Lecture 6 Chapter 4 Protein Structure

Question 1

What will be the weight of a protein consisting of 250 amino acid residues?
a. 27,500 g mol–1
b. 22,000 g mol–1
c. 5500 g mol–1
d. 25,000 g mol–1
e. 250 kDa

Answer 1

a. 27,500 g mol–1

Question 2

What groups of amino acids are linked in the primary sequence?
a. β-amino group and α-carboxyl group
b. α-amino group and β-carboxyl group
c. α-amino group and α-carboxyl group
d. α-nitro group and α-carboxyl group
e. β-nitro group and β-carboxyl group

Answer 2

c. α-amino group and α-carboxyl group

Question 3

What does polarity mean?
a. ends of a polypeptide chain have different charges of the carboxyl group
b. ends of a polypeptide chain always have different amino acid residues
c. ends of an amino acid residue can link only the same amino acid residue
d. a polypeptide chain has the amino-terminal residue and the carboxyl-terminal residue
e. a polypeptide chain has the amino-terminal residue with a different charge

Answer 3

d. a polypeptide chain has the amino-terminal residue and the carboxyl-terminal residue

Question 4

Which statements about the polypeptide Gly-Tyr-Gly-Phe-Met-Ser are CORRECT? Select all that apply.
a. Glycine is the C-terminal residue.
b. Serine is the N-terminal residue.
c. Serine is the C-terminal residue.
d. Methionine is the N-terminal residue.
e. Glycine is the N-terminal residue.

Answer 4

c. Serine is the C-terminal residue./ e. Glycine is the N-terminal residue.

Question 5

. What is the regularly repeating part of a polypeptide called?
a. the distinctive side chain
b. a variable part
c. a peptide
d. the backbone
e. an oligopeptide

Answer 5

d. the backbone

Question 6

What is the distance between the nitrogen and carbon atoms in a peptide bond?
a. 1.45 Å
b. 1.27 Å
c. 1.51 Å
d. 5.4 Å
e. 1.32 Å

Answer 6

e. 1.32 Å

Question 7

Why are peptide bonds of proteins found mainly in the trans configuration in nature?
a. In the cis configuration, side chains of amino acids are most distant from each other but steric clashes between the groups are necessary.
b. In the trans configuration, side chains of amino acids are most distant from each other and steric clashes between the groups are excluded.
c. In the trans configuration, side chains of amino acids are least distant from each other and steric clashes between the groups are excluded.
d. In the trans configuration, the two adjacent rigid peptide units may rotate about amino acid bonds.
e. The trans configuration contributes to the rotation of radicals in a clockwise direction.

Answer 7

In the trans configuration, side chains of amino acids are most distant from each other and steric clashes between the groups are excluded.

Question 8

What is the difference between a peptide and a protein?
a. the number of amino acid residues
b. the configuration of peptide bonds
c. the structure of amino acid residues
d. the charge of functional groups
e. torsion angles

Answer 8

a. the number of amino acid residues

Question 9

. What structures of polypeptide chains were proposed by Linus Pauling and Robert Corey?
a. primary structures
b. turns and loops
c. secondary structures
d. the alpha helix and the beta pleated sheet
e. cis and trans configurations

Answer 9

d. the alpha helix and the beta pleated sheet

Question 10

What helices are energetically more favorable?
a. right-handed
b. counterclockwise
c. left-handed
d. twisted ribbons
e. disulfide-bonded

Answer 10

a. right-handed

Question 10

In the formation of the alpha helix, the carbonyl group is connected by:
a. a hydrogen bond not with a neighboring NH group, but with a NH group located at a distance of four amino acid residues from it.
b. a hydrogen bond with a neighboring NH group.
c. a disulfide bond not with a neighboring NH group, but with a NH group located at a distance of four amino acid residues from it.
d. a peptide bond with a neighboring NO group.
e. a hydrogen bond with a single amino acid on an adjacent strand.

Answer 10

a. a hydrogen bond not with a neighboring NH group, but with a NH group located at a distance of four amino acid residues from it.

Question 10

What is the distance between adjacent amino acids along the α helix and along the β strand (respectively)?
a. 3.5 Å and 1.5 Å
b. 5.4 Å and 45 Å
c. 5.4 Å and 3.6 Å
d. 1.5 Å and 36 Å
e. 1.5 Å and 3.5 Å

Answer 10

e. 1.5 Å and 3.5 Å

Question 11

Aspartate can’t form the α-helix because it:
a. has a ring structure.
b. has closely located radicals that have a tendency to steric clashes.
c. has hydrogen-bond acceptors that compete for the main chain groups.
d. is a too short amino acid to form the α-helix.
e. does not have NH groups.

