Biochemistry

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Biochemistry

  1. 1. Honours Modules in Biochemistry, Genetics and Molecular Biology DNA, Cytogenetics and Human Evolution BGM2036 Semester 2, 30 credits The module comprises three strands: DNA Synthesis, Repair and Recombination, Cytogenetics, and Phylogenetics and Evolution. The first strand explains how DNA is replicated and how damaged dNA is repaired. It aims to provide a sound understanding of the molecular mechanisms underlying the replication, repair and recombination of DNA and to demonstrate the unique importance of the accuracy of these processes. It also aims to demonstrate the resolving power (and limits) of classical genetics using microbial eukaryotes to probe the mechanism of eukaryotic meiotic recombination. The second strand introduces students to the study of human chromosomes. Emphasis is given to the clinical impact of chromosome abnormalities on the development of the people who carry them and also the reproductive consequences of chromosome abnormality. The third strand introduces the conceptual frameworks used to establish phylogenetic relationships between organisms using sequence data and aims to equip students with the practical skills needed to use computer programmes to retrieve and align DNA sequences and build phylogenetic trees from those alignments. In course assessment is by written essay, data analysis, practicals and tutorials and is worth a total of 30% of the module mark. The remaining assessment is by a written examination. Keywords: Biology, Biosciences, Medical Sciences, Biomedical Sciences, Genetics, Biochemistry, Molecular Biology, DNA, Evolution Genetics and Evolution BGM2049 Semester 2, 30 credits The module comprises three strands: Genetic Analysis, Cell Cycle Genetics, and Evolution. The first strand looks at examples of different types of genetic analysis and the solution of various genetic problems and should enable students to design or interpret genetic analyses • to show if mutations are dominant or recessive • To show that genes are sex-linked or autosomal • To recognise if genes are in the same linkage group • To construct simple genetic maps • To recognise the effects of different chromosomal rearrangements on gene segregation
  2. 2. The second strand covers the regulation of the eukaryotic cell division cycle. Consideration is given to Saccharomyces cerevisiae and Schizosaccharomyces pombe as model eukaryotic systems and how the genetics of these organisms have provided a basic understanding of the control of the eukaryotic cell division cycle. The third strand aims to provide insight into modern evolutionary theory, the RNA world hypothesis and theories about the origin of life. Finally it provides information on genetic systems and the control of variation, speciation and natural selection. In course assessment is by written essay, a Flymap practical, practicals and structured questions and is worth a total of 30% of the module mark. The remaining assessment is by a written examination. Keywords: Biology, Biosciences, Medical Sciences, Biomedical Sciences, Genetics, Biochemistry, Molecular Biology, DNA, Evolution Biochemistry & Drug Targets** BGM2037 Semester 2, 30 credits **MAY NOT BE TAKEN WITH BGM2038 The aim of this module is develop students’ understanding of the kinetic parameters that describe enzyme catalysis and allosteric regulation, and of structural features of enzymes, including active sites and allosteric binding sites. The course emphasises how a deeper understanding of how enzyme action is dependent on a combination of different experimental and theoretical approaches. The course also describes how foreign compounds (xenobiotics) are handled in the body, the factors that influence this process and how xenobiotic metabolism is studied experimentally. Students are provided with an understanding of the molecular mechanisms underlying the replication and repair of DNA and the unique importance of the accuracy of these processes is emphasised. Students are shown how the genetic models for eukaryotic recombination can be tested at the molecular level using molecular biology techniques. Finally an overview is presented of the latest molecular evidence in combination with genetic data to produce a generalised model for the molecular basis of recombination in eukaryotes. In course assessment is by tutorial assignment, seminars, data analysis, prepared essay written under examination conditions and is worth a total of 30% of the module mark. The remaining assessment is by a written examination. Keywords: Biology, Biosciences, Medical Sciences, Biomedical Sciences, Genetics, Biochemistry, Molecular Biology, Pharmacology Proteins: Form Function & Trafficking BGM2055 Semester 2, 30 credits
  3. 3. The course aims to explain protein secondary structure, super secondary structure and tertiary folds. It introduces protein folding and discusses why proteins are the shape they are. Students are introduced to experimental measurements of protein folding. A second aim of the course is to explain how specific interactions between enzymes and substrates are determined by protein structure and how substrate binding leads to enzyme catalysis. The course also describes the enzyme complexes of the respiratory chain and how ATP is synthesised. Emphasis is also put on the common and recurrent themes by which proteins are delivered to their correct cellular address. This includes the role of molecular chaperones in protein trafficking and examples of post-translational modifications in cellular trafficking. Finally the course considers biological membranes, looking at micelles and bilayered liposomes, detergents, recognising membrane proteins from their polypeptide sequences, how membrane proteins are synthesized and end up where they should go, and a comparison of the different types of membrane –viral, bacterial, archeal, sub- cellular and cellular. In course assessment is by tutorial assignment, practicals, data analysis, and prepared essay written under examination conditions and is worth a total of 30% of the module mark. The remaining assessment is by a written examination. Keywords: Biology, Biosciences, Medical Sciences, Biomedical Sciences, Genetics, Biochemistry, Molecular Biology Biochemistry & Immunology** BGM2038 Semester 2, 30 credits **MAY NOT BE TAKEN WITH BGM2037 The aim of this module is to develop students’ understanding of the kinetic parameters that describe enzyme catalysis and allosteric