Biochem

Question 1

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–Phe–Leu–Gly–Lys–Lys–Phe–Met–Gly.
c. His–Leu–Gly–Lys–Lys–Phe–Phe–Gly–Met.
d. Met–Leu–Phe–Lys–Phe–Gly–Gly–Lys–His.
e. His–Leu–Phe–Gly–Lys–Lys–Phe–Met–Gly.

Answer 1

e. His–Leu–Phe–Gly–Lys–Lys–Phe–Met–Gly

Question 2

All of the following are considered “weak” interactions in proteins, except:

a. peptide bonds
b. hydrogen bonds
c. ionic bonds
d. hydrophobic interactions
e. van der Waals forces

Answer 2

a. peptide bonds

Question 3

An average protein will be denatured by the compounds below, except:

Select one:

a. pH 10.
b. urea.
c. iodoacetic acid.
d. a detergent such as sodium dodecyl sulfate.

Answer 3

c. iodoacetic acid.

Question 4

At pH 3, aspartic acid (pKs are alpha-carboxylate 1.99, alpha-amino 9.9, beta-carboxylate 3.9 ) would be charged as follows:

Select one:

a. -1 alpha-carboxylate, +1 alpha-amino, 0 beta-carboxylate, 0 net charge
b. -1 alpha-carboxylate, +1 alpha-amino, -1 beta-carboxylate, -1 net charge
c. alpha-carboxylate, +1 alpha-amino, +1 beta-carboxylate, +2 net charge
d. alpha-carboxylate, -1 alpha-amino, 0 beta-carboxylate, -1 net charge
e. +1 alpha-carboxylate, +1 alpha-amino, +1 beta-carboxylate, +3 net charge

Answer 4

a. -1 alpha-carboxylate, +1 alpha-amino, 0 beta-carboxylate, 0 net charge

Question 5

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

Select one:

a. There is not enough information to answer the question.
b. It will stay the same.
c. It will become more positive.
d. It will become more negative
e. The answer depends on the salt concentration.

Answer 5

d. It will become more negative

Question 6

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

Select one:

a. It will become more positive.
b. It will become more negative
c. There is not enough information to answer the question.
d. the answer depends on the salt concentration.
e. It will stay the same.

Answer 6

e. It will stay the same.

Question 7

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

Select one:

a. separate proteins exclusively on the basis of molecular weight.
b. determine the amino acid composition of the protein.
c. determine an enzyme’s specific activity
d. preserve a protein’s native structure and biological activity
e. determine a protein’s isoelectric point

Answer 7

a. separate proteins exclusively on the basis of molecular weight.

Question 8

Compare the following sequences taken from four different proteins, and select the answer that best characterizes their relationships.
A B C
1 DVEKGKKIDIMKCS HTVEKGGKHKTGPNLH GLFGRKTGQAPGYSYT
2 DVQRALKIDNNLGQ HTVEKGAKHKTAPNVH GLADRIAYQAKATNEE
3 LVTRPLYIFPNEGQ HTLEKAAKHKTGPNLH ALKSSKDLMFTVINDD
4 FFMNEDALVARSSN HQFAASSIHKNAPQFH NLKDSKTYLKPVISET

Select one:

a. Protein 4 is the protein that shows the greatest overall homology to protein 1.
b. Based only on sequences in column B, protein 4 reveals the greatest evolutionary divergence.
c. Comparing proteins 1 and 2 in column A reveals that these two proteins have diverged the most throughout evolution.
d. The portions of amino acid sequence shown suggest that these proteins are completely unrelated.
e. Proteins 2 and 3 show a greater evolutionary distance than proteins 1 and 4

Answer 8

b. Based only on sequences in column B, protein 4 reveals the greatest evolutionary divergence.

