分子生物学A教学大纲

《分子生物学A》教学大纲

课程英文名称 Molecular Biology

课程代码： BB035301 学时：54 学分：3

理论学时： 54 实验或讨论学时：

适用专业： 生物工程、生物科学、生物技术 课程性质：必修

执笔人： 白吉刚、刘红梅 审定人：郭兴启

一、说明（500字左右）

1、课程的性质、地位和任务

从广义上讲，核酸、蛋白质等生物大分子的结构和功能的研究均属于分子生物学的范畴，即该学科从分子水平上阐明生命现象和生物规律；从狭义上说，分子生物学是核酸的分子遗传学，是研究基因的结构、表达及表达调控的科学。分子生物学是现代生物学发展的生长点，已成为新技术革命的重要支柱，对人类的生产、生活将产生不可估量的影响。分子生物学的任务是研究基因或DNA的复制、转录、表达和调节控制等过程以及与这些过程有关的蛋白质和酶的结构与功能。

2、课程教学的基本要求

本课程安排在学生完成植物学、动物学、微生物学、生物化学、遗传学等有关基础和专业基础课程之后的第五学期。内容上注意与以上学科及基因工程课程的衔接，并避免不必要的重复，课程教学应力求使学生弄清楚基本概念，掌握基本内容，使学生在掌握DNA的主要性质和结构特点的基础上，重点掌握基因的结构与功能、基因表达的调节等过程。授课老师在吃透教材的基础上，应广泛阅读有关参考资料，紧跟本学科发展前沿，备课过程中随时补充新内容，使学生及时了解到本学科的重要进展及发展动向。

3、课程教学改革

选用国外大学经典原版教材，实行双语教学。分子生物学的理论知识较抽象，为提高学生的学习兴趣，在主要章节均增加了理论知识在将来实际的应用等内容。为避免与生物化学、基因工程等课程重复，以便在有限的教学时间内尽可能多地传授给学生有关分子生物学方面的理论知识，在保证知识体系完整的前提下，大分子的结构以及实验操作等内容略讲，重点讲授大分子的功能和协同作用

等内容。

二、教学大纲内容

Chapter 1 Macromolecules (1 h)

Types of the major macromolecules; Noncovalent interactions that determine the three-dimensional structures of proteins and nucleic acids; Two-dimensional gel electrophoresis of proteins; Gel electrophoresis of nucleic acids.

Cruces:

Noncovalent interactions that determine the three-dimensional structures of proteins and nucleic acids.

Questions:

1. What are the monomers of which proteins, nucleic acids, and polysaccharides are composed?

2. A mixture of different proteins is subjected to electrophoresis in three polyacrylamide gels, each having a different pH value. In each gel five bands are seen. (a) Can one reasonably conclude that there are only five proteins in the mixture? Explain. (b) Would the conclusion be different if a mixture of linear DNA fragments were being sized?

Chapter 2 Structure and properties of nucleic acids and proteins (5 h)

Major and minor groove in DNA double helix; Satellite DNA; Features of A, B and Z forms of DNA; Concepts of positive and negative supercoiling DNA; A cruciform structure of DNA existing in a palindromic region; Types of topoisomerases; Melting and renaturation curves of DNA; Unique and repetitive DNA sequences; Method of hybridizing DNA to nitrocellulose filters; DNA molecules to be heteroduplexed; Classes and secondary structure of RNA; Hydrolysis of nucleic acids by nucleases and ribozymes; Sanger procedure of DNA sequencing reactions; Chemical synthesis of DNA; A future practical application of sequence databases.

A hypothetical globular protein having several types of side-chain interactions; Three-dimensional structure of an IgG molecule; A future practical application of specific inhibitors to kinases and phosphatases.

Key concepts:

Major and minor groove; Satellite DNA; Positive and negative supercoiling DNA; Ribozyme. Questions:

1. In what circumstances does a double-stranded DNA molecule form an A helix? a B helix? a Z helix?

2. What features of the DNA double helix facilitate its replication? What features might make its replication complicated?

3. What is meant by the primary, secondary, and tertiary structure of a protein?

Chapter 3 Macromolecular interactions and the structure of complex aggregates (3 h) Highly supercoiled E. coli chromosome; Types of histones; Various stages in forming a metaphase chromosome; Many proteins bind to DNA using their domains (such as helix-turn-helix domain, helix-loop-helix domain, zinc finger domain and leucine zippers); Proteins are embedded into a lipid bilayer of the membrane; Eukaryotic cytoskeleton consists of protein complexes; A future practical application of protein-protein interaction to interrupt malaria.

Cruces:

Various stages in forming a metaphase chromosome.

Questions:

What are the differences between a nucleosome, a core particle, and an octameric disc? Which directly involve the histone H1?

