (en-yme units) in a milligram of protein.C) is the acti%ity (en-yme units) of a specific protein.

D) refers only to a purified protein.

E) refers to proteins other than en-ymes.



hich of the follo'ing refers to particularly stable arrangements of amino acid residues in a protein

that gi%e rise to recurring patterns*

A) rimary structure

B) 2econdary structureC) Tertiary structure

D) Guaternary structure

E) one of the abo%e


Page: &2 Difficulty: 1 Ans: D

hich of the follo'ing describes the o%erall three9dimensional folding of a polypeptide*

A) rimary structure

B) 2econdary structureC) Tertiary structureD) Guaternary structure

E) one of the abo%e

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32. he co-alent structure of proteins


The functional differences# as 'ell as differences in three9dimensional structures# bet'een t'odifferent en-ymes from E.coliresult directly from their different:

A) affinities for AT.

B) amino acid se6uences.C) roles in DA metabolism.

D) roles in the metabolism of E.coli.

E) secondary structures.


Page: &! Difficulty: 2 Ans: C

ne method used to pre%ent disulfide bond interference 'ith protein se6uencing procedures is:

A) clea%ing proteins 'ith proteases that specifically recogni-e disulfide bonds.

B) protecting the disulfide bridge against spontaneous reduction to cysteinyl sulfhydryl groups.

C) reducing disulfide bridges and pre%enting their re9formation by further modifying the 12+

groups.D) remo%ing cystines from protein se6uences by proteolytic clea%age.

E) se6uencing proteins that do not contain cysteinyl residues.


Pages: "&7 Difficulty: 3 Ans: C

A nonapeptide 'as determined to ha%e the follo'ing amino acid composition: (Lys)!# (ly)!# (he)!#

+is# Leu# Het. The nati%e peptide 'as incubated 'ith ?9fluoro9!#F9dinitroben-ene (@DB) and then

hydroly-ed& !#F9dinitrophenylhistidine 'as identified by +LC. hen the nati%e peptide 'as

exposed to cyanogen bromide (CBr)# an octapeptide and free glycine 'ere reco%ered. 5ncubation of

the nati%e peptide 'ith trypsin ga%e a pentapeptide# a tripeptide# and free Lys. !#F9Dinitrophenyl9

histidine 'as reco%ered from the pentapeptide# and !#F9dinitrophenylphenylalanine 'as reco%ered

from the tripeptide. Digestion 'ith the en-yme pepsin produced a dipeptide# a tripeptide# and atetrapeptide. The tetrapeptide 'as composed of (Lys) !# he# and ly. The nati%e se6uence 'as

determined to be:

A) lyIheILysILysIlyILeuIHetIheI+is.

B) +isILeuIlyILysILysIheIheIlyIHet.

C) +isILeuIheIlyILysILysIheIHetIly.

D) +isIheILeuIlyILysILysIheIHetIly.

E) HetILeuIheILysIheIlyIlyILysI+is.


Pages: "&7 Difficulty: 1 Ans: C

E%en 'hen a gene is a%ailable and its se6uence of nucleotides is 3no'n# chemical studies of theprotein are still re6uired to determine:

A) molecular 'eight of the protein.

B) the amino9terminal amino acid.

C) the location of disulfide bonds.

D) the number of amino acids in the protein.

E) 'hether the protein has the amino acid methionine in its se6uence.

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Page: 1'' Difficulty: 1 Ans: C

The term proteome has been used to describe:

A) regions (domains) 'ithin proteins.

B) regularities in protein structures.

C) the complement of proteins expressed by an organism,s genome.D) the structure of a protein9synthesi-ing ribosome.

E) the tertiary structure of a protein.


Pages: &$"1'' Difficulty: 2 Ans: C

A maor ad%ance in the application of mass spectrometry to macromolecules came 'ith the

de%elopment of techni6ues to o%ercome 'hich of the follo'ing problems*

A) Hacromolecules 'ere insoluble in the sol%ents used in mass spectrometry.

B) Hass spectrometric analyses of macromolecules 'ere too complex to interpret.

C) Hass spectrometric analysis in%ol%ed molecules in the gas phase.

D) Host macromolecules could not be purified to the degree re6uired for mass spectrometricanalysis.

