+1 2. Write out the primary sequence of the RNA transcript starting at +1 and co
ID: 165084 • Letter: #
Question
+1
2. Write out the primary sequence of the RNA transcript starting at +1 and continuing until the end of the sequence provided in Box I on the last page of this handout. (Write out the ‘...’s as well.)
*Hint: Have one group member read out the bases from the correct strand in the correct 5’ 3’ direction, and have another write them down.
Part 2: The mature mRNA
The sequence you have written out above corresponds to the pre-mRNA including the 5’ and 3’ untranslated sequences (5’ and 3’ UTRs), exon 1, intron 1, and exon 2 (the last exon in the gene). Introns are noncoding regions of the gene that are spliced out of the primary transcript as part of RNA processing.
Splicing requires a 5’ splice site and a 3’ splice site in addition to a branch point.
3. In the sequence you have, much of the intron 1 sequence is not given and is replaced by “...”.
Find and underline the sequence corresponding to the intron in the pre-mRNA sequence you wrote out in Box I.
*Hint: Look for the four nucleotide stretch AGGU, which is invariant in the 5’ consensus sequence, and then look at anking nucleotides to determine if they match the rest of the 5’ consensus sequence. Subsequently, look for the four nucleotide stretch CAGG, which is invariant in the 3’ consensus sequence.
4. Write the sequence of the mature mRNA a er intron 1 has been spliced out in Box II (on the last page of this handout).
Make sure you make the correct junction between exon 1 and exon 2 by paying attention to the precise 5’ and 3’ splice sites.
After RNA processing, the mature mRNA is exported from the nucleus to the cytoplasm. At this point the mature mRNA can be translated based on its reading frame and the genetic code. e position of the start codon de nes the reading frame of the mature mRNA.
5. Identify and underline the start codon in the mRNA sequence that you wrote out in Box II.
*Hint: In the gene Q mRNA the start codon is located closest to the 5’ end of the mature mRNA.
Once the reading frame start is located, the rest of the codons can be identi ed by organizing the nucleotides into contiguous sets of three at a time. e end of the reading frame is de ned by the presence of one of the three possible stop codons in the same frame.
6. For the mature mRNA sequence above (Box II), identify the reading frame and all of the codons, including the stop codon, in the mature mRNA. Underline the start codon, circle the three bases that code for each following codon, and draw a square around the stop codon.
7. Based on the genetic code and mature gene mRNA sequence, write out the primary sequence (the sequence of amino acids of protein Q).
You have the mutant version of gene Q below. e base pair di erence is highlighted and underlined.
+1
5’...TACTAATCGA AAATTGCAGA CTGTAATGGG AGTCAGATGA
3’...ATGATTAGCT TTTAACGTCT GACATTACCC TCAGTCTACT
TGCATTAAGG TAAGT......A...TCAG GAGAAATTGA AATAAA...3’
8. What consequence would this have on the protein? Would it a ect the sequence of the protein, the length, or both?
*Hint: Consider where the start codon is in the original gene sequence and consider the frame a er introduction of the mutation.
1. Which sequences are present in both the pre-mRNA and the mature mRNA? (Select all that apply.)
a. exons
b. introns
c. 5’ UTR
d. 3’ UTR
2. Which sequences are important to predict the protein sequence from the DNA sequence? (Select all that apply.)
a. start codon
b. stop codon
c. intron splice sites
d. the transcription start site
3. How many amino acids are translated from a gene with no introns and 15 codons?
a. 16
b. 15
c. 14
d. 10
Explanation / Answer
1. Which sequences are present in both the pre-mRNA and the mature mRNA: exons, 5’ UTR, 3’ UTR
introns are spliced out from pre mRNA.
5'-UTR and 3'-UTR are untranslated regions but not untranscribed regions. hence, they would not appear in protein sequence, but appear in mRNA.
2. Which sequences are important to predict the protein sequence from the DNA sequence: intron splice sites, the transcription start site
start codon and stop codon are also useful in predicting protein sequence. but codons are generally represented by trinucleotide sequences in mRNA.
3. How many amino acids are translated from a gene with no introns and 15 codons: 14
each codon codes for an amino acid. however, a gene would contain stop codon at the end, which does not code for any amino acid. therefore, 14 amino acids will be coded from a gene 15 codons
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