Biochemistry - BSc (Hons)

This course will provide an introduction to biomolecules in living matter. The simplicity of the building blocks of macromolecules (amino acids, monosaccharides, fatty acids and purine and pyrimidine bases) will be contrasted with the enormous variety and adaptability that is obtained with the different macromolecules (proteins, carbohydrates, lipids and nucleic acids). The nature of the electronic and molecular structure of macromolecules and the role of non-covalent interactions in an aqueous environment will be highlighted. The unit will be delivered though lectures, formative practicals and related feedback sessions to ensure students fully understand what is expected of them. Short tests (formative assessment) will be used throughout the unit to test students' knowledge and monitor that the right material has been extracted from the lectures.

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This course aims to introduce the 'workers' present in all cells – enzymes, and their role in the chemical reactions that make life possible.

The fundamental characteristics of enzymes will be discussed – that they are types of protein that act as catalysts to speed up reactions, or make unlikely reactions more likely. Methods for analysis of enzymic reactions will be introduced (enzyme kinetics). Control of enzyme activity, and enzyme inhibition will be discussed.

Following on from this the pathways of intermediary metabolism will be introduced. Enzymes catalyse many biochemical transformations in living cells, of which some of the most fundamental are those which capture energy from nutrients. Energy capture by the breakdown (catabolism) of complex molecules and the corresponding formation of NADH, NADPH, FADH2 and ATP will be described. The central roles of the tricarboxylic acid cycle and oxidative phosphorylation in aerobic metabolism will be detailed. The pathways used in animals for catabolism and biosynthesis (anabolism) of some carbohydrates and fat will be covered, as well as their control. Finally how humans adapt their metabolism to survive starvation will be discussed.

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This module addresses key themes and experimental techniques in molecular and cellular illustrated by examples from a range of microbes animals and plants . It covers basic cell structure, and organisation including organelles and their functions, cytoskeleton, cell cycle control and cell division. The control of all living processes by genetic mechanisms is introduced and an opportunity to handle and manipulate genetic material provided in the laboratory. Monitoring of students' knowledge and progress will be provided by a multi-choice test and the laboratory report, with feedback.

Functional Geography of Cells: Introduction to cell organisation, variety and cell membranes. Molecular traffic in cells. Organelles involved in energy and metabolism. Eukaryotic cell cycle. Chromosome structure & cell division. Meiosis and recombination. Cytoskeleton.

Molecular biology: The structure and function of genetic material. Chromosomes, chromatin structure, mutations, DNA replication, DNA repair and recombination, Basic mechanisms of transcription, mRNA processing and translation.

Techniques in molecular and cellular biology: Methods in cell Biology - light and electron microscopy; cell culture, fractionation and protein isolation/electrophoresis; antibodies, radiolabelling. Gene Cloning – vectors, enzymes, ligation, transformation, screening; hybridisation, probes and blots, PCR, DNA sequencing. Applications of recombinant DNA technology.

Laboratory: PCR amplification of DNA and gel analysis.

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This module will consider the anatomy and function of normal tissues, organs and systems and then describe their major pathophysiological conditions. It will consider the aetiology of the condition, its biochemistry and its manifestation at the level of cells, tissues and the whole patient. It may also cover the diagnosis and treatment of the disease condition.

Indicative topics will include:

Cells and tissues

Membrane dynamics

Cell communication and homeostasis

Introduction to the nervous system

The cardiovascular system

The respiratory system

The immune system and inflammation

Blood cells and clotting

The Urinary system

The digestive system, liver and pancreas

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Subject-based and communication skills are relevant to all the bioscience courses. This module allows you to become familiar with practical skills, the analysis and presentation of biological data and introduces some basic mathematical and statistical skills as applied to biological problems. It also introduces you to the computer network and its applications and covers essential skills such as note-taking and essay writing.

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Students with A2 Chemistry (equivalent) on entry take Phases 2+3+4

Biology students with A2 Chemistry (or equivalent) will obtain additional chemical concepts (Phase 4) as their chemistry qualification at A2 will already furnish them with concepts from Phase 1. All students will participate in the core section: Phase 2.

Phases 2+3+4 students will use the Phase 1 coursework test as a formative assessment to recognise their required chemical knowledgebase as obtained at A2 level. This provides an opportunity to identify students requiring additional support.

This module links to Biological Chemistry A with identically designed phases (1, 2 and 3) to maximise teaching efficiency across all programs in the School of Biosciences.

