MOLECULAR
BIOLOGY
课程性质：专业基础课/必修课程
所属一级学科：生物学
所属二级学科：生物化学与分子生物学
授课对象：三年级的生命科学学院本科生、全校生物类的硕士研究生
开课系及教科组：生命科学学院
学分数：4 学分
总学时数：每周 4 学时，共 68 学时
预备知识：遗传学、生物化学、细胞生物学基础知识。
单位：安徽师范大学
1
第一章
引言
Chapter 1
Introduction
【教学目的】
通过本章教学，使学生明确分子生物学的学科性质、基本内容和学习意义，掌握分
子生物学中几个常用术语的涵义及其相互区别，了解本门课程的教学要求和学习方法。
【重点难点】
明确分子生物学的概念及研究内容。
【教学方法】
多媒体教学
English Animation
【课时安排】
2 课时
主要教学内容
1. Introduction
2. History of Molecular Biology
(1) The Early Years of Genetics
(2) The Birth of Biotechnology
(3) The Revolution of the Biotechnology
(4) Welcome to the Genomics Era
3. What is Molecular Biology?
Molecular biology is the study of biology at a molecular level. It chiefly concerns itself
with understanding the interactions between the various systems of a cell, including the
interrelationship of DNA, RNA and protein synthesis and learning how these interactions are
regulated.
4. Contents of Molecular Biology
(1) Central dogma
(2) Contents of molecular biology
5. Progress and Future of Molecular Biology
(1) 2008 Ten Scientific Discoveries from TIME
(2) Future of Molecular Biology
2
Animations

English Animation: Charles Darwin’s Story

English Animation: Evolution of Skull

Animation: Hershey and Chase’s Experiment
Main References
1.
Genes VIII. Benjamin Lewin, 2004, Benjamin-Cummings Pub Co.
2.
Molecular Biology of Cell. Fourth Edition, Bruce Alberts, et al. 2002, NCBI e-book.
3.
Biochemistry. Fifth Edition, Jeremy M. Berg, et al. 2002, NCBI e-book.
4.
The Human Genome. Carina Dennis, 2002, Palgrave Macmillan.
5.
《现代分子生物学》 第 3 版, 朱玉贤等, 2002, 高等教育出版社
6.
The Cell. Fourth Edition, Geoffrey M. Cooper et al. 2007, ASM Press and Sinauer
Associates, Inc.
7.
分子克隆实验指南(上、下册)，第三版，2002，科学出版社
第二章
Chapter 2
基因和染色体
Genes and Chromosomes
【教学目的】
本章要求学生掌握原核生物和真核生物基因组的区别、染色体的组成、真核生物基
因组的复杂性、DNA 的结构等；掌握 DNA 复制的复杂性、几种 DNA 的复制方式、原
核生物 DNA 复制的酶、真核生物 DNA 复制的酶、DNA 的修复、重组和转座等。
【重点难点】
基本概念的掌握，清楚 DNA 复制、修复、重组及转座机制。
【教学方法】
讲述式和启发式教学 (适当结合讨论法)
多媒体教学
English Animation
【课时安排】
14 课时
3
主要教学内容
2.1 DNA and DNA structure
1.
Nucleoside & Nucleotide
2. Nucleic Acid Chain
3. DNA Primary Structure
(1) DNA Primary Structure: nucleotide acid sequence
(2) DNA Secondary Structure: double helix
 Right-handed helix -- A-DNA, B-DNA

Left-handed -- Z-DNA
(3) DNA Supercoiling:
(4) DNA Denaturation and Renaturation
2.2
Gene and Chromosomes
1. Concepts of Gene
(1) Gene
(2) Regulatory Gene
(3) Structural Gene
(4) Gene Cluster
(5) Gene family
2. Genome
(1) Genome
(2) Genomics
(3) Functional Genomics
(4) Structural Genomics
3. Size of Genome(1)
Prokaryotic cell
vs
Eukaryotic cell
(2) Relationship of genomic size and evolution
4.
Model Organisms
(1) Bacteria (E. coli, several others)
(2) Yeast (Saccharomyces cerevisiae)
(3) Plant (Arabidopsis thaliana)
(4) Caenorhabditis elegans
(5) Fruit fly
(6)
Zebrafish
(7) Mouse
(8) Human
4
2.3 Features of Genomic Organization
1.
Features of prokaryotic genomes
2.
Genomes of Prokaryotes
(1) E.coli Genome
(2) Phage genome
(3) Mu phage3.
Features of Eukaryotic Genomes
(1) Big size, big content
(2) Repeat sequence
(3) Single cistron
(4)
Interrupted gene - exon and intron
(5) Pseudogene
(6) Organelle genes
4. Genome of Eukaryotes
(1) Human genome
(2) Other genomes of Eukaryotes
 Mouse genome
 Yeast
 Drosophila
 C. elegans
 Arabidopsis thaliana
2.4
Nucleosome & Chromosome
1. Histones and Non-histone
2. Nucleosome
(1) Concept
(2) Packing
3. DNA Coiling into a Chromosome
2.5 DNA Replication
1. Semiconservative replication
(1) Models of DNA replication
 Semiconservaticve model
 Conservative model
 Dispersive model
(2) Replication elements
5
 Origin (ori)
 Replicon
 Replication fork
 Bi-directional replication
2. Enzymes involved in DNA replication
(1) DNA topoisomerase
(2) DNA helicase
(3) SSB - DNA single strand binding protein
(4) Primase and primosome
(5) DNA polymerase (see next part)
(6) DNA ligase
3. DNA Replication in Prokaryotes
(1) Ori in E.coli
(2)
Initiation of DNA replication in E.coli
(3) DNA polymerases

