Biochemistry

This module aims to provide a foundation in the core techniques utilised in protein purification.

Each week the lectures and practicals lead students through the variety of techniques used to purify proteins. The lectures provide students with an understanding of the biochemical methods commonly used and their significance within a protein purification strategy. Practicals will be tightly linked to the lectures, with students being required to follow a purification strategy over the course of the module. Starting with a mixture of proteins, students are set the task of purifying one of the proteins on the basis of their biochemical properties.

This module has four core topics that direct students through the purification process. They are:

• Introduction to protein purification and bulk preliminary purification techniques
• Chromatography techniques for protein purification
• Protein and enzyme assay techniques
• Gel electrophoresis and associated techniques.

This module is an introduction to cellular biochemistry focusing on the core pathways of intermediary metabolism which are central to cellular function. Specifically, it focuses on two related and key areas of biochemistry. The first is enzymology; how do proteins function as biological catalysts and how are chemical reactions controlled within a cell? Students will investigate how the many chemical reactions which participate in metabolism are accurately regulated and organised.

The second is cellular metabolism; particularly, how do cells obtain energy from their surroundings to maintain their complex order?

The module will cover several seminal and Nobel Prize winning research topics including a detailed look at the key reactions of the citric acid cycle and the coupling of electron transport, proton pumping and ATP synthesis. The concepts and areas of biochemistry covered will be further illustrated by reference to the pathological state and human diseases which result from specific malfunctions in biochemical pathways and reactions.

This module provides a comprehensive introduction to the basics of bioinformatics. The laboratory sessions will introduce students to software for sequence manipulation, genome visualization, phylogenetics, searching for related sequences using BLAST, primer design, structural biology and more. A lab manual written specially for the module is used to guide students step-by-step through learning the software.

Each student is assigned a virus genome sequence to which they will apply the techniques learned in the lab sessions to produce a coursework portfolio. By the end of the module, students will be prepared for more advanced bioinformatics techniques that they will encounter in third and fourth year modules, and which may also be of use to them in their dissertation projects.

This module explores the interactions that take place both within and between cells and which allow them to perform their function in the whole organism. Students will consider five key topics within cell biology:

• The methods used to study cells and the dynamic nature of the cytoskeleton
• The mechanisms and physiological significance of transport across membranes
• The mechanisms involved in cells receiving and acting upon information from outside of the cell
• The mechanisms of development of whole organisms, examining how individual cells become committed to a particular function as development occurs
• The regulation of the cell cycle, growth, and development. We will illustrate these topics using examples drawn from a range of biological system.

This module introduces advanced techniques of eukaryotic recombinant DNA technology, DNA sequencing, genomics and functional genomics. Bioinformatics, the computer-based analysis of data that result from genome sequencing and the genomic approaches to understanding gene function and expression are introduced and developed in the workshops. The module practicals provide hands-on experience of quantitative gene expression analysis employing widely used state of the art PCR (polymerase chain reaction) based technology.

Students will gain knowledge and understanding of these techniques, which will provide the basis for the informed reading and comprehension of primary experimental biological research literature required for subsequent undergraduate research projects. These technologies underpin an increasing proportion of modern biological research, particularly in the Biomedical disciplines and form the basis for rapidly developing applications in the field of personalised medicine.

The aim of this module is to provide students with the skills they need to begin their future careers. The module will enhance career awareness, develop oral communications skills and develop CV and cover letter writing. Workshops include sessions on LinkedIn, information skills, assessment centres, interview techniques and entrepreneurship.

This module takes a molecular approach to understanding heredity and gene function in organisms ranging from bacteria to man. It begins by reviewing genome diversity and how genomes are replicated accurately, comparing and contrasting replication processes in bacteria and man. The module discusses in detail molecular mechanisms, particularly those that ensure information encoded in the genome is transcribed and translated appropriately to produce cellular proteins.

Students will focus on the importance of maintaining genome stability and damaging effects of mutations in the genome on human health. Examples are drawn from a range of inherited genetic diseases such as phenylketonuria and sickle cell anaemia, paying particular focus to how mutations in key genes are driving cancer development.

