Deck 6: Proteins: Secondary, tertiary, and Quaternary Structure

Question 1

Which component is involved with hydrogen bonding of the carbonyl oxygen in a b-turn of peptide chain?

A)the amide proton on the next amino acid down the chain
B)the amide proton of the glutamine side chain
C)the amide proton of the residue 3 positions down the chain
D)the amide proton of the asparagine side chain

Answer 1

C

Question 2

Which combination of atoms forms the resonance structure within the "amide plane"?

A)CaH-NH-CO-C-CaH
B)CaH-NH-CO
C)Ca-NH-CO-Ca
D)NH-CO-Ca

Answer 2

C

Question 3

Which compound(s)can be used at high concentrations to dampen out electrostatic interactions among amino acid residues?

A)water
B)organic solvents
C)salts
D)heat

Answer 3

C

Question 4

Between which of the following amino acid pairs might an electrostatic interaction occur within a protein at typical physiological pH?

A)Ser/Asn
B)Asp/Glu
C)Arg/Cys
D)Lys/Asp

Question 5

Which of the following is/are capable of forming hydrogen bonds with the amino acid side chains located on the surface of a protein?

A)the water solvent
B)the protein interior
C)distant surface amino acid side chains
D)interior amino acid side chains

Question 6

When the peptide (AEFFLAMEP)forms an a-helix,which amino acid residue would be closest to being in the same position on the same face of the helix as is the initial alanine residue?

A)F(3)
B)A(6)
C)E(8)
D)P(9)

Question 7

Which 2 amino acids act as helix breakers due to their unique structure,which fixes the value of the Cₐ-N-C bond angle?

A)histidine and lysine
B)proline and hydroxyproline
C)arginine and lysine
D)serine and threonine

Question 8

What type of amino acids can be found on the surface of a protein?

A)only polar
B)only non-polar
C)mostly non-polar
D)both polar and non-polar

Question 9

Between which of these amino acid pairs might a hydrophobic interaction occur?

A)Ser/Ile
B)Val/Leu
C)Tyr/Cys
D)His/Val

Question 10

What is/are the primary stabilizer(s)of a-helices?

A)hydrogen bonds between the main-chain peptide bond component atoms
B)hydrophobic interactions between the a-carbons of the main chain
C)hydrogen bonding between the R groups
D)hydrophobic interactions between R groups and the solvent water

Question 11

Polylysine is a random coil when the pH is less than 11,while it forms an a-helix if the pH is raised to greater than 12.What happens at pH 12 to account for this?

A)The lysine residues are negatively charged,which electrostatically stabilizes the helix.
B)The positive charges on the lysine residues stabilize the a-helix.
C)The lysine residues are neutral,which eliminates electrostatic repulsion between the R groups.
D)The high concentration of OH⁻ ions in solution reduces the electrostatic repulsion between the R groups.

Question 12

What type of structure does an amino acid sequence have?

A)primary
B)secondary
C)tertiary
D)quaternary

Question 13

How many residues further up the a-helical chain is each peptide carbonyl group hydrogen bonded to the peptide N-H group?

A)1
B)2
C)3
D)4

Question 14

If the following section of a polypeptide is folded into an a-helix,to which amino acid is the carbonyl group of alanine hydrogen bonded?
Ala-Ser-Val-Asp-Glu-Leu-Gly

A)aspartic acid
B)glutamic acid
C)leucine
D)valine

Question 15

Which of the following is a feature of antiparallel b-sheets?

A)They progress from N- to C-termini in the same direction.
B)Usually all their hydrophobic residues are on one side of the sheet.
C)They consist of all hydrophobic residues.
D)The fibres can be stretched or extended,but are not flexible.

Question 16

What can be deduced from a Ramachandran plot?

A)the amino acid residues that have the greatest degree of rotational freedom
B)the sterically allowed rotational angles between R groups and a-carbons in a peptide
C)the sterically allowed rotational angles between Ca and the amide nitrogen (Ca-N),as well as between Ca and the amide carbonyl carbon (Ca-CO)
D)the sterically allowed rotational angles about the amide nitrogen (NH)and CO

Question 17

Rotation is allowed about which bond within a polypeptide chain?

