The green fluorescent protein and 4-methylideneimidazole-5-one (MIO) containing enzymes, have a cofactors made from the cyclization of three amino acids. Draw the structure of MIO and the green fluorescent protein chromophore, then circle atoms derived from each amino acid.

An octapeptide with the amino acids < Ile, Arg, Met, Phe, Pro, Thr, Tyr, Val > was subjected to digestion reactions A, B and C in order to deduce its amino acid sequence. The following results were obtained. The exact position occupied by each of the amino acids (positions 1-8 in the sequence) will be known when the results are analyzed

A. Digestion with Trypsin yielded a [Thr-Arg] dipeptide and a [hexapeptide] with the remaining amino acids.

Question (A1): Explain the reasoning for the fragmentation pattern
Question (A2): What can you deduce regarding the exact positions occupied by Thr and Arg in the

sequence?

B. Cyanogen bromide treatment of the octapeptide also yielded a dipeptide [Phe-Pro] and a hexapeptide. Question (B1): Explain the reasoning for the above fragmentation pattern

Question (B2): What can you deduce regarding the exact positions occupied by Phe and Pro in the sequence?

C. Chymotrypsin cleaved the octapeptide into two tetrapeptides, one with and the other

Question (C1): Explain the reasoning for the above pattern
Question (C2): What can you deduce regarding the exact positions occupied by Val and Ile in the

sequence?

Question (D): What is the sequence of the peptide?

1)   TAGs are broken down into glycerol and fatty acids, what happens to them?

2)    Fats feed glucogenesis in a very efficient way, what is this way?

3)    What are the primary differences between glycolysis and gluconeogenesis?

10. Briefly describe:

a. Anaerobic glycolysis:

b. Ketogenesis:

c. Where lipogenesis occurs:

d. How fatty acids are anabolized (built):

e. How glycerol is anabolized:

f. How triglycerides and phospholipids are anabolized:

A strain of E. coli carries a mutation that completely inactivates the enzyme encoded in the gene. Several revertants, mutants of the mutant with partly or fully restored activity, were selected, and the amino acid sequence of the enzyme was determined. The only differences found were at position 10 in the polypeptide chain.

Revertant 1 had Thr.

Revertant 2 had Glu.

Revertant 3 had Met.

Revertant 4 had Arg.

Assume that the initial mutation itself, as well as each revertant, resulted from a single nucleotide substitution.

a. What amino acid is present at position 10 in the mutant protein?

b. What codon in the mRNA would encode this amino acid?

Please provide explanations and not just correct answers.

Consider a alpha-helix "stretch" of a protein consisting of 20 amino acid residues compared to a Beta-strand "stretch" of a protein consisting of 20 amino acids(which of course is part of a Beta-sheet). What is the length of this alpha-helix and Beta-strand portion of the protein in angstroms?

DNA encodes proteins by reading the sequence in ordered triplets. For example, the three ordered triplets in the ACCAGGTTA sequence are ACC, AGG, and TTA. That is, a different triplet can encode a different amino acid. How many different amino acids can be coded for each ordered triplet?

Oxytocin is a nonprotein peptide (therefore has less than 40 amino acids). What is the charge on this peptide at pH 6.8?

1. Identify ketogenic and glucogenic amino acids and their pathways to produce acetyl CoA or glucose respectively (enzymes are not necessary) (20 points).