E) The speciali-ed instruments re6uired 'ere prohibiti%ely expensi%e.


Pages: &$"1'' Difficulty: 3 Ans: C

Identify the pair of peptides below that cannot be distinguished by tandem massspectrometry.

A) JT2LKAE and JTCLKAEB) JT2LKAE and JT2LKADE

C) JT2LKAE and JT25KAE

D) JT2LKAE and J2TLKAEE) All of the abo%e

39. Protein se.uences and e-olution

Pages: 1'2"1'# Difficulty: 3 Ans: A

Compare the follo'ing se6uences ta3en from four different proteins# and select the ans'er that bestcharacteri-es their relationships.

A B C

? DJE5D5HC2 +TJE+TL+ L@0TGAK2KT

! DJG0AL5DLG +TJEA+TAJ+ LAD05AKGAATEE

> LJT0LK5@EG +TLEAA+TL+ AL22DLH@TJ5DD

F @@HEDALJA022 +G@AA225+AG@+ LD2TKLJ52ET

A) Based only on se6uences in column B# protein F re%eals the greatest e%olutionary di%ergence.

B) Comparing proteins ? and ! in column A re%eals that these t'o proteins ha%e di%erged the most

throughout e%olution.

C) rotein F is the protein that sho's the greatest o%erall homology to protein ?.

D) roteins ! and > sho' a greater e%olutionary distance than proteins ? and F.

E) The portions of amino acid se6uence sho'n suggest that these proteins are completely unrelated.

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Chapter 3 Amino Acids, Peptides, and Proteins3'


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/hort Ans+er Questions

40. Amino acids

Page: 72 Difficulty: 1

hat are the structural characteristics common to all amino acids found in naturally occurring

proteins*

Ans:All amino acids found in naturally occurring proteins ha%e an carbon to 'hich are attached a

carboxylic acid# an amine# a hydrogen# and a %ariable side chain. All the amino acids are also in the Lconfiguration.

41. Amino acids

Page: 7! Difficulty: 1

nly one of the common amino acids has no free 9amino group. ame this amino acid and dra' its

structure.

Ans:The amino acid L9proline has no free 9amino group# but rather has an imino group formed by

cycli-ation of the 09group aliphatic chain 'ith the amino group (see @ig. >94# p. 8;).

42. Amino acids

Pages: 7("77 Difficulty: 2

Briefly describe the fi%e maor groupings of amino acids.

Ans:Amino acids may be categori-ed by the chemistry of their 0 groups: (?) nonpolar aliphatics& (!)

polar# uncharged& (>) aromatic& (F) positi%ely charged& (4) negati%ely charged. (2ee @ig. >94# p. 8;.)

43. Amino acids

Pages: 73"7! Difficulty: 2

A B C D E__________________________________________________________________Tyr9Lys9Het ly9ro9Arg Asp9Trp9Tyr Asp9+is9lu Leu9Jal9he

hich one of the abo%e tripeptides:

$$$$(a) is most negati%ely charged at p+ 8*

$$$$(b) 'ill yield D9tyrosine 'hen reacted 'ith l9fluoro9!#F9dinitroben-ene and

hydroly-ed in acid*

$$$$(c) contains the largest number of nonpolar 0 groups*

$$$$(d) contains sulfur*

$$$$(e) 'ill ha%e the greatest light absorbance at !/" nm*

Ans:(a) D& (b) A& (c) E& (d) A& (e) C

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44. Amino acids

Pages: 73"7! Difficulty: 2

Dra' the structures of the amino acids phenylalanine and aspartate in the ioni-ation state you 'ouldexpect at p+ 8.". hy is aspartate %ery soluble in 'ater# 'hereas phenylalanine is much less soluble*

Ans:Aspartate has a polar (hydrophilic) side chain# 'hich forms hydrogen bonds 'ith 'ater. 5n

contrast# phenylalanine has a nonpolar (hydrophobic) side chain. (2ee @ig. >94# p. 8; for structures.)

45. Amino acids

Pages: 77"7$ Difficulty: 3

ame t'o uncommon amino acids that occur in proteins. By 'hat route do they get into proteins*

Ans:2ome examples are F9hydroxyproline# 49hydroxylysine# 9carboxyglutamate#N9methyllysine#

desmosine# and selenocysteine. Mncommon amino acids in proteins (other than selenocysteine)

usually result from chemical modifications of standard amino acid 0 groups after a protein has been

synthesi-ed.

