Exam 2 Information And Content Review PDF

Exam 2 General Information + Content Review Monday, October 28, 2024  Exam 2 Overview This exam is CLOSED NOTE Between 15-20 Multiple Choice Questions (Scantron) 1 hour to complete it - rest of class time is for collecting papers ○ Accommodations Students - Check your Canvas...

Exam 2 General Information + Content Review Monday, October 28, 2024  Exam 2 Overview This exam is CLOSED NOTE Between 15-20 Multiple Choice Questions (Scantron) 1 hour to complete it - rest of class time is for collecting papers ○ Accommodations Students - Check your Canvas mail!!! Covers content from Topics 9-15 Questions very similar to the homework and quizzes What to Bring REQUIRED Writing Utensil: Scantron - Pencil is better in case you make mistakes but only if you write DARK; pen is fine too REQUIRED UT ID: You NEED your ID to turn in exams OPTIONAL Other Writing Utensils: Feel free to bring highlighters, pens, anything you might want to show work and solve problems - you will have space on the exam booklet to solve problems, but we will keep extra scratch paper. NO CALCULATOR What will Test Day look like? If you are in the 11am section - show up to the 11am class. If you are in the 12:30pm section - show up to the 12:30pm class. ○ (Accommodations students have different instructions!) Leave everything (bags, phones, electronics)) except for writing utensils and ID at the front of the room - TRY NOT TO BLOCK PATHWAY Try to spread out Scantrons and exams will all be collected You NEED your UT ID Card to turn in exams Test Day Instructions Leave everything (bags and phones) against the wall. Silence/Turn off electronics. Bring writing utensils and ID to your seat. Try to have at least one seat between you and the next person When you are done, bring your exam, scantron, and ID to turn in exams at the front. You don’t need to put in the unique number on the scantron - Name and EID If we see a phone, ipad, smart watch, other electronic device out, we will take your exam and you will receive a 0. What to Study Quizzes: Exam problems very similar to quiz problems. Homework: Homework problems help prepare you for quiz and exam problems. Homework is a good way to assess if you are able to apply what you have learned in class. Slides: Dr. Engler’s Slides are good for content review and base understanding Textbook: Textbook is good for content review and context for particular confusing topics. Be sure to know key vocabulary. How, where, and when to ask questions Come to Discussion where we go over FAQs! Come to office hours - See ‘TA and UGCA Office Hours’ page on Canvas. Post homework questions on Discussion ED Email someone on the teaching team with quiz questions Teaching team will respond to emails sent up until NOON on Sunday. We cannot guarantee a response after that. Where to find homework answers Solutions Manual and Study Guide You can find all the homework answers and explanations on Connect or on the Canvas Home page! What if I cannot take this exam on Monday because of an emergency? There are no make-ups and no drops. We will handle personal emergencies on an individual basis. Please email Dr. Engler, Damini, AND Ece if you have to miss the exam and report any emergencies to Student Emergency Services. Note: The Following slides are Summary Slides intended to help review the material. These slides are NOT comprehensive. The best way to study is reviewing quizzes, homework, and lecture/discussion/review slides as well as being sure you can do homework and quiz problems without notes. This is just to help you START studying! TOPIC 9: DNA Replication + Recombination  Review OF DNA Structure: Double Stranded Polar (5’ and 3’ ends) Complementary Base Pairing ○ A and T ○ C and G Pyrimidines: CUT (cut pie); Purines: AG  Replication is OVERVIEW OF DNA AND SEMICONSERVATIVE REPLICATION: Look at Feature Figure 6.23 (Chapter 6.4 DNA Replication)  WHAT ARE THE REQUIREMENTS OF DNA Primer, Template, 4 dNTPs POLYMERASE? DNA Recombination: Look at Feature Figure 6.27 (Chapter 6.5 Homologous Recombination at the DNA Level)  Fungal Tetrad Analysis Why Study Fungi? Ascus: a sac that contains all 4 products of single meiosis Ascospores: haploid cells Tetrad: assemblage of 4 ascospores in a single ascus ALL GAMETE PRODUCTS FROM SAME MEIOSIS STAY TOGETHER  3 tetrad types produced by meiosis of Gene Conversion… only case where dihybrid yeast: recombination is not reciprocal. Parental ditype (PD): all 4 spores have parental configuration of alleles Nonparental ditype (NPD): 4 recombinant spores, 2 of each type Tetratype (T): 4 different kinds of spores, 2 recombinant (one of each type) and 2 parental (one of each type). Topic 9: some of the especially helpful homework problems Chapter 6 #29 ***If the solutions manual explanation is confusing, there is a handwritten explanation and answer posted on ED Discussion. Look at that before asking the teaching team!