Deck 3: Protein I: Composition and Structure

Question 1

Covalent modifications of collagen include all of the following EXCEPT

A) hydroxylation of proline and lysine.
B) glycosylation of hydroxylysine.
C) oxidation of lysine or hydroxylysine.
D) formation of covalent cross-links by virtue of the reactivity of allysine or hydroxyallysine aldehyde groups.
E) stabilization of the mature fiber with disulfide bonds.

Answer 1

stabilization of the mature fiber with disulfide bonds.

Question 2

A major force that contributes to the conformation of proteins and, in globular proteins, occurs primarily in their interior is

A) hydrogen bonds.
B) charged dipoles.
C) hydrophobic interactions.
D) disulfide bridges.
E) hydration by water.

Answer 2

hydrophobic interactions.

Question 3

The amino acid side-chain which most commonly interacts to form covalent bonds in proteins

A) contains an amino group.
B) can form an ester with an alcohol.
C) contains a sulfhydryl group.
D) is that of histidine.
E) is that of glutamate.

Answer 3

contains a sulfhydryl group.

Question 4

An amino acid containing an amide function in its side chain

A) proline.
B) lysine.
C) arginine.
D) asparagine.
E) histidine.

Question 5

All of the following statements are correct about lipoproteins EXCEPT

A) they are a complex of protein, phospholipids and neutral lipids.
B) they are found in the plasma and cellular membrane.
C) they are covalent complexes of lipids and proteins.
D) the lipids and proteins are separable from one another by treatment with detergent.
E) most or all of the lipid can be removed from the protein by extraction with chloroform-methanol mixtures.

Question 6

SDS/polyacrylamide gel electrophoresis separates proteins based on

A) size of the polypeptide chain
B) net charge of the native protein
C) net charge of the denatured protein
D) all of the above
E) none of the above

Question 7

The peptide bond has all of the following characteristics EXCEPT

A) planarity.
B) freedom to rotate.
C) polarity.
D) greater stability in TRANS configuration.
E) partial double bond character.

Question 8

At their isoelectric point proteins have:

A) no ionized groups.
B) no positively charged groups.
C) no negatively charged groups.
D) equal numbers of positively and negatively charged groups.
E) an increased affinity for substrate.

Question 9

Proteins will normally exhibit minimum solubility in aqueous solutions at

A) a pH values above Pi.
B) a pH values below Pi.
C) a pH value = Pi.
D) low salt concentrations.
E) none of the above

Question 10

All of the following are involved as factors governing the folding of a protein EXCEPT which one?

A) Hydrogen bonds between groups involved in peptide bonding.
B) Hydrogen bonds between amino acid side chains.
C) Electrostatic interactions.
D) Hydrophobic bonding.
E) They are all involved.

Question 11

Adding an organic solvent to a protein solution may cause all of the following EXCEPT which one?

A) aggregation.
B) denaturation.
C) alteration of electrostatic interactions.
D) rupture of covalent bonds.
E) rupture of hydrophobic bonds.

Question 12

Bonding attraction and repulsion are determined by the distance between the two bonding atoms. Which type of bonding includes a type of repulsion called steric hindrance?

A) Covalent
B) Electrostatic
C) Hydrogen
D) Hydrophobic
E) Van der Waals

Question 13

Hemoglobin A differs from hemoglobin S in having two more anionic groups (both hemoglobins have a molecular weight of approximately 67,000). Which one of the following separation methods is most likely to distinguish between these two hemoglobins?

A) Precipitation with ethanol
B) Gel filtration
C) Ultracentrifugation
D) Electrophoresis

Question 14

In N-linked or type 1 glycoproteins, the linkage between the protein and the oligosaccharide is to which of the following amino acid residues?

A) serine
B) threonine
C) lysine
D) hydroxylysine
E) asparagines

Question 15

Which amino acid residue is least likely to be found on surfaces of globular proteins in aqueous solution?

A) Glutamate
B) Serine
C) Valine
D) Glutamine
E) Arginine

Question 16

The following protein separation techniques take advantage of the charge differences between various proteins EXCEPT for:

A) Diethylaminoethyl (DEAE) chromatography
B) Two dimensional gel electrophoresis
C) Isoelectric focusing
D) Gel filtration chromatography

Question 17

Which of the following is responsible for the maintenance of protein secondary structure?