46. Amino acids

Pages: 7$"7& Difficulty: 1hy do amino acids# 'hen dissol%ed in 'ater# become -'itterions*

Ans:ear p+ 7 8# the carboxylic acid group (1C+) 'ill dissociate to become a negati%elycharged 1CIgroup# and the 1+!amino group 'ill attract a proton to become a positi%ely

charged 1+>=group.

47. Amino acids

Page: 7& Difficulty: 1

As more +Ie6ui%alents (base) are added to an amino acid solution# 'hat titration reaction 'ill

occur around p+ 7 ;.4*

Ans:Around p+ 7 ;.4# the 1+>=group 'ill be titrated according to the reaction: 1+>== +I 1+!= +!.

48. Amino acids

Page: $' Difficulty: 3

5n the amino acid glycine# 'hat effect does the positi%ely charged 1+>=group ha%e on the pKaof

an amino acid,s 1C+ group*

Ans:The positi%ely charged amino group stabili-es the negati%ely charged ioni-ed form of the

carboxyl group# 1CI# and repels the departing +=thereby promoting deprotonation. The effect is

to lo'er the pKaof the carboxyl group. (2ee @ig. >9??# p. /".)

49. Amino acids


+o' does the shape of a titration cur%e confirm the fact that the p+ region of greatest buffering

po'er for an amino acid solution is around its pK,s*

Ans:5n a certain range around the pKa,s of an amino acid# the titration cur%e le%els off. This

indicates that for a solution 'ith p+ pK# any gi%en addition of base or acid e6ui%alents 'ill result in

the smallest change in p+1'hich is the definition of a buffer.

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50. Amino acids


Leucine has t'o dissociable protons: one 'ith a pKaof !.># the other 'ith a pKaof ;.8. 23etch a

properly labeled titration cur%e for leucine titrated 'ith a+& indicate 'here the p+ 7 pKand the

region(s) in 'hich buffering occurs.

Ans:2ee the titration cur%e for glycine in @ig. >9?"# p. 8;.

51. Amino acids


hat is the p5# and ho' is it determined for amino acids that ha%e nonioni-able 0 groups*

Ans:The p5 is the isoelectric point. 5t occurs at a characteristic p+ 'hen a molecule has an e6ual

number of positi%e and negati%e charges# or no netcharge. @or amino acids 'ith nonioni-able 0

groups# p5 is the arithmetic mean of a molecule,s t'o pKa%alues:

p5 7 ?N! (pK?= pK!)

52. Amino acids


The amino acid histidine has a side chain for 'hich the pKais


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54. Amino acids

Page: $1 Difficulty: 2

hat is the uni6uely important acid9base characteristic of the histidine 0 group*

Ans:nly the imida-ole ring of the histidine 0 group has a pKanear physiological p+ (pKa7 /# 'hy do biochemists di%ide a

protein,s molecular 'eight by ??" to estimate its number of amino acid residues*

Ans:@or each peptide bond formed# a molecule of 'ater is lost# bringing the a%erage molecular

'eight do'n to ?!". To reflect the preponderance of lo'9molecular9'eight amino acids# the a%erage

molecular 'eight is lo'ered further to ??".

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Page: $( Difficulty: 2

Lys residues ma3e up ?".4Q of the 'eight of ribonuclease. The ribonuclease molecule contains ?"Lys residues. Calculate the molecular 'eight of ribonuclease.

Ans:@rom the structure of lysine# 'e can calculate its molecular 'eight (?F


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(a) protein S from protein A*

(b) protein S from protein B*

(c) protein S from protein C*

Ans:(a) 2i-e9exclusion (gel filtration) chromatography to separate on the basis of si-e& (b) ion9

exchange chromatography or isoelectric focusing to separate on the basis of charge& (c) specific

affinity chromatography# using immobili-ed DA.