A)the a-carbon and carbonyl carbon
B)the b-carbon and carbonyl carbon
C)the carbonyl carbon and the nitrogen of the peptide bond
D)the a-carbon and nitrogen of the peptide bond

Question 18

Which characteristic of a peptide contains all the information necessary for folding the peptide chain into its "native" structure?

A)its amino acid sequence
B)its amino acid composition
C)its configuration
D)its amino acid side chain charges

Question 19

Which of the following does NOT determine secondary and higher orders of structure?

A)hydrophobic interactions
B)hydrogen bonds
C)van der Waals forces
D)peptide bonds

Question 20

Which non-covalent interaction between tightly packed amino acid side chains in the interior of the protein is a major contributor to protein structure?

A)hydrogen bonding
B)electrostatic interactions
C)covalent ester bonding
D)van der Waals interactions

Question 21

The "permanent" part of adding wave in hair is due primarily to which of these actions?

A)rearrangement of hydrogen bonds between hair fibres
B)reduction and re-oxidation of disulfide bonds in hair fibres
C)reestablishment of new ionic interactions between hair fibres
D)breaking and reforming peptide bonds in the hair polypeptides

Question 22

What type of polypeptide chains produces long fibres or large sheets in fibrous proteins?

A)those with an abundance of aromatic amino acids
B)those with an abundance of hydrophilic amino acids
C)those organized approximately parallel along a single axis
D)those with amino acids arranged in a repeating (-a-b-c-d-)n sequence

Question 23

What is the "Greek key" topology composed of?

A)adjacent a-helices oriented in the opposite direction
B)discreet regions of b-sheet oriented in an antiparallel fashion
C)discreet regions of b-turns
D)parallel b-sheet structures connected by a-helices

Question 24

What defines tertiary structure?

A)the sequence of amino acids
B)the folding of a single polypeptide chain in 3-dimensional space
C)hydrogen-bonding interactions between adjacent amino acid residues into helical or pleated segments
D)the way in which separate,folded,monomeric,protein subunits associate to form oligomeric proteins

Question 25

Which structure consists mainly of polar and charged residues on its outward face and mostly non-polar,hydrophobic residues on its inner face?

A)b-sheet
B)triple helix
C)b-turn
D)amphiphilic helix

Question 26

Which of the following is NOT a characteristic of collagen?

A)Tropocollagen is the basic structural unit.
B)Both intermolecular and intramolecular crosslinks help to stabilize the collagen fibrils.
C)Modification of prolines occurs prior to collagen synthesis.
D)Inextensible fibrous proteins are components of connective tissues.

Question 27

Which of the following structures form between 2 normal b-structure hydrogen bonds and are comprised of 2 residues on 1 strand and 1 residue on the opposite strand?

A)b-barrels
B)parallel b-sheets
C)b-turns
D)b-bulges

Question 28

How are the parallel b-sheets in a b-barrel connected?

A)by regions of a-helix
B)by b-turns
C)by electrostatic interactions
D)by disulfide bonds

Question 29

Which amino acid residue participates in stabilizing the staggered triple helix along its centre?

A)Glu
B)Lys
C)Pro
D)Gly

Question 30

Why should the core of most globular and membrane proteins consist almost entirely of a-helix and b-sheets?

A)Hydrogen bonded structures must be kept away from water solvent.
B)Highly polar N-H and C=O moieties of the peptide backbone must be neutralized in the hydrophobic core of the protein.
C)Hydrogen bonding occurs only in the core of proteins.
D)Trapped water stabilizes the helix and sheet structures.

Question 31

Silk fibres consist of fibroin proteins that are comprised of which alternating amino acid residues?

A)glycine;alanine;serine
B)glycine;proline;leucine
C)alanine;glycine;serine
D)glycine;alanine;threonine

Question 32

Which of these characteristics does NOT apply to a-keratin?