Question 9

Consider an acetate buffer, initially at the same pH as its pKa (4.76). When sodium hydroxide (NaOH) is mixed with this buffer, the:

Select one:

a. pH remains constant.
b. sodium acetate formed precipitates because it is less soluble than acetic acid.
c. pH rises more than if an equal amount of NaOH is added to an acetate buffer initially at pH 6.76.
d. pH rises more than if an equal amount of NaOH is added to unbuffered water at pH 4.76.
e. ratio of acetic acid to sodium acetate in the buffer falls

Answer 9

e. ratio of acetic acid to sodium acetate in the buffer falls

Question 10

Experiments on denaturation and renaturation after the reduction and reoxidation of the —S—S— bonds in the enzyme ribonuclease (RNase) have shown that:

Select one:

a. the enzyme, dissolved in water, is thermodynamically stable relative to the mixture of amino acids whose residues are contained in RNase.
b. folding of denatured RNase into the native, active conformation requires the input of energy in the form of heat.
c. the primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure.
d. native ribonuclease does not have a unique secondary and tertiary structure.
e. the completely unfolded enzyme, with all —S—S— bonds broken, is still enzymatically active.

Answer 10

c. the primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure.

Question 11

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:

Select one:

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 11

b. a net positive charge.

Question 12

Humans usually wish each other happy birthday, happy holiday, or nice weekend, but some of them wish to their colleagues to have the lowest entropy. This wish usually means that they want their colleagues to:

Select one:

a. have a great activation energy
b. have a lower metabolism
c. be organized
d. be disorganized
e. have more free energy
f. have a dynamic steady state

Answer 12

c. be organized

Question 13

hydronium ion:

Select one:

a. has the structure H3O+.
b. is a hydrated hydrogen ion.
c. is the usual form of one of the dissociation products of water in solution.
d. is a hydrated proton.
e. All of the above are true.

Answer 13

e. All of the above are true.

Question 14

If the free energy change Delta G for a reaction is -46.11 kJ/mol, the reaction is:

Select one:

a. endothermic.
b. at equilibrium.
c. exergonic.
d. endergonic.
e. exothermic

Answer 14

c. exergonic

Question 15

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

Select one:

a. ribonuclease A Mr = 13,700
b. immunoglobulin G Mr = 145,000
c. RNA polymerase Mr = 450,000
d. cytochrome c Mr = 13,000
e. serum albumin Mr = 68,500

Answer 15

e. serum albumin Mr = 68,500

Question 16

In an alpha helix the hydrogen bonds:

Select one:

a. are roughly parallel to the axis of the helix.
b. are roughly perpendicular to the axis of the helix.
c. occur mainly between electronegative atoms of the R groups.
d. occur only near the amino and carboxyl termini of the helix.
e. occur only between some of the amino acids of the helix.

Answer 16

a. are roughly parallel to the axis of the helix

Question 17

In an alpha helix, the R groups on the amino acid residues:

Select one:

a. are found on the outside of the helix spiral.
b. stack within the interior of the helix.
c. alternate between the outside and the inside of the helix.
d. cause only right-handed helices to form.
e. generate the hydrogen bonds that form the helix

Answer 17

a. are found on the outside of the helix spiral.

Question 18

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

Select one:

a. Mass spectrometric analysis involved molecules in the gas phase.
b. Mass spectrometric analyses of macromolecules were too complex to interpret.
c. Most macromolecules could not be purified to the degree required for mass spectrometric analysis.
d. Macromolecules were insoluble in the solvents used in mass spectrometry.
e. The specialized instruments required were prohibitively expensive.

Answer 18

a. Mass spectrometric analysis involved molecules in the gas phase.

Question 19

Of the 20 standard amino acids, only ___________ is not optically active. The reason is that its side chain ___________.

Select one:

a. glycine; is unbranched
b. proline; forms a covalent bond with the amino group
c. alanine; is a simple methyl group
d. lysine; contains only nitrogen
e. glycine; is a hydrogen atom

Answer 19

e. glycine; is a hydrogen atom

Question 20

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

Select one:

a. removing cystines from protein sequences by proteolytic cleavage.
b. sequencing proteins that do not contain cysteinyl residues.
c. reducing disulfide bridges and preventing their re-formation by further modifying the —SH groups.
d. cleaving proteins with proteases that specifically recognize disulfide bonds.
e. protecting the disulfide bridge against spontaneous reduction to cysteinyl sulfhydryl groups.

Answer 20

c. reducing disulfide bridges and preventing their re-formation by further modifying the —SH groups.

