A protein has a molecular mass of 400 kDa when measured by gel filtration. When subjected to gel electrophoresis in the presence of sodium dodecyl sulfate (SDS), the protein gives three bands with molecular masses of 180, 160, and 60 kDa. When electrophoresis is carried out in the presence of SDS and dithiothreitol, three bands are again formed, this time with molecular masses of 160, 90, and 60 kDa. Determine the subunit composition of the protein..

2. Pepsin is the name given to a mix of several digestive enzymes secreted( as larger precursor proteins) by glands that line the stomach. These glands also secrete hydrochloric acid, which dissolves the particulate matter in food, allowing pepsin to enzymatically cleave individual protein molecules. The resulting mixture of food, HCl, and digestive enzymes is known as chyme and has a pH near 1.5. What pI would you predict for the pepsin proteins? What functional groups must be present to confer this pI on pepsin? Which amino acids in the proteins would contribute such groups?

3. Histones are proteins found in eukaryotic cell nuclei, tightly bound to DNA, which has many phosphate groups. The pI of histones is very high, about 10.8. What amino acid residues must be present in relatively large numbers in histones? In what way do these residues contribute to the strong binding of histones to DNA?

4. At pH 7.0, in what order would the following three peptides be eluted from a column filled with a cation-exchange polymer? Their amino acid compositions are:

Protein A: Ala 10%, Glu 5%, Ser 5%, Leu 10%, Arg 10%, His 5%, Ile 10%, Phe 5%, Tyr 5%, Lys 10%,

Gly 10%, Pro 5%, and Trp 10%.

Protein B: Ala 5%, Val 5%, Gly 10%, Asp 5%, Leu 5%, Arg 5%, Ile 5%, Phe 5%, Tyr 5%, Lys 5%, Trp 5%, Ser 5%, Thr 5%, Glu 5%, Asn 5%, Pro 10%, Met 5%, and Cys 5%.

Protein C: Ala 10%, Glu 10%, Gly 5%, Leu 5%, Asp 10%, Arg 5%, Met 5%, Cys 5%, Tyr 5%, Phe 5%, His 5%, Val 5%, Pro 5%, Thr 5%, Ser 5%, Asn 5%, and Gln 5%.

5. Glutenin, a wheat protein rich in disulfide bonds, is responsible for the cohesive and elastic character of dough made from wheat flour. Similarly, the hard, tough nature of tortoise shell is due to

the extensive disulfide bonding in its a-keratin. What is the molecular basis for the correlation

between disulfide-bond content and mechanical properties of the protein?

6.Most globular proteins are denatured and lose their activity when briefly heated to 65 C. However, globular proteins that contain multiple disulfide bonds often must be heated longer at

higher temperatures to denature them. One such protein is bovine pancreatic trypsin inhibitor

(BPTI), which has 58 amino acid residues in a single chain and contains three disulfide bonds.

On cooling a solution of denatured BPTI, the activity of the protein is restored. What is the

molecular basis for this property?

7. Is myoglobin a motif, a domain, or a complete three-dimensional structure?

8.Several small aromatic molecules, such as phenol red (used as a non-

toxic drug model), have been shown to inhibit the formation of amyloid in laboratory model systems. A

goal of the research on these small aromatic compounds is to find a drug that would efficiently inhibit

the formation of amyloid in the brain in people with incipient Alzheimer’s disease.

(a) Suggest why molecules with aromatic substituents would disrupt the formation of amyloid.

(b) Some researchers have suggested that a drug used to treat Alzheimer’s disease may also be effective in treating type 2 (adult onset) diabetes mellitus. Why might a single drug be effective in

treating these two different conditions?

9. Under appropriate conditions, hemoglobin dissociates into its four

subunits. The isolated a subunit binds oxygen, but the O2-saturation curve is hyperbolic rather than sigmoid. In addition, the binding of oxygen to the isolated a subunit is not affected by the presence of H+, CO2, or BPG. What do these observations indicate about the source of the cooperativity in hemoglobin?

10. A host organism needs time, often days, to mount an immune response against a new antigen, but memory cells permit a rapid response to pathogens previously encountered. A vaccine to protect against a particular viral infection often consists of weakened or killed virus or isolated proteins from a viral protein coat. When injected into a human patient, the vaccine generally does not cause an infection and illness, but it effectively “teaches” the immune system. what the viral particles look like, stimulating the production of memory cells. On subsequent infection, these cells can bind to the virus and trigger a rapid immune response. Some pathogens, including HIV, have developed mechanisms to evade the immune system, making it difficult or impossible to develop effective vaccines against them. What strategy could a pathogen use to evade the immune system? Assume that a host’s antibodies and/or T-cell receptors are available to bind to any structure that might appear on the surface of a pathogen and that, once bound, the pathogen is destroyed.

11. When a vertebrate dies, its muscles stiffen as they are deprived of ATP, a state called rigor mortis. Explain the molecular basis of the rigor state.

12. The sweet taste of freshly picked corn (maize) is due to the high level of sugar in the kernels. Store-bought corn (several days after picking) is not as sweet, because about 50% of the free sugar is converted to starch within one day of picking. To preserve the sweetness of fresh corn, the husked ears can be immersed in boiling water for a few minutes (“blanched”) then cooled in cold water. Corn processed in this way and stored in a freezer maintains its sweetness. What is the biochemical basis for this procedure?