Chapter 4 DNA replication (5 h)

Mechanisms of covalent extension initiation and de novo initiation; The formation of a bidirectionally enlarging replication bubble; Relaxation of DNA overwinding by topoisomerases; Topoisomerase I unwinds a local region; The unwinding events in a replication fork; Elongation of newly synthesized strands; Sequence of events in assembly of lagging strand fragments; The complete DNA replication system and mutiple subunits of DNA polymerase; Replication of eukaryotic chromosomes is accomplished by having multiple initiation sites; Enzymology of eukaryotic replication; DNA is unwound from the nucleosomes at the replication forks; Telomere replication; Replication of adenovirus; A future practical application of AZT in an AIDS patient. Cruces:

The complete DNA replication system and mutiple subunits of DNA polymerase; Enzymology of eukaryotic replication; Replication of adenovirus.

Questions:

1. Name three enzymatic activities of DNA polymerase I.

2. What two reactions are coupled when nick translation occurs?

3. What specific constraint to DNA replication occurs at the ends of linear DNA molecules? How does replication occur at the ends of linear DNA molecules?

Chapter 5 Transcription (4 h)

Mechanism of the chain-elongation reaction catalyzed by RNA polymerase; RNA polymerase

bind to DNA at a promoter, Initiation of RNA synthesis in E. coli; Stages in RNA synthesis of E. coli; Terminators of prokaryotes; mRNA is transcribed and translated simultaneously in bacteria; Pre-rRNA and pre-tRNA processing in E. coli; Functions of RNA polymerases in eukaryotes; Pre-rRNA and pre-tRNA processing of eukaryotes; Southern transfer technique; A future practical application of antisense RNA.

Cruces:

Stages in RNA synthesis; Pre-rRNA and pre-tRNA processing; Functions of RNA polymerases in eukaryotes.

Questions:

1. Describe the differences, if any, between the chemical reactions catalyzed by DNA polymerase and RNA polymerase.

2. What chemical groups are present at the origin and terminus of a molecule of mRNA that has just been synthesized?

3. What could be the consequence(s) of mutations in various regions of a promoter?

Chapter 6 Translation (6 h)

Outline of translation; The universal genetic codes and their deviation; Three dimensional tRNA; Steps of aminoacyl-tRNA charging; Classes and proofreading of aminoacyl-tRNA synthetase; Wobble hypothesis; Polycistronic and monocistronic mRNA; Overlapping genes; Composition of ribosomes; Polysome; Stages of polypeptide synthesis in prokaryotes and eukaryotes; Functions of antibiotics in polypeptide synthesis; A future practical application of unnatural amino acids.

Cruces:

Steps of aminoacyl-tRNA charging; Stages of polypeptide synthesis.

Questions:

1. List three differences between prokaryotic and eukaryotic translation (ignore differences in ribosome structure)?

2. Which processes in protein synthesis require hydrolysis of GTP?

3. How might various antibiotics be used to study the process of translation?

Chapter 7 Mutations, repair and transposition (5 h)

Types of point mutations; Concept of reversion; Base-pairing between the rare imino form of adenine and cytosine and the enol form of thymine and guanine; A mechanism of 5-bromouracil-induced mutagenesis; Spontaneous depurination of DNA; Photoproducts induced

by UV irradiation; Actions of nitrous acid and hydroxylamine; Misalignment mutagenesis generated by intercalation of an acridine molecule in the replication fork; Action of alkylating agents; Mutated by transposons; Photoreactivation; Mechanism of alkyltransferase; Excision repair; Mismatch repair; Recombination repair; SOS repair leads to error-prone DNA replication; Holliday model of homologous recombination; Proteins involved in homologous recombination; Site-specific recombination between DNA of phage λ and bacteria, Mechanisms of transposition; Transposition process of prokaryotic transposons (such as TnA family, insertion sequences, composite transposons and transposable phages); Types of eukaryotic transposons; A future practical application of mutations in p53 gene and defects in DNA repair systems.

Cruces:

DNA repair systems and transposons.

Questions:

1. In what two ways does 5-bromouracil (BU) function as a mutagen? What type of mutations would occur from its use?

2. Consider the effects of life on Earth of the breakdown of the ozone layer (which would allow more UV light to penetrate to the Earth's surface). What might be the eventual outcome of that situation?

3. What is the difference between conservative and replicative transposition? What base-sequence is duplicated in both types?

Chapter 8 Regulation of gene activity in prokaryotes (5 h)

Principles of regulation; Concepts of negtative and positive regulation; Genetic map of lactose operon; Lac mRNA is made only if cAMP-CRP is present and repressor is absent; Regulation of galactose operon; Regulatory proteins of arabinose operon; Attenuation control in tryptophan operon; Translation of lac mRNA into proteins; Secondary structure of mRNA controls initiation of translation; Autoregulation; Conformational change of an enzyme by binding of an allosteric effector; Feedback inhibition of the pathway for synthesizing isoleucine; A future practical application of bacteria lacking one or more proteases.