A) salt bridges
B) hydrogen bonds
C) van der Waals forces
D) hydrophobic interactions
E) disulfide crosslinks

Question 18

Which of the following statements about protein structure is correct?

A) The alpha-helix conformation is stabilized by hydrophobic interactions.
B) The beta-sheet conformation is rarely found in globular proteins.
C) The folding of a polypeptide into a globular structure results in an interior enriched with hydrophobic amino acids.
D) The primary structure does not influence the native tertiary structure.
E) The subunits of proteins with quaternary structure associate through covalent bonds.

Question 19

Which of the following amino acids will terminate an alpha helical structure in globular proteins?

A) Tryptophan
B) Proline
C) Tyrosine
D) Histidine
E) Isoleucine

Question 20

If two proteins have the same molecular weight then it follows that they also have

A) the same amino acid composition.
B) the same sedimentation coefficient.
C) the same diffusion coefficient.
D) the same conformation.
E) none of the above

Question 21

Which of the following statements about cystine is true?

A) cystine is two cysteine molecules covalently attached by a disulfide bridge
B) cystine is formed by the reduction of two cysteines
C) cystine is a dipeptide
D) cystine is a tripeptide
E) cystine forms disulfide bridges with methionine

Question 22

The primary sequence of proteins is best described by the statement that proteins

A) contain amino acids.
B) include all the nitrogen compounds of tissues.
C) are salts of amino acids linked with one another.
D) are polymers formed by hydrogen bonding between the amino acids.
E) are polymers formed by amide linkages between the carboxyl and alpha-amino groups of alpha-amino acids.

Question 23

Which of the following mutations would you expect to cause the most drastic alteration in the functional performance of a polypeptide chain? (Assuming the replacement is not at the active site)

A) Replacement of glutamate with lysine.
B) Replacement of valine with alanine.
C) Replacement of aspartic acid with glutamic acid.
D) Replacement of lysine with arginine.

Question 24

Edman degradation refers to

A) a metabolic pathway for catabolism of proteins.
B) a chemical method for determination of the N-terminal amino acid sequence of proteins and polypeptides.
C) an enzymatic method for determination of the C-terminal sequence of proteins and polypeptides.
D) a chemical method for determination of the C-terminal sequence of proteins and polypeptides.
E) None of the above statements correctly refer to the Edman degradation.

Question 25

All of the following statements about the alpha-helix are true EXCEPT:

A) the alpha-helix is right-handed.
B) there are 3.6 amino acids per turn of the alpha-helix.
C) the R groups of the amino acids are externally directed.
D) the alpha-helix is stabilized primarily by hydrophobic interactions.
E) the structure of the alpha-helix was predicted before it was observed in a protein

Question 26

The following is the structure of which amino acid? (CH3)2-CH-CH2-CHNH2-COOH

A) isoleucine
B) threonine
C) arginine
D) valine
E) lysine

Question 27

Which statement below is most correct regarding the alpha helical structure of polypeptide chains in proteins?

A) It is primarily dependent upon hydrogen bonding.
B) It is primarily dependent upon disulfide linkages.
C) It is found in all proteins.
D) It refers to interactions between adjacent chains in fibrous proteins.

Question 28

When a protein is hydrolyzed there is

A) a decrease in free carboxyl groups.
B) an increase in free amino groups.
C) a large decrease in pH.
D) formation of peptide bonds.
E) a decrease in free amino groups.

Question 29

Which of the following is not an example of secondary structure;

A) Beta-pleated sheet
B) collagen triple helix
C) Alpha-helix
D) Beta-bend
E) disulfide bridge

Question 30

Hemoglobin A differs from hemoglobin S in having two more anionic groups (both hemoglobins have a molecular weight of approximately 67,000). Which one of the following separation methods is most likely to distinguish between these two

A) Precipitation with ethanol
B) Gel filtration
C) Ultracentrifugation
D) Electrophoresis

Question 31

The formation of a peptide bond between two amino acids

A) creates partial double-bond character among three atoms.
B) permits unrestricted rotations about each chemical bond.
C) places the alpha-carbons in the "centers" of two different planes.
D) retains the chemical properties of the typical ester bond.

Question 32

What leads to "superfolds"?

