Biochem homework chapter 5

Which structure below is appropriate for glycine at neutral pH? H2NCH2COOH +H3NCH2COO- +H3NCH2COOH H2NCH2COO-

+H3NCH2COO-

At the isoelectric pH of an amino acid which has two pKa values the net charge is ________. 0 0.5 -1 1

0

The side chain of ________ has a pKa in the physiological pH range and is therefore often involved in proton transfer during enzymatic catalysis. Arg His Glu Asp

His

Which of the following modified amino acids is incorporated during translation rather than being modified post-translationally? Selenocysteine N-ε-acetyllysine γ-carboxyglutamate Phosphoserine

Selenocysteine

All amino acids have a chiral α-carbon EXCEPT ________. Tryptophan Proline Alanine Glycine

Glycine

Protein biosynthesis uses only ________. L-amino acids R-amino acids D-amino acids S-amino acids

L-amino acids

Histidine has pKa values of 1.8, 6.0 (R-group) and 9.3. At pH 8.0, the net charge on histidine is ________. Positive Negative Neutral (uncharged) Insufficient information to tell

Neutral (uncharged)

The pKa of a certain weak acid is 4.0. Calculate the ratio of proton acceptor to proton donor at pH 7.0. 20:1 3:1 1000:1 1:1

1000:1

If the R group of an amino acid is -CH3, then the name of this compound is ________. Alanine Isoleucine 3-methyl amino acid 3-aminopropanoic acid

Alanine

The R group of an amino acid determines if it is ________. Hydrophilic or hydrophobic Polar or nonpolar Charged or uncharged All of the above

All of the above

Alanine, valine, leucine and isoleucine are important in three dimensional structure because they ________. Are highly hydrophobic Are branched Attract water molecules Are highly hydrophilic

Are highly hydrophobic

Which of the following amino acids would most likely be found on the surface of a protein? Proline Valine Leucine Aspartic acid

Aspartic acid

Which of the following statement is true about a protein in aqueous solution that has a pH equal to the isoelectric point (pI) of the protein? At pH = pI, there is a net positive charge on the protein. At pH = pI, there is a net negative charge on the protein. At pH = pI, there is no net charge on the protein. There is not enough information to answer this question.

At pH = pI, there is no net charge on the protein.

Amino acids with non-ionizable side chains are zwitterions when they are ________. In alkaline solutions only At physiological pH, pH = 7.4 In acidic solutions only In any solution

At physiological pH, pH = 7.4

Disulfide bridges can form in proteins ________. Between any two methionine or cysteine Only between cysteine residues side-by-side in the protein sequence Between cysteine residues that are close in three-dimensional space, but not necessarily close in the primary structure Between two cysteine residues in proteins

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

The trans configuration of most peptide groups is adopted in cells because it ________. Is the only one available Is favored in protein synthesis Minimizes steric hindrance of R groups Both minimizes steric hindrance of R groups and is favored in protein synthesis

Both minimizes steric hindrance of R groups and is favored in protein synthesis

The amino acids in polypeptide chains which contain sulfur (S) are ________. Cysteine Cysteine, lysine, and methionine Methionine only Cysteine and methionine

Cysteine and methionine

Name the N-terminal and C-terminal residues for the following peptide sequence. Peptide sequence: EASY Aspartic acid is the N-terminal residue; tyrosine is the C-terminal residue. Glutamic acid is the N-terminal residue; tyrosine is the C-terminal residue. Tyrosine is the N-terminal residue; glutamic acid is the C-terminal residue. Glutamic acid is the N-terminal residue; tryptophan is the C-terminal residue.

Glutamic acid is the N-terminal residue; tyrosine is the C-terminal residue.

The primary structure of a protein specifically describes the ________. Linear sequence of amino acids Φ and Ψ angles for each amino acid Location of disulfide bonds Overall three-dimensional shape

Linear sequence of amino acids

The ionic charges associated with a protein molecule are ________. Contributed by only the N-terminal and C-terminal residues Mostly contributed by the side chains of constituent amino acids Determined by the contribution from the α-carboxyl group, α-amino group and side chain of every amino acid in the protein Independent of the amino acid composition and depend only on pH

Mostly contributed by the side chains of constituent amino acids

Proteins have what charge on their carboxyl terminals at physiological pH? Positive Zero Negative Not enough information to determine

Negative

Which of the following characteristics are true about a typical peptide (amide) bond? 1. The bond is planar. 2. There is free rotation about the carbonyl carbon and nitrogen bond. 3. There is substantial double-bond character to this bond. 4. There is a net negative charge on nitrogen and net positive charge on oxygen. Only statements 1, 2, and 4 are correct. Only statements 2 and 3 are correct. Only statements 1 and 3 are correct. All of the listed statements are correct.