*** Topic 9: some of the especially helpful homework problems Chapter 6 #33 Chapter 6 Solved Problem 1 TOPIC 10: MUTATION  What is mutation? Mutation: a heritable change in the Point Mutation: only affects a few bases, 3 types base-pair sequence of DNA Forward Mutation: WT→mutant Reverse Mutation: Mutant→WT Spontaneous Mutations Rate LOW Because Repair Rates vary among genes. Why? Size of genes Higher mutation rate in sperm or eggs? Sperm! More replications Trinucleotide Repeat Expansions Natural processes cause spontaneous mutations: Mutagens induce mutations: Mutagen: induces mutations at higher rates Ames Test: Is this a mutagen? Mueller=proving x-rays increase rate of mutation Why Screen for reverse mutations and not forward? ○ Mutation rate lower for reverse! Less to count. Topic 10: some of the especially helpful homework problems Ch 7 Solved Problem 1 Ch 7 Solved Problem 2 Topic 10: some of the especially helpful homework problems Ch 7 # 9 Ch 7 # 11 Topic 10: some of the especially helpful homework problems Ch 7 # 12 Ch 7 # 20 Ch 7 # 21 TOPIC 11: Deciphering the Genetic Code Genetic Code is Colinear and non-overlapping Generated TRP- mutants in E-COLI that carried mutations in trpA (tryptophan synthase) Purified and found aa sequence of mutant tryptophan synthase subunits Linear order of DNA changes aligns with order of altered aa → Found that Genetic Code is Colinear Each mutant has 1 amino acid different from wt —> Found that Genetic Code Doesnt overlap Supplementation Tests Try to make your own table like the one on the left for the tryptophan synthesis pathway! Frameshift mutations used to which triplets make which AA? determine that genetic code is read in triplets  Topic 11: some of the especially helpful homework problems Ch 9 # 2  Topic 11: some of the especially helpful homework problems Ch 9 # 4 Ch 9 # 6  Topic 11: some of the especially helpful homework problems Ch 9 # 7  Topic 11: some of the especially helpful homework problems Ch 9 #9 Ch 9 # 12a  Topic 11: some of the especially helpful homework problems Ch 9 # 11 Ch 9 # 15 TOPIC 12: How the Genetic Code Works  TRNAs Central Dogma Aminoacyl-tRNA synthetases? ○ Charged tRNA: tRNA covalently coupled to to its amino acid WOBBLE Silent mutations TRNAs Missense mutations ○ Conservative vs. Nonconservative Substitutions 32 TRNAS for 64 codons for 20 amino acids Nonsense mutations Frameshift mutations The Genetic Code is Degenerate  Topic 12: some of the especially helpful homework problems Ch 9 # 26  Topic 12: some of the especially helpful homework problems Ch 9 # 28 Ch 9 # 29 Ch 9 # 31  Topic 12: some of the especially helpful homework problems Ch 9 # 30 ab Ch 9 # 59  Topic 12: some of the especially helpful homework problems Ch 9 # 33ab Topic 12: some of the especially helpful homework problems Ch 9 # 57ab TOPIC 13: Eukaryotic Gene Structure and Allele CLassification Eukaryotic Genes DNA mRNA Post-transcriptional SPLICING! modifications: Translation: What is the What are the start codon? STOP codons? AUG UAA, UGA, (Methionine) UAG loss-of-function alleles gain-of-function alleles *Usually recessive *Usually Dominant Amorphic/null alleles Hypomorphic (weak) allele Hypermorphic (overactive) alleles Haploinsufficiency is when Neomorphic alleles (new function) loss-of-function alleles can be dominant Antimorphic alleles (dominant negative)  Topic 13: some of the especially helpful homework problems Ch 9 # 21 Ch 9 # 24  Topic 13: some of the especially helpful homework problems Ch 9 # 36 a-o  Topic 13: some of the especially helpful homework problems Ch 9 # 42 Ch 9 # 50  Topic 13: some of the especially helpful homework problems Ch 9 # 48 Ch 9 # 47 TOPIC 14: Human Genome Project 1 - Sequencing  Creating Recombinant DNA molecules with Restriction Enzymes plasmid vectors: What enzymes are needed ? DNA ligase DNA Restriction Enzyme What features does your plasmid vector have? Selectable Marker (Antibiotic Resistance Gene - Ampr ) Genome Libraries: Genomic library: ○ A long-lived collection of cellular clones that contains copies of every sequence in the whole genome inserted into a suitable vector. Host cells take up and amplify recombinant DNA ○ Transformation Identification and isolation of transformed cells ○ Ampicillin Cells w/ plasmid = Part of a human grow genomic DNA Cells w/o plasmid = library cannot grow 1 colony = a cellular clone Sanger Sequencing- What do you need? Sanger Sequencing- ANALYSIS What is different between the dATP and ddATP? What is the impact of a ddATP on polymerization of DNA? Gel Electrophoresis Separates DNA fragments based on their size! Commonly use agarose gel (separates larger DNA fragments)  Topic 14: some of the especially helpful homework problems Ch 10 #Solved Problem 1 Topic 14: some of the especially helpful homework problems Ch 10 #2 Topic 14: some of the especially helpful homework problems Ch 10 #7 Topic 14: some of the especially helpful homework problems Ch 10 #8 Topic 14: some of the especially helpful homework problems Ch 10 #19  Topic 14: some of the especially helpful homework problems Ch 10 #22 TOPIC 15: Human Genome Project 2 - Annotation Whole-genome shotgun sequencing Paired-end Shotgun Sequencing 1. Obtained two sequence from each BAC clone, one from each end of the insert a. two sequences from each BAC clone must have originated from the same region of the genome (200-300kb apart) 2. Allowed for proper alignment of the unique sequences that flank each repeat region. Making cDNA Libraries cDNA does not have introns!  Topic 15: some of the especially helpful homework problems Ch 10 #Solved Problem 2  Topic 15: some of the especially helpful homework problems Ch 11 #6 Ch 11 #8 Ch 11 #9  Topic 15: some of the especially helpful homework problems Ch 11 #24