Answer 11

c. has hydrogen-bond acceptors that compete for the main chain groups.

Question 12

Collagen has:
a. pyrrolidine rings, which stabilize helices and glycine residues at every third position (because only glycine residues can fit inside of the super-helical cable).
b. pyrrolidine rings, which can push off and destabilize the helix and glycine residues at every second position (because only glycine residues can fit inside of the super-helical cable).
c. rings of proline and glutamine residues at every second position.
d. rings of glycine, which can stabilize helices and proline residues at every third position (because only proline residues can fit inside of the super-helical cable).
e. rings of proline and glycine residues at every second position.

Answer 12

a. pyrrolidine rings, which stabilize helices and glycine residues at every third position (because only glycine residues can fit inside of the super-helical cable).

Question 13

What tertiary structure does myoglobin have?
a. eight β sheets and α helices, turns and loops
b. eight α helices, turns and loops between helices, and heme group
c. eight β sheets, turns and loops between helices, and heme group
d. seven β sheets, turns and loops between helices
e. seven α helices, turns and loops between helices

Answer 13

b. eight α helices, turns and loops between helices, and heme group

Question 14

Where are the majority of nonpolar residues located in myoglobin?
a. The outside of myoglobin.
b. The interior of myoglobin.
c. Myoglobin consists of only nonpolar residues.
d. The outside and the interior of myoglobin.
e. The outside of the super helix.

Answer 14

b. The interior of myoglobin.

Question 15

How can you protect side chains of the main chain from interaction with water?
a. pair all of the NO and CO groups by peptide bonding
b. convert all nonpolar residues to polar ones
c. form α helices and β sheets
d. form quaternary structure
e. form superhelices

Answer 15

c. form α helices and β sheets

Question 16

What is a helix-turn-helix motif?
a. supersecondary structure in which an α helix is separated from another α helix by a turn
b. supersecondary structure in which a β sheet is separated from a helix by a turn
c. secondary structure in which two right-handed α helices are intertwined
d. secondary structure in which two left-handed α helices are intertwined
e. secondary structure in which an α helix is separated from a β sheet by a loop

Answer 16

a. supersecondary structure in which an α helix is separated from another α helix by a turn

Question 17

What types of interactions are in the quaternary structure? Select all that apply.
a. disulfide bonds
b. ionic bonds
c. hydrogen bonds
d. peptide bonds
e. van der Waals forces

Answer 17

b. ionic bonds
c. hydrogen bonds
e. van der Waals forces

Question 18

A denatured protein is a protein:
a. devoid of enzymatic activity.
b. with destroyed noncovalent bonds.
c. in which the disulfides are fully converted into sulfhydryls.
d. that was treated with β-mercaptoethanol.
e. that has been transformed into a random coiled peptide incapable of normal activities.

Answer 18

e. that has been transformed into a random coiled peptide incapable of normal activities.

Question 19

Proteins that are exceptions to the paradigm that a given protein amino acid sequence will fold into a particular three-dimensional structure are those that:
a. perform different functions in different conditions and with a different partner.
b. are only hydrophobic.
c. are only hydrophilic.
d. perform different functions with the same partners.
e. have a different structure.

Answer 19

a. perform different functions in different conditions and with a different partner.

Question 20

What led to the conclusion that information about catalytic activity is contained in the primary sequence?
a. Anfinsen’s experiment, which showed that denatured protein can spontaneously restore its structure after exposure to denaturing agents
b. Sanger’s experiment, which showed that a protein has a precisely defined amino acid sequence
c. Sanger’s experiment, which showed that denatured protein can spontaneously restore its structure after exposure to denaturing agents
d. Ramachandran’s experiment about the φ and ψ angles
e. Anfinsen’s experiment, which showed that a protein has a precisely defined amino acid sequence

Answer 20

a. Anfinsen’s experiment, which showed that denatured protein can spontaneously restore its structure after exposure to denaturing agents

Question 21

What is the difference between calculated and actual folding time called?
a. Dawkins’ paradox
b. folding funnel
c. Ramachandran plot
d. Levinthal’s paradox
e. Anfinsen’s paradox

Answer 21

d. Levinthal’s paradox

Question 22

. What proteins have multiple conformations?
a. ribonuclease and α-keratin
b. collagen and prions
c. synuclein and lymphotactin
d. myoglobin and lymphotactin
e. synuclein and collagen

Answer 22

c. synuclein and lymphotactin

Question 23

Prions are:
a. proteins that are normally present in the brain.
b. agents that are similar in size to viruses but consist only of protein.
c. agents causing viral brain diseases.
d. uncommon for brain proteins with a complex structure.
e. proteins contributing to the correct folding of proteins.

