Thakkar_Vraj_Wk5

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250

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Biology

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Apr 3, 2024

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docx

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MCB 250 Spring 2024 Discussion Week 5 – Feb. 22-26 1. A promoter for an E. coli gene that is transcribed by a -70 RNA polymerase has the following sequence: -30 -20 -10 +1 | | | | 5’GGCTTTACACTTTATGCTTCCGGCTCGTATGTTGTGTGGA 3’CCGAAATGTGAAATACGAAGGCCGAGCATACAACACACCT The transcription start site (+1) is identified. a. Identify the –10 and –35 sequences. How close are they to the consensus –10 and –35 sequences? The -10 sequence 5' TATGTT 3' and the -35 sequence 5' TTTACA 3' are regions within a promoter sequence. The consensus -35 sequence, which is the most common sequence found at the -35 region, is 5' TTGACA 3'. When comparing the given -35 sequence 5' TTTACA 3' to the consensus, we can see they are very similar, with only a single base difference. This close similarity to the consensus sequence suggests the given promoter sequence is likely a strong promoter that can effectively initiate transcription. b. What is the spacing between the –10 and the –35 sequences? How does this compare with the consensus spacing? They are separated by 17 bases, i.e consensus spacing . c. The sequence of bases in a transcribed RNA is identical (except for U's instead of T's) to the non-template strand. Explain. - The template strand of DNA is the strand that is used as the template for mRNA synthesis. The mRNA sequence is complementary to the template strand. - The non-template strand has a sequence that matches the mRNA transcript, except that in RNA, thymine (T) bases are replaced by uracil (U) bases. So the non-template DNA strand and the mRNA transcript are essentially identical in sequence, with U substituted for T. - The template and non-template DNA strands are complementary to each other with A-T and G-C base pairing. 1
So in essence, the mRNA transcript matches the non-template DNA strand except for substituting U where there are T bases. This allows the mRNA to convey the same genetic code information as the non-template DNA strand. d. Define promoter strength. The promoter's strength is defined by its ability to bind with RNA polymerase for the execution of transcription. The degree of binding strength directly influences the extent of gene transcription. e. Predict the effect of the following mutations on the strength of this promoter (stronger, weaker, no change). The changes indicated show the sequence as top strand/complementary strand. 1) Replacement of CTT/GAA at –23 to –20 with AAG/TTC. No change bc promotor ends bind to -10 and -35 sites only. 2) Replacement of G/C at –9 with A/T. This will give sequence 5' TATATT 3'. This sequence is pretty much similar to the original one - 5' TATAAT 3'. That's why it will be a strong promoter. 3) Replacement of T/A at –12 with C/G. This will give the sequence as 5' CATGTT 3'. This sequence is less similar to the original JAta sequence. Hence, the promoter will be weak. 4) Replacement of G/C at –38 with C/G. No change. Promotor wont bind . 5) Insertion of AT/TA between –18 and –17. No change. Promotor wont bind. 2. Alternative splicing is a key feature of the eukaryotic transcription-translation process. a) In eukaryotes, alternative splicing of pre-mRNAs can result in the production of many structurally distinct proteins from information encoded in a single gene. Explain. Alternative splicing is a mechanism wherein segments (exons) of pre-mRNA are rearranged in different combinations, resulting in the generation of multiple mRNA molecules from a single gene. These mRNA variants give rise to distinct protein isoforms. The splicing machinery identifies splice sites, allowing for the selective inclusion or exclusion of specific exons. This dynamic process contributes to the diversification of protein functions by introducing variations in structure, function, and interaction partners. 2
b) Do lower eukaryotes (such as yeast, Saccharomyces cerevisiae ) have the same opportunity to use alternative splicing to generate a vast array of proteins from a single gene? Explain. In lower eukaryotes such as yeast, alternative splicing is a phenomenon that occurs, but it is less frequent and complex compared to higher eukaryotes. This is primarily attributed to the simpler gene structures and fewer introns present in yeast genomes. Instead of relying heavily on alternative splicing for protein diversity, yeast employs alternative mechanisms. These mechanisms include gene duplication, diverse gene expressions, and post-translational modifications like phosphorylation or acetylation. These alternative strategies contribute to the generation of protein diversity in yeast, compensating for the relatively limited role of alternative splicing in comparison to higher eukaryotes. c) What other events can lead to additional diversity in the repertoire of proteins that could be encoded by a single gene? Hint: think of the N and C terminal ends. What about a post- translational mechanism. Name one. Indeed, various splicing-related mechanisms play crucial roles in enhancing protein diversity. Alternative start codon usage allows for the translation of different N-terminal sequences, affecting protein localization and function. Alternative polyadenylation generates mRNA transcripts with varying 3' UTR lengths, impacting mRNA stability, localization, and translation efficiency. Additionally, alternative exon usage at the C-terminal end can lead to variations in protein domains or interaction sites. Furthermore, post-translational modifications, including phosphorylation, glycosylation, acetylation, and ubiquitination, modify protein properties, stability, and cellular localization. These modifications contribute significantly to the diversification of functional proteins, adding an additional layer of complexity to the regulation of cellular processes. The combined effects of these splicing-related mechanisms and post-translational modifications contribute to the intricate and diverse landscape of functional proteins in cells. 3
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