Pol I: implicated in DNA repair

Pol II: involved in replication of damaged DNA

Pol III: elongates in DNA replication

Pol IV: a Y-family DNA polymerase

Pol V: a Y-family DNA polymerase; participates in bypassing DNA damage.
(4) Semicontinuous replication
(5) Termination of Replication
(6) Rolling Circle Replication
3. DNA Replication in Eukaryotes
(1) Multiple replicons
(2) DNA polymerase

Pol α:
Acts as a primase (synthesizing a RNA primer), and then as a DNA Pol
elongating that primer with DNA nucleotides. After around 20
nucleotides elongation is taken over by Pol δ (on the lagging strand) and
ε (on the leading strand).

Pol β:
Implicated in repairing DNA, in base excision repair and gap-filling
synthesis.

Pol γ: Replicates mitochondrial DNA.

Pol δ: Highly processive and has proofreading 3'->5' exonuclease activity.
Thought to be the main polymerase involved in lagging strand synthesis,
though there is still debate about its role.
6

Pol ε:
Also highly processive and has proofreading 3'->5' exonuclease activity.
Highly related to Pol δ, and thought to be the main polymerase involved
in leading strand synthesis……still debate about its role.
(3) Replication of Telomere
A telomere is a region of repetitive DNA at the end of chromosomes, which
protects the end of the chromosome from destruction.
(4)

Telomerase

Replication of Telomere
mtDNA Replication - D-loop replication
4. Proofreading of Replication
Error correction is a property of some, but not all, DNA polymerases. This process
corrects mistakes in newly-synthesized DNA. When an incorrect base pair is recognized,
DNA polymerase reverses its direction by one base pair of DNA. The 3'->5' exonuclease
activity of the enzyme allows the incorrect base pair to be excised (this activity is known as
proofreading). Following base excision, the polymerase can re-insert the correct base and
replication can continue.
2.6 DNA Mutagenesis
1. Types of Mutagenesis
(1) Base Substitution
(2) Frameshift Mutations
(3) Exon skipping
2. Mutagens
3. Significance of mutation
2.7
DNA Repair
1. Excision Repair -- Dark Repair
2. Directed Repair – Photoreactivation (Light Repair)
3. Recombinational Repair
4.
SOS Response - Error-prone repair
(1) Concept
(2)
Involved Genes and Proteins
(3) Mechanism
7
2.8
DNA Recombination
1. Overview
(1) Important Contributions of Genetic Recombination
(2) Types of DNA recombination
2. Homologous recombination
3.
Site-specific Recombination
4. DNA Transposition and Retrotransposition
(1) Definition
(2) Types and Structural Features
(3) Mechanism of Transposition and Retrotransposition
(4) The difference between Transposition and Retrotransposon
(5) Use of Transposons
(6) Transposons in eukaryote
Animations