Teaching is delivered by a series of lectures supported by varied practical work, workshops, guided reading and online resources. Laboratory practicals include investigating how exposure of bacteria to ultraviolet light induces mutations – providing a model for understanding how skin cancer may develop as a consequence of excessive sun exposure.

When we look at ourselves in the mirror the last thing we consider is that we are only 10% human due to our body comprising ten times more bacterial cells than human cells! There is no mistaking the importance of our bacterial communities in maintaining our proper functioning, eg digesting food, but microbes also cause disease and it is this that normally attracts media attention.

The ‘good vs bad’ nature of microbes is covered in the module Medical Microbiology (the pre-requisite to this module) together with methods for controlling exposure to pathogens; particularly in a hospital setting. But what about the household setting? How dangerous are the microbes living on your household surfaces (including your toothbrush!)? Do disinfectants really kill 99.9% of germs (as stated by all manufacturers)? These questions, and others, are addressed in this module whilst students learn the essential practical techniques necessary to work in both industrial and hospital laboratories. The module also explores the use of microbes as artistic media in the up and coming field of BioArt.

The first part of this module focuses on conformational analysis of chains and rings, with a particular focus on conformations of acyclic and cyclic hydrocarbons, and the conformations and reactivity of substituted cyclohexanes. Conformations and reactivity of cyclohexene, cyclohexanone, strained and bridgehead-containing rings will also be explored. Students will then concentrate on the application of spectroscopic methods in organic structure determination. The importance of geminal, vicinal and long range coupling in 1H NMR will be assessed, as will the uses of Nuclear Overhauser effect. 2D NMR in structure elucidation will be examined as well.

Students will gain knowledge, understanding and skills in the conformational analysis and structural determination of organic molecules. Additionally, they will improve their skills in problem solving and analysing and interpreting data.

Students will be introduced to the importance of molecular, metabolic and cellular interactions within parasitic protists, and between a range of parasitic protists and their hosts.

The course will provide students with an understanding of how the life cycle strategies used by protists enable them to gain access to, and survive within, the host as well as the impact that protist parasites have on human health. Practicals will provide an opportunity for students to apply immunological skills to investigate the host-parasite interaction.

Understanding how life works depends to a great extent on understanding how proteins work. Thanks to the Human Genome Project, we now have a catalogue of all the proteins that are encoded in the human genome. This might be thought of as life’s toolbox. The next questions are: how do those tools work; how do they interact with each other; and how have they evolved over the billions of years of evolutionary time that have led to us? This module introduces modern techniques for the study of protein structure, function and evolution.

Lectures cover: structural-functional relationships in proteins; methods for detecting the action of Darwinian selection in protein evolution; methods for reconstructing the evolutionary events that have led to present-day proteins; and, the new lab techniques that are allowing us to study protein function on a large scale. In the practical sessions, students will gain hands-on experience of molecular phylogenetics – the main tool for studying evolution at the molecular level – as it is applied to proteins. Assessment is by an exam and a coursework essay on a protein of your choice, giving students a chance to apply their new knowledge of protein biochemistry to any of their own areas of interest in biology.

Electrochemistry and Advanced Spectroscopy explores electricity and chemical changes. The module considers the application of electricity to elicit chemical reactions and provides the fundamentals of electrochemistry and modern electrochemistry. Students will learn to analyse simple electrochemical behaviour. The spectroscopy section of the module gives an overview of a range of optical spectroscopic techniques. Students will gain an understanding of Raman theory including advancements and real world applications of Raman spectroscopy as well as luminescence spectroscopy.

This module introduces students to ion mobility and column chromatography techniques of analytical separation. The principles of these separation techniques will be described and exemplified, with an emphasis on understanding how each component within a given separation technique contributes to the analytical quality and efficiency of the overall separation process. The practice of analytical chromatography will be described in terms of the application of advanced methods that enable the optimisation of separation resolution, detection sensitivity, and analysis time.

Students will gain an appreciation of how analytical separation systems rely on a combination of components working together and how the performance of any individual component affects the overall separation process. Throughout, practical examples of separation applications will be used to illustrate the principles and practice taught in the module. The module also demonstrates how an understanding of the fundamental chemical principles of a technique may be used to assist method development and the optimisation of the practical application of a technique. A study of analytical separations brings together both qualitative and quantitative analysis of chemical data.

