Biochem Questions Test 1

Replication

DNA to DNA

Transcription

Synthesis of RNA from DNA

A protease is an enzyme that catalyzes the hydrolysis of the peptide bonds of target proteins. How might a protease bind a target protein so that its main chain becomes fully extended in the vicinity of the vulnerable peptide bond?

A segment of the main chain of the protease could hydrogen bond to the main chain of the substrate to form an extended parallel or antiparallel pair of B strands.

A common practice of sprinters is to breathe rapidly and deeply before a race. Their blood pH may rise from 7.4 to 7.6. Why does this happen and how is this useful to a runner?

By hyperventilating, a person clears more CO2 out of their lungs. Based on bicarbonate buffering system, lower CO2 values lower H+ concentration, raising pH. This is not really useful to a runner as breathing rate involves sensors that respond to levels of CO2 as opposed to oxygen uses.

The shape of hair is determined in part by the pattern of disulfide bonds in keratin, its major protein. How can curls be induced?

Disulfide bonds in hair are broken by adding a thiol and applying gentle heat. The hair is curled, and an oxidizing agent is added to reform disulfide bonds to stabilize the desired shape.

Identify the groups in a protein that can form hydrogen bonds or electrostatic bonds with an arginine side chain at pH 7.

Glutamate, aspartate, and the terminal carboxylate can form salt bridges with the guanidinium group of arginine. In addition, this group can be a hydrogen bond donor to the side chains of glutamine, asparagine, serine, threonine, aspartate, and glutamate, and to the main chain carbonyl group.

Glycine, the smallest of the 20 naturally occurring amino acids, is often a highly conserved residue in the evolution of protein structures. Why is that the case?

Glycine has an R group of only a hydrogen atom. It is often used to create space as a linear peptide chain folds into its native 3D structure. Its small size and volume allows a 3D protein to bend or move without having atoms or side chains bumping into each other. So to conclude, it is a "spacer" per say. It also reduces steric hindrance and gives a protein flexibility.

Glycine is a highly conserved amino acid residue in the evolution of proteins. Why?

Glycine has the smallest side chain of any amino acid. Its size often is critical in allowing polypeptide chains to make tight turns or to approach one another closely.

Poly L - leucine (a polymer made exclusively of leuc ine residues that forms an α - helix) can be produced in a number of different organic solvents. Poly L - isoleucine (a polymer made exclusively of isoleucine residues) does not form an α - helix under the same conditions in the same organic solvents. Why does this happen for these two amino acids when they are in the same solvent solutions?

Isoleucine and leucine have similar structures, yet different beta carbons. The beta carbon on isoleucine has a methyl attached to it whereas the beta carbon in leucine has two hydrogens. These steric differences affect area, volume, and chemical properties. This means that they will behave very differently in solutions.

Translate the following amino acid sequence into one-letter code: Leu-Glu-Ala-Arg-Asn-Ile-Asn-Gly-Ser-Cys-Ile-Glu-Asn-Cys-Glu-Ile-Ser-Gly-Arg-Glu-Ala-Thr.

LEARNINGSCIENCEISGREAT.

Proteins that span biological membranes often contain α helices. Given that the insides of membranes are highly hydrophobic, predict what type of amino acids would be in such a helix. Why is an α helix particularly suited to exist in the hydrophobic environment of the interior of a membrane?

The amino acids inside would be hydrophobic in nature. An a helix is especially suited to cross a membrane because all of the amide hydrogen atoms and carbonyl oxygen atoms of the peptide backbone take part in intrachain hydrogen bonds, thus stabilizing these polar atoms in a hydrophobic environment.

All l amino acids have an S absolute configuration except l-cysteine, which has the R configuration. Explain why l-cysteine is designated as the R absolute configuration.

The assignment of absolute configuration requires the assignment of priorities to the four groups connected to a tetrahedral carbon. For all amino acids except cysteine, the priorities are 1) amino groups; 2) carbonyl groups; 3) side chain; 4) hydrogen. For cysteine, because of the sulfur atom in its side chain, the side chain has a greater priority than the carbonyl group, leading to the assignment of an R rather than S.

Proteins are quite stable. The lifetime of a peptide bond in aqueous solution is nearly 1000 years. However, the ΔG°′ of hydrolysis of proteins is negative and quite large. How can you account for the stability of the peptide bond in light of the fact that hydrolysis releases much energy?

The energy barrier that must be crossed to go from the polymerized state to the hydrolyzed state is large even though the reaction is thermodynamically favorable.

A mutation that changes an alanine residue in the interior of a protein to valine is found to lead to a loss of activity. However, activity is regained when a second mutation at a different position changes an isoleucine residue to glycine. How might this second mutation lead to a restoration of activity?

The first mutation destroys activity because valine occupies more space than alanine does, and so the protein must take a different shape, assuming that this residue lies in the closely packed interior. The second mutation restores activity because of a compensatory reduction of volume; glycine is smaller than isoleucine.

Poly-l-leucine in an organic solvent such as dioxane is α helical, whereas poly-l-isoleucine is not. Why do these amino acids with the same number and kinds of atoms have different helix-forming tendencies?

The methyl group attached to the B-carbon atom of isoleucine sterically interferes with a-helix formation. In leucine, this methyl group is attached to the y-carbon atom, which is farther from the main chain and does not interfere.

An enzyme that catalyzes disulfide-sulfhydryl exchange reactions, called protein disulfide isomerase (PDI), has been isolated. PDI rapidly converts inactive scrambled ribonuclease into enzymatically active ribonuclease. In contrast, insulin is rapidly inactivated by PDI. What does this important observation imply about the relation between the amino acid sequence of insulin and its three-dimensional structure?

The native conformation of insulin is not the thermodynamically most stable form since it contains two separate chains linked by disulfide bonds. Insulin is formed from proinsulin, a single-chain precursor, that is cleaved to form insulin with 33 residues once the disulfide bonds have formed.

For an amino acid such as alanine, the major species in solution at pH 7 is the zwitterionic form. Assume a pKa value of 8 for the amino group and a pKa value of 3 for the carboxylic acid and estimate the ratio of the concentration of neutral amino acid species (with the carboxylic acid protonated and the amino group neutral) to that of the zwitterionic species at pH 7.

Using the Henderson-Hasselbach equation, we find the ratio of alanine-COOH to alanine-COO- at pH 7 to be 10-4. The ratio of alanine-NH2 to alanine-NH3+, determined in the same fashion, is 10-1. Thus, the ratio of neutral alanine to zwitterionic species is 10-4 × 10-1 = 10-5.

Aspirin is a weak acid with a pKa of 3.5. It is absorbed into the bloodstream through cells lining the stomach and small intestine. Absorption through cell membranes is determined by the polarity of the molecule with neutral hydrophobic molecules passing much more rapidly than polar molecules. The pH of gastric juice in the stomach is about 1.5 and the pH of the small intestine is about 6. Is more aspirin absorbed into the bloodstream from the stomach or small intestine. Explain.

With a pKa of 3.5, aspirin is in its protonated form at pH below 2.5. At higher pH, it becomes increasingly deprotonated (anionic). Thus, it is better absorbed in the more acidic environment of the stomach bc absorption requires passage through the plasma membrane, the rate of which is determined by the polarity of the molecule: charged and highly polar molecules pass slowly, whereas neutral hydrophobic ones pass rapidly (Membrane is nonpolar tails so nonpolar molecules go through more quickly)

Translation

synthesis of protein from RNA