English Animation: DNA Structure

English Animation: Model Organisms

English Animation: DNA Replication Fork

English Animation: Mechanism of Transposition
Summary
1. Concepts:
Gene
Exon
Substitution
Regulatory Gene
Intron
Mismatch Repair
Structural Gene
Pseudogene
Excision Repair
Gene Cluster
DNA Primary Structure
Directed Repair
Gene Family
DNA Secondary Structure
Recombination Repair
Genome
DNA Supercoiling
Error-prone Repair (SOS response)
Genomics
DNA Denaturation
Homologous Recombination
Functional Genomics
DNA Renaturation
Site-specific Recombination
Structural Genomics
Semi-conservative Replication
Transposition
C value
Replication Fork
Transposon
C value paradox
Semi-discontinous Replication
Retrotransposon
2. Genomes of prokaryotes and eukaryotes
3. Genomic structure of prokaryotes and eukaryotes
4. DNA polymerase of prokaryotes and eukaryotes
8
5. Mechanism of DNA replication in prokaryotes and eukaryotes
6. Mechanism of DNA mutation, repair and recombination
7. Mechanism of DNA transposition and retrotransposition
第三章 生物信息的传递(上)——From DNA to RNA
Chapter 3 The Transfer of Genetic Information— From DNA to RNA
教学目的：
本章要求学生掌握中心法则及其进展、原核生物的 RNA 聚合酶和启动子及其结构、
真核生物的 RNA 聚合酶和启动子及其结构、真核生物的 RNA 聚合酶及其启动子、真核
基因转录产物的修饰和剪切等。
重点与难点：
1、原核生物和真核生物的转录机器
2、启动子的结构与转录起始
3、RNA 转录的延伸与终止
4、RNA 的加工
教学方法：
讲述式和启发式教学 (适当结合讨论法)
多媒体教学
English Animation
课时安排：
8 课时
主要教学内容：
3.1 Transcription Overview
1. Gene Expression Processes
(1) Gene Expression
(2) Steps
2. Coding Strand & Antisense Strand
3. Steps are required for the transcription
(1) Template recognition
(2)
Initiation
(3) Elongation
(4) Termination
9
3.2
Main Component of Transcription
1.
RNA Pol in Prokaryotes - E.coli
2.
RNA Polymerases in Eukaryotes
3.3 Transcription in Prokaryotes
1. DNA Elements for Transcription in Prokaryotes
2. Initiation of Transcription in Prokaryotic
3. Elongation and Termination of Transcription in Prokaryotic
(1) Elongation
(2) Termination
(3) Antitermination
3.4 Transcription in Eukaryotes
1. DNA Elements for Transcription in Eukaryotes
(1) Core Element of Promoter
(2) Upstream Promoter Element (UPE) or Upstream Activating Sequence (UAS)
2.
Initiation of Transcription in Eukaryotes
(1) RNA Pol II - induced initiation of transcription
(2) RNA Pol I - induced initiation of transcription
(3) RNA Pol III - induced transcription
(4) Transcription of 5S rRNA gene
3.
3.5
Elongation and Termination of Transcription in Eukaryotes
RNA Processing
1. Coding RNA and non-coding RNA
(1) Coding RNA - mRNA
(2) Non-coding RNAs(ncRNA)
2. Types of RNA processing
3. End-modification of RNA Primary Transcript
(1) 5’-Cap
(2) Poly-(A) Tail
4. RNA Splicing
(1) Types of Introns
(2) Pre-mRNA Splicing (GU-AG, AU-AC)
10
(3)
(4)
(5)
(6)
(7)
(8)
5.
(1)
(2)
6.
SR protein:
AU-AC intron
Self-splicing of Type I Intron
Self-splicing of Type II Intron
Significance of RNA Splicing
Cis-splicing and Trans-splicing
Cutting Events
Pre-rRNA processing
Pre-tRNA processing
RNA Editing
(1)
(2)
(3)
7.
Definition
Editing mechanism
Biological significances
RNA Chemical Modification
8.
mRNA Degradation
3.6
Reverse Transcription
1. Reverse Transcriptase
2. Processes of Reverse Transcription
◆A retrovirus-specific cellular tRNA hybridizes with a complementary region called the
primer-binding site (PBS).
◆A DNA segment is extended from tRNA based on the sequence of the retroviral
genomic RNA.
◆The viral R and U5 sequences are removed by RNase H.
◆First jump: DNA hybridizes with the remaining R sequence at the 3' end.
◆A DNA strand is extended from the 3' end.
◆Most viral RNA is removed by RNase H.
◆A second DNA strand is extended from the viral RNA.
◆Both tRNA and the remaining viral RNA are removed by RNase H.
◆Second jump
◆Extension on both DNA strands. LTR stands for "long terminal repeat".
3.7 Ribozymes
1. Discovery
2. Concept
3. Mechanism of Ribozyme
4. Ribozyme and RNA world hypothesis
11
5. Different types of ribozymes
6. Naturally occurring ribozymes
Animations
 English Animation: Transcription
 English Animation: RNA Splicing
Summary
1. Regulatory elements of prokaryotes and eukaryotes for RNA transcription
2. RNA polymerase of prokaryotes and eukaryotes
3.
4.
5.
6.
Procedures of RNA transcription
mRNA structure of prokaryotes and eukaryotes
Types of RNA processing
Types of RNA splicing and their mechanisms
7. RNA editing mechanism
8. Mechanism of reverse transcription
9. Ribozyme and silencing mechanism
第四章 生物信息的传递(下)——From mRNA to Protein
Chapter 4 Protein Biosynthesis: RNA → Protein
教学目的：
本章要求学生掌握遗传密码、tRNA 的结构、核糖体的结构、蛋白质合成过程及相
关因子、分子伴侣的功能、蛋白质转运机制、蛋白质的降解机制等。
重点与难点：
1、核糖体的结构
2、分子伴侣的功能
3、蛋白质转运机制
4、蛋白质的降解机制
教学方法：
讲述式和启发式教学 (适当结合讨论法)
多媒体教学
English Animation
课时安排：
8 课时
12
主要教学内容：
4.1 Translation System of Protein Biosynthesis
1. Genetic Codon and Features
(1) Genetic codon
(2) Features
(3) Wobble hypothesis
2.
tRNA
(1) Secondary Structure – Cloverleaf
(2) Tertiary structure –Upside-down “L”
3. Aminoacyl-tRNA Synthetase
4. Ribosome
(1) Component of ribosome
(2) Structure of ribosome
(3) Cycle of ribosome
5. Relative Factors Involved in the Protein Biosynthesis
(1)
Initiation factor
(2) Elongation factor
(3) Release factor
4.2 Protein Biosynthesis in Prokaryotes
1. Features of mRNA Structure in Prokaryotic
2.
Initiation of Protein Biosynthesis in Prokaryotes
 IF-3 binds to the 30S ribosomal subunit, freeing it from its complex with the 50S
subunit. IF-1 assists binding of IF-3 to the 30S ribosomal subunit. Binding of IF-1
also occludes the A site domain of the small ribosomal subunit, helping to insure that
the initiation aminoacyl-tRNA, fMet-tRNAfMet, can bind only in the P site and that no
other aminoacyl-tRNA can bind in the A site during initiation.