Answer 23

a. proteins that are normally present in the brain.

Question 24

In a Ramachandran plot:
a. the values of 0 to +180 for the angle of the N–αC bond and of 0 to –180 for the angle of the αC–C bond are strongly disfavored.
b. the φ angle is positive if the amino group is rotated to the left from the α carbon.
c. only a small part of conformations is sterically excluded because two atoms cannot be in the same place at the same time.
d. clockwise rotations of the torsion angles correspond to the negative values.
e. the ψ angle corresponds to the bond between the amino group and α carbon.

Answer 24

a. the values of 0 to +180 for the angle of the N–αC bond and of 0 to –180 for the angle of the αC–C bond are strongly disfavored.

Question 25

Choose the CORRECT statement concerning the folding funnel.
a. As the percentage of protein residues in native conformation increases, the total energy of the protein decreases, which increases the entropy of the protein.
b. The energy of the protein grows as more hydrophobic interactions occur upon protein folding.
c. In the nucleation-condensation model, both local and long-range interactions take place to lead to the formation of the native state.
d. The molten globule model assumes that local interactions facilitate long-range hydrophobic interactions upon protein folding.
e. The molten globule state has a lower energy than the partially correct intermediate.

Answer 25

c. In the nucleation-condensation model, both local and long-range interactions take place to lead to the formation of the native state.

Question 25

. Which amino acids of the portion of the polypeptide AIGHTSM will be hydrogen-bonded to each other in the α helix?
a. A-T, I-S, G-M
b. A-H, I-T, G-S
c. A-G, I-H, G-T
d. A-I, G-H, T-S
e. A-M, I-S, G-T

Answer 25

a. A-T, I-S, G-M

Question 26

Choose the CORRECT statement concerning prions.
a. The prion precursor contains mostly extended structural elements rather than tightly coiled ones.
b. A large number of β strands prevents extensive contacts between different proteins.
c. The difference in the free energy between PrP and PrPSC is small.
d. Prions usually consist of two subunits of the normal PrP protein.
e. The decrease in the content of α-helical structural elements is unique for prions and always leads to pathological conditions.

Answer 26

c. The difference in the free energy between PrP and PrPSC is small.

Question 27

In the study of a new protein, you have observed the existence of several distinct stable conformations of the protein depending on presence or absence of other proteins in the solution. One form is 100% α helical, another contains about 75% α helices, and for the third one half of the protein had no distinctive secondary elements. Explain the results of your study.
a. Most if not all of the forms are intermediates of the native protein.
b. The protein should belong to the IDP class and is most likely involved in some signaling pathway.
c. An intrinsically disordered form of the protein should have been present in the absence of any other protein, while in the presence of some other protein the folding should have proceeded as implied by the model of molten globule.
d. The protein doesn’t adhere to the paradigm of the folding funnel, and the existence of several forms strongly implies that the protein belongs to the metamorphic proteins.
e. The protein doesn’t adhere to the paradigm of the folding funnel, and the intrinsically disordered structure implies that this protein is metamorphic.

Answer 27

B. The protein should belong to the IDP class and is most likely involved in some signaling pathway.

Question 28

Choose the CORRECT statement about the secondary structure of protein.
a. Adjacent strands in the parallel β sheet can be formed from the amino acids that are neighbors in the protein sequence.
b. Loops and turns are required only to connect β strands while α helices are taking the whole length of the protein.
c. Neighboring amino acids can form any possible secondary structure.
d. Adjacent strands in the antiparallel β sheet can be formed from the amino acids that are neighbors in the protein sequence.
e. One β strand is stable enough to exist in the protein structure.

Answer 28

d. Adjacent strands in the antiparallel β sheet can be formed from the amino acids that are neighbors in the protein sequence.

Question 29

How many hydrogen bonds should be present within the antiparallel β sheet that curls into a closed barrel-like structure if overall it has 8 β strands each 5 amino acids long? Do not consider the bonds that should be present in turns between the strands.
a. 10
b. 30
c. 36
d. 44
e. 80

Answer 29

c. 36

Question 29

34. Compact globular units, called _______, are polypeptide chains folded into two or more compact regions.

Answer 29

ANSWER: domains

Question 30

Every third residue in the protein collagen is:
a. leucine.
b. glycine.
c. proline.
d. tyrosine.
e. titin.