For 50 years, thanks to evolutionary theory, we’ve known why we are fated to age and die, but our understanding of the mechanisms has been a lengthy evolution in itself. Only relatively recently, with the use of modern molecular biology tools, do we begin to understand the mechanistic basis of the ageing process, from early notions about rates of living to current ideas about modular yet interacting mechanisms including autophagy, protein synthesis, nutrient sensing, insulin-like signalling and disease resistance. Even now we do not clearly know what makes us age. Ageing is perhaps the most multidisciplinary area of study and is certainly one of the last great mysteries in biology.

This module introduces the area and the methodologies with which ageing is studied. Teaching is through lectures, workshops, practical work, individual and group-based coursework and private study.

In this module students are given an overview of the cellular and molecular processes that underpin the development of cancer. This will enable students to discuss the various factors that can affect cancer susceptibility. Students will look at the approaches taken to treat cancer, including some of the new generation of molecularly-targeted cancer therapies.

The ability of cells to communicate with one another using signalling pathways is of fundamental importance in multicellular organisms such as mammals. Cell signalling enables the transmission of information that is required for the correct co-ordination of metabolism, growth and development.

This module revises the basic principles of cellular communication, exploring the molecular basis of signalling in detail by using key signalling pathways as examples. The combination of Lectures and Workshops allows students to evaluate influential scientific discoveries, whilst Laboratory practicals provide the opportunity to put theory into practice.

This module explores some of the key roles played by ion channels and calcium ions in the communication that takes place within and between cells. The module is split into two linked themes. Firstly, an introduction to the diversity of ion channel families and their biological functions including the many different cellular processes throughout the life history of cells that are regulated by calcium ions as signals. Secondly, an investigation of the importance of ion channels and calcium signalling in animals, and human physiology in particular, using examples of diseases that are caused when ion channels malfunction (e.g. myotonia, malignant hyperthermia, sudden heart arrest caused by long QT syndrome.) or calcium signalling is disrupted (e.g. Alzheimer’s disease, polycystic kidney disease, pancreatitis). Students also gain hands-on experience of the techniques used to study ion channels and calcium signalling in cells.

Every day our body does something remarkable, but we are completely unaware of it most of the time: our immune system is constantly protecting us from pathogens in our environment as well as threats from within. This highly evolved, interdependent collection of organs, cells and chemical messengers is continually scanning our tissues for any unwanted intruders or abnormal cells. When we get ill, with a cold for example, full mobilisation of our immune system sends armies of cells and molecules to fight the problem in what can sometimes literally be a fight to the death. Fortunately for us, our immune system wins the battle almost every time!

In this module we examine the various components of the immune system – the organs, cells, and messengers, and how they function in health and illness. We look at particular threats such as allergies, infectious diseases and cancer, providing students with a good understanding of how this vital component of our bodies keeps us well.

Research and practice in biomedicine continues to evolve more rapidly than at any other time in history, raising fascinating but complex moral and ethical challenges for those studying and working in the field. Understanding ethics in biomedicine and the relationship between science and society has become an essential element in biomedical degree training.

This module builds on the Biomedicine and Society module, aiming to help students develop a deeper understanding of key ethical principles used in biomedicine and some major cultural, social and political influences that define research agendas and fuel ethical debates in the public perception of biomedicine.

The module takes on a seminar format structured around three core themes:

• The development of ethical principles in biomedicine
• Ethical practice and current debates in animal and human research including clinical trials
• Ethical challenges such as those emerging in genetics and regenerative medicine and how these are debated in the media.

How is DNA, the fundamental building block of life, organised and expressed in different types of organisms such as bacteria and humans? Lectures comparing eukaryotic and prokaryotic gene organisation and expression, chromatin structure and DNA repair will seek to answer this question. In addition, students will study the application of genetics to science and technology during practical and workshop sessions, providing them with the opportunity to develop group and independent working skills whilst reinforcing theoretic concepts.