Cruces:

Lac mRNA is made only if cAMP-CRP is present and repressor is absent; Attenuation control in tryptophan operon.

Questions:

1. What distinguishes negative from positive regulation? How would you distinguish between negative and positive autoregulation?

2. Imagine an enzyme that must be synthesized in response to an environmental stimulus (e.g., lacZ in response to lactose). What are the advantages and disadvantages for regulating this enzyme at the transcriptional versus posttranscriptional level?

3. Why is the autogenous type of regulation common for abundant proteins that are incorporated into macromolecular assemblies? (For example, ribosomal proteins in prokaryotes are autogenously regulated at the level of translation.)

Chapter 9 Bacteriophage (4 h)

Properties of the nucleic acid of several phage types; Replication of T4 DNA; Transcription map of phage T7; Replication of phage M13; Replication sequence of phage λ; Regulatory genes of phage λ; A practical application of bacteriophage vectors.

Cruces:

Regulatory genes of phage λ.

Questions:

What kind of nucleic acids is found in the following phages: T4, T7, M13, λ? Tell about circularity also.

Chapter 10 Regulation of gene activity in eukaryotes (11 h)

Potential control levels for the regulation of gene expression in eukaryotes; The production of the mature k-type L chain mRNA of a particular lgG molecule; The joining of V and J DNA segments during B-cell differentiation; Controlling chromatin structure; Models for regulation of RNA synthesis; Structure and role of specific transcription factors; Splicing pathway for GU-AG introns; Models of alternative splicing; Trans splicing; RNA editing; Regulation of nucleocytoplasmic mRNA transport; Regulation of histone and tubulin mRNA Stability; Regulation of transferring mRNA translation; Two principal pathways for intracellular protein translocation; Chemical modification of proteins and proteolytic cleavage; Posttranslational regulation of glucocorticoid receptor; Protein degradation; A practical application to construct artifical tissues.

Cruces:

Models for regulation of RNA synthesis; Splicing pathway for GU-AG introns; Models of alternative splicing; Trans splicing and RNA editing.

Questions:

1. What RNA polymerase(s) transcribe eukaryotic genes? Name the polymerase(s) and the type of gene(s) it transcribes.

2. Give the two types of splicing that can occur in the processing of eukaryotic mRNA, and state the differences between them.

Chapter 11 Plasmids (2 h)

Plasmid encoded proteins; Transfer of F plasmid DNA from an F+ male cell to an F- female cell using a rolling circle replication; Conjugation between an Hfr male bacterium and an F- female bacterium; Plasmid DNA replication; A practical application of Agrobacterium tumefaciens contains a plasmid.

Cruces:

Replication of plasmid DNA.

Questions:

How have plasmid-borne genes for antibiotic resistance and toxins affected medical treatment and pharmaceutical development?

Chapter 12 Recombinant DNA and genetic engineering (3 h)

Some restriction enzyme classes and their cleavage sites; Procedure of preparing a restriction enzyme map for a DNA fragment; Chromosome walking and jumping; PCR (Polymerase chain Reaction) yields large quantities of a specific sequence; Directional cloning into a plasmid vector; Detection of transformed cells; Site-specific mutagenesis of a gene cloned into an M13 phage; Production of transgenic mice; Restriction fragment length polymorphisms associated with sickle cell anemia; DNA fingerprint resulting from the presence of variable numbers of tandem repeats. Cruces:

Directional cloning into a plasmid vector; Detection of transformed cells.

Questions:

1. Two types of cuts are made by restriction enzymes. What are they? These two types of cuts produce three possible types of DNA termini. Describe them.

2. You have the cDNA clones for two human genes, A and B, which you believe may be closely linked on a human chromosome, since these two genes are known to be close together in rats. Briefly describe the tools and procedures you would use to answer this question.

3. Describe the general procedure used to produce a DNA fingerprint.

附：教学参考书目

[1] 《Genes Ⅷ》Lewin著, Published by Pearson Prentice Hall, 2004

[2] 《Molecular Biology》P C Turner等著，科学出版社，1999

[3] 《Genomes》T A Brown著，Published by BIOS Scientific Publishers Limited，1999

[4] 《Molecular Biology》Robert F Weaver著，Published by McGraw-Hill，2005

[5] 《Introduction to Molecular Biology》 Peter Paolella著，清华大学出版社，2002

[6] 《Molecular Biology of the Gene》 J D Watson等著，Published by Pearson Education，2004