Deck 3: Amino Acids, peptides, and Proteins

Question 1

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

A)has no net charge.
B)is a carboxylic acid.
C)is bonded to four different chemical groups.
D)is in the l absolute configuration in naturally occurring proteins.
E)is symmetric.

Answer 1

is bonded to four different chemical groups.

Question 2

Which of the following is correct with respect to the amino acid composition of proteins?

A)Larger proteins have a more uniform distribution of amino acids than smaller proteins.
B)Proteins contain at least one each of the 20 different standard amino acids.
C)Proteins with different functions usually differ significantly in their amino acid composition.
D)Proteins with the same molecular weight have the same amino acid composition.
E)The average molecular weight of an amino acid in a protein increases with the size of the protein.

Answer 2

Proteins with different functions usually differ significantly in their amino acid composition.

Question 3

For amino acids with neutral R groups,at any pH below the pI of the amino acid,the population of amino acids in solution will have:

A)a net negative charge.
B)a net positive charge.
C)no charged groups.
D)no net charge.
E)positive and negative charges in equal concentration.

Answer 3

a net positive charge.

Question 4

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)two free amino and two free carboxyl groups.
E)two free carboxyl groups,both on glycyl residues.

Question 5

At the isoelectric pH 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 zero.
D)there are four ionic charges.
E)two internal amino acids of the tetrapeptide cannot have ionizable R groups.

Question 6

Titration of valine by a strong base,for example NaOH,reveals two pK's.The titration reaction occurring at pK₂ (pK₂ = 9.62)is:

A)-COOH + OH^- $\rightarrow$ -COO^- + H₂O.
B)-COOH + -NH₂ $\rightarrow$ -COO^- + -NH₂⁺.
C)-COO^- + -NH₂⁺ $\rightarrow$ -COOH + -NH₂.
D)-NH₃⁺ + OH^- $\rightarrow$ -NH₂ + H₂O.
E)-NH₂ + OH^- $\rightarrow$ -NH^- + H₂O.

Question 7

At pH 7.0,converting a glutamic acid to $\gamma$ -carboxyglutamate,will have what effect on the overall charge of the protein containing it?

A)It will become more negative
B)It will become more positive.
C)It will stay the same.
D)There is not enough information to answer the question.
E)The answer depends on the salt concentration.

Question 8

The formation of a peptide bond between two amino acids is an example of a(n)______________ reaction.

A)cleavage
B)condensation
C)group transfer
D)isomerization
E)oxidation reduction

Question 9

Which two amino acids differ from each other by only one atom?

A)Ser and Thr
B)Leu and Ile
C)Ala and Ser
D)Asp and Asn
E)Ser and Cys

Question 10

Which of the following statements about cystine is correct?

A)Cystine forms when the -CH₂-SH R group is oxidized to form a -CH₂-S-S-CH₂- disulfide bridge between two cysteines.
B)Cystine is an example of a nonstandard amino acid,derived by linking two standard amino acids.
C)Cystine is formed by the oxidation of the carboxylic acid group on cysteine.
D)Cystine is formed through a peptide linkage between two cysteines.
E)Two cystines are released when a -CH₂-S-S-CH₂- disulfide bridge is reduced to -CH₂-SH.

Question 11

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.

Question 12

Which of the following statements about aromatic amino acids is correct?

A)All are strongly hydrophilic.
B)Histidine's ring structure results in its being categorized as aromatic or basic,depending on pH.
C)On a molar basis,tryptophan absorbs more ultraviolet light than tyrosine.
D)The major contribution to the characteristic absorption of light at 280 nm by proteins is the phenylalanine R group.
E)The presence of a ring structure in its R group determines whether or not an amino acid is aromatic.

Question 13

At pH 7.0,converting a proline to hydroxyproline,will have what effect on the overall charge of the protein containing it?

A)It will become more negative
B)It will become more positive.
C)It will stay the same.
D)There is not enough information to answer the question.
E)The answer depends on the salt concentration.

Question 14

In a highly basic solution,pH = 13,the dominant form of glycine is:

A)NH₂-CH₂-COOH.
B)NH₂-CH₂-COO^-.
C)NH₂-CH₃⁺-COO^-.
D)NH₃⁺-CH₂-COOH.
E)NH₃⁺-CH₂-COO^-.

