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,
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.
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
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.
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?
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?
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?
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
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
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
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 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
Key points of chapter 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
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
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
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
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 s factors,NtrC,MerR,Gal rep,
araBAD operon
---after transcription initiation,the trp
operon,riboswitch,regulation of the
synthesis of ribosomal proteins
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.
---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
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?
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,
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.
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
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.
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?
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?
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?
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
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
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
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 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
Key points of chapter 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
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
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
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
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 s factors,NtrC,MerR,Gal rep,
araBAD operon
---after transcription initiation,the trp
operon,riboswitch,regulation of the
synthesis of ribosomal proteins
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.
---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
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?
