Please answer the following questions. IMPORTANT: When referring to specific nucleotides, give the letters of the bases (A,C,G or T), as well as their numerical positions in the original DNA sequence. For questions 1-6, please just give me the bases and their numbers, or the range of bases--don't include the question or add any editorial material. (Ex. "GAC at 234, 235, 236" or "pre-mRNA = 456-879" if I am asking for a range of nucleotides).
1. a. How many nucleotides in the entire sequence entry?
b. How many exons are in the gene?
c. How many introns are in the gene?
To help you answer later questions, please highlight the three exons.
2. Transcription is initiated by the binding of transcription factors to the promoter region at the front end of the gene. The promoter region usually includes a variable number of nucleotides that lie in front of exon 1, and often includes approximately the first third of exon 1. Transcription factor binding sites sometimes have characteristic sequences. Among these are what people cutely call the "cat box motif," which involves the nucleotides C, A and T in some arrangement that spells out CAT or something like it, examples: CAAT, CCAATT, CATAAAA.Please identify two sequences that might serve as "cat box" promoter sequences. First remind yourself where to look--think about where the promoter region of the gene is, compared to the gene's coding sequence.
3. Which nucleotides are used to make the pre-mRNA (aka the primary transcript)?
4. Recall what happens as the pre-mRNA is processed into mRNA. Which nucleotides are present in the mRNA?
5. Codon 31 begins with nucleotide 244. Which three nucleotides from the DNA sequence are contained in codon 31 of the mRNA?
6. Recall that the bases at the very beginning and very end of the mRNA are not actually read as instructions to chain the amino acids together; they help stabilize the mRNA and get the mRNA to where it needs to go to be translated. The CDS contains the nucleotides that were actually used to direct the ribosome to chain the appropriate amino acids together during translation. Look at the CDS to determine exactly where translation begins and ends. Which three nucleotides make up the translation initiation codon, aka the START codon? (Hint: its sequence is always ATG)
7. Again using the CDS to tell you where translation began and stopped, please tell me which of the three STOP codons the beta-globin gene uses to signal to the ribosome that it can stop adding amino acids to the polypeptide? Give me the three nucleotides and their positions in the original DNA sequence.
8. If there was a deletion that took out nucleotides 1-103, what effect would that deletion have on the beta-globin gene's activity, and why?
9. Codon 9 is an AAG codon; it causes lysine to be incorporated as the ninth amino acid in the polypeptide. Which would be more deleterious to the function of the protein, an AG change 5 involving the first A in the codon (new codon = GAG) or an AG change involving the second A in the codon (new codon = AGG)? Why do you say this?
Genetic Code Table
