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1. What features of a protein-coding gene might be found in a non-coding gene?
2. What features are unnecessary in a non-coding gene?
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- Some exons in the human genome are quite small (lessthan 75 bp long). Identification of such “microexons” isdifficult because these distances are too short to reliablyuse ORF identification or codon bias to determine ifsmall genomic sequences are truly part of an mRNAand a polypeptide. What techniques of “gene finding”can be used to try to assess if a given region of 75 bpconstitutes an exon?a. Very few if any eukaryotic genes contain tractswith more than 25 As or Ts in a row, yet almost alleukaryotic mRNAs have a tract with more than100 As in a row. How is this possible?b. Scientists know the nucleotide sequences that directthe termination of bacterial gene transcription, butthey generally have little idea about the nature ofthe nucleotide sequences that direct transcriptiontermination in eukaryotic cells. Explain the basisof this statement.Shown below is a portion of a wild-type DNA sequence that encodes the last amino acids of a protein that is 270 amino acids long. The first three bolded base pairs indicate the frame and include the coding region. 5^ ...GCTAAGTATTGCTCAAGATTAGGATGATAAATAACTGG 3^ 3^.. CGATTCATAACGAGTTCTAATCCTACTATTTATTGACC 5^ Which strand is the template strand for transcription of this gene? Briefly explain how you know. An insertion of one base pair causes the protein to decrease in length by seven amino acids. With respect to the sequence given above, where does this insertion occur? A change of one base pair leads to the protein increasing in the length by one amino acid. With respect to the sequence given above, which base pair would you change, and what would you change this base pair for the protein to increase in the length by one amino acid?
- Alternative splicing is a common mechanism for eukaryotes toexpand their repertoire of gene functions. At least one estimateindicates that approximately 50 percent of human genes usealternative splicing, and approximately 15 percent of diseasecausingmutations involve aberrant alternative splicing. Differenttissues show remarkably different frequencies of alternativesplicing, with the brain accounting for approximately 18 percentof such events. Why might some tissues engage in more alternative splicingthan others?A research group has sequenced the cDNA and genomic DNA for a particular gene. The cDNA is derived from mRNA, so it does not contain introns. Here are the DNA sequences. cDNA: 5′–ATTGCATCCAGCGTATACTATCTCGGGCCCAATTAATGCCA– GCGGCCAGACTATCACCCAACTCGGTTACCTACTAGTATATC– CCATATACTAGCATATATTTTACCCATAATTTGTGTGTGGGTATA– CAGTATAATCATATA–3′ Genomic DNA (contains one intron): 5′-ATTGCATCCAGCGTATACTATCTCGGGCCCAATTAATGCCAG CGGCCAGACTATCACCCAACTCGGCCCACCCCCCAGGTTTA– CACAGTCATACCATACATACAAAAATCGCAGTTACTTATCCCA– AAAAAACCTAGATACCCCACATACTATTAACTCTTTCTTTCTAG– GTTACCTACTAGTATATCCCATATACTAGCATATATTTTAC– CCATAATTTGTGTGTGGGTATACAGTATAATCATATA–3′ Indicate where the intron is located. Does the intron contain the normal consensus sequences for splicing, based on those shown? Underline the splice site sequences, and indicate whether or not they fit with the consensus sequences.The entire genome of the yeast Saccharomyces cerevisiaehas been sequenced. This sequencing has led to the identification of all the open reading frames (ORFs, gene-sizesequences with appropriate translational initiation andtermination signals) in the genome. Some of these ORFsare previously known genes with established functions;however, the remainder are unassigned reading frames(URFs). To deduce the possible functions of the URFs,they are being systematically, one at a time, convertedinto null alleles by in vitro knockout techniques. The results are as follows:15 percent are lethal when knocked out.25 percent show some mutant phenotype (alteredmorphology, altered nutrition, and so forth).60 percent show no detectable mutant phenotype at alland resemble wild type.Explain the possible molecular-genetic basis of thesethree mutant categories, inventing examples wherepossible.
