Pierce_Gene to Protein_Handout

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Union County College *

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240

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Biology

Date

Jan 9, 2024

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pdf

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5

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Name: From Gene to Protein Page 1 of 5 From Gene to Protein Activity Background You have identified a (fictional!) gene Q . This gene is thought to play a role in liking chocolate. You have the wild-type se- quence of this gene. In talking to a coworker, you learn that she detests chocolate, so you ask to sequence her gene Q . When you get the sequence back, you realize she has a mutation in this gene. 1. Based on what you know about the genetic code, would a mutation in a gene always lead to an altered protein? In this activity, you will transcribe and translate the wild-type gene Q , and then determine whether your coworker’s mutation alters protein Q (and therefore whether it’s possible that your coworker detests chocolate because of this mutation). Part 1: The pre-mRNA The sequence of the (fictional) gene Q is below. Here, the bottom strand is the template strand. +1 5’…TACTAATCGA AAATTGCAGA CTGTAATGGA GTCAGATGAT 3’…ATGATTAGCT TTTAACGTCT GACATTACCT CAGTCTACTA GCATTAAGGT AAGT……A…TCAGG AGAAATTGAA ATAAA…3’ CGTAATTCCA TTCA……T…AGTCC TCTTTAACTT TATTT…5’ 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.
Name: From Gene to Protein Page 2 of 5 These sequences can be identified based on their perfect or high identity to the consensus sequences as shown below. In the sequence you have, much of the intron 1 sequence is not given and is replaced by “…”. 3. 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 flanking 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 after 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. Check in with your instructor before proceeding to translate protein Q! Part 3: Translating mRNA to protein 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. The position of the start codon defines 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 identified by organizing the nucleotides into contiguous sets of three at a time. The end of the reading frame is defined 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.
Name: From Gene to Protein Page 3 of 5 During translation amino acids are incorporated into a protein according to the genetic code. Each codon specifies an amino acid. The genetic code is shown below: 7. Based on the genetic code and mature gene mRNA sequence, write out the primary sequence (the sequence of amino acids of protein Q) in Box III (last page of this handout). Check with your instructor that you have the correct amino acid sequence! Part 4: Does the mutant gene Q code for an altered protein? You have the mutant version of gene Q below. The base pair difference is highlighted and underlined. +1 5’…TACTAATCGA AAATTGCAGA CTGTAATG G G AGTCAGATGA 3’…ATGATTAGCT TTTAACGTCT GACATTAC C C TCAGTCTACT TGCATTAAGG TAAGT……A…TCAG GAGAAATTGA AATAAA…3’ ACGTAATTCC ATTCA……T…AGTC CTCTTTAACT TTATTT…5’ 8. What consequence would this have on the protein? Would it affect 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 after introduction of the mutation.
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