Answer 30

b. glycine.

Question 30

Select all that apply. Human hemoglobin:
a. is the oxygen-carrying protein in mitochondria.
b. exists as an α2β2 tetramer.
c. consists of α helices and β sheets.
d. contains heme groups.
e. has a tertiary structure.

Answer 30

b. exists as an α2β2 tetramer./ d. contains heme groups.

Question 31

38. The amino acid residue that would MOST likely be buried in the interior of a water-soluble globular protein is:
    a. aspartate.
    b. serine.
    c. phenylalanine.
    d. lysine.
    e. glutamine.

Answer 31

d. lysine.

Question 32

The folding of a protein into its native shape can best be described as a(n):
a. random event.
b. random event catalyzed by ribosome proteins to maintain a low energy structure.
c. series of controlled folds with a few random-shaped structures.
d. series of repeatable random events where the lowest energy structure is maintained.
e. event where the highest possible energy state is stabilized with discrete folding intermediates.

Answer 32

d. series of repeatable random events where the lowest energy structure is maintained.

Question 33

What structures did Pauling and Corey predict in 1951? Select all that apply.
a. α helix
b. β sheet
c. turns between β sheets
d. loops between α helices
e. β strand

Answer 33

a. α helix
b. β sheet

Question 34

Peptides differ from proteins in:
a. the direction of β strands.
b. the number of amino acid residues.
c. the three-dimensional structure.
d. the primary structure.
e. polarity.

Answer 34

b. the number of amino acid residues.

Question 35

Lymphotactin is an example of:
a. metamorphic proteins.
b. peptides.
c. protein hormones.
d. fatty-acid-binding proteins.
e. fibrous proteins.

Answer 35

a. metamorphic proteins.

Question 36

Two amino acids undergo oxidation to form a dimer called:
a. proline.
b. glycine.
c. cystine.
d. tyrosine.
e. leucine.

Answer 36

c. cystine.

Question 36

What determines a protein’s function?
a. its structure
b. its gene sequence
c. N-terminal amino acids
d. time of its formation
e. C-terminal amino acids

Answer 36

a. its structure

Question 37

Why is the peptide bond planar?
a. Bulky side chains prevent free rotation around the bond.
b. It exhibits partial double-bond character, preventing rotation.
c. Hydrogen bonding between the NH and C=O groups limits movement.
d. The bond can have either cis conformation or trans conformation.
e. It has different peptide bonds.

Answer 37

b. It exhibits partial double-bond character, preventing rotation.

Question 38

Where are β turns and loops often found?
a. in a hydrophobic pocket
b. on the interior cleft
c. at the protein interface with a ligand
d. on the surface of proteins
e. between β sheets

Answer 38

d. on the surface of proteins

Question 39

Your study group is trying to identify differences in the four levels of protein structure. The secondary structure but not the tertiary structure is stabilized by:
a. ionic attractions between oppositely charged side chains.
b. H-bonding between polar side chains.
c. hydrophobic interactions between nonpolar side chains.
d. H-bonding between the oxygen of the backbone carbonyl and the hydrogen of the backbone amine.
e. van der Waals forces.

Answer 39

d. H-bonding between the oxygen of the backbone carbonyl and the hydrogen of the backbone amine.

Question 40

A clinician friend comes to you and tells you she has a patient that she thinks has some sort of defect in the collagen structure. She wants to know what kinds of structural differences there might be. Which of the following is FALSE for defects leading to scurvy or brittle bone disease?
a. Proline residues are not hydroxylated.
b. Glycine is replaced by other amino acids.
c. Prolyl hydroxylase activity is deficient.
d. Accumulation of defective collagen causes cell death.
e. There is violation of the quaternary structure.

Answer 40

e. There is violation of the quaternary structure.

Question 41

Which of the following structures is lost when a peptide bond is formed between two amino acids?
a. amino group
b. water
c. carboxyl group
d. carbonyl group
e. amino-terminal residue

Answer 41

b. water

Question 42

Which of the following proteins contains examples of the α-helical character? Select all that apply.
a. keratin
b. ferritin
c. myosin
d. tropomyosin
e. CD4

Answer 42

a. keratin
b. ferritin
c. myosin
d. tropomyosin