Question 1

What was the initial evidence for the existence of mRNA?

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Question 2

Describe the structure of RNA polymerase in bacteria. What is the core enzyme? What is the role of the ? subunit?

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Question 3

Write a paragraph describing the abbreviated chemical reactions that summarize RNA polymerase-directed transcription.

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Question 4

Messenger RNA molecules are very difficult to isolate in prokaryotes because they are rather quickly degraded in the cell. Can you suggest a reason why this occurs? Eukaryotic mRNAs are more stable and exist longer in the cell than do prokaryotic mRNAs. Is this an advantage or a disadvantage for a pancreatic cell making large quantities of insulin?

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Question 5

Present an overview of various forms of posttranscriptional processing in eukaryotes. For each, provide an example.

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Question 6

One form of posttranscriptional modification of most eukaryotic RNA transcripts is the addition of a poly-A sequence at the 3? end. The absence of a poly-A sequence leads to rapid degradation of the transcript. Poly-A sequences of various lengths are also added to many prokaryotic RNA transcripts where, instead of promoting stability, they enhance degradation. In both cases, RNA secondary structures, stabilizing proteins, or degrading enzymes interact with poly-A sequences. Considering the activities of RNAs, what might be general functions of 3?-polyadenylation?

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Question 7

Describe the role of two forms of RNA editing that lead to changes in the size and sequence of pre-mRNAs. Briefly describe several examples of each form of editing, including their impact on respective protein products.

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Question 8

Substitution RNA editing is known to involve either C-to-U or A-to-I conversions. What common chemical event accounts for each?

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Question 9

It has been suggested that the present-day triplet genetic code evolved from a doublet code when there were fewer amino acids available for primitive protein synthesis.
(a) Can you find any support for the doublet code notion in the existing coding dictionary?
(b) The amino acids Ala, Val, Gly, Asp, and Glu are all early members of biosynthetic pathways (Taylor and Coates, 1989) and are more evolutionarily conserved than other amino acids (Brooks and Fresco, 2003). They therefore probably represent "early" amino acids. Of what significance is this information in terms of the evolution of the genetic code? Also, which base, of the first two, would likely have been the more significant in originally specifying these amino acids?
(c) As determined by comparisons of ancient and recently evolved proteins, cysteine, tyrosine, and phenylalanine appear to be late-arriving amino acids. In addition, they are considered to have been absent in the abiotic earth (Miller, 1987). All three of these amino acids have only two codons each, while many others, earlier in origin, have more. Is this mere coincidence, or might there be some underlying explanation?

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Question 10

An early proposal by George Gamow in 1954 regarding the genetic code considered the possibility that DNA served directly as the template for polypeptide synthesis. In eukaryotes, what difficulties would such a system pose? What observations and theoretical considerations argue against such a proposal?

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Question 11

In a mixed copolymer experiment, messages were created with either 4/5C:1/5A or 4/5A:1/5C. These messages yielded proteins with the following amino acid compositions.
  Using these data, predict the most specific coding composition for each amino acid.

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Question 12

Shown here are the amino acid sequences of the wild-type and three mutant forms of a short protein. Use this information to answer the following questions:
  (a) Using Figure, predict the type of mutation that led to each altered protein.
(b) For each mutant protein, determine the specific ribonucleotide change that led to its synthesis.
(c) The wild-type RNA consists of nine triplets. What is the role of the ninth triplet?
(d) Of the first eight wild-type triplets, which, if any, can you determine specifically from an analysis of the mutant proteins? In each case, explain why or why not.
(e) Another mutation (Mutant 4) is isolated. Its amino acid sequence is unchanged, but the mutant cells produce abnormally low amounts of the wild-type proteins. As specifically as you can, predict where this mutation exists in the gene.
Figure
  
The coding dictionary. AUG encodes methionine, which initiates most polypeptide chains. All other amino acids except tryptophan, which is encoded only by UGG, are represented by two to six triplets. The triplets UAA, UAG, and UGA are termination signals and do not encode any amino acids.

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Question 13

The genetic code is degenerate. Amino acids are encoded by either 1, 2, 3, 4, or 6 triplet codons. (See Figure.) An interesting question is whether the number of triplet codes for a given amino acid is in any way correlated with the frequency with which that amino acid appears in proteins. That is, is the genetic code optimized for its intended use? Some approximations of the frequency of appearance of nine amino acids in proteins in E. coli are given in the following:
  (a) Determine how many triplets encode each amino acid.
(b) Devise a way to graphically compare the two sets of information (data).
(c) Analyze your data to determine what, if any, correlations can be drawn between the relative frequency of amino acids making up proteins and the number of codons for each. Write a paragraph that states your specific and general conclusions.
(d) How would you proceed with your analysis if you wanted to pursue this problem further?
Figure
  
The coding dictionary. AUG encodes methionine, which initiates most polypeptide chains. All other amino acids except tryptophan, which is encoded only by UGG, are represented by two to six triplets. The triplets UAA, UAG, and UGA are termination signals and do not encode any amino acids.

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Question 14

Klemke et al. (2001) discovered an interesting coding phenomenon in which an exon within a neurologic hormone receptor gene in mammals appears to produce two different protein entities (XL ? s, ALEX). Following is the DNA sequence of the exon's 5? end derived from a rat. The lowercase letters represent the initial coding portion for the XL ? s protein, and the uppercase letters indicate the portion where the ALEX entity is initiated. (For simplicity, and to correspond with the RNA coding dictionary, it is customary to represent the noncoding, nontemplate strand of the DNA segment.)5?-gtcccaaccatgcccaccgatcttccgcctgcttctgaagATGCGGGCCCAG
(a) Convert the noncoding DNA sequence to the coding RNA sequence.
(b) Locate the initiator codon within the XL ? s segment.
(c) Locate the initiator codon within the ALEX segment. Are the two initiator codons in frame?
(d) Provide the amino acid sequence for each coding sequence. In the region of overlap, are the two amino acid sequences the same?
(e) Are there any evolutionary advantages to having the same DNA sequence code for two protein products? Are there any disadvantages?

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Question 15

The concept of consensus sequences of DNA was defined in this chapter as sequences that are similar (homologous) in different genes of the same organism or in genes of different organisms. Examples were the Pribnow box and the ?35 region in prokaryotes and the TATA-box region in eukaryotes. One study found that among 73 isolates from the virus HIV-Type 1C (a major contributor to the AIDS epidemic), a GGGNNNNNCC consensus sequence exists (where N equals any nitrogenous base) in the promoter-enhancer region of the NF- ? B transcription factor, a cis -acting element that is critical for initiating HIV transcription in human macrophages (Novitsky et al., 2002). The authors contend that finding this and other conserved sequences may be of value in designing an AIDS vaccine. What advantages would knowing these consensus sequences confer? Are there disadvantages as a vaccine is designed?

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Question 16

Recent observations indicate that alternative splicing is a common way for eukaryotes to expand their repertoire of gene functions. Studies indicate that approximately 50 percent of human genes exhibit alternative splicing and approximately 15 percent of disease-causing mutations involve aberrant alternative splicing. Different tissues show remarkably different frequencies of alternative splicing, with the brain accounting for approximately 18 percent of such events (Xu et al., 2002. Nuc. Acids Res. 30: 3754-3766).
(a) Define alternative splicing and speculate on the evolutionary strategy alternative splicing offers to organisms.
(b) Why might some tissues engage in more alternative splicing than others?

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Quiz 13: The Genetic Code and Transcription