- You have just gotten back the results from an RNA-seq analysis of mRNAs from liver. You had anticipatedcounting the number of reads of each mRNA to deter-mine the relative abundance of different mRNAs. But youare puzzled because many of the mRNAs have given youresults like those shown in Figure Q8–4. How is it that dif-ferent parts of an mRNA can be represented at differentlevels?The code for a fully functional protein is actually coming from an mRNA transcript that has undergone post transcriptional processing which is essentially way too different from the original code in the DNA template. Given: Cytosine; a Protein with known amino acid sequence (amino acid sequence given below) MATIVNTKLGEHRGKKRVWLEGQKLLREGYYPGMKYDLELKDSQVVLRVKEEGKFTISKRERNGRVSPII DLTVQELATVFDGVEMLRVFIRNGAIVISAHHQQERVIERVNRLISKLENGESLSVCSLFHGGGVLDKAI HAGFHKAGIASAISVAVEMEGKYLDSSLANNPELWNEDSIVIESPIQAVNLSKRPPQVDVLMGGIPCTGA SKSGRSKNKLEFAESHEAAGAMFFNFLQFVEALNPAVVLIENVPEYQNTASMEVIRSVLSSLGYSLQERI LDGNEFGVIERRKRLCVVALSHGIDGFELEKVQPVRTKESRIQDILEPVPLDSERWKSFDYLAEKELRDK AAGKGFSRQLLTGDDEFCGTIGKDYAKCRSTEPFIVHPEQPELSRIFTPTEHCRVKGIPEELIQGLSDTI AHQILGQSVVFPAFEALALALGNSLWSWVGMMPIMVEVVDESQPVIGGEDFHWATALVDAKGTLKLSPAA KKQGMPFNIMDGQLAVYSPNGTKKSCGHEPCEYLPVMMSGDAIMVTSSLVH Requirement: Original DNA code (itemize the steps you would take to get to know the original DNA code of Cytosine in focus)Alternative splicing is a common mechanism for eukaryotes toexpand their repertoire of gene functions. At least one estimateindicates that approximately 50 percent of human genes usealternative splicing, and approximately 15 percent of diseasecausingmutations involve aberrant alternative splicing. Differenttissues show remarkably different frequencies of alternativesplicing, with the brain accounting for approximately 18 percentof such events. Define alternative splicing and speculate on the evolutionarystrategy alternative splicing offers to organisms.
- mRNA sequence of A gene If we have the following mutations, find the type of the mutation (silent or missense or nonsense?) 17CàU 36GàA 49GàU 115AàC 5’ AAACUGUGACUGAACCUCAAACCCCAAACCAGCCCGAGGAGAACCACAUUCUCCCAGGGA CCCAGGGCGGGCCGUGACCCCUGCGGCGGAGAAGCCUUGGAUAUUUCCACUUCAGAAGCC UACUGGGGAAGGCUGAGGGGUCCCAGCUCCCCACGCUGGCUGCUGUGCAGAUGCUGGACG ACAGAGCCAGGAGGGAGGCCGCCAAGAAGGAGAAGGUAGAGCAGAUCCUGGCAGAGUUCCAGC UGCAGGAGGAGGACCUGAAGAAGGUGAUGAGACGGAUGCAGAAGGAGAUGGACCGCGGCCUGA GGUAGAAGCCGCUGGGGCUUGGGGCU-3’Which of the following set(s) of primers a–d couldyou use to amplify the following target DNA sequence, which is part of the last protein-coding exonof the CFTR gene?5′ GGCTAAGATCTGAATTTTCCGAG ... TTGGGCAATAATGTAGCGCCTT 3′3′ CCGATTCTAGACTTAAAAGGCTC ... AACCCGTTATTACATCGCGGAA 5′a. 5′ GGAAAATTCAGATCTTAG 3′;5′ TGGGCAATAATGTAGCGC 3′b. 5′ GCTAAGATCTGAATTTTC 3′;3′ ACCCGTTATTACATCGCG 5′c. 3′ GATTCTAGACTTAAAGGC 5′;3′ ACCCGTTATTACATCGCG 5′d. 5′ GCTAAGATCTGAATTTTC 3′;5′ TGGGCAATAATGTAGCGC 3′Sequence: CCACCTGTACCCGGACACACCCTGGTGTCC Provide the FULL protein sequence encoded by the gene. Are different splice variants known for this gene?