regulation, and of structural features of enzymes, including active sites and allosteric binding sites. The course emphasises how a deeper understanding of how enzyme action is dependent on a combination of different experimental and theoretical approaches. This module also aims to provide a sound understanding of the molecular mechanisms underlying the replication and repair of DNA and to demonstrate the unique importance of the accuracy of these processes. It also shows how the genetic models for eukaryotic recombination can be tested at the molecular level using molecular biology techniques. It provides an overview of the latest molecular evidence in combination with genetic data to produce a generalised model for the molecular basis of recombination in eukaryotes. The immunology component of the module describes the causes and consequences of immunodeficiency, describe the mechanisms by which self-tolerance is achieved and how autoimmune diseases might arise. It aims to explain how qualitative regulation of
  4. 4. immune responses is important in determining the outcome in infectious, allergic and autoimmune diseases. The role of the immune system in cancer, tissue transplantation and in pregnancy is also described. Finally the way in which the immune responses can be modulated to the benefit of the host in a range of disease situations and the various ways in which immune function can be assessed are described. In course assessment is by prepared tutorial, data analysis, and prepared essay written under examination conditions and is worth a total of 30% of the module mark. The remaining assessment is by a written examination. Keywords: Biology, Biosciences, Medical Sciences, Biomedical Sciences, Genetics, Biochemistry, Molecular Biology, Immunology Biochemistry of Chronic Diseases BGM3001 Semester 1, 10 credits (examined end of semester 2) This module aims to provide an understanding of the biochemistry and clinical aspects of a number of chronic human diseases, including Type 1 and 2 diabetes, liver disease and neurodegenerative disorders and to explain how knowledge of the biochemistry of a disorder can be used to develop rational drug design for treatment. Topics covered include: G-protein coupled receptors in health and disease; the epidemic of obesity and Type 2 diabetes; physiological insulin replacement in Type 1 diabetes; the pathogenesis of type 2 diabetes; fatty liver diseases; metals and disease, drug development for treatment of chronic diseases; mitochondrial function and human disease. In course assessment (worth 20% of the module mark) is a prepared essay written under examination conditions. The remaining assessment is by a written examination. Keywords: Biology, Biosciences, Medical Sciences, Biomedical Sciences, Genetics, Biochemistry, Molecular Biology Protein DNA Interactions BGM3009 Semester 1, 10 credits (examined end of semester 2) “In living systems the only phenomenon of any importance is the interaction of proteins with DNA and the consequences thereof” (Dr S.E. Halford, University of Bristol). Certainly many of the most significant cellular events such as DNA replication, transcription and recombination, the specific switching on and off of genes, DNA methylation, and DNA restriction are mediated through precise interactions of sets of proteins with DNA. These interactions are of tremendous medicinal importance and when aberrant are often the causes of diseases such as cancer. Furthermore many of the proteins and enzymes that interact with DNA (e.g.
  5. 5. restriction endonucleases and DNA polymerases) are of crucial importance in the biotechnology industry. The high academic, therapeutic and industrial significance of protein-DNA interactions provides the rational for their study. This module aims to address these interactions. Topics encountered in this course include: A, B and Z-DNA families; the helix-turn- helix motif; the use of beta-ribbons to interact with DNA; zinc-finger DNA binding proteins; the leucine zipper motif and the related helix-loop-helix structure, restriction endonucleases; DNA methylation; base flipping and DNA repair; and a review of chromatin structure. In course assessment (worth 20% of the module mark) is a tutorial for which the student prepares a review of one of the common techniques used to study protein- DNA interactions. The remaining assessment is by a written examination. Keywords: Biology, Biosciences, Medical Sciences, Biomedical Sciences, Genetics, Biochemistry, Molecular Biology The Molecular Basis of Cancer BGM3024 Semester 1, 10 credits (examined end of semester 2) Cancer is one of the major causes of mortality. This module provides a background to the biochemistry and molecular biology of cancer. The course introduces cancer as a genetic disease and how the onset of cancer is a multi-step process. It discusses the role of oncogenes and tumour suppressor genes particularly with respect to retinoblastoma and p53. An overview is given of familial cancers and examples of inherited predisposition to cancer. The roles of failures in the DNA repair mechanisms in causing cancer are also described. The factors that lead to metastasis (the development of secondary tumours at sites remote from the primary) are also discussed. Mention is made of experimental genetic models of tumour development and the advantages of transgenic animal models over cell lines highlighted. An important part of this module is a discussion of the methods of anticancer treatment. Many anticancer drugs are themselves carcinogens. Some tumour cells can become drug resistant. The ways in which drugs can be targeted to the tumours are described. Examples and mechanisms of treatments based on growth factors and hormone mechanisms (e.g. breast cancer and prostate cancer) are mentioned, along with new approaches for tumour specificity: targeting surface receptors; targeting cytotoxic drugs to tumour cells; specific inhibition of key tumour enzymes (in leukaemia); gene array techniques for identifying new targets. Finally current and future stem cell therapies are described and an overview given of the various approaches to human gene therapy with special reference to the techniques of gene transfer (viral vectors versus physical DNA transfer methods) and the safety aspects along with critical assessment of the problems encountered. In course assessment (worth 20% of the module mark) is an essay written after a tutorial discussion. The remaining assessment is by a written examination.