Question 21

Phosphoric acid is tribasic, with pKa’s of 2.14, 6.86, and 12.4. The ionic form that predominates at pH 3.2 is:

Select one:

a. None of the above
b. PO43–
c. HPO42–
d. H3PO4.
e. H2PO4–

Answer 21

e. H2PO4–

Question 22

Roughly how many amino acids are there in one turn of an alpha helix?

Select one:

a. 4.2
b. 1.9
c. 3.6
d. 3.8
e. 10

Answer 22

c. 3.6

Question 23

Stereoisomers that are nonsuperimposable mirror images of each other are known as:

Select one:

a. cis-trans isomers.
b. enantiomers.
c. geometric isomers.
d. diastereoisomers.
e. anomers.

Answer 23

b. enantiomers.

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?

Select one:

a. 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.
b. The number 138 represents the molecular weight of conjugated amino acids.
c. 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.
d. The number 110 is based on the fact that the average molecular weight of a protein is 110,000 with an average of 1,000 amino acids.
e. The number 110 takes into account the relatively small size of nonstandard amino acids.

Answer 24

d. The number 110 is based on the fact that the average molecular weight of a protein is 110,000 with an average of 1,000 amino acids

Question 25

The bacterium E. coli requires simple organic molecules for growth and energy—it is therefore a:

Select one:

a. lithograph.
b. lithotroph.
c. chemoheterotroph.
d. photoautotroph.
e. chemoautotroph.
f. phototraph.

Answer 25

c. chemoheterotroph

Question 26

The enzyme fumarase catalyzes the reversible hydration of fumaric acid to l-malate, but it will not catalyze the hydration of maleic acid, the cis isomer of fumaric acid. This is an example of:

Select one:

a. racemization.
b. biological activity.
c. stereospecificity.
d. stereoisomerization.
e. chiral activity.

Answer 26

c. stereospecificity.

Question 27

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:

Select one:

a. proteins with similar isoelectric points can become free of charge
b. the individual bands undergo a second, more intense isoelectric focusing.
c. the proteins in the bands separate more completely because the second electric current is in the opposite polarity to the first current.
d. proteins with similar isoelectric points become further separated according to their molecular weights.
e. the individual bands become stained so that the isoelectric focus pattern can be visualized

Answer 27

d. proteins with similar isoelectric points become further separated according to their molecular weights.

Question 28

The Henderson-Hasselbalch equation:

Select one:

a. employs the same value for pKa for all weak acids.
b. does not explain the behavior of di- or tri-basic weak acids
c. relates the pH of a solution to the pKa and the concentrations of acid and conjugate base.
d. allows the graphic determination of the molecular weight of a weak acid from its pH alone.
e. is equally useful with solutions of acetic acid and of hydrochloric acid.

Answer 28

c. relates the pH of a solution to the pKa and the concentrations of acid and conjugate base.

Question 29

The major carrier of chemical energy in all cells is:

Select one:

a. uridine diphosphate.
b. FedEx
c. adenosine monophosphate.
d. acetyl triphosphate.
e. cytosine tetraphosphate.
f. adenosine triphosphate.

Answer 29

f. adenosine triphosphate

Question 30

The most important contribution to the stability of a protein’s conformation appears to be the:

Select one:

a. stabilizing effect of hydrogen bonding between the carbonyl group of one peptide bond and the amino group of another.
b. entropy increase from the decrease in ordered water molecules forming a solvent shell around it.
c. sum of free energies of formation of many weak interactions between its polar amino acids and surrounding water.
d. entropy increase from the increase in ordered water molecules forming a solvent shell around it.
e. maximum entropy increase from ionic interactions between the ionized amino acids in a protein.

Answer 30

b. entropy increase from the decrease in ordered water molecules forming a solvent shell around it

Question 31

The pH of a sample of blood is 7.4, while gastric juice is pH 2.4. The blood sample has:

Select one:

a. 100,000 times lower [H+] than the gastric juice.
b. 6 times lower [H+] than the gastric juice.
c. 0.189 times the [H+] as the gastric juice.
d. 5.29 times lower [H+] than the gastric juice.
e. a million times lower [H+] than the gastric juice

Answer 31

a. 100,000 times lower [H+] than the gastric juice.