Question 15

The peptide alanylglutamylglycylalanylleucine has:

A)a disulfide bridge.
B)five peptide bonds.
C)four peptide bonds.
D)no free carboxyl group.
E)two free amino groups.

Question 16

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

A)acid or a base.
B)neutral molecule or an ion.
C)polar or a nonpolar molecule.
D)standard or a nonstandard monomer in proteins.
E)transparent or a light-absorbing compound.

Question 17

Of the 20 standard amino acids,only ___________ is not optically active.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 covalent bond with the amino group

Question 18

What is the approximate charge difference between glutamic acid and $\alpha$ -ketoglutarate at pH 9.5?

A)0
B)½
C)1
D)1½
E)2

Question 19

Two amino acids of the standard 20 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.

Question 20

The uncommon amino acid selenocysteine has an R group with the structure -CH₂-SeH (pK_a $\approx$ 5).In an aqueous solution,pH = 7.0,selenocysteine would:

A)be a fully ionized zwitterion with no net charge.
B)be found in proteins as d-selenocysteine.
C)never be found in a protein.
D)be nonionic.
E)not be optically active.

Question 21

Only one of the common amino acids has no free $\alpha$ -amino group.Name this amino acid and draw its structure.

Question 22

To determine the isoelectric point of a protein,first establish that a gel:

A)contains a denaturing detergent that can distribute uniform negative charges over the protein's surface.
B)exhibits a stable pH gradient when ampholytes become distributed in an electric field.
C)is washed with an antibody specific to the protein of interest.
D)neutralizes all ionic groups on a protein by titrating them with strong bases.
E)relates the unknown protein to a series of protein markers with known molecular weights,M_r.

Question 23

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

A)VTSPLYANEGK and VTCPLYANEGK
B)VTSPLYANEGK and VTSPLYADEGK
C)VTSPLYANEGK and VTSPIYANEGK
D)VTSPLYANEGK and VSTPLYANEGK
E)All of the above

Question 24

The average molecular weight of the 20 standard amino acids is 138,but biochemists use 110 when estimating the number of amino acids in a protein of known molecular weight.Why?

A)The number 110 is based on the fact that the average molecular weight of a protein is 110,000 with an average of 1000 amino acids.
B)The number 110 reflects the higher proportion of small amino acids in proteins,as well as the loss of water when the peptide bond forms.
C)The number 110 reflects the number of amino acids found in the typical small protein,and only small proteins have their molecular weight estimated this way.
D)The number 110 takes into account the relatively small size of nonstandard amino acids.
E)The number 138 represents the molecular weight of conjugated amino acids.

Question 25

The term specific activity differs from the term activity in that specific activity:

A)is measured only under optimal conditions.
B)is the activity (enzyme units)in a milligram of protein.
C)is the activity (enzyme units)of a specific protein.
D)refers only to a purified protein.
E)refers to proteins other than enzymes.

Question 26

The term "proteome" has been used to describe:

A)regions (domains)within proteins.
B)regularities in protein structures.
C)the complement of proteins expressed by an organism's genome.
D)the structure of a protein-synthesizing ribosome.
E)the tertiary structure of a protein.

Question 27

What are the structural characteristics common to all amino acids found in naturally occurring proteins?

Question 28

The first step in two-dimensional gel electrophoresis generates a series of protein bands by isoelectric focusing.In a second step,a strip of this gel is turned 90 degrees,placed on another gel containing SDS,and electric current is again applied.In this second step:

A)proteins with similar isoelectric points become further separated according to their molecular weights.
B)the individual bands become stained so that the isoelectric focus pattern can be visualized.
C)the individual bands become visualized by interacting with protein-specific antibodies in the second gel.
D)the individual 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.

Question 29

Even when a gene is available and its sequence of nucleotides is known,chemical studies of the protein are still required to determine:

A)molecular weight of the protein.
B)the amino-terminal amino acid.
C)the location of disulfide bonds.
D)the number of amino acids in the protein.
E)whether the protein has the amino acid methionine in its sequence.