A) Evolutionary development
B) Ratio of a-helices to b-pleated sheets
C) Similar function
D) Similar primary structure
E) Thermodynamic stability

Question 33

The isoelectric point of arginine is approximately

A) 1
B) 3
C) 5
D) 7
E) 11

Question 34

Which of the following statements about protein structure is correct?

A) Disulfide interactions are required for the stability of globular structures.
B) Hydrophobic sidechains commonly occur clustered in interior areas of globular proteins.
C) The alpha-helix is maintained chiefly by hydrophobic interactions.
D) Covalent linkages between the protomeric chains are a common feature of globular oligomeric proteins such as hemoglobin and lactate dehydrogenase (LDH).
E) Pleated-sheet structures are found only in fibrous proteins.

Question 35

Each of the following statements about the side chains of amino acid residues is true EXCEPT which one?

A) Isoleucine, valine and tryptophan tend to be in the interior of protein molecules.
B) Catalytically functional groups include aspartate, histidine and cysteine.
C) Tyrosine, phenylalanine and threonine participate in hydrogen bond formation.
D) Lysine, arginine and glutamate form ionic bonds with substrates and other protein components.
E) Lysine, cysteine and tyrosine have pKa's higher than 7.0.

Question 36

At the isoionic point

A) proteins are least soluble.
B) the net ionic charge is zero.
C) repulsive forces between proteins are at a minimum.
D) the pH of the solution may vary widely from protein to protein.
E) all of the above

Question 37

Which of the following is a kind of physical/chemical interaction of major quantitative importance in the overall structure of most globular proteins and occurs chiefly in the interior areas of the molecule?

A) Disulfide bridges.
B) Hydrophobic bonds.
C) Amide linkages between amino acid sidechains.
D) Ester linkages between sidechains of acidic and alcoholic amino acids.
E) Hydrogen bonds to water molecules.

Question 38

amino acids are classified according to the nature of their side chain. All of the following amino acids are correctly classified EXCEPT

A) Serine : polar, uncharged.
B) Glutamic : polar, acidic.
C) Arginine : polar, basic.
D) Histidine : nonpolar, uncharged.
E) Phenylalanine : nonpolar, uncharged.

Question 39

At a pH more acidic than its isoelectric point, an amino acid will carry

A) a net negative charge.
B) a net positive charge.
C) a positive charge equal to the negative charge.
D) no ionic charge.
E) an unknown charge, since its concentration is not specified.

Question 40

The alpha helix structure of a protein can be considered an example of:

A) quaternary structure
B) tertiary structure
C) secondary structure
D) primary structure
E) none of the above

Question 41

Information on which of the following features of a protein can be obtained by means of optical rotary dispersion?

A) helical content
B) subunit content
C) disulfide interactions
D) ligand binding specificity
E) isoionic point

Question 42

Within the native tertiary structure of a typical globular protein, interactions between an alpha-helix and a beta_sheet would occur primarily

A) after the incorporation of a prosthetic group during polypeptide folding.
B) by non-covalent interactions among the amino acid side chains.
C) following the hydrolysis of ATP.
D) in the presence of one or more chaperones.
E) near the ends of these structural conformations.

Question 43

Which of the following tripeptides will move anodically (positive electrode) during electrophoresis at pH 5?

A) asp-his-lys
B) arg-pro-gly
C) asn-glu-val
D) gln-his-arg

Question 44

When a protein has alpha-helical structure, how many amino acid residues are there per turn of the helix?

A) 2.6
B) 3.2
C) 3.6
D) 4.2
E) none of the above

Question 45

Which of the following techniques is best suited for the determination of the subunit molecular weight of an oligomeric protein?

A) circular dichroism
B) sedimentation velocity ultracentrifugation
C) SDS polyacrylamide gel electrophoresis
D) gel chromatography in dilute buffer
E) cellulose acetate electrophoresis

Question 46

An amino acid residue which forms a covalent link to sugar moieties in collagen is

A) hydroxylysine.
B) proline.
C) lysine.
D) glycine.
E) desmosine.

Question 47

L-amino acids are the most common form. L signifies

A) the absolute configuration of the asymmetric C-atom as compared to L-glyceraldehyde.
B) the levorotation of plane polarized light by solutions of these compounds.
C) the fact that the amino group is attached to C-atom #1.
D) the designation is of historical origin and bears no relationship to structure.
E) none of the above

Question 48

If gly has a positive charge in a buffer at pH 1, then gly-gly-gly in the same buffer should have which of the following charges?