  6. 6. Keywords: Biology, Biosciences, Medical Sciences, Biomedical Sciences, Genetics, Biochemistry, Molecular Biology, Cancer Plant and Animal Biotechnology BGM3037 Semester 1, 10 credits (examined end of semester 2) This module will provide knowledge about the commercial application of molecular genetic techniques in plants and animals. Biotechnology is growing very rapidly and this course aims to give a broad picture of exciting developments in the subject. It will highlight those areas where the fundamental information of molecular genetics, molecular biology and biochemistry is being applied to: 1) the improvement of crops, 2) commercial application in whole animals, 3) how the genetic modification of animals can be exploited to understand the role of specific genes in mammalian physiology and biochemistry, 4) the development of new products. Finally the biology and potential therapeutic uses of both stem cells derived by nuclear cloning and adult stem cells will be discussed. Continual assessment (worth 20% of the module mark) is by prepared work for a tutorial presentation. The remaining assessment is by a written examination. Keywords: Biology, Biosciences, Medical Sciences, Biomedical Sciences, Genetics, Biochemistry, Molecular Biology, Biotechnology Structural and Molecular Biology in Biotechnology BGM3038 Semester 1, 10 credits (examined end of semester 2) Proteins are the molecules in all cells that perform the routine tasks, such as the provision of energy, that are essential for life. Proteins are increasingly useful and valuable in commercial and medical applications and therefore an appreciation of protein function is vital in the biotechnology industry. Protein function is dictated by protein structure and in turn by protein (and thus DNA) sequence. To comprehend protein function, it is necessary to understand protein structure and the experimental methods by which protein structures can be deduced and analysed, and how their functions can be adapted, to perhaps improve a bioprocess. Topics to be covered include protein folding and protein structure determination by X-ray crystallography and NMR; the link between structural and molecular biology; the means to alter the properties of proteins; structural and molecular biology in drug design; worked examples of protein engineering, such as the swapping of loops and circular permuted proteins; other biophysical techniques used to study protein structure and function, such as EPR, CD and DSC.
  7. 7. Continual assessment (worth 20% of the module mark) is by group presentations of relevant scientific papers. The remaining assessment is by a written examination. Keywords: Biology, Biosciences, Medical Sciences, Biomedical Sciences, Genetics, Biochemistry, Molecular Biology, Biotechnology Genes and Development BGM3011 Semester 1, 10 credits (examined end of semester 2) Developmental genetics is a particularly fast moving field. Much of the early work was performed on Drosophila (the fruit fly) and a huge amount is known about how genes control the early development of this organism. This module describes the first experiments that identified the genes involved in determining the regions along the anterior posterior axis of the Drosophila embryo. These genes are first expressed in the developing oocyte in the adult female’s ovary and some of their gene products, in the form of RNA or protein, are deposited in specific regions of the oocyte. When this process is upset for instance by mutation in one of the genes then the embryo shows abnormal development. The course takes the students through the whole process of oogenesis describing which genes are expressed, where they are expressed, what their products are, what their roles are in the process, where the products end up in the oocyte, and how this is achieved. After the oocyte is fertilised and laid the process of embryogenesis begins. The course goes on to describe how the positional information laid down during oogenesis is interpreted and leads to the expression of the three groups of segmentation genes whose products are responsible for producing the segmented embryo. Finally the homeotic genes are described that determine the identity of the segments along the anterior posterior axis of the embryo. The module not only recounts the course of events that happen to give rise to the normal Drosophila embryo but also describes many of the ingenious experiments that were performed to elucidate the complex pattern of events. In course assessment (worth 20% of the module mark) is an essay, the remainder of assessment being in the form of a written examination. Keywords: Biology, Biosciences, Medical Sciences, Biomedical Sciences, Genetics, Biochemistry, Molecular Biology Analysis and Manipulation of Animal Genomes BGM3012 Semester 1, 10 credits (examined end of semester 2) This course aims to introduce the students to the most frequently used techniques applied in manipulating animal genomes with particular emphasis on Drosophila (the
