Deck 4: Protein Structure

Question 1

If the isoelectric point (pI) for an amino acid is at point A, what is the charge on the amino acid at point B?

A) "0"
B) "-2"
C) "+2
D) "-1"

Answer 1

"-2"

Question 2

For the alanine titration curve shown below, which best describes point A?

A) a buffer region
B) isoelectric point
C) second equivalence point
D) pH = pK_a

Answer 2

isoelectric point

Question 3

What is the peptide sequence Asp-Gln-Gly-Ser, using one-letter abbreviations for the amino acids?

A) AGYS
B) DNGC
C) DQGS
D) EGYS

Answer 3

DQGS

Question 4

The amino acid with the neutral side chain at neutral pH is

A) asparagine.
B) aspartate.
C) arginine.
D) glutamate.

Question 5

The chirality of naturally occurring amino acids in proteins is

A) R.
B) L.
C) D.
D) the same as glyceraldehyde.

Question 6

Which amino acid side chain from the list below is the most polar?

A) Gln
B) Ala
C) Leu
D) Phe

Question 7

What is the pI of the dipeptide shown? (Use the pK as given.)

A) 0
B) 5
C) 9
D) 10.5

Question 8

Which statement about amino acids is true?

A) Most common natural amino acids in proteins are L-amino acids.
B) All naturally occurring amino acids in proteins are chiral.
C) Most naturally occurring amino acids in proteins are D-amino acids.
D) Naturally occurring amino acids in proteins occur as a mixture of enantiomers.

Question 9

If the titration curve shown below is for the amino acid glycine, at which point in the curve is the pI?

A) A
B) B
C) C
D) D

Question 10

Using the pKas shown, what is the isoelectric point of the amino acid tyrosine?

A) <1.0
B) 5.5
C) 7.0
D) 9.75

Question 11

Which amino acid has the highest pKa?

A) glutamate
B) asparagine
C) cysteine
D) lysine

Question 12

At what point does the isoelectric point or pI occur?

A) when all of the acidic protons are neutralized with base
B) at pH = 7.0
C) at the pH when all negative charges on a zwitterion counter the positive charges
D) when the molecule has a single electric charge

Question 13

Which amino acid contains a hydroxyl group?

A) valine
B) cysteine
C) threonine
D) aspartate

Question 14

What are the three-letter and one-letter abbreviations for the amino acid tyrosine?

A) Tyo, T
B) Tyr, R
C) Tro, Y
D) Tyr, Y

Question 15

Which of the following are negatively charged amino acids at pH = 7?

A) Glu, Asp
B) Gln, Asn
C) Thr, Tyr
D) Cys, Asn

Question 16

Consider the whole amino acid alanine at pH =7. How many atoms (including Hs) are found in the molecule?

A) 15
B) 13
C) 10
D) 8

Question 17

Of the 20 common amino acids, how many have a chiral $\alpha$ -carbon?

A) 0
B) 1
C) 19
D) 20

Question 18

The amino acid with the most hydrophobic side chain is

A) asparagine.
B) aspartate.
C) valine.
D) threonine.

Question 19

A polypeptide has a high pI value. Which amino acids might comprise it?

A) arginine and lysine residues
B) aspartate and glutamate residues
C) the large nonpolar amino acids
D) a mixture of aspartate and arginine residues

Question 20

What is the approximate net charge of the molecule shown below at pH 7?

A) "+1"
B) "0"
C) "-1"
D) "-2"

Question 21

To what organic reaction class does peptide bond formation belong?

A) condensation
B) isomerization
C) oxidation
D) addition

Question 22

Which statement regarding protein secondary structures is correct?

A) " $\beta$ -strands allow $\alpha$ -helices to interact with one another."
B) "Protein $\alpha$ -helices alternate with $\beta$ -strands in stabilizing protein structure."
C) "Protein $\alpha$ -helices are left handed, whereas $\beta$ -sheets are right handed in arrangement."
D) "Protein $\alpha$ -helices and $\beta$ -strands differ in that $\alpha$ -helices are stabilized by intrahelical hydrogen bonds, whereas $\beta$ -strands are stabilized by hydrogen bonds across adjacent strands."