 IF-2 is a small GTP-binding protein. IF-2-GTP binds the initiator fMet-tRNAfMet and
helps it to dock with the small ribosome subunit.
 As the mRNA binds, IF-3 helps to correctly position the complex such that the
tRNAfMet interacts via base pairing with the mRNA initiation codon (AUG). A region
of the mRNA upstream of the initiation codon, the Shine-Dalgarno sequence, base
pairs with the 3' end of the 16S rRNA. This positions the small ribosomal subunit in
relation to the initiation codon.
 As the large ribosomal subunit joins the complex, GTP bound to IF-2 is hydrolyzed,
leading to dissociation of IF-2-GDP and dissociation of IF-1.The large ribosomal
subunit serves as GAP (GTPase activating protein) for IF-2.
13
 Once the two ribosomal subunits come together, the mRNA is threaded through a
curved channel that wraps around the "neck" region of the small subunit.
3. Elongation of Protein Biosynthesis in Prokaryotes
 New entry. EF-Tu-GTP binds and delivers an aminoacyl-tRNA to the A site on the
ribosome. EF-Tu recognizes & binds all aminoacyl-tRNAs with approximately the
same affinity, when each tRNA is bonded to the correct (cognate) amino acid. tRNAs
for the different amino acids have evolved to differ slightly in structure, to
compensate for different binding affinities of amino acid side-chains, so that the
aminoacyl-tRNAs all have similar affinity for EF-Tu.
 Peptide synthesis. The peptide attached to the peptidyl-tRNA at the P site is transferred
to the new aminoacyl-tRNA at the A site, generating a peptidyl-tRNA with a longer
peptide. This step is catalyzed by peptidyl transferase.
 Translocation. The empty tRNA at the P site is ejected from the ribosome and the
peptidyl-tRNA generated at the A site takes over the vacant P site. In the mean time,
the ribosome moves one codon down the mRNA chain.
The A to P switch is
catalyzed by the elongation factor EF-G in bacteria.
4.
Termination of Protein Biosynthesis in Prokaryotes
 RF-1 and RF-2 recognize and bind to STOP codons. One or the other binds when a
stop codon is reached.
 RF-3-GTP facilitates binding of RF-1 or RF-2 to the ribosome. Once the release factors
occupy the A site on the ribosome, the ribosomal Peptidyl Transferase catalyzes
transfer of the peptidyl group to water (hydrolysis). Hydrolysis of GTP on RF-3, to
GDP + Pi, causes a conformational change that results in dissociation of release
factors.
 A ribosomal recycling factor (RRF) is required, with EF-G-GTP and IF-3, for
release of uncharged tRNA from the P site, and dissociation of the ribosome from
mRNA with separation of the two ribosomal subunits.
4.3 Protein Biosynthesis in Eukaryotes
1. Features of mRNA Structure in Eukaryotes
2. Initiation of Protein Biosynthesis in Eukaryotes
 Initiation of protein synthesis is much more complex in eukaryotes, and requires a
large number of protein factors. Some eukaryotic initiation factors (e.g., eIF3 and
eIF4G) serve as scaffolds, with multiple domains that bind other proteins during
assembly of large initiation complexes.
14
 Usually a pre-initiation complex forms, including several initiation factors along with
the small ribosomal subunit and the loaded initiator tRNA, Met-tRNAiMet. This then
binds to a separate complex that includes mRNA and other initiation factors which
interact with the 5' methylguanosine cap and the 3' poly-A tail of mRNA.
 Within this complex mRNA is thought to be circularized via interactions between
factors that associate with the 5' cap and with a poly-A binding protein. A simplified
diagram of the eukaryotic initiation complex once it has reached the initiation codon is
found in the.
 After the initiation complex assembles, it translocates along the mRNA in a process
called scanning, until the initiation codon is reached. Scanning is facilitated by
eukaryotic initiation factor eIF4A, which functions as an ATP-dependent helicase to
unwind mRNA secondary structure while releasing bound proteins.
 A short sequence of bases adjacent to the AUG initiation codon may aid in recognition
of the start site. After the initiation codon is recognized, there is hydrolysis of GTP
and release of initiation factors, as the large ribosomal subunit joins the complex and
elongation commences.
 Some eukaryotic mRNAs have what is called an internal ribosome entry site (IRES),
far from the 5' capped end, at which initiation may occur without the scanning process.
3. Elongation and Termination of Protein Biosynthesis in Eukaryotes
4. Processing of Protein Precursor
 Removing fMet or Met at the N-end
 Formation of S-S bond
 Chemical modification of amino acid
 Intein splicing
5. Inhibitors of Protein Biosynthesis
4.4 Molecular Chaperone
1. Functions of Molecular Chaperone
2. Main Types of Molecular Chaperone
 Molecular Chaperones
 Discovery
 Structure
 Function and regulation
 Family members
 Eukaryotic organisms express several slightly different Hsp70 proteins.
 Hsc70 or Hsp73
15
 Hsp70 or Hsp72
 BiP or Grp78
 mtHsp70 or Grp75
 Prokaryotes express three Hsp70 proteins
 DnaK
 HscA (Hsc66)
 HscC (Hsc62).
 Chaperonins
 Structure
 Categories of Chaperonins
 Group I
 GroEL
 GroES
 Group II
 TRiC (TCP-1 Ring Complex, also called CCT)
 Mechanism of action
 Trigger Factor (TF)
4.5 Transmembrane Transport of Proteins
1. Co-Translation and Transport
(1) Signal peptide
(2) Signal hypothesis
2. Posttranslational Transport
4.6 Protein Degradation
1. Ubiquitin
(1) Components of Ubiquitin
(2) Ubiquitination (Ubiquitylation)
2. Proteasomes
(1) Concept
(2) Structure of proteasome
 Core Particle (CP):
 Regulatory Particle (RP)
(3) Functions
3.
Protein Degradation Pathways
16
(1) Ubiquitin-dependent degradation
(2) Ubiquitin-independent degradation
Animations

