11.01 Because of the way the genetic code works, the specific nucleotide sequence of a gene exactly specifies the amino acid sequence in the corresponding protein that is the product of that gene. Explain how the sequence of bases of the DNA is transcribed into mRNA and how the mRNA is translated into the sequence of amino acids in the polypeptide chain. For discussion purposes use a hypothetical gene that codes for a hypothetical protein three amino acids long. State the functions of all of the components involved.

11.02 The diagram below depicts an electron micrograph taken of a thin fiber from an E. coli cell. The main fiber has attached strings of granules (each about 20 nm in diameter). DNase treatment destroys the main fiber but not the strings of granules, whereas RNase removes the granular strings from the main fiber.

(a) Which of these structures represents: a portion of the E. coli chromosome? ribosomes? mRNA?

(b) Could some of the granules be RNA polymerase molecules? If so, which ones and why?

(c) Explain what processes are occurring here and how that are related.

(d) What other major components involved in these processes might be visible if the resolution of the micrograph could be increased?

11.03 At any given time, each functioning ribosome is attached to only one growing polypeptide chain. Why must this be true?

11.04 A segment of DNA has the following base-pair sequence:

strand A 3' - T A C G A T T G A A G C - 5'

strand B 5' - A T G C T A A C T T C G - 3'

If Strand A serves as the template for transcription:

(a) Give the sequence of bases of the mRNA. Show the 5' and 3' ends.

(b) Which three bases of the template will be transcribed first?

(c) Which three bases of the mRNA will be translated first once the RNA attaches to a ribosome?

11.05 We tend to think of RNA as a single-stranded molecule, but certain RNAs can have double-stranded regions (e.g. tRNA). A particular fragment of an RNA molecule has the following percentages of bases: A = 23%, U = 42%, C = 21%, and G = 14%.

(a) Is this piece of RNA single stranded or double stranded? How can you tell?

(b) What would be the percentages of bases in the DNA template strand that this RNA was transcribed from?

(c) Now consider the entire double-stranded DNA molecule (both template and non-template strands together). What would be the G+C ratio of this DNA?

11.06 Consider a promoter with a -10 box having the following sequence: 5'-T-A-G-T-A-C-3'.

(a) If a mutation occurred that changed the C to a T, would this likely be an up or a down mutation? Explain. (Note: an up mutation is one that makes a promoter more active; a down mutation makes it less active. You will need to understand consensus sequences to answer this question. Look this up in your textbook).

(b) Would changing the T in the first position to an A be an up or a down mutation?

11.07 The diagram illustrates the process of translation.

(a) Label all of the following elements on the diagram: 5' and 3' ends of the mRNA, A and P sites of the ribosome, the start codon, the stop codon, tRNA, amino and carboxyl ends of the growing polypeptide chain.

(b) What will be the anticodon of the next tRNA that attaches to the ribosome?

(c) What will be the next amino acid added to the polypeptide chain?

11.08 Suppose that you charged a methionine tRNA with methionine, then chemically changed the attached methionine to alanine. Then you used this used this synthesized alanyl-tRNA in an in vitro translation reaction.

(a) What do you predict would be the result? Would the alanine go into the protein where an alanine is supposed to go or where a methionine is supposed to go? Explain?

(b) What does this say about the importance of the specificity of aminoacyl-tRNA synthase enzymes?

11.09 The DNA fragment shown below is a small piece of a gene. Assume that the bottom strand is used as the template for transcription.

3' - A G C A G A G G G A T G A C C C A T - 5'

5' - T C G T C T C C C T A C T G G G T A - 3'

(a) Write the sequence of bases on the mRNA that would be synthesized from this DNA. (Be sure to mark the 3' and 5' ends.)

(b) How many codons does this message contain?

(c) When this RNA is translated, what would be the anticodon on the tRNA carrying the third amino acid of the protein? (Be sure to mark the 3' and 5' ends.)

(d) What would be the amino acid sequence of the polypeptide that would result from the translation of this message? Write the amino acids in the order in which they are assembled.

11.10 What would be the effect on reading frame and on the resulting polypeptide if the following mutations happened?

(a) Two bases are inserted into the middle of a gene?

(b) Three bases are inserted into the middle of a gene?

(c) One base is inserted into a gene, and one base is deleted from the gene very near to the insertion?

11.11 If the length of each codon was six bases rather than three, what kind of product would you expect from the translation of a repeating tetranucleotide such as poly(UUCG)? That is, how many different amino acids would the polypeptide contain, and what order would they be in. You can use AA-1, AA-2, AA-3, etc. to abbreviate the amino acids.

11.12 You have discovered a new virus and are trying to characterize its DNA. The capsule of this virus contains 12 different proteins. The average molecular weight of these proteins is 25,000. Approximately what would be the minimum length of the virus's DNA molecule in micrometers if it contains one gene for each of the 12 proteins. (Notes: The average molecular weight of an amino acid is 137. The distance between two base pairs of DNA is 0.34 nm.)

11.13 Consider different E. coli strains with each of the following mutations. Explain what effect each mutations would have on the function of the lac operon (assuming no glucose is present)?

(a) A mutant lac operator that cannot bind to the repressor.

(b) A mutant lac repressor that cannot bind to the operator.

(c) A mutant lac repressor that cannot bind to allolactose.

(d) A mutant lac promoter that cannot bind to RNA polymerase.