Phase 2: Autumn Term (9 lectures, 2 x 2 hr Workshop, 3 extra support lectures)

Chemical and biochemical thermodynamics. Topics covered are: (i) energetic and work, (ii) enthalpy, entropy and the laws of thermodynamics (iii) Gibbs free energy, equilibrium and spontaneous reactions, (iv) Chemical and biochemical equilibrium (including activity versus concentration and Le Chatelier's principle). The two hour workshop is designed to be delivered as small group sessions to cover the applications and practice of thermodynamics concepts.

Chemistry applied to biological concepts: bonding, valence, hybridisation as well as biological applied thermodynamic process (biomolecular association/dissociation).

Assessment feedback (1 session/lecture)

Phase 3: Spring Term (17 lectures, 2 x 2 hr workshop)

Fundamental organic chemistry with biological examples. Topics covered: (i) Introduction and basic functional chemistry, (ii) Isomerism and stereochemistry, (iii) Reaction mechanisms, (iv) Alkanes/alkyl halides/alkenes/alkynes, (v) Aromatic compounds, (vi) Heterocyclic compounds, (vii) Amines and alcohols (viii) Carbonyl compounds and carboxylic acids and (ix) Biological inorganic chemistry. The two workshops is designed to be delivered as small group sessions to cover the applications of reaction mechanisms and reaction schemes.

Phase 4: Spring Term (8 lectures, 2 x 1 hr workshop)

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This module is an introduction to Mendelian genetics, and it will also address human pedigrees, quantitative genetics, and mechanisms of evolution.

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The module deals with the molecular mechanisms of gene expression and its regulation in organisms ranging from viruses to man. This involves descriptions of how genetic information is stored in DNA and RNA, how that information is decoded by the cell and how this flow of information is controlled in response to changes in environment or developmental stage. Throughout, the mechanisms in prokaryotes and eukaryotes will be compared and contrasted and will touch on the latest developments in how we can analyse gene expression, and what these developments have revealed.

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The cell is the fundamental structural unit in living organisms. Eukaryotic cells are compartmentalized structures that like prokaryotic cells, must perform several vital functions such as energy production, cell division and DNA replication and also must respond to extracellular environmental cues. In multicellular organisms, certain cells have developed modified structures, allowing them to fulfil highly specialised roles. This module reviews the experimental approaches that have been taken to investigate the biology of the cell and highlights the similarities and differences between cells of complex multicellular organisms and microbial cells. Initially the functions of the cytoskeleton and certain cellular compartments, particularly the nucleus, are considered. Later in the unit, the mechanisms by which newly synthesised proteins are secreted or shuttled to their appropriate cellular compartments are examined.

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This module will consider the anatomy and function of the immune system and immunopathology and then consider the diseases and microorganisms that affect the different organs and tissues of the human body. Indicative topics will include inflammation, innate and adaptive immunity to pathogens, immune defence mechanisms against bacterial, viral and parasitic infections, antibody classes and functions, antigen processing and presentation, complement, the generation of antibody diversity, cell communication and immunopathology, including autoimmunity, hypersensitivity and transplant rejection. In the medical microbiology section of the module, indicative topics will include epidemiology, virology, parasitology, fungal infections, skin infections, GI tract infections, CNS infections, respiratory tract infections, UTI and STD infections.

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This module will consider the anatomy and function of normal tissues, organs and systems and then describe their major pathophysiological conditions. It will consider the aetiology of the condition, its biochemistry and its manifestation at the level of cells, tissues and the whole patient. It may also cover the diagnosis and treatment of the disease condition. Indicative topics will include the reproductive system; muscle; nervous system; and endocrine system.

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This module covers the general principles of metabolic disorders and focuses on pathways, enzyme mechanisms, and diseases associated with defects in metabolism.

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This module will cover the following areas:

* Principles of metabolic regulation: Allostery, cooperativity, phosphorylation, and hormonal control. Metabolic regulation in response to cellular energy status. Transcriptional regulation.

* Plant metabolism: Photosynthesis and carbon fixation.

* Microbial metabolism: Nitrogen metabolism, stress responses, metals, and secondary metabolites.

* Metabolism in biotechnology: Manipulating microbial metabolism for the production of useful compounds. Manipulating mammalian cell metabolism in biotechnology.

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One-on-one meetings and small group tutorials focused on academic progression and the development of key skills to support the core curriculum and future study or employment. Students meet with their Academic Advisor individually or in small groups at intervals during the academic year. Individual meetings review academic progress, support career planning etc. Themed tutorials develop transferable skills; indicative topics are presentation skills, problem solving etc. The tutorials are informal involving student activity and discussion. Year group events deliver general information e.g. on University resources, application to 4-year programmes, module selection etc.

