Exam 3: Amino Acids, Peptides, and Proteins

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

What does the molecule SDS do to proteins?

The "signature sequence" shown below represents a portion of a protein from four different organisms. a. At which position(s) are amino acid residues invariant? b. At which position(s) are amino acids limited to positively charged residues? c. At which position(s) are amino acids limited to negatively charged residues? d. At which position(s) are amino acids limited to nonpolar residues?

The amino acid proline is unique because the R group:

By convention, polypeptides are read in which order?

The MOST useful way to classify amino acids is by:

You are given a solution containing an enzyme that converts B into A. Describe what you would do to determine the specific activity of this enzyme solution.

The pK_a of lysine's carboxyl group, amino group, and side chain are 2.2, 9.0, and 10.5, respectively. If lysine is in a pH 13 solution, what is the net charge on each lysine molecule?

Amino acids without ionizable R-groups can act as a zwitterion in a(n) _____ solution.

Iodoacetamides, maleimides, benzyl halides, and bromomethyl ketones can all be used to modify the _____ group on _____ residues.

How are sequential reactions controlled in the Edman degradation procedure?

A biochemist wishes to determine the sequence of a protein that contains 123 amino acid residues. After breaking all of the disulfide bonds, the protein is treated with cyanogen bromide (CNBr), and it is determined that that this treatment breaks up the protein into seven conveniently sized peptides, which are separated from each other. It is your turn to take over. Outline the steps you would take to determine, unambiguously, the sequence of amino acid residues in the original protein.

For amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of amino acids in solution will have:

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

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

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?

Which item is NOT a biochemical use/function of peptides of small molecular weight?

The gel below illustrates the purification of the RecA protein from E. coli. This gel was loaded from the top. Which statement BEST describes how proteins "run" in an SDS gel?

In the amino acid glycine, what effect does the positively charged -NH₃⁺ group have on the pK_a of an amino acid's -COOH group?

What factors would make it difficult to interpret the results of a gel electrophoresis of proteins in the absence of sodium dodecyl sulfate (SDS)?