1. Key points for Chapter 6 1.Definitions: topoisomerase, ribozyme, double helix, DNA denaturation, Tm, linking number, pseudoknot. 2.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 1.Definitions: nucleosome, gene density, core histones (structure and function), Nucleosome remodeling complexes 2.Describe the important functions of packing of DNA into chromosome. 3.Why genes make up only a small proportion of the eukaryotic genome.

3. Key points for Chapter 7 4.Briefly describe roles of three critical DNA elements important for chromosome duplication & segregation 5.Briefly describe how the higher- order chromatin structure is formed

4. Key points for Chapter 8 1.Definitions: replication fork, leading strand, lagging strand, Okazaki fragment, processivity, proofreading exonuclease, replisome, pre- replicative complexes (pre-RCs) 2.Describe the function and mechanism of DNA polymerase. 3.Describe DNA replication process and proteins involved at a replication fork.

5. Key points for Chapter 8 4.How is the DNA replication tightly controlled in E. coli and in eukaryotic cells? 5.What is the end replication problem? how does cell resolve the problem?

6. Key points for Chapter 9 1.Definitions: replication errors, spontaneous DNA damage, DNA mutations, double-strand break (DSB) repair pathway. 2.How does the mismatch repair system accurately detect, remove and repair the mismatch resulting from inaccurate replication? 3.What are the environmental factors that cause DNA damage?

7. Key points for Chapter 9 4.How could a DNA damage be converted to DNA mutation? 5.What are the mechanisms to repair a DNA damage? Describes how base excision and repair and nucleotide excision repair work? 6.What is translesion DNA synthesis? Why it is important?

8. Key points for Chapter 10 1.Definitions: Mating-type switching, gene conversion, Holliday junction 2.Compare the two models for homologous recombination, which model finds more evidence? 3.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 1.Conservative site-specific recombination (CSSR): definition, consequence, mechanism and examples. 2.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 1.The central dogma, 2.Transposon and transposition: definitions, consequence, basic structural feature of three principle classes of transposable elements, and the mechanism of viral-like retrotransposons/retroviruses

11. 1.RNA polymerases (RNAP, 真核和原核的异同 ) and transcription cycle 2.Transcription cycle in bacteria: Initiation: (1) promoters and promoter recognition by  factor (4 domains) and  CTD. (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 Key points of chapter 12

12. 3.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. 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? Key points of chapter 13

14. 1.The main challenge of translation and the solution 2.The structure and function of four components of the translation machinery. 3.Translation initiation, elongation and termination ( 具体过程和翻译因子的作用 ) 4.The mRNA and protein stability dependent on translation ( 生物学问题是 什么，怎么解决的 ) Key points of chapter 14

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)? Key points of chapter 15

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

17. 3.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. 1.How to clone a gene, to screen for the recombinant plasmid-containing colonies, to express a gene, and to purify an encoded protein? 2.How to create a genomic DNA and a cDNA library?