Only statements 1 and 3 are correct.

An amide bond between the α-carboxylic acid group of one amino acid and the α-amino group on another is called a ________. Noncovalent bond Peptide bond Protein bond Phosphoester bond

Peptide bond

At pH=0, the net charge on a polypeptide will be ________. Zero Positive Negative Not enough information to determine

Positive

Basic amino acids are ________ (positive, negative) at pH 7 and acidic R group amino acids are ________ (positive, negative) at pH 7. Negative; positive Positive; negative Negative; negative Positive; positive

Positive; negative

Arginine is the most basic of the 20 amino acids because its side chain is ________ under most cell conditions. Titrated Hydrophobic Protonated Very highly charged

Protonated

For an amino acid such as aspartic acid, what impact would you expect a neighboring carboxylic acid to have on the apparent pKa value of the side chain? The apparent pKa value for aspartic acid increases. The aspartic acid and the neighboring carboxylic acid would form a salt bridge, therefore the apparent pKa value is not affected. The neighboring carboxylic acid would have no impact on the pKa value for aspartic acid. The apparent pKa value for aspartic acid decreases.

The apparent pKa value for aspartic acid increases.

Proline is distinct among the 20 commonly found amino acids because ________. It is hydrophilic and ionic It is a ring compound The nitrogen of the amino group is cyclized in a ring The carbon of the carboxyl group is cyclized in a ring

The nitrogen of the amino group is cyclized in a ring

How does the pKa values of an ionizable side chain compare when the amino acid is free versus when it is in a polypeptide chain? The pKa of the side chain is always lower for the free amino acid. The pKa of the side chain is usually higher in a polypeptide chain due to stabilization from nearby residues in the three-dimensional structure. The pKa of the side chain is independent of whether the amino acid is in a polypeptide chain or is free. The pKa of the side chain may be lower or higher in a polypeptide chain due to weaker inductive effects and differences in their microenvironments.

The pKa of the side chain may be lower or higher in a polypeptide chain due to weaker inductive effects and differences in their microenvironments.

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

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

The pH inside cells is normally near pH 7. At pH 7 which statement is TRUE about the charges (ionization state) of the α-Carboxyl and α-Amino groups of an amino acid? The α-Carboxyl group is 1+ and the α-Amino group is 1-. The α-Carboxyl group is 1- and the α-Amino group is 1+. Both groups are uncharged (not ionized) at pH 7. The α-Carboxyl group is 1- and the α-Amino group is uncharged.

The α-Carboxyl group is 1- and the α-Amino group is 1+.

The pKa 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? The side chain is a different functional group than the α-carboxyl group. The α-carboxyl group has less steric hindrance and is therefore ionized more easily. The side chain has more possible resonance structures. The α-carboxyl group is closer to the α-amino group than the side chain is.

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

For the amino acid lysine, the Henderson-Hasselbalch equation can be applied to ________ ionization group(s). One Two Three Four

Three

Ultraviolet (UV) light can be used to estimate protein solution concentrations because ________. Phenylalanine absorbs at 260 nm All the amino acids absorb UV light Aromatic amino acids absorb at 280 nm Tryptophan and tyrosine absorb at 280 nm

Tryptophan and tyrosine absorb at 280 nm

What is the N-terminal for the pentapeptide Val-Ile-Glu-Arg-Tyr? 'Tryptophan Tyrosine The NH3+ group on the side chain of Arg Valine

Valine

At neutral pH, the net charge of serine is ________. Negative Zero Positive None of the above

Zero

At physiological pH, the carboxylic acid group of an amino acid will be ________, while the amino group will be ________, yielding the zwitterion form. deprotonated, protonated protonated, protonated deprotonated, deprotonated protonated, deprotonated

deprotonated, protonated

According to the Henderson-Hasselbalch equation, when the concentrations of proton acceptor and proton donor are the same, then ________. pH = pKa The carboxylic acid is totally neutralized pKa = log[proton acceptor]/[proton donor] Only salt forms are present

pH = pKa