Question 30

A nonapeptide was determined to have the following amino acid composition: (Lys)₂, (Gly) ₂, (Phe) ₂,His,Leu,Met.The native peptide was incubated with 1-fluoro-2,4-dinitrobenzene (FDNB)and then hydrolyzed;2,4-dinitrophenylhistidine was identified by HPLC.When the native peptide was exposed to cyanogen bromide (CNBr),an octapeptide and free glycine were recovered.Incubation of the native peptide with trypsin gave a pentapeptide,a tripeptide,and free Lys.2,4-Dinitrophenyl-histidine was recovered from the pentapeptide,and 2,4-dinitrophenylphenylalanine was recovered from the tripeptide.Digestion with the enzyme pepsin produced a dipeptide,a tripeptide,and a tetrapeptide.The tetrapeptide was composed of (Lys) ₂,Phe,and Gly.The native sequence was determined to be:

A)Gly-Phe-Lys-Lys-Gly-Leu-Met-Phe-His.
B)His-Leu-Gly-Lys-Lys-Phe-Phe-Gly-Met.
C)His-Leu-Phe-Gly-Lys-Lys-Phe-Met-Gly.
D)His-Phe-Leu-Gly-Lys-Lys-Phe-Met-Gly.
E)Met-Leu-Phe-Lys-Phe-Gly-Gly-Lys-His.

Question 31

For the study of a protein in detail,an effort is usually made to first:

A)conjugate the protein to a known molecule.
B)determine its amino acid composition.
C)determine its amino acid sequence.
D)determine its molecular weight.
E)purify the protein.

Question 32

Which of the following refers to particularly stable arrangements of amino acid residues in a protein that give rise to recurring patterns?

A)Primary structure
B)Secondary structure
C)Tertiary structure
D)Quaternary structure
E)None of the above

Question 33

Which of the following describes the overall three-dimensional folding of a polypeptide?

A)Primary structure
B)Secondary structure
C)Tertiary structure
D)Quaternary structure
E)None of the above

Question 34

In a conjugated protein,a prosthetic group is:

A)a fibrous region of a globular protein.
B)a nonidentical subunit of a protein with 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 with "protomer."

Question 35

The functional differences,as well as differences in three-dimensional structures,between two different enzymes from E.coli result directly from their different:

A)affinities for ATP.
B)amino acid sequences.
C)roles in DNA metabolism.
D)roles in the metabolism of E.coli.
E)secondary structures.

Question 36

By adding SDS (sodium dodecyl sulfate)during the electrophoresis of proteins,it is possible to:

A)determine a protein's isoelectric point.
B)determine an enzyme's specific activity.
C)determine the amino acid composition of the protein.
D)preserve a protein's native structure and biological activity.
E)separate proteins exclusively on the basis of molecular weight.

Question 37

Prosthetic groups in the class of proteins known as glycoproteins are composed of:

A)carbohydrates.
B)flavin nucleotides.
C)lipids.
D)metals .
E)phosphates.

Question 38

A major advance in the application of mass spectrometry to macromolecules came with the development of techniques to overcome which of the following problems?

A)Macromolecules were insoluble in the solvents used in mass spectrometry.
B)Mass spectrometric analyses of macromolecules were too complex to interpret.
C)Mass spectrometric analysis involved molecules in the gas phase.
D)Most macromolecules could not be purified to the degree required for mass spectrometric analysis.
E)The specialized instruments required were prohibitively expensive.

Question 39

One method used to prevent disulfide bond interference with protein sequencing procedures is:

A)cleaving proteins with proteases that specifically recognize disulfide bonds.
B)protecting the disulfide bridge against spontaneous reduction to cysteinyl sulfhydryl groups.
C)reducing disulfide bridges and preventing their re-formation by further modifying the -SH groups.
D)removing cystines from protein sequences by proteolytic cleavage.
E)sequencing proteins that do not contain cysteinyl residues.

Question 40

In a mixture of the five proteins listed below,which should elute second in size-exclusion (gel- filtration)chromatography?

A)cytochrome c M_r = 13,000
B)immunoglobulin G M_r = 145,000
C)ribonuclease A M_r = 13,700
D)RNA polymerase M_r = 450,000
E)serum albumin M_r = 68,500

Question 41

As more OH^- equivalents (base)are added to an amino acid solution,what titration reaction will occur around pH = 9.5?

Question 42

For each of these methods of separating proteins,describe the principle of the method,and tell what property of proteins allows their separation by this technique.
(a)ion-exchange chromatography
(b)size-exclusion (gel filtration)chromatography
(c)affinity chromatography

Question 43

Briefly describe the five major groupings of amino acids.

Question 44

Why do smaller molecules elute after large molecules when a mixture of proteins is passed through a size-exclusion (gel filtration)column?