In this module students will work together as a team to propose a solution to a problem of biological relevance, for example antibiotic resistance, invasive species or healthy ageing. The solution may be a patentable, commercial product or a policy proposal. Weekly workshop sessions will be held for the whole class which will include presentations from external speakers on topics such as intellectual property, project management and negotiating skills. Each team will choose a leader who will be responsible for organising regular meetings in which ideas are developed, tasks assigned and information gathered. The team will produce a report in the form of a patent application or policy document which will form part of the module assessment. The remainder of the assessment will be based on an oral presentation. Peer-assessment will be used to adjust tutors' marks according to individual contribution to the project.

This module aims to provide an understanding of the organisation of the human genome, how disease genes are mapped and how mutations are identified leading to the development of diagnostic tests. The impacts of massively parallel next generation DNA sequencing, microarrays and SNP genotyping on gene discovery and disease diagnosis are examined. The application of modern genetic techniques to identifying susceptibility genes for complex, multifactorial traits will also be studied. A range of diseases will be examined in detail both in lectures and in case study workshop sessions. The final lecture looks at gene therapy and considers the future for treatment of genetic disorders. The practical session aims to give students an opportunity to study their own DNA in a forensics scenario, using techniques that are widely applicable in modern molecular genetics.

Nervous system function, from formation in the embryo to sensory systems and the neural control of complex behaviours, is the focus of this module. The emphasis is on model systems and the use of genetic tools to elucidate developmental pathways and neural circuits. Practical exercises are used to illustrate some of the functions of nervous systems and how these can be manipulated by genetic intervention.

Students are encouraged to access and evaluate information from a variety of sources and to communicate the principles in a way that is well-organised, topical, and recognises the limits of current hypotheses. On completion of the module, students will be equipped with practical techniques including data collection, analysis and interpretation.

Microbiology for the biomedical scientist comprises screening samples to identify and assess microbiological pathogens that cause disease and, enable front line medical staff to choose the correct therapy for successful eradication of the infection. Increasing numbers of these infections are community acquired and many are contracted from, or in, the environment. The environment therefore plays an increasing role in the life cycle and ecology of many pathogens. This in turn, is having an increasing impact on human health and national health services. The increase is a combination of changing environmental conditions (such as land use changes, global warming) and an ever evolving microbial community, most of which do not harm but a few can cause mild to fatal diseases when the opportunity arises. Also cycling in the environment are obligate pathogens which will cause infections if contracted. Furthermore, there are new diseases emerging (e.g. Ebola) and others thought to have been controlled are now re-emerging such as cholera. Using specific microbial pathogens as examples, this module examines the factors and interactions that allow microbial infections to be transmitted from the environment to humans and how their life cycle plays an important role in their emergence, persistence, transmission and infection. It also examines antibiotic resistance: how it has emerged, the different types of resistance, its management and the complications that it imposes on the treatment of these diseases.

Assessment:

1. Exam: 2 hour paper with two questions in sections A and B. Students are required to answer one question from each.

2. Coursework is an extended essay of 2000 words based on the lectures and field trip. The title will be announced in the first lecture.

This module describes the use of chemical contrast agents in biological and medical imaging. Various techniques will be introduced with a discussion of their strengths and weaknesses and the requirements for chemical agents to enhance their usefulness. The design and synthesis of general classes of agents and specific examples of clinical imaging agents (e.g. FDG, Myoview) will be presented, showing how the biological/pharmaceutical properties (membrane transport, toxicity) and physical properties required for imaging can be successfully balanced with molecular design. Finally, the area of multi-modal agents will be introduced and real-life applications of selected agents is illustrated.

The module will introduce key concepts relating to the chemistry behind and the design, synthesis and application of chemical agents in MRI; PET; SPECT; Fluorescence microscopy and other optical techniques. Finally the module will introduce the concept of multimodal imaging and explore the issues involved and prospects for development in this area.

This module provides an advanced introduction into nuclear magnetic resonance (NMR), which is the principal spectroscopic technique used by chemists, biochemists, and biologists, to determine the structure of molecules and study their dynamics. In modern usage, NMR is an extremely powerful technique as the experiments can be performed in a way that enhances or removes certain types of information from the spectra, facilitating their interpretation.