Question 23

The peptide bond is stronger than the ester bond. What structural feature of the peptide bond gives it additional bond strength?

A) Resonance structures give the peptide bond some double bond character.
B) The peptide bond is between carbon and nitrogen instead of carbon and oxygen atoms.
C) The peptide bond is more polar.
D) Peptide bonds can hydrogen bond.

Question 24

How many possible unique triplet codons could there be in a genome?

A) 3
B) 20
C) 36
D) 64

Question 25

Which interaction largely stabilizes protein secondary (2 $\degree$ ) structures?

A) disulfide bonds
B) hydrogen bonding
C) hydrophobic packing
D) metal ions

Question 26

Which linear sequence of bonded atoms can be found in the backbone of polypeptides?

A) C-N-N-C
B) C-C-N-C
C) N-C-C-C
D) C-O-C-N

Question 27

Protein secondary structures such as $\alpha$ -helices and $\beta$ -sheets are stabilized mainly by

A) ionic interactions.
B) disulfide bond formation.
C) van der Waals forces.
D) hydrogen bond formation.

Question 28

Which represents the correct arrangement of bonding in a peptide bond?

A)
B)
C)
D)

Question 29

What do Ramachandran plots show?

A) Only some $\Psi$ and $\phi$ angles are commonly found in proteins.
B) The chiral carbon in amino acids is found largely in the S configuration.
C) Peptide backbones form mostly linear chains.
D) The $\alpha$ -carbon is chiral.

Question 30

The dipole moment associated with a peptide bond proceeds from which amide?

A) the C to the O atom
B) the C to the N atom
C) the O to the H atom
D) the H to the O atom

Question 31

All of the following are stabilizing forces in maintaining a stable protein tertiary (3 $\degree$ ) structure, EXCEPT

A) H bonds.
B) temperature.
C) hydrophobic interactions.
D) electrostatic attractions.

Question 32

The peptide bond

A) is most stable in the cis configuration.
B) has a mix of single and double bond characters.
C) can rotate around the carbonyl and N bond but not around the $\alpha$ -carbon and N bond.
D) can function as a weak acid and weak base.

Question 33

The $\phi$ and $\Psi$ angles are the

A) flatness of the peptide bond.
B) torsion angles on either side of the $\alpha$ -carbon.
C) angles of each amino acid side chain.
D) peptide bond plane angle.

Question 34

A mutation in a gene results in the least amount of damage to the resulting protein.

A) missense
B) nonsense
C) frameshift
D) silent

Question 35

All of the following are types of protein secondary structure EXCEPT

A) " $\beta$ -sheets."
B) " $\alpha$ -helixes."
C) " $\beta$ -helixes."
D) " $\beta$ -turns."

Question 36

How many possible protein primary structures are there for a tripeptide given the 20 amino acids?

A) 3²⁰
B) 400
C) 20³
D) 1.27 *10¹³⁰

Question 37

Trace directly the covalently bonded backbone atoms from the N to C terminus of a dipeptide. Which atoms are found in this trace?

A) NCCNCC
B) NCCONCCO
C) NCONCO
D) CNCCNC

Question 38

Use the table below to determine how many possible RNA sequences could code for the dipeptide Pro-Ala.

A) 1
B) 16
C) 8
D) 64

Question 39

Using the table below, determine the kind of gene mutation illustrated. ATG_AAT_CAC $\rightarrow$ ATG_AAG_CAC

A) missense mutation
B) nonsense mutation
C) frameshift mutation
D) silent mutation

Question 40

The points in the Ramachandran plot are derived by

A) counting the number of amino acids and placing points in allowed regions.
B) measuring the $\phi$ and $\Psi$ angles in an experimentally determined protein crystal structure.
C) placing each amino acid in regions commonly occupied by that amino acid.
D) experimentally measuring the optical rotation of polarized light.

