Amino Acids

Question 1

At pH 7.0, converting a glutamic acid to y-carboxyglutamate, will have what effect on the overall charge of the protein containing it?

Answer 1

It will become more negative

Question 2

At pH 7.0, converting a proline to hydroxyproline, will have what effect on the overall charge of the protein containing it?

Answer 2

It will stay the same

Question 3

At pH 7.0, converting a proline to a hydroxyproline, will have what effect on the overall charge of the protein containing it?

Answer 3

It will stay the same

Question 4

What is the approximate charge difference between glutamic acid and a-ketoglutarate at pH 9.5?

Answer 4

1/2

Question 5

The formation of a peptide bond between two amino acids is an example of a(n)

Answer 5

Condensation reaction.

Question 6

The peptide alanylglutamylglycylalanylleucine has:

Answer 6

four peptide bonds

Question 7

An octapeptide composed of four repeating glycylalanyl units has:

Answer 7

one free amino group on a glycyl residue and one free carboxyl group on an alanyl residue

Question 8

At the isoelectric pH of a tetrapeptide

Answer 8

The total net charge is zero

Question 9

Which of the following is correct with respect to the amino acid composition of proteins?

Answer 9

Proteins with different functions usually differ significantly in their amino acid composition

Question 10

The average molecular weight of the 20 standard amino acids is 138 , but biochemists use 110 when estimating the number of amino acids in a protein of known molecular weight. Why?

Answer 10

The number 110 reflects the higher proportion of small amino acids in proteins, as well as the loss of water when the peptide bond forms.

Question 11

In a conjugated protein, a prosthetic group is:

Answer 11

A part of the protein that is not composed of amino acids

Question 12

Prosthetic groups in the class of proteins known as glycoproteins are composed of:

Answer 12

Carbohydrates

Question 13

For the study of a protein in detail, an effort is usually made to first:

Answer 13

Purify the protein

Question 14

In a mixture of the five proteins listed below, which should elute second in size-exclusion (gel-filtration) chromatography?

Answer 14

immunoglobulin G Mr= 145,000

Question 15

By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to:

Answer 15

separate proteins exclusively on the basis of molecular weight

Question 16

To determine the isoelectric point of a protein, first establish that a gel:

Answer 16

exhibits a stable pH gradient when ampholytes become distributed in an electric field.

Question 17

The first step in two-dimensional gel electrophoresis generates a series of protein bands by isoelectric focusing. In a second step, a trip of this gel is turned 90 degrees, placed on another gel containing SDS, and electric current is again applied. In this second step:

Answer 17

Proteins with similar isoelectric points become further separated according to their molecular weights.

Question 18

The term specific activity differs from the term activity in that specific activity:

Answer 18

is the activity ( enzyme units ) in a milligram of protein.

Question 19

Which of the following refers to particularly stable arrangements of amino acid residues in a protein that give rise to recurring patterns?

Answer 19

Secondary Structure

Question 20

Which of the following describes the overall three dimensional folding of a polypeptide?

Answer 20

Quaternary structure

Question 21

The functional differences, as well as difference in three-dimensional structures, between two different enzymes from E. Coli result directly from their different:

Answer 21

Amino acids sequences.

Question 22

One method used to prevent disulfide bond interference with protein sequencing procedures is:

Answer 22

reducing disulfide bridges and preventing their re-formation by further modifying the -SH groups

Question 23

A nonapeptide was determined to have the following amino acid composition: (Lys)2, (Gly)2, (Phe)2, His, Leu, Met. The native peptide was incubated with 1-fluoro-2,4-dinitrobenzene (FDNB) and then hydrolyzed; 2,4-dinitrophenylhistidine was identified by HPLC. When the native peptide was ezxposed to cyanogen bromide (CNBr), an octapeptide anad free glycine were recovered. Incubation of the native peptide with trypsin gave pentapeptide, a tripeptide, and free Lys. 2,4- Dinitrophenyl-histidine was recovered from the pentapeptide, and 2,4- dinitrophenylphenylalanine was recovered from the tripeptide. Digestion with the enzyme pepsin produced a dipeptide, a tripeptide. Digestion with the enzyme pepsin produced a dipeptide, a tripeptide, and a tetrapeptide. The tetrapeptide was composed of (Lys) 2, Phe, and Gly. The native sequence was determined to be:

Answer 23

His-Leu-Phe-Gly-Lys-Lys-Phe-Met-Gly

Question 24

Even when a gene is available and its sequence of nucleotides is known, chemical studies of the protein are still required to determine:

Answer 24

the location of the disulfide bonds.

Question 25

The term “ proteome” has been used to describe:

Answer 25

the complement of proteins encoded by an organism’s DNA.

Question 26

A major advance in the application of mas spectrometry to macromolecules came with the development of techniques to overcome which of the following problems?

Answer 26

Mass spectrometric analysis involved molecules in the gas phase.

