The

final exam will be comprised of 2 parts each with a separate answer sheet. The cumulative portion of the exam (Ch 1-2 and 4-19) will be a total of 80 points 60 points of which will be verbatim questions from each of the exams. This includes practice exams and midterms for all 4 exams (8 total). The remaining 20 points of this part will be new questions taken solely from the lecture slides. These questions will address more general points no mechanism questions here. For this portion of the final you will want to review the practice exam and midterm for each of the 4 exams. In addition, you should review the lecture slides for this portion of the course. It is not necessary to review the homework or end-of-the-chapter questions for this section of the final. The second part of the exam (new material) will be 60 points and will be very similar to the previous exams in terms of the types of questions and point values. It will cover all of the material since and not included on Exam 4 Ch 20-22 and Ch 3. For this part, you should know each of the following items, listed by chapter. Youll also want to review all of the lecture slides and the end-of-chapter questions listed on Blackboard for each chapter. Each part of the final will contain 1-, and 2-point questions. There will be NO 3-point questions for either part (your welcome!). I will NOT be posting a practice for the final.

Final Exam Study Guide: Spring 2012

Chapter 3 Know the structural difference between purines and pyrimidines o You dont have to know the specific chemical structure of the 4 bases Know that RNA uses the base uracil in place of thymine used in DNA Know the difference between a nucleoside and a nucleotide Know the structure of DNA o Know the structure of a single strand the 5 and 3 ends o Know the structure of the double helix Includes knowing that it is rotated by 30 and what is the effect of this twist o Know the types of base pairs that form (A:T or G:C) and the number of H bonds in each o Know what contributes to the stability of the double helix and why Know what is meant by melting DNA and what factors contribute to the melting temperature o How is the degree of melting detected and measured? o How is the DNA renatured? Know the principles of the Central Dogma Know the general principles of the genetic code o DONT need to know the code itself o Know that it is degenerate and contains 3 stop codons o Know the universal start codon Know the following methods and how they are performed: o DNA sequencing o PCR o Cloning, including use of restriction endonucleases 1

 Chapter 20 Know that the standard DNA helix is a B-type helix o Know that it is a right-handed helix Know the difference between twist and write and how they contribute to the linking number Know the main structural difference between positive and negative supercoiling o Positive supercoiling creates overwound DNA o Negative supercoiling creates slightly underwound DNA o Know that most organisms have negatively supercoiled DNA Which organisms do not? The function of the different types of topoisomerases o Type I and Type II o Know that the human topoisomerase I utilizes an active site tyr residue to nick the backbone The steps and components involved in prokaryotic DNA replication o See the DNA replication animation Know that replication is semi-conservative and what this means The differences between replication on the leading and lagging strands Know the general characteristics and structure of DNA polymerase o Need to know function of active site Asp residues and Mg2+ ions o Mechanism involved in proofreading ability o Where are there multiple DNA polymerases? Know the function and mechanism of DNA ligase The structure and function of telomeres and telomerases o Uses RNA template to make DNA (reverse transcriptase) o How are ssDNA ends of telomeres protected from nuclease digestion Types of DNA damage that can occur and how o Mis-matched bases o Oxidation of G residues o Depurination o Deamination o Thymine dimers Mechanisms for repair of DNA o Mismatch repair o Base excision repair o Nucleotide excision repair o Double-strand breaks Nonhomologous end joining Homologous recombination Structure and packaging of DNA o Heterchromatin vs. euchromatin o Core nucleosome and its components o 30 nm fiber 2

Final Exam Study Guide: Spring 2012

Final Exam Study Guide: Spring 2012

Modifications to chromatin o Why necessary for replication and transcription o Types of modifications to histones (acetylation, phosphorylation, methylation) o Modifications to DNA CpG islands and DNA methylation