Question 41

An $\alpha$ -helix has the sequence: NH₃⁺-Ser-Glu-Gly-Asp-Trp-Gln-Leu-His-Val-Phe-Ala-Lys-Val-Glu-COO-. The carbonyl oxygen (in the peptide bond) of the histidine residue is hydrogen bonded to the amide nitrogen of

A) Asp.
B) Lys.
C) Trp.
D) Ala.

Question 42

Which one of the following statements comparing alpha keratin and silk fibroin is true?

A) Both have covalently cross-linked strands.
B) Both are primarily $\alpha$ -helical in character.
C) Both fibers are intracellularly located.
D) Both fibers are heavily stabilized by hydrogen bonds.

Question 43

How many $\beta$ -turns or $\beta$ -loops are required to construct a $\beta$ -sheet composed of four antiparallel strands?

A) 0
B) 3
C) 4
D) 5

Question 44

Which statement about the $\alpha$ -helix is true?

A) "The hydrophobic interior of $\alpha$ -helices is stabilized by the side chains of hydrophobic amino acids."
B) "The amino acid side chains point out to the sides with every third amino acid roughly lining up on one side of the helix."
C) " $\alpha$ -Helices have backbone amide groups that are hydrogen bonded to amino acid side chains."
D) " $\alpha$ -Helices have 5 amino acids per one turn of the helix."

Question 45

Protein tertiary structures

A) require the formation of disulfide bonds in order to achieve their native state.
B) are always irreversibly destroyed by the addition of denaturants, such as urea and salts, even when the denaturants are subsequently removed.
C) are often disrupted by the either very low pH or very high pH values as a result of alterations in the ionization states of acidic or basic amino acids.
D) are generally poorly defined and cannot be determined experimentally.

Question 46

Which of the following statements about $\beta$ -sheet structures is true?

A) The individual strands of all $\beta$ -sheet structures are connected by turns, helices, or loops.
B) All amino acid side chains in antiparallel and parallel $\beta$ -sheet structures point to one side of the sheet.
C) Parallel $\beta$ -sheet structures have backbone amides that directly hydrogen bond between strands, whereas antiparallel $\beta$ -sheets have hydrogen bonds that are offset.
D) All $\beta$ -sheet structures form a spiraling backbone chain.

Question 47

The common protein fold shown below is the fold.

A) "Greek key"
B) "Rossman"
C) "FERM domain"
D) " $\alpha$ / $\beta$ barrel"

Question 48

What is the dominant secondary structure found in hair keratin?

A) " $\alpha$ -helices"
B) "disulfide bonds"
C) " $\beta$ -sheets"
D) "loop structures"

Question 49

The proteins collagen, silk fibroin, and hair keratin have all of the following in common, EXCEPT that they

A) are fibrous proteins.
B) are composed of repeating amino acid sequences.
C) are composed of $\alpha$ -helical structures.
D) play important structural roles in biology.

Question 50

How many different protein folds are recognized in the formal system of organization, referred to as SCOP: Structure Organization of Proteins?

A) 4
B) >10
C) >100
D) >1000

Question 51

Which of the following statements regarding protein domains is true?

A) Each protein has one unique domain.
B) Multiple domains require multiple subunits and a quaternary structure.
C) A domain can be composed of smaller structural units called motifs.
D) A domain is a region absent of $\alpha$ -helices and $\beta$ -sheets.

Question 52

Which class of protein structures does the protein shown below fit into?

A) predominantly $\alpha$ -helical
B) predominantly $\beta$ -sheet
C) intermixed $\alpha$ -helix and $\beta$ -sheet
D) domains of $\alpha$ -helix adjacent to domains of $\beta$ -sheet

Question 53

What is the minimum number of amino acids needed to make one turn of an $\alpha$ -helix?

