Biochem Final- Week 3

Basic amino acids are ________ (positive, negative) at pH 7 and acidic R group amino acids are ________ (positive, negative) at pH 7. Select one: A. positive; negative B. negative; negative C. positive; positive D. negative; positive

A. positive; negative

The RS system of nomenclature describes Select one: A. the absolute configuration about chiral carbon centers . B. the relative sizes of molecules. C. the way the amino acid side chains are arranged. D. the strength of the chemical groups in amino acids.

A. the absolute configuration about chiral carbon centers

Proline is not often found in α-helices of proteins because it Select one: A. lacks a hydrogen atom on its amide nitrogen. B. interacts with adjacent amino acids. C. has a very bulky side chain. D. has a small, uncharged side chain.

A. lacks a hydrogen atom on its amide nitrogen

The ________ is the single shape a protein adopts under physiological conditions. Select one: A. native conformation B. primary structure C. most stable enantiomer D. minimal configuration

A. native conformation

________ is a technique used to analyze the macromolecular structure of proteins in solution. Select one: A. NMR B. X-ray crystallography C. SDS-PAGE D. Affinity chromatography

A. NMR

Which represents the backbone of a protein? Note: R = amino acid side chain N = nitrogen Cα = alpha carbon C = carbonyl carbon Select one: A. Repeating units of N-Cα-C. B. Repeating units of N-C. C. R1R2R3R4R5. D. Repeating units of Cα-C.

A. Repeating units of N-Cα-C

Disulfide bridges can form in proteins ________. Select one: A. between cysteine residues that are close in three-dimensional space, but not necessarily close in the primary structure B. between any two methionines or cysteines C. between two cystine residues in proteins D. only between cysteine residues side-by-side in the protein sequence

A. between cysteine residues that are close in three-dimensional space, but not necessarily close in the primary structure

A protein that contains more isoleucine, phenylalanine and leucine than asparagine, lysine and arginine is most likely Select one: A. hydrophobic. B. low on the hydropathy index scale. C. neutral. D. hydrophilic

A. hydrophobic

Proline is distinct among the 20 commonly found amino acids because Select one: A. the nitrogen of the amino group is in a ring. B. it is hydrophilic and ionic. C. it is a ring compound. D. it has little effect on protein structure. E. the carbon of the carboxyl group is in a ring.

A. the nitrogen of the amino group is in a ring

The three ionizable groups of arginine have the following pKa's Carboxyl = 1.8 Amino = 9.0 Side Chain = 12.5 Identify the predominant charge state for each group of Arginine at pH 7.0 What is the pI of the amino acid free in solution?

Amino Group- Positive Carboxyl Group- Negative Side Chain Group- Positive pI = 10.75

The pKa's of arginine's α-Carboxyl group, α-Amino group and side chain are 1.8, 9.0 and 12.5, respectively. Calculate the isoelectric point. Select one: A. 7.2 B. 10.8 C. 7.8 D. 5.4

B. 10.8

How many monomers are there in an oligomeric protein designated αβ2γ2? Select one: A. 4 B. 5 C. 2 D. 3

B. 5

What feature does a Ramachandran plot display? Select one: A. Preferred amino acids in an α-helix. B. Allowed angles of phi and psi for a polypeptide backbone. C. The variation of pH versus volume of base added during titration to determine the pKa. D. The hydropathy of amino acids.

B. Allowed angles of phi and psi for a polypeptide backbone.

Which statement is NOT true about an α-helix? Select one: A. It is stabilized by hydrogen bonding. B. It frequently contains proline residues. C. It is usually right-handed. D. It is a type of secondary structure.

B. It frequently contains proline residues.

The last common ancestor of modern organisms must have used Select one: A. D amino acids. B. L amino acids. C. both D and L amino acids. D. either D or L amino acids.

B. L amino acids

To what level of structure do α-helices belong? Select one: A. Quaternary B. Secondary C. Primary D. Tertiary

B. Secondary

Which statement is not true about the peptide bond? Select one: A. The carbonyl oxygen and the amide hydrogen are most often in a trans configuration with respect to one another. B. The peptide bond is longer than the typical carbon-nitrogen bond. C. Rotation is restricted about the peptide bond. D. The peptide bond has partial double-bond character.

B. The peptide bond is longer than the typical carbon-nitrogen bond.

Which is not true about β-sheets? Select one: A. The range of allowed phi and psi angles is broader than for those in the α-helix. B. The side-chains of all amino acids point to the same side of the sheet. C. The polypeptide chains in the sheet are nearly fully extended. D. In antiparallel sheets the hydrogen bonds between adjacent strands are nearly perpendicular to the backbones of the strands

B. The side-chains of all amino acids point to the same side of the sheet.

The pKa's of the side chain group and the α-carboxyl group of glutamate are 4.1 and 2.1, respectively. Which statement accounts for this difference? Select one: A. The side chain has more possible resonance structures. B. The α-carboxyl group is closer to the α-amino group than the side chain is. C. The α-carboxyl group has less steric hindrance and is therefore ionized more easily. D. The side chain is a different functional group than the α-carboxyl group.

B. The α-carboxyl group is closer to the α-amino group than the side chain is.

The overall shape of a protein is greatly influenced by Select one: A. hydrophilic amino acids. B. amino acid R group properties. C. charged amino acids. D. pH. E. hydrophobic amino acids.

B. amino acid R group properties

The amino acids in polypeptide chains which contain sulfur (S) are Select one: A. cystine. B. cysteine and methionine. C. cysteine only. D. methionine only. E. cysteine, cystine, and methionine.

B. cysteine and methionine

The amino acid that destabilizes alpha-helical structures and is usually found at the ends of alpha helices is Select one: A. glutamate. B. glycine. C. alanine. D. asparagine.