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Communication Skills in Biosciences: Essay writing, oral presentations, laboratory reports, the scientific literature and literature reviews. Working in groups.

Techniques in Biomolecular Science: Immunochemistry. Monoclonal and polyclonal antibody production, immuno-chromatography, ELISA and RIA. Electrophoresis, Immunoblotting, Protein Determination, Activity Assays, Purification.

Computing for Biologists: Bioinformatics, phylogenetic trees, database searches for protein/DNA sequences.

Mini-project – introduction to research skills: Students will work in groups of eight to undertake directed experimental work (Group Project) before extending the project further through self-directed experiments working as a pair (Mini Project).

Careers: The programme will be delivered by the Careers Advisory Service and will review the types of careers available for bioscience students. The sessions will incorporate personal skills, careers for bioscience graduates, records of achievement, curriculum vitae preparation, vacation work, postgraduate study, interview skills and action planning.

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Introduction and basic principles of drug action: key drug targets including major receptor subtypes, ion channels, transporters, and structure-function relationships

Systems pharmacology: the biological basis of diseases states affecting different physiological systems, therapeutic approaches to treating these diseases, and the cellular/molecular mode of action of drugs used. Indicative diseases may include hypertension, asthma, Parkinson's disease, schizophrenia, infertility, depression and anxiety.

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You study the diversity of animal life throughout evolution, including elements of functional anatomy and physiology such as circulation and gaseous exchange, the digestive system, the nervous system and reproduction.

Topics:

A. Comparative physiology - in this section the diversity of different physiological systems will be studied including circulation, gaseous exchange, feeding and digestion, excretion, nervous tissue and the senses, reproduction and immunology.

B. Form and Function - in this section a diverse range of taxonomic groups and their characteristics will be studied to understand the relationship between structure and function. How these characteristics equip the animal to survive and succeed in its particular environment will be explored.

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The module deals with the molecular mechanisms underlying the ecological, medical, scientific and commercial importance of microorganisms (including prokaryotic and eukaryotic microorganisms). This involves descriptions of how microbial genetic information is stored in DNA, how that information is decoded by the cell and how this flow of information is controlled in response to changes in environment. The Module also discusses microbial interaction with humans and the environment. Throughout the module, the mechanisms in prokaryotes and eukaryotes will be compared and contrasted and will touch on the latest tool development in microbiology.

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This module will introduce students to the importance of genome-wide DNA sequence analysis in a range of different fields of study including forensic science, medical diagnosis and historical research. They will acquire a full grounding in the basic biology of how sequence data is acquired and analysed, and engage with up-to-date methods of DNA sequence analysis in the practical sessions. At the broad level, the module will be structured around the following 4 themes:

What is a genome? This addresses genome content and structure, including both functional and non-functional elements of the genome such as the simple "junk" DNA repeats used for forensic identification.

Understanding genomic variation. This addresses the molecular causes of genomic variation between individuals – i.e. what makes us all unique – and the technical methodologies used to detect genomic variation.

What are the implications of being able to read DNA? This covers the extent to which we can infer phenotype from genomic sequence – e.g. how much you can tell about a person once their genome has been sequenced. Specific examples may be drawn from forensic science, medical diagnosis and historical analysis.

What are the implications of being able to write or edit DNA? This addresses nascent and future technology for genome editing – what can it achieve, what are the risks, what are the ethical issues?

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Projects are designed by individual members of staff in keeping with their research interests and fall into one of four categories:

• Wet/Dry Laboratory and Computing: practical research undertaken in the teaching laboratories, or on computers followed by preparation of a written report

• Dissertation: library-based research leading to production of a report in the style of a scientific review

• Business: development of a biotechnology business plan

• Communication: similar to dissertation projects but with an emphasis on presenting the scientific topic to a general, non-scientist audience

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Cells and subcellular compartments are separated from the external milieu by lipid membranes with protein molecules inserted into the lipid layer. The aim of this module is to develop understanding of both the lipid and protein components of membranes as dynamic structures whose functions are integrated in cellular processes.

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The module will cover the structural analysis of proteins and protein assemblies using techniques such as fluorescence, circular dichroism, mass spectrometry, atomic-force microscopy, cryo-EM, X-ray crystallography and NMR. It will also look at protein folding, molecular processing, de novo design, engineering and modelling. The module will also investigate the relationship between protein structure and function and cover the principles and practice of enzymology, ligand binding, and enzyme catalysis.

