Lecture 5: Review of Genetic Code and Translation

1. The genetic code is organized into units called codons.

a. What constitutes a codon?
b. How many different codons are possible, based on the structural organization of individual codons?
c. How many different codons are there that specify amino acids in the "standard" version of the genetic code?
d. What is the function of the codons that do not code for amino acids?
e. Compare the number of amino acid-coding codons with the number of amino acids that are coded for and explain how cells deal with the discrepancy in the two numbers.

2. What effect on the coded protein do you expect from each of the following:

a. Deletion of one nucleotide from near the 5'-end of the coding sequence?
b. Deletion of one nucleotide from near the 3'-end of the coding sequence?
c. Deletion of three nucleotides from near the middle of the coding sequence?
d. Inserting one nucleotide near the 5'-end of the coding sequence.
e. Deleting one nucleotide near the 5' end of the coding sequence and inserting one nucleotide nine nucleotides downstream from the deletion.

3. Is the genetic code universal? Justify your answer.

4. Parts of this question will require speculative answers based on reasonable extrapolation from information that has been given.

a. In a random DNA sequence read three bases at a time, how frequently would you expect to encounter a stop codon?
b. How would you determine whether a known prokaryotic DNA sequence that is 1000 base pairs in length contains a protein-coding gene. (Assume for purposes of this question that any functional protein would be at least 100 amino acids in length. Also, keep in mind the possibility that the protein could be coded for in any of the three possible reading frames, and that the coding could be in a 5' to 3' direction on either of the two strands of DNA, since you do not know whether the sequence you have was read from the sense or the antisense strand.).
c. What characteristic features would you expect to be contained in a complete coding sequence for a protein?
d. What additional features would you expect to see upstream from the coding sequence for a protein?
e. What additional features would you expect to see downstream from the coding sequence for a protien?
f. What added complication might you encounter with eukaryotic DNA?

5. The table of codons in the textbook lists only RNA codons. What changes would be necessary to show DNA codons?

6. Which amino acid does each of the following DNA codons specify?

a. ATG
b. TAA
c. TTT
d. CAT
e. TGG

7. Describe all of the parts of a full-length eukaryotic mRNA that do not code for amino acids.

8. Translation is a complex process that involves many different molecular species.

A. What is the name of the molecular species that matches specific amino acid structural properties to specific nucleic acid structural properties during the process of translation? Describe the major function(s) of such molecules.

B. What is the name of the molecular species that reads the triplet code on the mRNA? How does that molecular species become associated with the amino acid that corresponds to the codon triplet(s) it reads?

C. What molecular species are associated with the actual formation of peptide bonds between two amino acids? Be as specific as you can.

D. What molecular species are associated with the termination of translation and release of the new protein from the ribosome?

E. What molecules provide the energy needed for translation?

9. Describe the roles of the A and P sites on the ribosome during translation.

10. Describe the sequence of events involved in assembling together the messenger RNA, the ribosomal subunits, and the first two amino acids involved in translation of a specific protein. Include in your summary a brief description of the various accessory molecules and carrier molecules that are involved.

11. What signals (plural) identify the start site for protein synthesis in prokaryotic cells?

12. What signals identify the termination site for protein synthesis?

13. What is meant by the term "redundancy"as it is applied to the genetic code?

14. What is the physical location where new peptide bonds are formed during protein synthesis? Be as precise as you can.

15. How much energy (measured in terms of high energy bonds) is consumed for each new amino acid added to a growing protein? Summarize the energy consuming steps.

16. Distinguish between the following pairs in a way that makes it clear that you know what each is and how they differ.

a. Initiation factor and elongation factor.
b. ATP and GTP
c. 16S rRNA and 21S rRNA
d. EF-Tu and EF-G
e. AUG codon and UAG codon
f. 70S and 80S ribosomes
g. The first amino acid in a prokaryotic protein and the first amino acid in an eukaryotic protein

17. What does the presence of intact 80S ribosomes in an electron micrograph tell you about the physiological state of the cell at the time it was fixed and used for specimen preparation.

18. Compare the mRNA signals that are needed for initiation of translation in prokaryotic and eukaryotic cells. What features are different and what features are shared in common.

19. What is the wobble hypothesis, and what is its importance for translation.

20. Transfer RNA plays a critical role in translation.

a. What is the nature of the bond between the amino acid and the tRNA?
b. How is that bond formed?
c. How is that bond broken?
d. What is the nature of the tRNA sequence adjacent to the point of attachment of the amino acid?
e. How does the correct amino acid become matched up with each molecular species of tRNA?
f. What happens if the wrong amino acid becomes attached to a tRNA?
g. What is unusual about the nucleotides conained in tRNA molecules?
h. How do you explain the fact that a typical cell does not contain as many different molecular species of tRNA as the number of different codons that are present in its messenger RNAs.
i. Is the cloverleaf diagram an accurate representation of a tRNA molecule? Explain your answer.

21. The amino acid hydroxyproline is found in substantial amounts in collagen proteins, but there is no codon for hydroxyproline. How can you explain this apparent discrepancy?

22. What is a polysome and what is its significance?

23. What is meant by post-translational modification of proteins?

24. Prions are unusual infectious agents.

a. Explain what a prion is believed to consist of.
b. Where is the genetic code for prion proteins located?
c. What changes are involved in the acquisition of pathogenic properties by prions?
d. How is prion infectivity believed to be achieved?
e. What properties of prions make prion diseases particularly difficult to control?

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