English Animation: Translation
Summary
1. Structure of tRNA and ribosome for protein translation
2. Procedures of protein translation in prokaryotes and eukaryotes
3.
List three differences between prokaryotic and eukaryotic translation
4. What is the function of intein splicing?
5. Types of molecular chaperone and their functions
6. What is signal peptide? What is signal hypothesis?
7. Ubiquitin and mechanism of protein degradation
第五章 蛋白质的结构与功能
Chapter 5 Structure & Function of Protein
教学目的：
本章要求学生简单了解蛋白质分子生物学的基本内容，了解肽链的组成及结构特
点，蛋白质的结构特点以及结构与功能关系，酶的结构特点及作用机理等。
重点与难点：
1、基本概念
2、肽链的组成及结构特点
3、蛋白质的结构与功能关系
4、酶的作用机理
教学方法：
多媒体教学
讲述式教学
English Animation
课时安排：
4 课时
主要教学内容：
5.1 Protein Components
1. Amino Acid: Basic Unit of Protein
17
 Structure
 Classification
2. Peptide Bond
 Peptide plane
 Dihedral angle
3. Peptide and Polypeptide
4. Peptide Classes
5.
Peptides Applications
5.2 Protein Structure
1. Primary Structure:
2. Secondary Structure
(1) Basic Secondary Structure
 -helix
 -strand, -sheet, β-barrel, -turn
(2) Motifs
3. Tertiary Structure
4. Quaternary Structure
5. Bonds & Forces for Protein Structure
6. Denaturation & Renaturation
(1)
Protein Denaturation
Definition: Protein denaturation is commonly defined as any noncovalent change in the
structure of a protein.
Causes of Protein Denaturation
▲thermal denaturation
▲pH denaturation
▲changes in dielectric constant
▲denaturation at interfaces
▲ionic strength
(2) Protein Renaturation
5.3 Protein Folding
1. Concept of Protein Folding
2. History
18
Protein folding - the unsolved problem
3. Models for Protein Folding
4. Protein Misfolding and Diseases
5.4 Enzyme
1. Function of Proteins and Classification
2. Enzyme
(1) Definition:
(2) Classification of enzymes
3. Structure of enzyme
(1) Essential group and active site
(2) The active site and enzyme specificity
4. Catalysis Mechanism of Enzyme
(1) Models of mechanism

Lock and key model

Induced-fit model
(2) Steps in an enzymatic reaction
(3) Features of catalytic reaction
(4) Factors affecting enzyme activity
(5) Reaction inhibition
5. Enzyme Kinetics (复习生物化学，自修)
Animations