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One-on-one meetings and small group tutorials focused on academic progression and the development of key skills to support the core curriculum and future study or employment. Students meet with their Academic Advisor or project supervisor individually or in small groups at intervals during the academic year. Individual meetings review academic progress, support career planning etc. Themed tutorials develop transferable skills; indicative topics are research and presentation skills. The tutorials are informal involving student activity and discussion. Year group events deliver general information, most at this stage focused on further study or employment.

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Recent events have illustrated the importance of ensuring that science is communicated effectively to non-scientific audiences. This module considers best practice in science communication, making use of case studies that illustrate its importance in developing an informed and empowered public, while developing skills in different modes of communication that enhance future employability.

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The module begins by overviewing the diverse mechanisms used by cells to communicate, considering the main modes of cell-cell communication, the major classes of signalling molecules and the receptor types upon which they act. It then focuses on nuclear, G-protein coupled, and enzyme linked receptors covering in molecular detail these receptors and their associated signal transduction pathways.

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The module introduces the student to cell cycle and teaches how its precise regulation is essential for all life. The course will introduce to the students the current understanding of cellular reproduction and how it emerged. The initial lectures will describe the important breakthroughs in cell cycle research in their historical and experimental context. The course will go on to give the students a detailed understanding of the key events that occur and how they are regulated by mechanisms conserved from yeast to man. Key topics that will be discussed include:

Mitotic kinases (including Cdks, Polo, aurora).

Microtubule reorganisation (including spindle formation and regulation).

Actin reorganisation (including regulation of cell growth, endocytosis, and cell division)

Checkpoints (including Spindle assembly checkpoint, DNA damage checkpoint).

Meiosis.

Apoptosis.

Organelle reorganisation (e.g. nuclear and golgi reorganisation).

Cancer and the cell cycle.

Cell cycle related pathologies.

The final lectures will then introduce the students to how generating computer models of the cell cycle are playing a crucial role in defining novel avenues for research into therapies for cell cycle related diseases.

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The module will develop understanding and analytical skills in virology, based around interactive seminars wherein students will analyse, present, and discuss the relevant research literature. The students will gain experience in scientific design, literature analysis, scientific communication, and the analysis of experimental data.

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The aim of this Advanced Immunology module is to review topical aspects of advanced immunology with emphasis on the regulation of the immune response, and the role of dysfunctional immune systems in the aetiology of a variety of disease states. Indicative topics include antigen processing and presentation, transplant rejection, autoimmunity, hypersensitivity, cell migration homing and extravasation, cytokines, tumour immunology, mucosal immunology and autophagy.

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Bioinformatics Data sources & Sequence analysis: Databases and data availability. Using sequence data for analysis – sequence searching methods, multiple sequence alignments, residue conservation, Protein domains and families.

Protein Bioinformatics Methods: Protein structure and function prediction. Prediction of binding sites/interfaces with small ligands and with other proteins. Bioinformatics analyses using protein data.

Genomics: An introduction to the analysis of genomic data, primarily focussing on the data available from genome sequencing – how it can be used to study genetic variants and compare genomes (i.e. comparative and functional genomics).

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Cancer formation and progression; underlying factors, cancer cell heterogeneity, uncontrolled cell division, invasive growth/metastasis formation.

The Molecular Biology of Cancer: (Proto-)oncogenes, tumour suppressor genes, cell cycle control, cell death.

Cancer therapies

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The module deals with basic neuroanatomy and molecular and cellular neurobiology, such as transmission of signals within the nervous system and sensory perception. It explores more complex functions of the nervous system, e.g. behavioural and cognitive functions including learning, memory, emotions and appetite control. Throughout the module both the normal nervous system and disorders that arise as a consequence of abnormalities will be covered.

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The module provides a detailed molecular basis for the ageing process. It reviews the organisms and experimental methods used to study ageing, and discusses the findings of this work to provide both knowledge and context to the process of ageing.

Topics may include: Importance and principles of ageing research

Why do organisms age and theories of ageing

Overview of processes and pathways controlling ageing

How ageing and lifespan is measured.

Signalling pathways that control ageing

Diseases of ageing

Ethics of ageing research

There will be two workshops: Workshop 1: Data analysis session (whole class or 2-3 groups).

Workshop 2: Group discussion of key ageing research paper(s) (small groups ).

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This module is designed to provide students across the university with access to knowledge, skill development and training in the field of entrepreneurship with a special emphasis on developing a business plan in order to exploit identified opportunities. Hence, the module will be of value for students who aspire to establishing their own business and/or introducing innovation through new product, service, process, project or business development in an established organisation. The module complements students' final year projects in Computing, Law, Biosciences, Electronics, Multimedia, and Drama etc.

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