Pages: $$"$& Difficulty: 2

hat factors 'ould ma3e it difficult to interpret the results of a gel electrophoresis of proteins in the

absence of sodium dodecyl sulfate (2D2)*

Ans:ithout 2D2# protein migration through a gel 'ould be influenced by the protein,s intrinsic net

charge1'hich could be positi%e or negati%e1and its uni6ue three9dimensional shape# in addition to

its molecular 'eight. Thus# it 'ould be difficult to ascertain the difference bet'een proteins based

upon a comparison of their mobilities in gel electrophoresis.

65. )or*ing +ith proteinsPages: &'"&1 Difficulty: 2

+o' can isoelectric focusing be used in conunction 'ith 2D2 gel electrophoresis*

Ans:5soelectric focusing can separate proteins of the same molecular 'eight on the basis of differing

isoelectric points. 2D2 gel electrophoresis can then separate proteins 'ith the same isoelectric points

on the basis of differing molecular 'eights. hen combined in t'o9dimensional electrophoresis# a

great resolution of large numbers of proteins can be achie%ed.

##0 )or*ing +ith proteins

Pages: &1"&2 Difficulty: 3

Kou are gi%en a solution containing an en-yme that con%erts B into A. Describe 'hat you 'ould do

to determine the specific acti%ity of this en-yme solution.

Ans:@irst# add a 3no'n %olume of the en-yme solution (say# "."? mL) to a solution of its substrate B

and measure the initial rate at 'hich product A is formed# expressed as molNmL of en-yme

solutionNmin. Then measure the total protein concentration# expressed as mgNmL. @inally# di%ide the

en-yme acti%ity (molNminNmL) by the protein concentration (mgNmL)& the 6uotient is the specific

acti%ity.

#70 )or*ing +ith proteins

Pages: &1"&2 Difficulty: 2

As a protein is purified# both the amount of total protein and the acti%ity of the purified protein

decrease. hy# then# does the specificactivityof the purified protein increase*

Ans:2pecific acti%ity is the units of en-yme acti%ity (mol of productNmin) di%ided by the amount of

protein (mg). As the protein is purified# some of it is lost in each step# resulting in a drop in acti%ity.

+o'e%er# other contaminating proteins are lost to a much greater extent. Therefore# 'ith each

purification step# the purified protein constitutes a greater proportion of the total# resulting in an

increase in specific acti%ity. (2ee also Table >94# p. //.)

#$0 Peptides and proteins

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Page: $( Difficulty: 1

Define the primary structure of a protein.

Ans:The primary structure of a protein is its uni6ue se6uence of amino acids and any disulfide

bridges present in the nati%e structure# that is# its co%alent bond structure.

#&0 he co-alent structure of proteinsPages: &("1'' Difficulty: 2

5n one or t'o sentences# describe the usefulness of each of the follo'ing reagents or reactions in the

analysis of protein structure:

(a) Edman reagent (phenylisothiocyanate)

(b) protease

(c) reducing agent (dithiothreitol or 9mercaptoethanol)

Ans:(a) Msed in determination of the amino acid se6uence of a peptide# starting at its amino

terminus& (b) used to produce specific peptide fragments from a polypeptide& (c) used to brea3disulfide bonds or bridges or to 3eep them from forming and to 3eep Cys residues in their reduced

form.

7'0 he co-alent structure of proteins

Pages: "&7 Difficulty: 2

A polypeptide is hydroly-ed# and it is determined that there are > Lys residues and ! Arg residues (as

'ell as other residues). +o' many peptide fragments can be expected 'hen the nati%e polypeptide is

incubated 'ith the proteolytic en-yme trypsin*

Ans:2ix fragments 'ould be expected# unless the carboxyl9terminal residue is Lys or Arg& in 'hich

case there 'ould be fi%e.

710 he co-alent structure of proteins

Pages: &("&! Difficulty: 2

The follo'ing reagents are often used in protein chemistry. Hatch the reagent 'ith the purpose for'hich it is best suited. 2ome ans'ers may be used more than once or not at all& more than one reagent

may be suitable for a gi%en purpose.

