The course aims to provide an advanced understanding of the core principles and topics of Biochemistry and their experimental basis, and to enable students to acquire a specialised knowledge and understanding of selected aspects by means of a stem/branch lecture series and a research project.
General Principles and Topics
The course aims to provide students with an advanced integrated knowledge and understanding of core topics, with general principles set in particular contexts:
- Structural and chemical biology, including nucleic acid structure and interactions, signaling proteins and membrane proteins, enzyme kinetics and drug discovery and protein design.
- From genome to proteome, including all steps in eukaryotic gene expression from chromatin accessibility to translation and mRNA turnover.
- The dynamic cell, including the dynamics of proteins and membrane-bound organelles in eukaryotic cells
- Signalling and cancer, including cell and molecular biology of signaling and cancer, DNA repair and apoptosis
- Bioengergy, including the exploitation of plants and algae for renewable energy generation.
- Molecular microbiology of infectious disease, including the examination of prokaryotes as agents of disease and as source of antibiotics, of virulence and resistance, and the molecular aspects of eukaryotic protozoan pathogens.
This course aims to develop the key transferable skills required in scientific work. These include
- Practical research skills
- Analytical and presentation skills
- Advanced scientific methods
Practical research skills
The course aims to provide training in research skills through the provision of a minimum eight week research project for each student.
Analytical and presentational skills
The course aims to provide the students with analytical and presentational skills. This will be achieved in methods and skills lectures, classes and seminars and small group teaching by the student undertaking:
- Two journal clubs which guide the student through a detailed analysis of a research paper.
- A critical review of a paper in the literature and oral presentation of the analysis.
- Exploration and oral presentation of contemporary biochemical topics.
- A problem-solving approach to experimental data.
- A short course on scientific report writing.
- A short course on basic statistics.
- Small group discussion on topics under the heading ‘Science that affects Society’ and practice at constructing reports on broad themes that integrate diverse scientific topics.
Advanced Scientific Methods
The course aims to develop students' understanding of three areas of widely used and advanced scientific methods – spectroscopic tools, molecular imaging and bioinformatics. This is achieved via lectures, classes, seminars and a bioinformatics problem based learning exercise.
By the end of the course, the students should be able to demonstrate advanced knowledge and understanding in the following core areas.
- Aspects of protein structure: genome to proteome. The principles of globular protein structure, as well as the techniques used for elucidation of structures and approaches to their prediction from sequence. The behaviour of proteins in solution and the principles of molecular recognition. The principles of membrane protein structure determination.
- Enzyme kinetic behaviour and mechanisms. Intermediates in enzyme-catalysed reactions and their investigations.
- Molecular imaging. Principles and application of modern imaging techniques.
- Bioinformatics. Identification/quantitation of polypeptide similarity. Identification of polypeptide families & superfamilies. Large scale sequencing projects, data analysis including comparative analysis.
- Chromatin structure in relation to gene expression. The contribution of chromatin structure to the regulation of transcription, both activation and repression. Control as exerted both at the level of higher order structure and nucleosome occlusion of promoters, both of which are naturally repressive. Nucleosome positioning in relation to promoter architecture; promoter remodelling. The roles of histone acetylation, and the targeted acetylases (and deacetylases), and the action of ATP-dependent 'chromatin remodelling machines'.
- Mechanism and control of DNA transcription in animals. Transcription initiation in eukaryotes is a highly complex, multi-step process. The role of general transcription factors in mediating the various steps in transcription initiation will be described. Models for about the appropriate temporal and spatial control of gene expression will be discussed.
- DNA damage repair, and integrity, immortalisation. The molecular basis of the processes that occur in DNA recombination and repair processes.
- RNAi and microRNA. The molecular basis of RNAi as a technique for gene silencing, and the role of microRNAs in control of gene expression in vivo.
- Protein synthesis and translational control. Protein synthesis mechanisms, especially with respect to ribosome structure-function and accuracy of translation, considered mainly in prokaryotes.
- Control of gene expression in eukaryotes. The principles and current research emphases of the control of eukaryotic gene expression at all stages: initiation of transcription; pre-mRNA processing; mRNA stability and translation. Co-ordination of expression of organelle and nuclear genomes.
- Protein targeting to the endoplasmic reticulum, internal organelles and the cell surface. Mechanisms and principles of eukaryotic intracellular vesicular trafficking and mechanisms of targeting, in particular to the ER and the secretory pathway. How a combination of genetic and biochemical methods have together made important contributions.
- Apoptosis, from molecules to function in disease. An understanding of apoptosis and its involvement in disease processes.
- Signal transduction in eukaryotes. An understanding of receptors that couple to guanine nucleotide-binding proteins (G proteins) and the mechanisms by which their signals are transduced in the eukaryotic cell. An understanding of signalling in relation to tumour cell biology.
- Oncogenes, tumour suppressor genes and carcinogenesis. The molecular biology of cancer, with a strong link between the basic scientific aspects including our current understanding of the entry into and exit from the cell cycle and the regulation of transitions between phases of the cycle; and clinical aspects, including epidemiology, tumour cell metabolism, cancer stem cells, DNA viruses, metastasis and therapeutic strategies.
By the end of the course, the students should be able to demonstrate advanced knowledge and understanding in one of the following specialised areas.
- Bioenergy. The harnessing of photosynthesis in plants and algae, whether directly using photovoltaic systems, or indirectly through production of oils or other forms of biomass, and the conversion of biomass to other fuels.
- Molecular microbiology of infectious disease. An understanding of the mechanisms of infection, antibiotic action, resistance and virulence. Molecular biology of sleeping sickness and of malaria.
Research, Analytical and Presentational skills
By the end of the course, students should be able to:
- Demonstrate knowledge of the objective, methods, results and conclusions of their research project.
- Demonstrate knowledge of the written presentation of research through the production of a written report on their research project.
- Critically analyse an original paper in the literature.
- Research and present orally contemporary biochemical topics.
- Research and present orally an analysis of an original paper.
- Critically analyse experimental data
- Employ basic statistical methods, where appropriate
Advanced Scientific Methods
By the end of the course students should understand the principles and limitations of spectroscopic tools, molecular imaging and bioinformatics.