English Animation: Protein Structure

English Animation: Protein Folding
Summary
1. Peptide, polypeptide
2. Hierarchical protein structure.
3. Motifs and domains of protein
4. Protein folding, misfolding and diseases
5. Protein functions and classification
6. Structure of enzyme and its specificity
19
第六章 原核生物的基因表达与调控
Chapter 6 Gene Expression and Regulation in Prokaryotes
教学目的：
本章要求学生掌握原核生物基因表达调控的基本理论、乳糖操纵子调控系统、色氨
酸操纵子、阿拉伯糖操纵子调控系统、核糖开关的调控、原核生物转录后的调控等。
重点与难点：
1、操纵子及其结构
2、乳糖操纵子调控系统
3、色氨酸操纵子调控系统
4、核糖开关的调控
教学方法：
讲述式和启发式教学 (适当结合讨论法)
多媒体教学
English Animation
课时安排：
8 课时
主要教学内容
6.1 Overview
1. What are Gene Expression and Regulation?
(1) Gene expression
(2) Gene regulation/control
2.
Affecting factors
3. Operon
(1) The operon - unit of transcription
 Promoter - RNA polymerase
 Operator - repressor
 Structural genes
(2) Operon types
 Inducible operon
 Repressible operon
(3)
Gene regulation of operon
 In negative inducible operons, a regulatory repressor protein is normally bound to the
operator and it prevents the transcription of the genes on the operon. If an inducer
molecule is present, it binds to the repressor and changes its conformation so that it
20
is unable to bind to the operator. This allows for the transcription of the genes on
the operator.
 In negative repressible operons, transcription of the genes on the operon normally
takes place. Repressor proteins are produced by a regulator gene but they are
unable to bind to the operator in their normal conformation. However certain
molecules called corepressors can bind to the repressor protein and change its
conformation so that it can bind to the operator. The activated repressor protein
binds to the operator and prevents transcription.
6.2 The Regulation of lac Operon
1. Structure of lac operon
 Three structural genes
 One promoter
 One operator
 One terminator
 Repressor of lac operon
2. Positive control of lac operon
3. Negative control of lac operon
6.3
1.
The Regulation of trp Operon
trp Operon Structure
 structural genes
 regulatory region
 leader region
2.
Repression of trp Operon
3.
Attenuation mechanism of trp Operon
(1) Attenuator
(2) Attenuation Mechanism
 In prokaryotes, upstream translation occurs simultaneously with transcription of
downstream genes.
 When RNA polymerase has created the mRNA for the leader sequence, it is being
translated. When the ribosome reaches the double-trp codons:
 The attenuator sequence at domain 1 contains instruction for peptide
synthesis that requires Trp. A high level of Trp will permit ribosomes to
translate the attenuator sequence domains 1 and 2, allowing domains 3 and 4
21
to form a hairpin structure, which results in termination of transcription of
the trp operon. No Trp is synthesised.
 In contrast, a low level of Trp means that the ribosome will stall at domain 1,
causing the domains 2 and 3 to form a different hairpin structure that does
not signal termination of transcription. Therefore the rest of the operon will
be transcribed and translated, so that Trp can be produced. Thus, domain 4 is
an attenuator. Without domain 4, translation can continue regardless of the
level of Trp.
4. Affecting factors of attenuation
5. Generality of attenuation
6.4
The Regulation of Other Operons
1. Regulation of ara Operon
(1) Structure of ara operon
(2) Regulation model of ara operon
 Activation
 Repression
2.
rRNA Operon
 7 rRNA operons: rrnA, rrnB, rrnC, rrnD, rrnE, rrnG, rrnH
 Each rRNA operon: 16S rRNA gene, 23S rRNA gene, 5S rRNA gene
but rrnD operon has two 5S rRNA genes
6.5 The Regulation of Riboswitches
1. What is a riboswitch?
2. The Regulation Mechanism of Riboswitches
 Inhibition of translation initiation
 Transcription termination
 Auto-cleavage
 Other methods of action
3. Tempting Targets
4. Riboswitches and the RNA World hypothesis
5. Riboswitches as Antibiotic Targets
22
6.6 Time Regulation
1. Time Regulation of Sigma Factors
2. Time Regulation of λ phage
(1) Structure
(2) The lysis-lysogeny decision by λ phage
 Uncommitted
 RNA inititates transcription at PR, resulting in expression of Cro protein.
 RNA inititates transcription at PL, resulting in expression of N protein.
 N protein prevents termination at tR1 and tL1 allowing expression of cII and cIII
proteins.
 Committment
 Lysogeny. If sufficient cII protein accumulates, cII binds to PRE and activates
transcription of cI gene and cII binds to PI and activates transcription of the int
gene. Because cII protein is rapidly degraded by a protease encoded by the host hfl
gene, accumulation of sufficient cII protein depends upon two factors:
 Lysis. If cII protein is degraded, RNAP is unable to initiate transcription from PRE
or PI, so transcription continues from PL and PR.
 Execution
Lysogeny
 activation of cI expression from PRE results in accumulation of cI protein
 expression of int from PI results in accumulation of integrase protein
 cI protein binds to OL and represses N expression ([N protein] rapidly
decreases because N is unstable)
 cI protein binds to OR and represses O, P, and Q expression
 cI protein binds to OR and activates its own expression from PRM
Lysis
 decreased [cII protein] cannot activate cI expression from PRE
 transcription from PR continues to express O, P, and Q proteins
 Q protein prevents termination at tR2 allowing expression of PLate operon
 [Cro protein] increases due to transcription from PR
 Cro protein binds to OR and OL and represses expression of early gene
products
6.7 Post-Transcriptional Regulation
1.
Translation Initiation of Regulation
23
(1) Ribosome binding site
(2) SD sequencing
(3) mRNA secondary structure
(4)
Initiational codon
2.
Regulation of Rare Codon
3.
Transcriptional Regulation of Overlapping Gene
4. Translational Repression
Animations