Question 32

The pH of a solution of 1 M HCl is:

Select one:

a. 0
b. 1
c. 10
d. 0.1

Answer 32

a. 0

Question 33

The positive charge on proteins in electrospray ionization mass spectrometry is the result of:

Select one:

a. a low pH.
b. protons fired at the gas-phase protein molecules.
c. electrons fired at the gas-phase protein molecules.
d. protonated Asp and Glu residues.
e. protonated Arg and Lys residues.

Answer 33

a. a low pH

Question 34

The three-dimensional structure of macromolecules is formed and maintained primarily through noncovalent interactions. Which one of the following is not considered a noncovalent interaction?

Select one:

a. van der Waals interactions
b. hydrogen-carbon bonds
c. hydrophobic interactions
d. hydrogen bonds
e. ionic interactions

Answer 34

b. hydrogen-carbon bonds

Question 35

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

Select one:

a. —NH3+ + OH? —NH2 + H2O.
b. —NH2 + OH? —NH + H2O.
c. —COOH + —NH2 —COO + —NH2+.
d. —COO + —NH2+ —COOH + —NH2.
e. —COOH + OH? —COO + H2O

Answer 35

a. —NH3+ + OH? —NH2 + H2O

Question 36

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

Select one:

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

Answer 36

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

Question 37

Which of the following is not known to be involved in the process of assisted folding of proteins?

Select one:

a. Peptide bond isomerization
b. Disulfide interchange
c. Peptide bond hydrolysis
d. Chaperonins
e. Heat shock proteins

Answer 37

c. Peptide bond hydrolysis

Question 38

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

Select one:

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

Answer 38

a. On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine.

Question 39

Which of the following statements about buffers is true?

Select one:

a. At pH values lower than the pKa, the salt concentration is higher than that of the acid.
b. The strongest buffers are those composed of strong acids and strong bases.
c. A buffer composed of a weak acid of pKa = 5 is stronger at pH 4 than at pH 6.
d. The pH of a buffered solution remains constant no matter how much acid or base is added to the solution.
e. When pH = pKa, the weak acid and salt concentrations in a buffer are equal.

Answer 39

e. When pH = pKa, the weak acid and salt concentrations in a buffer are equal.

Question 40

Which of the following statements about cystine is correct?

Select one:

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 formed by the oxidation of the carboxylic acid group on cysteine.
c. Cystine is an example of a nonstandard amino acid, derived by linking two standard amino acids.
d. Two cystines are released when a —CH2—S—S—CH2— disulfide bridge is reduced to —CH2—SH.
e. Cystine is formed through a peptide linkage between two cysteines.

Answer 40

a. Cystine forms when the —CH2—SH R group is oxidized to form a —CH2—S—S—CH2— disulfide bridge between two cysteines

Question 41

Which of the following statements concerning protein domains is true?

Select one:

a. They have been found only in prokaryotic proteins.
b. They are a form of secondary structure.
c. They are examples of structural motifs.
d. They consist of separate polypeptide chains (subunits).
e. They may retain their correct shape even when separated from the rest of the protein.

Answer 41

e. They may retain their correct shape even when separated from the rest of the protein.

Question 42

Which of the following statements concerning the process of spontaneous folding of proteins is false?

Select one:

a. It may be defective in some human diseases.
b. It may be an essentially random process.
c. It may involve initial formation of a highly compact state.
d. It may involve initial formation of local secondary structure.
e. It may involve a gradually decreasing range of conformational species

Answer 42

b. It may be an essentially random process.

Question 43

Which of the following statements is false?

Select one:

a. Collagen is a protein in which the polypeptides are mainly in the alpha-helix conformation.
b. Silk fibroin is a protein in which the polypeptide is almost entirely in the beta conformation.
c. Alpha-keratin is a protein in which the polypeptides are mainly in the alpha-helix conformation.
d. Disulfide linkages are important for keratin structure.
e. Gly residues are particularly abundant in collagen.

Answer 43

a. Collagen is a protein in which the polypeptides are mainly in the alpha-helix conforma