Chapter 21 Main differences in structure of RNA vs. DNA o Why is there no RNA double helix? Two types of genes: protein-coding and noncoding RNAs Where transcription takes place in the cell Methods and effects of chromatin remodeling Structure and general characteristics of RNA polymerases o Why are there multiple RNA polymerases in eukaryotes? o Specific structure of E. coli RNA polymerase Difference between core and holoenzyme Function of sigma factor General structure of prokaryotic promoters DNA elements that regulate and control transcription o Know these elements and their function: TATA box, Inr, enhancers, and silencers That eukaryotic transcription begins with general transcription factors o Know that TBP binds the TATA box Know that activators bind enhancers and repressors bind silencers o Often far upstream or downstream of promoter o Cause looping of DNA Know function and significance of Mediator complex o Binds to both general transcription factors + RNA polymerase and to activators/repressors Know that there are multiple regulatory elements and TFs that bind them and why o Prevents random transcription; more control The first steps in the formation of the pre-initiation complex at the TATA box o How TBP binds TATA box Know the helix-turn-helix motif of DNA-binding proteins Know the general structure of the lac operon and how it is regulated by LacI repressor and allolactose Know the general mechanism of RNA polymerase o Binds dsDNA o Separates strands and reads template o Clamp closes over template to increase processivity o Proofreading mechanism o That RNA:DNA hybrid helix forms o Helix near active site oscillates between bent and straight to rachet template along Know the switch from initiation to elongation o Phosphorylation of CTD of RNA polymerase Know the two types of transcription termination in prokaryotes 3

Final Exam Study Guide: Spring 2012

The steps and components by which eukaryotic RNA molecules are modified o 5 cap (general structure) o Poly A tail o Splicing Know the general mechanism and that it is catalyzed by splicesome How is splicing beneficial? o How does poly(A) tail shortening affect mRNA half-life RNA interference o siRNAs How tRNA is modified How to determine the sequence of an mRNA molecule from its DNA template or coding strand

Chapter 22 Know the concept of a reading frame that there are 3 possible reading frames due to the fact that the codons contain 3 nucleotides Know the types of RNA that participate in translation and their respective roles Know the general structure of tRNA o 1 RNA molecule o Only need to know the anticodon loop Know that it contains the anticodon that base pairs with the codon o Know that it has specific secondary and tertiary structure o Know that the acceptor stem is at the 3 end o What are isoacceptor tRNAs? Know how the tRNA is charged with its cognate amino acid o Know the general mechanism (what makes it irreversible?) o Know that it is catalyzed by aminoacyl tRNA synthetases o Know that these enzymes make contacts with both the anticodon loop and the acceptor stem to ensure the right amino acid gets added to the right tRNA molecule o Know the chemical link between the amino acid and its tRNA o Isoacceptor tRNAs recognized by same AARS The principle of the third base wobble and how this relates to translation of the mRNA code o How isoacceptor tRNAs bind multiple codons The general structure and components of the ribosome o How many rRNA molecules are present in each subunit o Contains protein but is mostly RNA o Know that there are differences between prokaryotic and eukaryotic but you DONT have to know the details o Two subunits contact each other on the RNA face o Contains binding sites for 3 tRNAs: A site; P site; E site (know their relative locations) The ordered steps in prokaryotic translation what binds when and why o See the translation animation 4

Final Exam Study Guide: Spring 2012

What is the initiator codon and what is the first amino acid o Met in eukaryotes; fMet in prokaryotes Know how translation initiation occurs in eukaryotes o Circularization of mRNA The various proofreading steps involved in translation o 50S subunit confirms correct pairing how? o Importance of EF-Tu in this process Order of addition of amino acids o Transferred from P to A site; N to C terminus How translocation occurs o Function of EF-G How translation termination occurs o Role of release factors Know how to translate an mRNA message into a sequence of amino acids or vice versa given the genetic code Know that transcription and translation is coupled in prokaryotes o Why is this possible for them and not for eukaryotes? o What is the advantage? Role of molecular chaperones in protein folding o Role of trigger factor o Role of DnaK o General role of GroEL/ES Folding occurs in the heptameric rings Provides protected environment so protein can fold itself Made possible by ATP hydrolysis Significance of binding GroES cap Components of the signal peptide important for translocation of a protein into the ER lumen o Bound by SRP o Contains segment of RNA what is its role? The types of post-translational modifications that can occur o Proteolysis o Glycosylation o Addition of chemical groups o Addition of lipid anchors of fatty acid chains o Significance of this: creates variability beyond the amino acid sequence contained in the genetic code

BEST WISHES TO ALL!