B. glycine

Protein subunits in a multisubunit protein are held to each other primarily by Select one: A. covalent bonds. B. hydrophobic and other weak interactions. C. hydrophobic interactions exclusively. D. both strong and weak interactions. E. All of the above.

B. hydrophobic and other weak interactions

Histidine has pKa values of 1.8, 6.0 (R-group) and 9. At pH 7.5, the net charge on histidine is: Select one: A. positive. B. neutral (uncharged). C. negative. D. Insufficient information to tell.

B. neutral (uncharged)

net charge is Select one: A. 1. B. 0.5. C. 0. D. -1.

C. 0

The pKa of a certain weak acid is 4.0. Calculate the ratio of proton acceptor to proton donor at pH 7.0. Select one: A. 1:1 B. 20:1 C. 1000:1 D. 3:1 E. The ratio cannot be calculated without knowing the structure of the weak acid.

C. 1000:1

The pKa's of isoleucine's α-Carboxyl group and α-Amino group are 2.3 and 9.8, respectively. Calculate the isoelectric point. Select one: A. 9.8 B. 2.3 C. 6.0 D. The isoelectric point cannot be calculated without the pKa value for the side chain.

C. 6.0

Which is true about the side chains of residues in an α-helix? Select one: A. They point toward the center of the helix. B. They extend above or below the pleats. C. They extend radially outward from the helix axis. D. They hydrogen bond extensively with each other.

C. They extend radially outward from the helix axis

Alanine, valine, leucine and isoleucine are important in three dimensional structure because they Select one: A. are highly hydrophilic. B. attract water molecules. C. are highly hydrophobic. D. are branched.

C. are highly hydrophobic.

An amino acid with two chiral carbon atoms Select one: A. is unstable. B. can form three possible stereoisomers. C. can form four possible stereoisomers. D. can exist in 4 forms, all of which are superimposable. E. can form five possible stereoisomers.

C. can form four possible stereoisomers

A change from one conformation of a molecule to another involves ________. Select one: A. breaking and reforming of covalent bonds B. inversion about a center of symmetry C. rotation about bonds only D. Any of the above

C. rotation about bonds only

At neutral pH, the net charge of serine is Select one: A. negative. B. positive. C. zero. D. None of the above.

C. zero

Which statement is false about a globular protein that performs its biological function as a single independent polypeptide chain? Select one: A. Non-covalent forces are the primary source of stability for the secondary and tertiary structure. B. Its tertiary structure is likely stabilized by the interactions of amino acid side chains in non-neighboring regions of the polypeptide chain. C. It could contain α-helices that are stabilized by hydrogen bonding. D. It likely has extensive quaternary structure to maintain its globular shape.

D. It likely has extensive quaternary structure to maintain its globular shape.

The conformation of the backbone of a polypeptide is described completely by the angle(s) of rotation about which bond(s)? Select one: A. N-Cα only. B. N-Cα, Cα-C and C-N bonds. C. The peptide bond only. D. N-Cα and Cα-C bonds only.

D. N-Cα and Cα-C bonds only

What is true about the rotation about bonds in a protein backbone? Select one: A. All bonds in the backbone have restricted rotation and partial double-bond character. B. The rotation is free about all bonds in the backbone, except for the bond between the nitrogen and the alpha carbon in proline residues. C. The rotation is free only about the peptide bond. The other bonds are restricted by steric hindrance and the presence of proline residues. D. The bond between the carbonyl carbon and nitrogen is restricted. Other bonds are free to rotate depending only on steric hindrance or the presence of proline residues

D. The bond between the carbonyl carbon and nitrogen is restricted. Other bonds are free to rotate depending only on steric hindrance or the presence of proline residues.

Which technique is commonly used to determine the three-dimensional conformation of a protein? Select one: A. The Edman degradation. B. SDS-PAGE. C. Isoelectric focusing. D. X-ray crystallography.

D. X-ray crystallography

Amino acids with non-ionizable side chains are zwitterions when they are ________. Select one: A. in acidic solutions only B. in alkaline solutions only C. in any solution D. at physiological pH, pH = 7.4 E. All of the above

D. at physiological pH, pH = 7.4

Amino acids are named that because each one Select one: A. has a standard configuration. B. is a carboxyl derivative of an amide acid. C. is a unique carboxylic acid. D. is an amino derivative of a carboxylic acid

D. is an amino derivative of a carboxylic acid

Concentrations of some proteins cannot be estimated by UV spectrophotometry because they are Select one: A. high in aromatic amino acids. B. low in protein. C. low in glycine and valine. D. low in tryptophan and tyrosine.

D. low in tryptophan and tyrosine

Tyrosine and tryptophan are less hydrophobic than phenylalanine because Select one: A. phenylalanine has an indole group. B. tyrosine and tryptophan have smaller R groups. C. phenylalanine is a phenol. D. phenylalanine has no polar group in the side chain. E. All of the above.

D. phenylalanine has no polar group in the side chain.

Ramachandran determined the "allowed" values of the phi and psi angles primarily by considering ________. Select one: A. hydrogen bonding effects B. pKa values of the amino acids C. the hydropathy of amino acids D. steric hindrance

D. steric hindrance

Nearly all peptide bonds are in the trans configuration because Select one: A. trans peptide bonds are stronger. B. cis peptide bonds are weaker. C. cis peptide bonds prevent R groups from interacting. D. trans peptide bonds minimize steric hindrance of R groups

D. trans peptide bonds minimize steric hindrance of R groups

Arginine is the most basic of the 20 amino acids because its side chain is ________ under most cell conditions. Select one: A. negatively charged B. titrated C. very highly charged D. hydrophobic E. protonated

E. protonated