Lecture 5: RNA Processing, Messenger RNA, Genetic Code
1. Summarize the overall organization of a typical eukaryotic gene and the RNA that is initially transcribed from it.
2. Describe three distinctly different ways in which eukaryotic messenger RNA is modified after the gene is transcribed.
3. Describe the "cap" that is added to the 5'-end of eukaryotic mRNA molecules. What unusual features does it have?
4. What role or roles are believed to be played by the 5'-cap on eukaryotic mRNAs?
5. What modification occurs at the 3'-end of most eukarytoic mRNAs? What is the signal that causes the modification to be made?
6. What is a snRNP, and what is its significance to message processing?
7. Summarize the major steps involved in removing introns from hnRNA, including the signals that are involved in determining what sequences are to be removed.
8. Describe the formation of a "lariat loop" during the removal of an intron. What is unusual about the bond that closes the loop?
9. How do ribosomal RNAs differ from their initial transcript?
10. Describe the steps involved in the flow of genetic information from DNA to protein in an eukaryotic cell. How does the overall process differ in prokaryotic cells?
11. 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 most common 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.
12. 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.
13. Is the genetic code universal? Justify your answer.
14. 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?
15. The table of codons in the textbook lists only RNA codons. What changes would be necessary to show DNA codons?
16. Which amino acid does each of the following DNA codons specify?
a. ATG
b. TAA
c. TTT
d. CAT
e. TGG
17. Describe all of the parts of a full-length eukaryotic mRNA that do not code for amino acids.
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