A)+3
B)+2
C)+1
D)-1
E)-2

Question 49

The surface shell of a lipoprotein such as a chylomicron or very low density lipoprotein (VLDL) is composed chiefly of

A) phospholipid.
B) cholesterol ester.
C) triglyceride.
D) ganglioside.

Question 50

In man, the serum lipoprotein with the highest cholesterol content is

A) alpha-lipoprotein
B) beta-lipoprotein
C) pre-beta-lipoprotein
D) chylomicrons
E) pre-albumin

Question 51

Protein-protein hydrogen bonding is involved in all of the following structural features in proteins EXCEPT

A) alpha-helix.
B) Beta-sheet conformation.
C) Reverse-turn (beta bend).
D) Random coil.
E) Collagen triple helix.

Question 52

All of the following statements about protein structure are correct EXCEPT which one?

A) Other than peptide bonds, hydrogen bonding is the most important interaction in pleated sheet and alpha-helical structures.
B) The peptide bond is one kind of amide linkage.
C) The native state of a protein is the least stable form under cell conditions and accordingly is easily denatured.
D) In the alpha helix, the amino acid side chains project out from the coiled backbone of the polypeptide chain.
E) Globular proteins often contain a pocket or groove into which a prosthetic group or substrate can fit.

Question 53

amino acid side chains which may be involved in hydrogen bonding in proteins include

A) leucine.
B) isoleucine.
C) alanine.
D) tyrosine.
E) phenylalanine.

Question 54

Which of the following is not a feature of collagen?

A) a repeating tripeptide sequence, Gly-Xaa-Pro or Gly-Xaa-HyPro
B) a long triple helix
C) the unusual amino acid hydroxyproline
D) glycine at every third residue of the helix
E) beta-pleated sheet secondary structure

Question 55

Cysteine can be converted to cystine by

A) acylation.
B) peptide bond formation.
C) reduction.
D) oxidation.
E) esterification.

Question 56

The term denaturation, when used in connection with nucleic acids or proteins refers to a change in structural characteristics due to

A) the disruption of covalent bonds.
B) the disruption of non-covalent bonds.
C) the binding of toxic compounds.
D) changes in primary structure.
E) changes in the state of aggregation.

Question 57

Which amino acid possesses a guanidinium group in the side chain?

A) Arginine
B) Aspartate
C) Methionine
D) Leucine
E) Serine

Question 58

Collagen is a protein whose conformation is characterized by

A) a triple helix.
B) a double alpha-helix.
C) antiparallel beta-sheet regions.
D) mostly random coil regions.
E) the lack of any stable conformation.

Question 59

What is the isoelectric point of cysteine? (pK1 = 1.96, pK2 = 8.18 and pK3 = 10.28).

A) 1.96
B) 5.07
C) 8.18
D) 9.23
E) 10.28

Question 60

Which of the following describes the side chain of leucine?

A) contains a sulfhydryl group
B) contains an alcoholic group
C) contains an branched chain hydrocarbon
D) doesn't have a side chain
E) contains an acidic group

Question 61

Information about the secondary structures of a protein most reliably and unambiguously derives from

A) complementary DNA analysis.
B) ion-exchange chromatography.
C) polyacrylamide gel electrophoresis.
D) ultraviolet spectroscopy.
E) x-ray crystallography.

Question 62

At their isoelectric point proteins have

A) no ionized groups.
B) no positively charged groups.
C) no negatively charged groups.
D) equal numbers of positively and negatively charged groups.
E) none of the above

Question 63

How many carbon and nitrogen atoms are there, respectively, in a single turn of an alpha-helix?

A)6 5
B)7 5
C)7 4
D)6 4
E)5 7

Question 64

Which of the following is a characteristic of the amino acid composition of a protein which has an isoelectric pH (pI) of 9.5 ?

A) no basic amino acids
B) no acidic amino acids
C) no neutral amino acids
D) more basic than acidic amino acids
E) more acidic than basic amino acids

Question 65

We have treated a protein with chymotrypsin (cleaves at aromatic amino acid residues) and have isolated a polypeptide fragment produced during the chymotryptic digestion. The amino acid composition of the polypeptide was found to be amino acid moles/mole polypeptide lysine (lys)2 glycine (gly) 1 serine (ser)1 phenylalanine (phe)1. The N-terminal amino acid, determined by the dansylation procedure, was serine. Treatment of the polypeptide with trypsin (cleaves at basic amino acid residues) gave two dipeptides plus free phenylalanine What is the amino acid sequence of this polypeptide?