A) 3
B) 4
C) 6
D) 7

Question 54

What is a difference between parallel and antiparallel $\beta$ -sheet secondary structures?

A) Antiparallel $\beta$ -sheets have a larger number of stabilizing H bonds between backbone amides than parallel $\beta$ -sheets.
B) Parallel $\beta$ -sheets require a larger loop connecting together the individual peptide strands in the sheet.
C) Parallel $\beta$ -sheets are longer than antiparallel sheets.
D) Parallel $\beta$ -sheets have amino acid side chains alternating up and down, whereas antiparallel side chains alternate down and up.

Question 55

In a standard $\alpha$ -helix, __________ H bonds and dipole moments are found per amino acid, which stabilizes the $\alpha$ -helical structure.

A) 1; 1
B) 1; 2
C) 2; 1
D) 2; 2

Question 56

Which of the following statements about $\alpha$ -helices and $\beta$ -sheets are FALSE?

A) They are both incompatible with the amino acid proline.
B) They both interact with other protein elements through amino acid side chains that stick out.
C) They both contain a recurring pattern of hydrogen bonds from one peptide bond to another peptide bond.
D) They both give rise to similar tertiary structures.

Question 57

Which stabilizing force in protein tertiary structures is a covalent bonding force?

A) ionic bonding
B) disulfide bonding
C) hydrophobic interactions
D) van der Waals bonding

Question 58

Which of the following statements is true about $\alpha$ -helices?

A) The center of the helix is an open channel.
B) There are about seven amino acids per helical turn.
C) The amide backbone dipoles line up in one direction.
D) The helical backbone structure is stabilized by ionic interactions.

Question 59

The protein fold known as the Rossman fold is found in proteins that commonly bind

A) " $\alpha$ -helices."
B) "nucleotides."
C) "cytochromes."
D) "membranes."

Question 60

Which of the following statements about Ramachandran plots is true?

A) They are good predictors of protein tertiary structure.
B) They are needed to determine the secondary structure of a protein.
C) They show equal distributions of $\phi$ and $\Psi$ angles for $\alpha$ -helical and $\beta$ -sheet containing proteins.
D) They show that $\beta$ -sheets and $\alpha$ -helices occupy different $\phi$ and $\Psi$ angles.

Question 61

Calculate the pI for the following dipeptide using the pKas shown.

Question 62

What is believed to be the underlying cause of prion protein plaque formation?

A) The PrP^Sc proteins are misfolded and aggregated from PrP^c proteins.
B) The unstructured N-terminal region of PrP^c is thought to remain unfolded.
C) The normal PrP^c proteins are aggregated.
D) The PrP^Sc protein adheres to and inhibits cell membranes.

Question 63

In multi-subunit proteins, such as hemoglobin, the different subunits are usually bound to one another by all of the following EXCEPT

A) hydrogen bonds.
B) electrostatic interactions.
C) hydrophobic interactions.
D) peptide bonds.

Question 64

Which of the following statements about the clamp-type chaperone protein Hsp70 is correct?

A) Hsp70 uses ATP binding and hydrolysis energy to assist in the folding of a protein.
B) Hsp70 is a multi-subunit protein shaped like a large barrel, inside of which the folding protein is protected.
C) Hsp70 is most active during cell division phases.
D) Hsp70 assists in protein unfolding by hydrolyzing and remaking the protein peptide bonds.

Question 65

Of the three proposed models of globular protein folding, which one describes formation of an initial disordered protein interior, followed next by ordering of secondary and tertiary structures?

A) mutant globule
B) hydrophobic collapse model
C) framework model
D) nucleation model

Question 66

Which gives rise to a favorable enthalpic ( $\Delta$ S) driving force for protein folding?

A) The lining up of hydrogen bonds as the protein folds.
B) The limiting of possible conformations as the protein folds.
C) The decrease in ordered water molecules as hydrophobic amino acids pack together.
D) The stabilization caused by favorable electrostatic interactions of amino acid side chains.

