Consider the codon “GAU” and answer the following questions:
a- Which amino acid is encoded by the given codon.
b- How many different codons can be generated by point mutation at the position of the second
nucleotide “A”. Show all possible codons and representing amino acids.

5. How could you take a protein with a known sequence of amino acids and use it to make an artificial gene?

Explain why all protein sources are not the same. (Hint: think about limiting amino acids and complementary proteins)

If carbohydrates are unavailable for cellular respiration, other organic molecules can be broken down and enter the cellular respiration process at the appropriate spot. Proteins can be broken down into a variety of amino acids. Some amino acids can be converted into glutamate which can then be converted into alpha- ketoglutarate. State which steps of the cellular respiration pathway, lead to the generation of the energy molecules. State the TOTAL number of ATP molecules the ONE of these converted alpha-ketoglutarate molecules can produce and explain how all the ATP molecules are generated.

Which of the following events occur during the initiation of translation in prokaryotic cells? (more than one answer will apply)

Select one or more:

a. The small ribosomal 30S subunit will bind the the Shine Dalgarno sequence in the mRNA.

b. tRNA carrying fMet will bind to the AUG start codon.

c. The large ribosomal 50S subunit will form a sandwich with the mRNA in between the two subunits

d. tRNAs will bring amino acids to the A site of the ribosome.

e. The ribosome will make peptide bonds between amino acids

You encounter an extraterrestrial organism that makes proteins consisting of a combination of 100 types of amino acids. You also discover that it only uses a combination of 2 possible nucleotides (P and W) in its DNA and RNA. If other aspects of this creature’s biology are more like those of terrestrial organisms, what would be the minimal length of codons needed to code for all 100 types of amino acids?

Question 7 options:

1.What type of bond holds amino acids together in a polypeptide chain?

A. Peptide Bond B. Phosphodiester Bond C. Hydrogen Bond   

2.Termination of translation takes place when the ribosome reaches:

A. A primer B. The promoter C. The start codon D. A stop codon

3. Which of the following is Different between prokaryotic and eukaryotic translation?

A. tRNA brings amino acids to the ribosome B. Codon is complementary to anticodon C. Coding dictionary D. Occurs in same place as transcription

A. What is the ? (alpha)- helical dipole and what is the molecular origin of that dipole?

B. Identify two amino acids that are preferred in ? (beta)- sheets. Why might these amino acids be preferred?

C. Peptide bonds are believed to by hydrated by three water molecules, with one hydrogen bond donated from the N-H and two hydrogen bonds being accepted by the lone pairs of electrons in the carbonyl group. Would you expect a significant entropic component to be associated with the formation of secondary structures like alpha-helicies and beta-sheets. Explain.

1.ATP in nitrogen fixation:

a. Is provided by the host plant

b. Directly drives the oxidation of Ferredoxin and reduction of Dinitrogenase reductase

c. Is required because flow of electrons from ferredoxin to nitrogenase is kinetically unfavorable

d. Both a and c

e. None of the above

2. Essential amino acids

a. Are not made at all or made to sufficient levels in our bodies

b. Must be obtained by animals by eating other organisms

c. include amino acids such as glutamate and glutamine

d. both a and b

e. all of the above

3. Formation of which amino acid represents the most common point for incorporation for NH4+ into metabolism?

a.   Asp

b.   Cys

c.   Ser

d.   Gly

e.   Glu

(a) Estimate the volumes of the various amino acids in units of nm^3.

(b) Estimate the mass of a "typical" amino acid in daltons. Justify your estimate by explaining how many of each type of atom you chose. Compare your estimate with the actual mass of several key amino acids such as glycine, proline, arginine, and tryptophan.

(c) On the basis of your result for part (b), deduce a rule of thumb for converting the mass of a protein (reported in kDa) into a corresponding number of residues. Apply this rule of thumb to myosin, G-actin, hemoglobin, and hexokinase and compare your results with the actual number of residues in each of these proteins. Relevant data for this problem are provided on the book’s website.

http://microsite.garlandscience.com/pboc2/data.html