A) ser-gly-lys-phe-lys
B) gly-lys-ser-lys-phe
C) ser-gly-lys-lys-phe
D) phe-lys-gly-ser-lys
E) ser-lys-gly-lys-phe

Question 66

Which one of the following factors is considered to be the major force which leads to conformational stability of globular proteins?

A) hydrogen bonding.
B) hydrophobic interactions.
C) ionic interactions.
D) disulfide bonding.
E) van der Waals forces.

Question 67

Which of the following amino acid residues may participate in strong hydrophobic bonding?

A) Glycine.
B) Isoleucine.
C) Lysine.
D) Serine.
E) Aspartate.

Question 68

Which of the following measurements can provide the most information about the overall shape of a protein?

A) Isoelectric point.
B) pH of maximum buffering.
C) Intrinsic viscosity.
D) amino acid composition.
E) Ultraviolet absorption.

Question 69

Which of the following describes the side chain of glutamine?

A) contains a branched chain hydrocarbon
B) contains a sulfhydryl group
C) contains an aromatic ring
D) contains a methyl group
E) contains an amide

Question 70

An essential element of the alpha-helical structure of proteins is

A) disulfide bonds.
B) hydrogen bonds perpendicular to the axis.
C) salt links.
D) hydrogen bonds randomly placed.
E) hydrogen bonds parallel to the axis.

Question 71

What is the reason for the planar geometry of the peptide bond in proteins?

A) Proteins contain only L amino acids.
B) Hydrogen bonding.
C) Steric hindrance.
D) The peptide bond is trans rather than cis.
E) The partial double bond character of the carbon-nitrogen bond.

Question 72

Information indicating that the final conformation of a protein is determined by the amino acid sequence in its polypeptide chains was obtained from

A) difference spectroscopy.
B) reversible denaturation.
C) atomic adsorption.
D) hydrodynamic analysis.
E) sequence analysis.

Question 73

The primary structure of a protein refers to its

A) ability to form intrachain hydrogen bonds.
B) amino acid sequence.
C) folding induced by disulfide linkages.
D) ability to form subunit structures.
E) ability to form interchain hydrogen bonds.

Question 74

Which of the following amino acids is most likely to be found on the interior of a protein?

A) lysine
B) threonine
C) isoleucine
D) arginine
E) aspartic acid

Question 75

All of the following statements regarding collagen are correct EXCEPT which one?

A) Collagen is the most abundant protein in the human.
B) Collagen has an amino acid composition typical of that found in most soluble proteins.
C) Collagen is a very inelastic protein in the native state.
D) Collagen is a very insoluble protein in the native state.
E) Collagen is made up of subunits termed tropocollagen.

Question 76

Which of the following amino acids would be considered the MOST polar?

A) Alanine.
B) Proline.
C) Isoleucine.
D) Threonine.
E) Phenylalanine.

Question 77

All of the following generalizations are correct with regard to the overall structure of a protein EXCEPT which one?

A) amino acid residues on the surface of the protein are polar.
B) amino acid residues in the interior are hydrophobic.
C) Charged amino acids on the protein interact with ions in the environment.
D) The alpha-helix or the pleated sheet is present in most proteins.
E) Hydrogen bonds in the peptide backbone play a minor role in the structure of the protein.

Question 78

Which of the following sections of a polypeptide chain have amino acid side chains, all of which are capable of forming hydrogen bonds?

A) leu-val-phe
B) cys-his-ala
C) ile-ser-trp
D) val-arg-pro
E) asp-lys-ser

Question 79

A peptide bond

A) contributes atoms to hydrophobic interactions.
B) exhibits unrestricted rotation around the C-N bond.
C) is formed between the side chains of Glu and Lys residues.
D) is planar and partially ionic.

Question 80

In X-ray crystallography, the atoms which can diffract X-rays and thus be located within 3-dimensional space are the following EXCEPT for

A) hydrogen
B) carbon
C) nitrogen
D) oxygen
E) sulfur