Question 27

Compare the following sequences taken from four different proteins, and select the answer that best characterizes their relationships.
A B C
1 DVEKGKKIDIMKCS HTVEKGGKHKTGPNLH GLFGRKTGQAPGYSYT
2 DVQRALKIDNNLGQ HTVEKGAKHKTAPNVH GLADRIAYQAKATNEE
3 LVTRPLYIFPNEGQ HTLEKAAKHKTGPNLH ALKSSKDLMFTVINDD
4 FFMNEDALVARSSN HQFAASSIHKNAPQFH NLKDSKTYLKPVISET

Answer 27

Based only on sequences in column B, protein 4 reveals the greatest evolutionary divergence.

Question 28

What are the structural characteristics common to all amino acids found in naturally occurring proteins

Answer 28

All amino acids found in naturally occurring proteins have an a-carbon to which are attached an carboxylic acid, an amine, a hydrogen, and a variable side chain. All the amino acids are also in the L configuration.

Question 29

Only one of the common amino acids has no free -amino group. Name this amino acid and draw its structure.

Answer 29

The amino acid L-proline has no free- amino group, but rather has an imino group formed cyclization of the R-group aliphatic chain with the amino group.

Question 30

Briefly describe the five major groupings of amino acids.

Answer 30

Amino acids may be categorized by the chemistry of their R groups: (1) non polar aliphatic; (2) polar, uncharged; (3) aromatic; (4) positively charged; (5) negatively charged.

Question 31

A B C D E
__________________________________________________________________
Tyr-Lys-Met Gly-Pro-Arg Asp-Trp-Tyr Asp-His-Glu Leu-Val-Phe

Which one of the above tripeptides:
__(a) is most negatively charged at pH 7?
__(b) will yield DNP-tyrosine when reacted with l-fluoro-2,4- dinitrobenzene and hydrolyzed in acid?
__(c) Contains the largest number of nonpolar R groups?
__(d) contains sulfur?
__(e) Will have the greatest light absorbance at 280 nm?

Answer 31

(a) D
(b) A
(c) E
(d) A
(e) C

Question 32

Name two uncommon amino acids that occur in proteins. By what route do they get into proteins?

Answer 32

Some examples are 4-hydroxyproline, 5-hydroxylysine, -carboxyglutamate, N-methyllysine, desmosine, and selenocysteine. Uncommon amino acids in proteins ( other than selenocysteine) usually result from chemical modification sof standard amino acid R groups after a protein has been synthesized.

Question 33

Why do amino acids, when dissolved in water, become zwitterions?

Answer 33

Near pH= 7, the carboxylic acid group (-COOH) will dissociate to become a negatively charged -COO- group, and the –NH2 amino group will attract a proton to become a positively charged –NH3+ group.

Question 34

As more OH- equivalents (base) are added to an amino acid solution, what titration reaction will occur around pH = 9.5?

Answer 34

Around pH = 9.5, the —NH3+ group will be titrated according to the reaction: —NH3+ + OH- —NH2 + H2O.

Question 35

In the amino acid glycine, what effect does the positively charged —NH3+ group have on the pKa of an amino acid’s —COOH group?

Answer 35

The positively charged amino group stabilizes the negatively charged ionized form of the carboxyl group, —COO-, and repels the departing H+ thereby promoting deprotonation. The effect is to lower the pKa of the carboxyl group

Question 36

How does the shape of a titration curve confirm the fact that the pH region of greatest buffering power for an amino acid solution is around its pK’s?

Answer 36

In a certain range around the pKa’s of an amino acid, the titration curve levels off. This indicates that for a solution with pH pK, any given addition of base or acid equivalents will result in the smallest change in pH—which is the definition of a buffer.

Question 37

Leucine has two dissociable protons: one with a pKa of 2.3, the other with a pKa of 9.7. Sketch a properly labeled titration curve for leucine titrated with NaOH; indicate where the pH = pK and the region(s) in which buffering occurs.

Answer 37

See the titration curve for glycine in Fig. 3-10, p. 79.

Question 38

What is the pI, and how is it determined for amino acids that have nonionizable R groups?

Answer 38

The pI is the isoelectric point. It occurs at a characteristic pH when a molecule has an equal number of positive and negative charges, or no net charge. For amino acids with nonionizable R groups, pI is the arithmetic mean of a molecule’s two pKa values:

Question 39

The amino acid histidine has a side chain for which the pKa is 6.0. Calculate what fraction of the histidine side chains will carry a positive charge at pH 5.4. Be sure to show your work.

Answer 39

pH = pKa + log

pKa - pH = log

antilog (pKa - pH) =

antilog (6.0 - 5.4) =

4 = [acid]/[conjugate base], or
4[conjugate base] = [acid]

Therefore, at pH 5.4, 4/5 (80%) of the histidine will be in the protonated form.