English Animation: lac Operon

English Animation: trp Operon
Summary
1. Concepts
Gene Expression
Operon
Attenuator
Constitutive Expression
Inducible Operon
Attenuation
Regulated Expression
Repressible Operon
Riboswitch
Gene Regulation
2. Differences between an inducible operon and a repressible operon
3. The regulation mechanism of lac operon
4. The regulation mechanism of trp operon (attenuation)
5. The regulation mechanism of ara operon
6. The regulation mechanism of riboswitches
第七章 真核生物的基因表达与调控
Chapter 7 Gene Expression and Regulation in Eukaryotes
教学目的：
本章要求学生掌握真核生物基因表达调控的基本理论，真核生物基因表达调控的多
个层次，顺式作用元件、反式作用因子及其相互关系、真核基因不同水平的表达调控机
制、基因表达与癌症等。
重点与难点：
1、顺式作用元件及其作用机制
2、反式作用因子及其作用机制
3、真核生物多层次基因表达调控的主要机制
24
教学方法：
讲述式(配合传统板书)
多媒体教学
English Animation
课时安排：
8 课时
主要教学内容：
7.1 Multilevel Gene Regulation in Eukaryotes
1. The Types of Regulation in Eukaryotes
 Transient regulation/ reversible regulation
 Developmental regulation / irreversible regulation
2. Gene Structure of Eukaryotes
 Interrupted gene: intron and exon
 Simple multigene family: rRNA gene family
 Complex multigene family: histone gene family
 Complex multigene family regulated by development: globin gene family
3. The Structural Features of Eukaryotic Genome
4.
Eukaryotic Gene Regulation Mechanisms (Multilevel Control)
7.2 Gene Regulation at the DNA Level – Chromatin Remodeling
1.
Changes of DNA Topo structure formation of ssDNA
2. DNA Methylation
 CPG islands
 Housekeeping gene
 Luxury gene
3. Histone Modifications
 Histone acetylation
 Histone methylation
4. Changes of Nucleosome
 Change mechanisms
 High mobility group (HMG) proteins
5.
Other Gene Regulation at DNA Level in Eukaryotes
25
7.3 Transcriptional Regulation
1. Cis-acting elements - DNA sequences in the vicinity of the structural portion of a gene
that are required for gene expression.
(1) Promoter
 Core promoter
 Proximal elements of promoter
(2) Terminator
(3) Enhancer
 Functional Features of Enhancer
 Relationship of Enhancer and Promoter
(4) Silencer
(5)
Insulator
2.
Trans-acting Factor - Usually they are proteins, that bind to the cis-acting elements to
control gene expression.
(1) RNA polymerase
(2) Transcription factors
 Basal/general TFs
 Specific TFs
 Mechanism of TFs
(3) Domains of trans-acting factors
 DNA binding domain (DBD)
 Helix-turn-helix (HTH) - The helix-turn-helix motif is a protein helix with a
bend. The helical region of the motif fits into the DNA major groove.
 Homeodomain – It consists of a 60-amino acid helix-turn-helix structure in
which three α-helices are connected by short loop regions.
Homeobox, Homeobox genes
Multiple Eyes Mutant
Bithorax Complex
Normal Fly
Antp Mutant
 Leucine zipper - The leucine zipper consist of a periodic repetition of leucine
residues at every seventh position over a distance covering eight
helical turns. The segments containing these periodic arrays of
leucine residues seem to exist in α-helical conformation.
26
 Zinc finger - is a large superfamily of protein domains that can bind to DNA.
Usually it comprises a pair of Cys residues in the beta strands and
two His (the C2H2 class) residues in the α-helix which are responsible
for binding a zinc ion.
 Helix-loop-helix (HLH) - Helix-loop-helix motifs regulate immune system
genes. They differ from the helix-turn-helix motif by having a loop
between helices rather than a turn. The helix-loop-helix family of
transcriptional regulatory proteins is key players in a wide array of
developmental processes.
 Transcription activation domain
 Acidic-rich activation domain
 Gln-rich activation domain
 Pro-rich activation domain
7.4 Post-Transcriptional Regulation
1. Gene Regulation of mRNA Processing
2. Gene Regulation at the Level of RNA Editing
3. Regulation of mRNA Transcript Longevity
4. Transport Control of mRNA through the Nuclear Envelope
5. RNA Interference (Silencing) - Post-transcription Controls
 miRNA, or microRNA
 siRNA (small interference RNA)
(1) History and discovery
(2) Regulation Mechanism of RNAi
(3) Biological functions
 Immunity
 Downregulation of genes
 Upregulation of genes
 Crosstalk with RNA editing
(4) Technological applications
 Gene knockdown
 Functional genomics
 Medicine
 Biotechnology
27
7.5 Translational and Post-translational Regulation
1.
Translation Control - Blocking mRNA Attachment to Ribosomes
2. Regulation of Post-Translational Processing
 Phosphorylation & Dephosphorylation
 Amino acid residus phosphorylated
 Mechanism of phosphorylation
 Catalysis features of actions
3.
Regulation of Protein Stability
The time a protein remains functional is also a genetic control. A tiny protein, ubiquitin,
which is recognized by huge protease enzymes called proteasomes, tags proteins targeted for
degradation. The tagged protein is readily degraded within the proteasome. In cystic fibrosis,
the chloride ion channel protein gets tagged and degraded before reaching the plasma
membrane. Mutations that make proteins resistant to tagging and hence not degraded by
proteasomes can lead to cancer.
7.6
Cancer and Gene Regulation
1. Features of Cancer Cells
2. Causes of Cancer
3. Proto-oncogene and Oncogene
4. Activation of Proto-oncogene
 gene deletion
 gene mutation
 gene amplification
 gene or chromosome rearrangement
5. p53 and Cancer
(1) p53 has many anti-cancer mechanisms:
 It can activate DNA repair proteins when DNA has sustained damage.
It can also hold the cell cycle at the G1/S regulation point on DNA damage
recognition (if it holds the cell here for long enough, the DNA repair proteins will
have time to fix the damage and the cell will be allowed to continue the cell cycle.)
It can initiate apoptosis, the programmed cell death, if the DNA damage proves to be
irreparable.
(2) Mechanism of p53
28
Animations