Question 67

The essential amino acids in adult humans are those that are required in our diet because of a lack of the biosynthetic pathway in our cells. The single-letter abbreviations for these amino acids are WVMILKFHT. Name these amino acids.

Question 68

Draw the structure of the amino acid glutamate showing the predominant form found at pH
7.0 (assume -NH₃⁺ pKa 9.0; Glu pK_R 4.0; -COOH pKa 2.0).

Question 69

Of the three proposed models of globular protein folding, which one describes the initial formation of all secondary structures, followed by the arrangement of those secondary structures into a final tertiary structure?

A) mutant globule
B) hydrophobic collapse model
C) framework model
D) nucleation model

Question 70

Which of the following statements about the chamber-type chaperone protein GroEL-GroES is correct?

A) GroEL-GroES requires the hydrolysis of multiple ATPs to assist in the folding of a protein.
B) GroEL-GroES recycles misfolded proteins by recovering individual amino acids.
C) GroEL-GroES assists in protein unfolding by hydrolyzing and remaking the protein peptide bonds.
D) GroEL-GroES uses GroEL as a cap, trapping an unfolded protein in the GroES chamber.

Question 71

At the interface between subunits of a protein with quaternary structure, which of the following interactions between amino acid side chains would contribute to the stability of the dimer?

A) glutamate-aspartate.
B) leucine-aspartate.
C) glutamate-lysine.
D) phenylalaninelysine.

Question 72

What is the difference between clamp-type and chamber-type chaperone proteins?

A) One uses ATP and the other does not.
B) One folds proteins, whereas the other just protects them from unfolding.
C) They are shaped differently.
D) One type is found extracellularly and one intracellularly.

Question 73

In the Anfinsen experiment with the unfolding of RNaseA, what order could the chemical reagents be removed in order to achieve an inactive protein?

A) Remove denaturant first and reductant second.
B) Simultaneously remove denaturant and reductant.
C) Remove reductant first, denaturant second, and then finally add back reductant.
D) Remove reductant first and denaturant second.

Question 74

Christian Anfinsen showed in a famous experiment that it is possible to unfold a protein and refold it to obtain a functional protein. Which two reagents were used in this experiment to unfold the protein?

A) detergent and salt
B) urea and $\beta$ -mercaptoethanol
C) acid and base
D) ethanol and $\beta$ -mercaptoethanol

Question 75

Cells deal with misfolded proteins by

A) storing them for later energy use.
B) collecting and excreting them from the cell.
C) aggregating them to maintain the cell's structural integrity.
D) degrading them to individual amino acids.

Question 76

Cystic fibrosis results from the misfolding of proteins that never get the chance to properly insert into the membranes of lung epithelial cells and perform their function. This is generally referred to as a disease.

A) loss-of-function protein folding
B) chaperonin-unassisted folding
C) gain-of-function protein folding
D) amyloid plaque-forming

Question 77

It is important for cells to degrade misfolded proteins. If misfolded proteins are not degraded, the misfolded proteins may

A) waste excessive ATP in attempts to refold them.
B) aggregate and interfere with normal cellular function.
C) eventually refold, but not until excessive and sometimes fatal levels of cellular energy are spent.
D) be excreted from the cell rather than recycled for building blocks.

Question 78

What is a current hypothesis that explains the infectious nature of prion diseases?

A) The virus responsible for prion diseases is transmissible.
B) Unfavorable environmental factors negatively influence healthy cells.
C) The small molecule denaturants found in infected cells are passed on to healthy cells.
D) The presence of an improperly folded prion protein promotes the misfolding of normal prion proteins.

Question 79

The following amino acid is discovered in a newly isolated protein. What would it be called, and does it represent a new amino acid?

Question 80

Shown is the titration curve for the amino acid aspartic acid. Draw the predominant protonation state of aspartic acid found at point A in the curve.