Short Answers Flashcards
What are the structural characteristics common to all amino acids found in naturally occurring proteins?
All amino acids found in naturally occurring proteins have an α carbon to which are attached a carboxylic acid, an amine, a hydrogen, and a variable side chain. All the amino acids are also in the L configuration.
Briefly describe the five major groupings of amino acids.
Amino acids may be categorized by the chemistry of their R groups:
(1) nonpolar aliphatics;
(2) polar, uncharged;
(3) aromatic;
4) positively charged;
(5) negatively charged. (
Why do amino acids, when dissolved in water, become zwitterions?
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.
Hydrolysis of peptide bonds is an exergonic reaction. Why, then, are peptide bonds quite stable?
Peptide bonds are stable because hydrolysis of peptide (or amide) bonds has a high activation energy and as a result occurs very slowly.
Define the primary structure of a protein.
The primary structure of a protein is its unique sequence of amino acids and any disulfide
bridges present in the native structure, that is, its covalent bond structure.
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.
First, add a known volume of the enzyme solution (say, 0.01 mL) to a solution of its substrate B and measure the initial rate at which product A is formed, expressed as μmol/mL of enzyme solution/min. Then measure the total protein concentration, expressed as mg/mL. Finally, divide the enzyme activity (μmol/min/mL) by the protein concentration (mg/mL); the quotient is the specific activity.
As a protein is purified, both the amount of total protein and the activity of the purified protein decrease. Why, then, does the specific activity of the purified protein increase?
Specific activity is the units of enzyme activity (μmol of product/min) divided by the amount of protein (mg). As the protein is purified, some of it is lost in each step, resulting in a drop in activity. However, other contaminating proteins are lost to a much greater extent. Therefore, with each purification step, the purified protein constitutes a greater proportion of the total, resulting in an increase in specific activity. (See also Table 3-5, p. 92.)
In one or two sentences, describe the usefulness of each of the following reagents or reactions in the analysis of protein structure:
(a) Edman reagent (phenylisothiocyanate)
(b) Sanger reagent (1-fluoro-2,4-dinitrobenzene, FDNB) (c) trypsin
Ans: (a) used in determination of the amino acid sequence of a peptide, starting at its amino terminus; (b) used in determination of amino-terminal amino acid of a polypeptide; (c) used to produce specific peptide fragments from a polypeptide.
Describe the relationship between a living organism and its surroundings in terms of both matter and energy.
Living organisms are open systems and exchange both matter and energy with their surroundings. They are not at equilibrium with their surroundings; that is, the concentrations of molecules inside the cells of the organism are not the same as their concentrations in the surroundings. To maintain this situation, the organism must acquire energy from its surroundings, either in the form of chemical energy or directly from sunlight.
The free-energy change for the formation of a protein from the individual amino acids is positive and is thus an endergonic reaction. How, then, do cells accomplish this process?
The endergonic (thermodynamically unfavorable) reaction is coupled to an exergonic (thermodynamically favorable) reaction through a shared intermediate, so that the overall free-energy change of the coupled reactions is negative (the overall reaction is exergonic).
What is meant by feedback inhibition and why is it important in a living organism?
Feedback inhibition is the regulation of a biochemical pathway in which a reaction product inhibits an earlier (usually the first) step in the pathway. It is an important type of regulation because it ensures that energy is not wasted by an organism producing molecules it does not need.