English Animation: Enhancer and Silencer

English Animation: RNAi
Summary
1. Genomic structure of eukaryotes
2. Regulation levels of eukaryotic gene expression.
3. Regulation at DNA level (DNA methylation, histone modification……)
4. Regulation at transcritional level
Cis-acting elements: promoter, terminator, enhancer, silencer, insulator
Trans-acting factors: basal TFs, specific TFs
DNA binding domains and transcription activation domain
5. Transcriptional regulation
6. The mechanism of RNAi
7. Translational and post-translational regulation: protein processing, protein modification,
protein stability
8. Protein phosphorylation and its mechanism
第八章 分子生物学研究新领域
Chapter 8 New Fields in Molecular Biology
教学目的：
本章要求学生简单了解分子生物学的研究进展和发展趋势，目前主要包括生物信息
学、蛋白质组学等方面的内容。
教学方法：
多媒体教学
课时安排：
2 课时
主要教学内容
8.1 Bioinformatics(生物信息学)
1. What is Bioinformatics?
2. Major research areas
(1) Sequence analysis
 sequence alignment in order to find similar sequences
29
(2)
 identification of gene-structures, reading frames, distributions of introns and exons
and regulatory elements
 prediction of protein structures
 genome mapping
 comparison of homologous sequences to construct a molecular phylogeny
Genome annotation
 Structural annotation consists in the identification of genomic elements.
ORFs and their localisation
gene structure
coding regions
location of regulatory motifs
 Functional annotation consists in attaching biological information to genomic
elements.
biochemical function
biological function
involved regulation and interactions
expression
(3) Computational evolutionary biology
(4) Measuring biodiversity
(5)
(6)
(7)
(8)
(9)
(10)
(11)
(12)
Analysis of gene expression
Analysis of regulation
Analysis of protein expression
Analysis of mutations in cancer
Prediction of protein structure
Comparative genomics
Modeling biological systems
High-throughput image analysis
3. Databases
BLAST ACCESS: Provides access to the main NCBI databases locally hosted in our
server, with a batch-processing option.
dbEST or Expressed Sequence Tags database—Manihot esculenta (cassava): A
division of NCBI's GenBank, containing a database on cassava (Manihot
esculenta); search possible by EST, contig, factor, and library; a BLAST service
available against this database.
AceDB databases: Genotypic databases for beans and cassava.
30
Phenotypic databases: Access to phenotypic databases for information about passports
and characterization of different crops; and information about the collections in
CIAT's Genetic Resources Unit.
LIMS: Laboratory Information Management System (LIMSYS). A software developed
by a Local Software Company (DataBio).
BASE: BioArray Software Environment. Database for managing and analyzing data
generated by microarray analyses.
MOLCAS: Access point to the Cassava Molecular Diversity Network.
8.2 Proteome & Proteomics
1. What is Proteome?
2. What is Proteomics?
3.
Protein databases
UniProt
PIR
Swiss-Prot
PDB
NCBI
Human Protein Reference Database
Proteopedia the collaborative, 3D encyclopedia of proteins and other molecules.
4. Branches of Proteomics
 Expressional Proteomics
 Functional Proteomics
 Structural Proteomics
(1) Why Expressional Proteomics?
 2D Gel Principles
 Protein Microarray
(2) Why Functional Proteomics?
(3) Why Structural Proteomics?
5. Relationships between Bioinformatics & Proteomics
8.3 Metabonomics
1. What is Metabonome?
2. What is Metabonomics?
3. Applications of Metabonomics
31
4. Future Directions
Develop comprehensive metabonomic database
Expand metabonomics applications to other species.
Evaluate crypoprobe technology for increased sensitivity or increased throughput.
Expand technology to novel targets:
– Cardiac toxicity
– Adrenal toxicity
32