Question 45

How does the shape of a titration curve confirm the fact that the pH region of greatest buffering power for an amino acid solution is around its pK's?

Question 46

What factors would make it difficult to interpret the results of a gel electrophoresis of proteins in the absence of sodium dodecyl sulfate (SDS)?

Question 47

How can isoelectric focusing be used in conjunction with SDS gel electrophoresis?

Question 48

If the average molecular weight of the 20 standard amino acids is 138,why do biochemists divide a protein's molecular weight by 110 to estimate its number of amino acid residues?

Question 49

In the amino acid glycine,what effect does the positively charged -NH₃⁺ group have on the pK_a of an amino acid's -COOH group?

Question 50

The amino acid histidine has three ionizable groups,with pK_a values of 1.8,6.0,and 9.2.
(a)Which pK_a corresponds to the histidine side chain?
(b)In a solution at pH 5.4,what percentage of the histidine side chains will carry a positive charge?

Question 51

What is the pI,and how is it determined for amino acids that have nonionizable R groups?

Question 52

Hydrolysis of peptide bonds is an exergonic reaction.Why,then,are peptide bonds quite stable?

Question 53

What is the uniquely important acid-base characteristic of the histidine R group?

Question 54

Why do amino acids,when dissolved in water,become zwitterions?

Question 55

Lys residues make up 10.5% of the weight of ribonuclease.The ribonuclease molecule contains 10 Lys residues.Calculate the molecular weight of ribonuclease.

Question 56

Draw the structure of Gly-Ala-Glu in the ionic form that predominates at pH 7.

Question 57

Name two uncommon amino acids that occur in proteins.By what route do they get into proteins?

Question 58

How can a polypeptide have only one free amino group and one free carboxyl group?

Question 59

The amino acid histidine has a side chain for which the pK_a is 6.0.Calculate what fraction of the histidine side chains will carry a positive charge at pH 5.4.Be sure to show your work.

Question 60

Draw the structures of the amino acids phenylalanine and aspartate in the ionization state you would expect at pH 7.0.Why is aspartate very soluble in water,whereas phenylalanine is much less soluble?

Question 61

Provide a brief definition for a polymorphic protein.

Question 62

A polypeptide is hydrolyzed,and it is determined that there are 3 Lys residues and 2 Arg residues (as well as other residues).How many peptide fragments can be expected when the native polypeptide is incubated with the proteolytic enzyme trypsin?

Question 63

Conjugated proteins contain chemical substituents in addition to amino acids.List three classes of conjugated proteins and identify the type of prosthetic group associated with each one.

Question 65

In one or two sentences,describe the usefulness of each of the following reagents or reactions in the analysis of protein structure:
(a)Edman reagent (phenylisothiocyanate)
(b)protease
(c)reducing agent (dithiothreitol or $\beta$ -mercaptoethanol)

Question 66

A biochemist wishes to determine the sequence of a protein that contains 123 amino acid residues.After breaking all of the disulfide bonds,the protein is treated with cyanogen bromide (CNBr),and it is determined that that this treatment breaks up the protein into seven conveniently sized peptides,which are separated from each other.It is your turn to take over.Outline the steps you would take to determine,unambiguously,the sequence of amino acid residues in the original protein.

Question 67

How are "signature sequences" useful in analyzing groups of functionally related proteins?

Question 68

Distinguish between homologs,paralogs,and orthologs as classes of related proteins.

Question 69

Define the primary structure of a protein.

Question 70

As a protein is purified,both the amount of total protein and the activity of the purified protein decrease.Why,then,does the specific activity of the purified protein increase?

Question 71

You are trying to determine the sequence of a protein that you know is pure.Give the most likely explanation for each of the following experimental observations.You may use a simple diagram for your answer.
(a)The Sanger reagent (FDNB,fluorodinitrobenzene)identifies Ala and Leu as amino-terminal residues,in roughly equal amounts.
(b)Your protein has an apparent M_r of 80,000,as determined by SDS-polyacrylamide gel electrophoresis.After treatment of the protein with performic acid,the same technique reveals two proteins of M_r 35,000 and 45,000.
(c)Size-exclusion chromatography (gel filtration)experiments indicate the native protein has an apparent M_r of 160,000.

Question 72

You are given a solution containing an enzyme that converts B into A.Describe what you would do to determine the specific activity of this enzyme solution.