In this module, the basic principles of the method are presented from a physical chemistry perspective. This is followed by discussion of the experimental methods appropriate to the study of both liquid and solid samples. Applications of NMR to the structure and dynamic of proteins, to solid-state inorganic materials and medical imaging are also explored.

Together with BIOL469 MSci Research Project, the projects comprise half of the final year assessment for MSci schemes. The literature review provides the opportunity for students to explore an area of bioscience, related to the research project, in depth. Published articles are summarised and critically reviewed to identify gaps in current knowledge and to provide the background for the student’s own research. The literature review consists of a 4,000 word dissertation which is written during the autumn term of the final year and submitted along with the research project in the summer term.

Together with BIOL470 MSci Project Literature Review, the projects comprise half of the final year assessment for MSci schemes. The research project allows students to spend an extended period of time in the research lab of a member of academic staff, carrying out original research and working alongside PhD students and other researchers. Students develop skills learned in the third year project to enhance student independence and provide experience of the laboratory based research environment. Students develop an adaptable, flexible, and effective approach to research questions and the ways in which their practical skills can be used to address such questions. Results of the research are reported in an 8,000 word dissertation submitted during the summer term of the final year.

Module convenor

• Dr Derek Gatherer

Timetable

• Week 17–18

Aims and scope

• This module aims to encourage students to access and evaluate information from a variety of sources and to communicate the principles in a way that is well-organised, topical and recognises the limits of current hypotheses. It also aims to equip students with practical techniques including data collection, analysis and interpretation.

Learning Outcomes

On successful completion of this module, students will be able to:

• Work effectively to produce a knowledgeable report
• Interpret data and design bioinformatics “experiments” (meaning planned sequences of computer analyses designed to shed light on a scientific problem)
• Perform a standard repertoire of bioinformatics skills
• Be able to describe the uses and limitations of the various ’omic technologies
• Be able to critically evaluate papers in the fields of bioinformatics
• Be able to understand and discuss topics in bioinformatics

Assessment

• Compulsory Exam 50%
• Compulsory Coursework 50%

Recommended reading

• Michael Agostino. Practical Bioinformatics. Garland Science. ISBN 978-0-8153-4456-8 Arthur M Lesk.
• Introduction to Bioinformatics 4th ed. Oxford Univ Press ISBN 978-0-19-965156-6
• Carl Zimmer & Douglas Emlen. Evolution. Making Sense of Life Roberts and Co. ISBN 978-1-93-622117-2
• AD Baxevanis & BFF Ouellette Bioinformatics 3rd ed. Wiley ISBN 0-471-47878-4
• Paul H Dear (ed) Bioinformatics. Scion ISBN 978-1-90-484216-330
• Masatoshi Nei & Sudhir Kumar Molecular evolution and phylogenetics (Also available on http://lib.myilibrary.com/Open.aspx?id=83437)
• Drummond AJ & and Bouckaert RR. Bayesian Evolutionary Analysis with BEAST. Cambridge University Press ISBN 978-1107019652

This module introduces the concept of protein misfolding disorders, and expands this through consideration of two major neurodegenerative diseases; Alzheimer’s disease and Parkinson’s disease. The role of oxidative stress and proteases in neurodegenerative diseases is covered in detail, before examining the role of lipids in various brain disorders. The module also considers how animal models can be used to study both normal brain aging and neurodegenerative diseases.

This module introduces principles involved in the discovery and development of a new drug from initial concept to the identification of a candidate compound to first use in man. This knowledge is extended by learning how the pharmaceutical industry and small biotech companies use contemporary scientific advances to identify drug targets and develop new drugs. How new drug entities are tested, developed and ultimately reach the market is examined using ‘real life’ examples in the form of case studies.

The aim of this module is to provide a broad understanding of the human immune system, more detailed knowledge of human immunological disorders and the application of cutting edge immunological research to biomedical science and clinical practice. Technical skills associated with this course include experience and data analysis of advanced flow cytometry techniques and insight into how research findings are reported and presented to the scientific community and media.

This module provides insight into the underlying molecular events in the development of cancer, how cancers spread through the body and explain how an understanding of the molecular basis of cancer has led to the development of novel cancer treatments. Workshops allow students to study the aetiology and progression of one particular type of cancer in depth, and also to understand how cancer is studied in practice.