(a) CBr (cyanogen bromide) (e) performic acid

(b) Edman reagent (phenylisothiocyanate) (f) chymotrypsin

(c) 2anger reagent (@DB) (g) trypsin

(d) reducing agent (dithiothreitol) (h) iodoacetamide

$$$ hydrolysis of peptide bonds on the carboxyl side of Lys and Arg

$$$ clea%age of peptide bonds on the carboxyl side of Het

$$$ brea3age of disulfide (12121) bonds

$$$ modification of sulfhydryl groups of Cys$$$ determination of the amino acid se6uence of a peptide

$$$ determining the amino9terminal amino acid in a polypeptide

Ans:g& a& d and e& h& b& c


Pages: &("&7 Difficulty: 2

Conugated proteins contain chemical substituents in addition to amino acids. List three classes of

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conugated proteins and identify the type of prosthetic group associated 'ith each one.

Ans:Any of the follo'ing are acceptable ans'ers:

Lipoproteins# 'ith lipid groups

lycoproteins# 'ith carbohydrate groups

Phosphoproteins with phosphoryl groups

!emoproteins with heme groups"la#oproteins with $a#in nucleotide groups%etalloproteins with metal ions &'inc iron calcium etc.)



ro%ide a brief definition for a polymorphic protein.

Ans:A polymorphic protein is one 'hose amino acid se6uence %aries among the human population.

The %ariants ha%e little or no differences in the function or acti%ity of the protein.

7(0 he co-alent structure of proteins

Pages: &("&7 Difficulty: 2A biochemist 'ishes to determine the se6uence of a protein that contains ?!> amino acid residues.

After brea3ing all of the disulfide bonds# the protein is treated 'ith cyanogen bromide (CBr)# and it

is determined that that this treatment brea3s up the protein into se%en con%eniently si-ed peptides#

'hich are separated from each other. 5t is your turn to ta3e o%er. utline the steps you 'ould ta3e to

determine# unambiguously# the se6uence of amino acid residues in the original protein.

Ans:(?) Mse Edman degradation to determine the se6uence of each peptide. (!) Create a second set

of peptides by treatment of the protein 'ith a specific protease (e.g.# trypsin)# and determine the

se6uence of each of these. (>) lace the peptides in order by their o%erlaps. (F) @inally# by a similar

analysis of the original protein 'ithout first brea3ing disulfide bonds# determine the number and

location of 12121 bridges.

7!0 he co-alent structure of proteins


Kou are trying to determine the se6uence of a protein that you 3no' is pure. i%e the most li3ely

explanation for each of the follo'ing experimental obser%ations. Kou may use a simple diagram for

your ans'er.

(a) The 2anger reagent (@DB# fluorodinitroben-ene) identifies Ala and Leu as amino9

terminal residues# in roughly e6ual amounts.(b) Kour protein has an apparent Mrof /"#"""# as determined by 2D29polyacrylamide gel

electrophoresis. After treatment of the protein 'ith performic acid# the same techni6ue

re%eals t'o proteins of Mr>4#""" and F4#""".

(c) 2i-e9exclusion chromatography (gel filtration) experiments indicate the nati%e protein has

an apparent Mrof ?4#""" subunits and t'o MrF"#""" subunits.

66. 7#0 he co-alent structure of proteins

Page: 1'1 Difficulty: 2

Describe t'o maor differences bet'een chemical synthesis of polypeptides and synthesis of

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19/19


polypeptides in the li%ing cell.

Ans:There are many such differences& here are a fe'. (?) Chemical synthesis proceeds from carboxyl

terminus to amino terminus& in the li%ing cell# the process starts at the amino terminus and ends at the

carboxyl terminus. 5n the li%ing cell# synthesis occurs under physiological conditions& chemical

synthesis does not. Chemical synthesis is only capable of synthesi-ing short polypeptides& cells can

produce proteins of se%eral thousand amino acids.

770 Protein se.uences and e-olution

Page: 1'2"1'( Difficulty: 2

Distinguish bet'een homologs# paralogs# and orthologs as classes of related proteins.

Ans: +omologs are any members of a particular protein family# paralogs are t'o homologs presentin the same species# and orthologs are are t'o homologs present in different species.

7$0 Protein se.uences and e-olution

Page: 1'! Difficulty: 2

+o' are signature se6uences useful in analy-ing groups of functionally related proteins*

Ans: 2uch se6uences are often present in one taxonomic group or shared by closely related

taxonomic groups but are absent in e%olutionarily more distant groups. They thus aid in constructing

more elaborate e%olutionary trees based on protein se6uences.

3&

lehninger principles of biochemistry test bank 6e ch03

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