LS7C Week 9 Pre-Class Reading Guide

.pdf

School

University of California, Los Angeles *

*We aren’t endorsed by this school

Course

Subject

Biology

Date

Dec 6, 2023

Type

pdf

Pages

Uploaded by DeaconWaterAnt60

LS7C Week 9 Pre-Class Reading Guide Fill out this worksheet as you complete your pre-class assignments. Bring your completed worksheet to class to use as a reference for in-class activities. After completing your pre-class assignments, you should be able to: • Identify elements of protein-coding genes • Interpret genome browser profiles summarizing data for coding and non-coding positions in a genome • Describe how properties of particular amino acids in a protein may affect protein structure and function • Define DNA/gene editing • Describe the structure and function of the CRISPR/Cas9 system and its application to human gene editing 1. The diagram below shows a gene model of a protein coding region of the genome. a. Indicate whether the sequence shown below is the template or non-template strand of this gene. b. Transcribe the primary mRNA and then write the sequence of the mature mRNA beneath the primary transcript. c. Translate the mRNA to show the amino acid sequence of the polypeptide produced. 2. The UCSC Genome Browser ( http://genome.ucsc.edu/ ) allows you to access data that many scientists have collected to understand the human genome. Find the gene SHH in the genome browser. You should try to be well acquainted with the Genome Browser before your Week 9 discussion. a. On what Chromosome is the SHH gene located? What is the total SHH gene transcript size? b. Draw the SHH gene model below. Be sure to include the direction the gene is transcribed. Label the 5’ and 3’ ends. Distinguish between exons and introns on the gene model. How many exons and introns are in the SHH gene? Number of exons: _____________ Number of Introns: ______________ c. The arrowheads on the gene model represent the direction in which the gene is transcribed. Where do you expect the promoter for the SHH gene to be? d. If upstream is defined as towards the 5’ end of a DNA strand, what is the closest protein coding gene downstream (to the left) of the SHH gene on this chromosome? You might try to zoom out. e. What is a non-coding RNA? Are there any non-coding RNAs in this region of the genome? Try looking further upstream of the SHH gene for a uniquely colored transcript. You might try to zoom out.

If you would like more practice using the genome browser, try looking up another gene and answering the same questions that you answered for SHH above. (Some ideas: TP53, BRCA1, ACTA1, INS, SLC2A1, ATP1A2, PFKB1, TBP) 3. In addition to the general navigation controls at the top of the genome browser, there are tools that allow you to explore the genome in more depth. Hold the Shift key down then click and drag your mouse across a region on the genome browser. A pop-up will appear with instructions on how to highlight a region of the genome or zoom in on that region. Practice using the highlight and zoom tools to label and explore a specific position in the SHH gene. a. Highlight the start codon for SHH. At what nucleotide position in this chromosome is the start codon for the SHH gene? Write the three nucleotides that represent the start codon of SHH as they would appear in the coding strand of DNA. b. Based on the direction of transcription, does the nucleotide sequence shown on the genome browser represent the coding or template strand of DNA for the SHH gene? c. Highlight the stop codon for SHH. At what nucleotide position in this chromosome is the stop codon for the SHH gene? Write the three nucleotides that represent the stop codon of SHH as they would appear in the coding strand of DNA. 4. Often eukaryotic genes make more than one possible mRNA. These different mRNA splice variants are displayed as different gene models (box and line illustrative renderings). They are also called isoforms. To best illustrate different isoforms, you should take a closer look at the RBM33 gene (from 2d above). a. Are there multiple gene isoforms for RBM33? What about SHH? How man isoforms did you count for each gene? b. The gene models illustrate changes in the way that the RBM33 gene is transcribed and how its introns are spliced. What differences do you notice between the isoforms of RBM33? List them out and describe how they differ. Pay particular attention to the start/stop codon locations, numbers of exons, and identity of exons.

Your preview ends here

Eager to read complete document? Join bartleby learn and gain access to the full version