  8. 8. fruitfly). Many of the molecular biology techniques are universally applicable, while others are peculiar to particular systems. The course describes the different methods of cloning genes that were developed for analysis of the Drosophila genome while emphasising those that are also applicable to other organisms. The ways in which the thousands of mutations and chromosomal aberrations have been exploited by the Drosophila geneticist in manipulating the Drosophila genome are also described. A key technique in genome analysis is determining where genes are located along the chromosomes and the time and place they are expressed during an organism’s lifetime. The way in which the technique of in situ hybridisation can be used to address these questions is discussed. A major feature of Drosophila genetics is the phenomenon of hybrid dysgenesis arising from the mobilisation of the P element transposon. The way in which this phenomenon was discovered and investigated experimentally is a major part of this module. A critical review of the work involved in characterising the P element and determining how it excises and reinserts in the genome is provided. In addition, there is equal emphasis put on the many different techniques to which the P element has been applied to generate mutations, identify genes, and generally manipulate the Drosophila genome. The zebrafish is now a major vertebrate model organism and many techniques first developed in Drosophila have now been applied to the zebrafish, not least the ability to perform whole genome screens for mutations in genes affecting development. The course describes how such screens can be performed and what other techniques have been developed for producing a genetic map of the zebrafish and why zebrafish has become such an important model organism. In course assessment (worth 20% of the module mark) is an essay, the remainder of assessment being in the form of a written examination. Keywords: Biology, Biosciences, Medical Sciences, Biomedical Sciences, Genetics, Biochemistry, Molecular Biology Human Genome Organisation and Function BGM3028 Semester 1, 10 credits (examined end of semester 2) This module aims to provide an understanding of the organisation and expression of the human genome and human genes. It provides an overview of the approaches being taken to study human genome function. The course begins with an overview of the Human Genome Project, followed by more detailed study of human genome organisation and regulatory mechanisms controlling gene expression. Identification of genes underlying human genetic disease is important for clinical reasons but is also a route to information about gene function. The principal approaches to mapping and identifying disease genes are outlined as are approaches to studying gene function, including information from model organisms and related genome projects.
  9. 9. Some of the topics covered in the course include: an outline of the Human genome Project, organisation and evolution of the human mitochondrial genome, coding and non-coding DNA, gene copy number, clustered multigene families, gene duplication and divergence of gene function, interspersed gene families, formation of pseudogenes, tandemly repetitive and interspersed non-coding DNA, human gene expression, disease gene mapping, and other genome projects in model organisms. In course assessment (worth 20% of the module mark) is an essay, the remainder of assessment being in the form of a written examination. Keywords: Biology, Biosciences, Medical Sciences, Biomedical Sciences, Genetics, Biochemistry, Molecular Biology Advanced Medical Genetics BGM3030 Semester 1, 10 credits (examined end of semester 2) Our understanding of the genetic basis of human disease has grown exponentially in the last few years and will have a dramatic effect on medicine in the future. This course applies basic principles to inherited disorders and considers ways of giving information about these to families. Several examples of different inheritance patterns of human diseases are described. These include autosomal recessive, autosomal dominant, variable expressivity and penetrance, X-linked traits such as Duchenne muscular dystrophy and Fragile X. The course also considers the relevance of genetics to the susceptibility to and the onset of cancer. Under this heading topics that are discussed include: familial adenomatous polyposis and hereditary non-polyposis colon cancer as examples of single gene disorders that cause bowel cancer; the genetic background to common and uncommon cancers including breast/ovarian cancer, Li-Fraumeni and Cowden syndromes. Other topics covered in the course include mitochondrial disease, and imprinting as a cause of glomus body tumours and Angelman and Prader Willi syndromes. There are practical/tutorial sessions on drawing a pedigree while watching a video reconstruction of a consultation between a family and a geneticist, a role play of a genetic counselling scenario with the students taking the role of client and geneticist in turn, and small group discussions on ethical issues surrounding medical genetics relating to family dynamics and societal issues such as insurance, genetic testing, prenatal diagnosis etc. In course assessment (worth 20% of the module mark) is on interpretation of diagnostic laboratory results, the remainder of assessment being in the form of a written examination. Keywords: Biology, Biosciences, Medical Sciences, Biomedical Sciences, Genetics, Biochemistry, Molecular Biology

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