Key points for Chapter 6

1. Key points for Chapter 6 • Definitions: topoisomerase, ribozyme, double helix, DNA denaturation, Tm, linking number, pseudoknot. • What are the structural differences between DNA and RNA? How the structural properties of DNA and RNA determine their distinct biological functions.

2. Key points for Chapter 7 • Definitions: nucleosome, gene density, core histones (structure and function), Nucleosome remodeling complexes • Describe the important functions of packing of DNA into chromosome. • Why genes make up only a small proportion of the eukaryotic genome.

3. Key points for Chapter 7 • Briefly describe roles of three critical DNA elements important for chromosome duplication & segregation • Briefly describe how the higher-order chromatin structure is formed

4. Key points for Chapter 8 • Definitions: replication fork, leading strand, lagging strand, Okazaki fragment, processivity, proofreading exonuclease, replisome, pre-replicative complexes (pre-RCs) • Describe the function and mechanism of DNA polymerase. • Describe DNA replication process and proteins involved at a replication fork.

5. Key points for Chapter 8 • How is the DNA replication tightly controlled in E. coli and in eukaryotic cells? • What is the end replication problem? how does cell resolve the problem?

6. Key points for Chapter 9 • Definitions: replication errors, spontaneous DNA damage, DNA mutations, double-strand break (DSB) repair pathway. • How does the mismatch repair system accurately detect, remove and repair the mismatch resulting from inaccurate replication? • What are the environmental factors that cause DNA damage?

7. Key points for Chapter 9 • How could a DNA damage be converted to DNA mutation? • What are the mechanisms to repair a DNA damage? Describes how base excision and repair and nucleotide excision repair work? • What is translesion DNA synthesis? Why it is important?

8. Key points for Chapter 10 • Definitions: Mating-type switching, gene conversion, Holliday junction • Compare the two models for homologous recombination, which model finds more evidence? • Describe RecBCD pathway and protein involved in bacteria, and the function of the eukaryotic homologue Spo11, MRX and Dmc1

9. Key points for Chapter 11 • Conservative site-specific recombination (CSSR): definition, consequence, mechanism and examples. • Transposon and transposition: definitions, consequence, basic structural feature of three principle classes of transposable elements, and the mechanism of viral-like retrotransposons/retroviruses

10. Key points for Chapter 12 • The central dogma, • Transposon and transposition: definitions, consequence, basic structural feature of three principle classes of transposable elements, and the mechanism of viral-like retrotransposons/retroviruses

11. Key points of chapter 12 • RNA polymerases (RNAP, 真核和原核的异同) and transcription cycle • Transcription cycle in bacteria: • Initiation: (1) promoters and promoter recognition by s factor (4 domains) and aCTD. (2) Transition from the closed complex to the open complex. (3) abortive initiation. • Elongation and proofreading by RNAP • Termination: Rho-independent and Rho-dependent mechanism

12. Transcription cycle in eukaryotes: • ---RNAP II transcription • Initiation: (1)Promoter and its recognition by GTF, (2) Assembly of the pre-initiation complex, (3) Initiation in vivo requires additional proteins____ • Elongation: (1) phosphorylation of the CTD tail of RNAP II, shedding most of its initiation factors, and recruiting factors for elongation and RNA processing. (2) How RNA processing is coupled with transcription? • Polyadenylation and termination • ---RNAP I and III transcription • GTFs and promoter recognition

13. Key points of chapter 13 • Definitions: exons, introns, RNA splicing, spliceosome; alternative RNA splicing, exonic splicing enhancer, SR proteins; trans-splicing; alternative spliceosome; RNA editing, ADAR enzyme, guild RNAs • The chemical reaction of RNA splicing • Describe the splicing pathway conducted by dynamic spliceosome assembly • Self-splicing introns and chemical reactions • How alternative splicing is regulated?

14. Key points of chapter 14 • The main challenge of translation and the solution • The structure and function of four components of the translation machinery. • Translation initiation, elongation and termination (具体过程和翻译因子的作用) • The mRNA and protein stability dependent on translation (生物学问题是什么，怎么解决的)

15. Key points of chapter 15 • Definitions: codon, degeneracy, synonyms, missense mutation, nonsense mutation, frameshift mutation, suppressor gene • What is the wobble concept? • What are the three rules governing the genetic code? • What are the benefits of the code universality (P475)?

16. Key points of chapter 16-17 • Principles of gene regulation.(1) The targeted gene expression events; (2) the mechanisms: by recruitment/exclusion or allostery • Regulation in bacteria • ---transcription initiation :the lac operon, alternative s factors, NtrC, MerR, Gal rep, araBAD operon • ---after transcription initiation:the trp operon, riboswitch, regulation of the synthesis of ribosomal proteins

17. Regulation in eukaryotes • --- Definitions: regulatory sequences, enhancers, insulators, gene silencing, ChIP, two hybrid assay, LCR, • --- Describe the similarity and differences of regulation between eukaryotes and prokaryote • --- Describe the DNA binding domains and activating regions that eukaryotic activators commonly use. • Regulation at transcription initiation: • ---Describe the two ways that eukaryotic activators recruit polymerase.

18. ---How signals are integrated by the function of activators (F17-14)? Give two examples. ---Describe the ways in which eukaryotic repressors work (F17-19) ---Use an example to illustrate that signals are often communicated to transcription regulators through signal transduction pathways (F17-21) Regulation after transcription initiation: --- Use an example to illustrate regulation of alternative mRNA splicing (F17-28) RNA in gene regulation ---Describe the production pathway and the function of siRNA and microRNA

19. Key points of chapter 19 • Definitions: cloning vector, expression vector; shotgun sequencing, comparative genomics, proteomics, mass spectometry (MS); restriction endonuclease, Northern hybridization, southern hybridization, Western blot, PCR; affinity chromatography, gel filtration chromatography, ion exchange chromatography, SDS PAGE. • How to clone a gene, to screen for the recombinant plasmid-containing colonies, to express a gene, and to purify an encoded protein? • How to create a genomic DNA and a cDNA library?