CHEM 3520 Biochemistry II Mid-Term Exam 1 2025 PDF

CHEM 3520 Biochemistry II Dr. John Bellizzi Mid-Term Exam 1 Information Spring 2025 Mid-Term Exam 1 is on Friday February 7 and will cover the slides from...

CHEM 3520 Biochemistry II Dr. John Bellizzi Mid-Term Exam 1 Information Spring 2025 Mid-Term Exam 1 is on Friday February 7 and will cover the slides from Lectures 1-8 and Chapters 24, 25, 26, and 27.1. There will be 12 questions worth a total of 100 points. Questions will have a variety of formats including fill in the blank, open-ended free response, multiple choice, and drawing structures/mechanisms. Office hours will be cancelled on the afternoon of Friday February 7. In addition to my normal office hours next week (Mon 1:30-2:30, Wed 11-12, Wed 3-4) I will hold extra office hours on Tuesday February 4 from 3-5 pm and on Thursday February 6 from 10:30 am-12 noon. An outline of topics to review is below. I. Big Picture Concepts 1. How biochemical information flows according the central dogma, and what the exceptions are. 2. The basic order of events and essential enzymes for key processes in central dogma and key areas of regulation (the big ones for this exam – DNA replication and transcription, along with recombination and various repair pathways). 3. Understand the different mechanisms for preserving the integrity and fidelity of biochemical information in the pathways we studied 4. Similarities and parallels between different processes, and recuring themes/mechanisms used for regulation and fidelity of the central dogma. 5. How our understanding of the processes of biochemical information flow has led to the development of advances in biotechnology as well as medical treatments. II. Big Questions How does the cell store and organize all the information required to make a living organism? What is the structure and size of these organizational units? How do you fit 2 meters of negatively charged DNA into a nucleus that is only 10-5 meters in diameter? Once you compact the DNA, how do you access the parts you need? How do you relieve the strain created by unwinding DNA to do replication and transcription? How is DNA replicated? What are the basic steps? Why does DNA replication require a primer? How do you replicate 3 billion base pairs per cell rapidly and with high fidelity? If DNA replication/proofreading has an error rate of 106-108 but overall error rate is 109 - 1010, where does the additional fidelity come from? What are the basic types of DNA damage and the pathways that repair them? What are common themes for different types of DNA repair? How is DNA repaired when there is no undamaged template? How do you repair DNA when there is no template strand? How are homologous chromosomes held together during meiosis? How has our understanding of recombination led to breakthroughs biotechnology? How much of our genome is actually coding for protein? How much of it is actually human DNA at all (and where did the non-human part come from)? What are the similarities and differences between transcription and DNA replication? What are the basic steps of transcription and how are they regulated? What experimental techniques can provide insights into transcription? How does transcription differ between eukaryotes and prokaryotes? What are three major types of mRNA modification and what is their purpose? How can human complexity arise from only 20,000 different genes? What are the similarities and differences between the three major types of mRNA splicing? What are the exceptions to the central dogma? What specific biotechnology application arose from the study of HIV genome replication? How do the COVID-19 vaccines work? Why do we have 64 codons for 20 amino acids? Why is protein synthesis referred to as “translation”?  How are the correct amino acids attached to the correct tRNA? II. Enzymes and Other Proteins, Molecular Structures, Reactions and Mechanisms 1. You should be able to explain the functions of proteins important for the pathways described in these lectures/chapters, or, if given a description of the function, be able to identify the protein that has that function. 2. Since you all took Biochemistry I, I am expecting that you still know how to draw detailed structures of nucleotides and segments of nucleic acids, since you learned that previously. There are no other new structures from these chapters that you are expected to know how to draw for an exam, but you are always free to sketch pictures or structures as part of your respond to an open-ended question if it will help you explain your answer 3. Compared to future exams, there really aren’t that many different reaction mechanisms that you have to study for this exam. a. This is because the majority of the important enzyme-catalyzed reations involve different applications of the same fundamental mechanisms (formation and/or hydrolysis and/or transesterification of phosphodiester linkages) are used. b. You should be able to write curved arrows to show electron flow in bond breakage/formation for those three types of mechanisms and know how to apply those to the reactions catalyzed by enzymes in this part of the course, including DNA and RNA polymerases, nucleases, DNA ligase, and self-splicing introns. III. Important Points to Emphasize from each Chapter: Chapter 24 Central dogma = DNA makes RNA makes protein Overall size and organization of genome Structure of DNA, genes, and chromosomes Role of specialized regions within chromosomes The challenges of DNA compaction and how chromosome structure overcomes this The role of histones and supercoiling in chromosome structure Mechanistic differences between type I and type II topoisomerases DNA supercoiling and linking number Know how to calculate linking number Chapter 25 Overview of DNA replication: semiconservative, bidirectional, semidiscontinuous Mechanism of DNA replication and need for RNA primers Regulation of DNA replication: Initiation, Elongation, & Termination Mechanisms for DNA replication fidelity Types and roles of different DNA polymerases Types of DNA damage Mechanisms of DNA Repair o Mismatch repair o Base Excision Repair o Nucleotide Excision Repair o Direct Repair o Translesion DNA Synthesis DNA recombination o Homologous DNA recombination in DNA repair and meiosis o Transposons o DNA recombination in generation of antibody diversity Chapter 26  DNA vs. RNA and Transcription vs. Translation vs. Replication Mechanism and regulation of transcription in prokaryotes o Recruitment of RNAP to promoter o Initiation of transcription o Elongation o Termination Transcription in eukaryotes o Different types of polymerases o Key differences between eukaryotes and prokaryotes RNA polymerases as drug targets RNA processing: Types and Purposes o 5’ capping o Splicing o Polyadenylylation Types and Mechanisms of RNA Splicing o Group I Introns o Group II Introns o Spliceosome Processing of special-function RNA (tRNA, rRNA) RNA degradation Retroviruses Use of reverse transcriptase for biotechnology Telomerase RNA viruses, RNA-dependent RNA polymerase, mRNA vaccines and pseudouridine Chapter 27.1 Overview of the genetic code How the genetic code facilitates information fidelity – ORFs and frame shift mutations – Wobble position in tRNAs Amino acyl tRNA synthetases – Mechanism of activation and proofreading – Amber suppression & manipulation of the genetic code