A)primary component in hair,claws,fingernails,and horns of animals
B)consists of 4 helical strands arranged as twisted pairs of 2-stranded coiled coils
C)has associated hydrophobic strips on the 2 coiled coils
D)principal constituent of connective tissues in animals

Question 33

How are the hydrophobic residues typically arranged in antiparallel b-sheets?

A)on both sides of the sheet
B)in the plane of the sheet
C)on one side of the sheet
D)unevenly distributed on either side of the sheet

Question 34

Which of the following does the tertiary structure of proteins NOT depend on?

A)Protein structure depends on primary structure.
B)Secondary structures form whenever possible.
C)Proteins are stable as a single-layer structure.
D)Peptide segments between secondary structures are short.

Question 35

Which amino acid residue is most likely to be found in a beta turn?

A)glycine
B)alanine
C)valine
D)leucine

Question 36

What type of amino acid residue fills the space between the helices in hemoglobin most efficiently and tightly?

A)hydrophobic
B)polar
C)acidic
D)basic

Question 37

Which of the following is NOT a characteristic of prolyl hydroxylase?

A)requires citric acid
B)is activated by Fe2+
C)requires molecular oxygen
D)requires a-ketoglutarate

Question 38

Which of the following does NOT apply to the collective motions of proteins?

A)The movements of groups of atoms are covalently linked in such a way that the group moves as a unit.
B)It includes trypsin ring flips.
C)It includes trans-cis isomerization of prolines.
D)It involves the flexible antigen-binding domains of immunoglobulins.

Question 39

Which amino acid commonly comprises flexible,disordered segments of proteins?

A)Leu
B)Lys
C)Ser
D)Asp

Question 40

Which structure accommodates the unique composition of collagen?

A)b-pleated sheet
B)triple helix
C)helix-turn-helix motif
D)coiled coil

Question 41

Which statement is correct about the b-a-b motif?

A)The 2 b-strands are antiparallel.
B)The peptide segment connecting the b-strands usually contains no more than 5 amino acids.
C)The peptide segment connecting the 2 b-strands commonly contains proline.
D)The crossover connection itself contains an a-helical segment.

Question 42

Which molecule is an example of an antiparallel a-helix protein?

A)pyruvate kinase
B)flavodoxin
C)hemoglobin
D)papain

Question 43

Which of these proteins help other proteins to fold?

A)immunoglobulins
B)phospholipases
C)synthetases
D)molecular chaperones

Question 44

Which of the following does NOT occur during the folding of globular proteins into a proper structure?

A)"molten globule" formation of assembled domains
B)formation of domains through cooperative aggregation of folding nuclei
C)adjustment in the confirmation of domains
D)rapid and reversible formation of local secondary structure

Question 45

Which of the following is NOT a class of globular proteins according to type and arrangement of secondary structure?

A)small metal- and disulfide-rich proteins
B)parallel or mixed b-sheets
C)antiparallel b-sheets
D)antiparallel b-turns

Question 46

Which statement is NOT correct regarding the tertiary structure of the enzyme triose phosphate isomerase?

A)Its b-strands are parallel.
B)Its a-helices are in the interior of the molecular structure.
C)It contains a b-barrel in the centre of its structure.
D)It is composed entirely of alternating a-helices and b-strands.

Question 47

Which of these molecules is an example of a disulfide-rich protein?

A)insulin
B)glyceraldehyde-3-phosphate dehydrogenase
C)hemoglobin
D)triose phosphate isomerase

Question 48

Which of the following in NOT a characteristic of triose phosphate isomerase's tertiary structure?

A)Its a-helices are in the interior core of the molecular structure.
B)It contains a b-barrel in the centre of its structure.
C)It is composed entirely of alternating a-helices and b-strands.
D)Hydrophobic residues are buried between concentric layers.

Question 49

Which characteristic is NOT a structural and functional advantage to quaternary structure?

A)cooperativity
B)instability
C)bringing catalytic sites together
D)genetic economy and efficiency