BMS 1062: Molecular Biology

• Convenor: Dr Peter Boag
• 6 points
• Monash Handbook

BMS1062, as a core unit, builds on the fundamental understanding of biological systems developed in the first semester units, BMS1011 ‘Biomedical chemistry’ and BMS1021 ‘Cells, tissues and organisms’, and is an essential forerunner to most of the second and third year BMS units, especially to BMS2042 ‘Human genetics’, BMS2062 ‘Bioinformatics and communication’ and BMS3021 ‘Molecular medicine and biotechnology’. For students studying BBNSc or BND it provides an introduction to the control of cellular processes, an understanding of which is essential for units such as BND2021 ‘Nutritional biochemistry’, BND2042 ‘Nutrition and Immunology’, BND2062 ‘Microbiology of food’, and a range of BNS units involving the study of brain function and/or chemistry.

BMS1062 introduces DNA as the genetic blueprint for life and explores how it functions within the cell at a molecular level. It provides a grounding in areas such as

• the structure, properties and maintenance of DNA
• how DNA is organised into functional units (i.e. genes) and how genes direct the development and growth of cells
• the scientific basis for, and the applications of, biotechnology, such as in gene cloning, treatment of disease, the human genome project.

In this unit students will also gain some laboratory-based experience in techniques commonly used in molecular biology research.

Lecturing Staff

Dr Peter Boag convenor and Lab 1 coordinator	Dr John Boyce	Dr Mark Prescott	Dr Amanda Walmsley
Dr Trudi Bannam	Mr Mohamed Mohideen Lab 2 coordinator	A/Prof Robyn Slattery	Dr Frank Alderuccio Lab 4 coordinator
Dr Saw Hoon Lab 3 coordinator

Organisation of the unit

The unit consists of two formal components (3 lectures per week and one 3 hr laboratory class per week), supported by a range of supplementary materials (e.g. textbook, on-line resources such as Blackboard, quizzes, websites). Enrolled students can access all unit information, lecture notes and supplementary material on the BMS1062 Blackboard site.

Topics covered

INTRODUCTION TO MOLECULAR BIOLOGY

Basic concepts in molecular biology

Universal features of cells. Central dogma of molecular biology. What is a gene? What is molecular biology?

DNA STRUCTURE AND PHYSICAL PROPERTIES

Structure of nucleic acids

Primary structure of DNA - nucleotides and their linkage, information storage in base sequences. Secondary structure of DNA - complementary base pairing, double-stranded helix, antiparallel orientation of strands, biological implications i.e. the role of both strands as templates. Generalised structure of RNA

 Organisation of DNA in microbial genomes

DNA can be packaged in various forms in microbial genomes.

Bacterial genomes are usually present in a single copy and circular, supercoiled, secured into loops, condensed into nucleoid. Plasmids are composed of dsDNA, usually multicopy and circular. Viral genomes (procaryotic and eucaryotic).

Genetic material can be transferred between bacterial cells.

Natural systems in bacteria: transformation and conjugation. Use of these systems in genetic manipulation. Transfection of eucaryotic cells.

Manipulation of DNA based on structural properties. Properties of DNA and their implications including: solubility, viscosity, UV absorption, denaturation and reannealing, hybridisation, probes, separation of DNA species by gel electrophoresis

Manipulation of DNA based on sequence properties

Fragmentation of DNA, restriction endonucleases - their characteristics and uses. Detection of specific DNA sequences using Southern blotting. Sequencing of DNA by the dideoxy method and its automation, brief introduction to the Human Genome Project

AN OVERVIEW OF DNA FUNCTION AND INFORMATION FLOW

Gene expression - from DNA → RNA → protein Central dogma, DNA as a template for replication and transcription. Transcription - overview including polymerisation reaction, limits of transcription (genes), nature of primary transcripts in prokaryotes, complexity of eukaryotes - exons and introns, processing of mRNA

The genetic code

Deciphering and key features of the genetic code. Transfer RNA (tRNA) - synthesis, structure, function, activation, interaction with mRNA

Protein synthesis

Ribosomal RNA (rRNA) - synthesis and structure. Ribosomes - structure and function.

Translation - general mechanism of peptide synthesis. Post-translational modification of proteins

MUTATION OF DNA SEQUENCES

Mutagenesis and the nature of mutations

Definition of mutation. General effects on protein structure / function. Germline vs. somatic mutations. Classes of mutation including base substitution, frameshift, deletion (large and small), duplication, inversion and trinucleotide repeat expansion with clinical examples of each. Causes including replicative and environmental (radiation, chemical, mechanical)

Mutation in evolution, disease and DNA fingerprinting

Good, bad and neutral mutations. Development of new genes / gene families. Comparative genomics and evolution. Generation of variation. Mutation and human disease- single gene to cancer. Heterozygote advantage. Polymorphisms and DNA fingerprinting - forensic, paternity testing

HIGHER ORDER GENETICS

Chromosome structure and function

How do cells manage to fit of their DNA inside the cell? How is chromatin organised? What is the structure and function of centromeres, telomeres and nucleosomes? Functional consequences of nucleosome structure.

Replicons

Discussion of the DNA replication cycle including initiation and termination. Mitochondrial genomes. Genes and psuedogenes, with particular reference to the globin gene cluster and thalassemias. Ribosomal RNA synthesis. Highly repetitive DNA

Mobile genetic elements

Structure and genetic organisation of insertion sequences and transposons. Bacterial transposons, transposons in eukaryotes. Retroviruses and retrotransposons

TRANSCRIPTION AND RNA PROCESSING

Overview of mRNA transcription

DNA to mRNA, coding (sense) strand and template strand, synthesis from 5' to 3' end. Life cycle of mRNA, differences in prokaryotic and eukaryotic cells, polyA 3' tails and 5' methylated caps

Bacterial operon

Concept of polycistronic messengers. Initiation of transcription in prokaryotes. RNA polymerase multiple subunits, core enzyme, sigma factors, holoenzyme Sigma factors control binding to DNA, recognition of promoter sequences Termination of transcription, rhodependent and rho-independent mechanisms

 Eukaryotic transcription

Eukaryotic RNA polymerases, different types of promoter elements. Processing of eukaryotic mRNA, adenylation and capping, cellular location and transport. Presence of introns and exons in eukaryotic genes, post-transcriptional splicing.

GENE REGULATION

Gene regulation I

The concept that cells do not express all of their genes all of the time is introduced and followed by an overview of regulatory mechanisms. Negative and positive regulatory systems and catabolite repression are discussed, with particular reference to the lac operon of Escherichia coli.

Gene regulation II

Continued discussion of regulatory mechanisms including repression of metabolic pathways and transcriptional attenuation, with particular reference to the trp operon of E.coli.

PERPETUATION OF DNA

DNA replication

Semi-conservative DNA replication, DNA polymerases, origin of replication,

Mechanisms of DNA replication

Priming DNA replication, coupling of leading and lagging strand synthesis, replication at telomeres, fidelity of DNA replication

Gene mutation and DNA repair

Spontaneous and induced mutations, biological repair mechanisms, excision repair, postreplication repair, SOS system, repair defects and human disease

DNA RECOMBINATION AND GENE CLONING

DNA recombination

Mechanisms of recombination, breakage and reunion, Holliday structures

Mechanisms of DNA recombination

Gene conversion, enzymatic mechanisms of homologous recombination

Recombinant DNA techniques

Making recombinant DNA, isolating, cutting and joining DNA, amplifying recombinant DNA

Cloning and its applications

Cloning vectors, genomic and cDNA libraries, finding specific clones, uses of cloned DNA, applications and uses of polymerase chain reaction, Human Genome Project