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.

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.

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.

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

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.

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)

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

This module covers the general principles of metabolic disorders and focuses on pathways, enzyme mechanisms, and diseases associated with:

Energy metabolism

Amino acid/nucleotide metabolism

The urea cycle

Cholesterol metabolism

Vitamin metabolism

Heme synthesis/breakdown

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

Plant metabolism: Photosynthesis, carbon fixation, and secondary metabolites.

Microbial metabolism: Nitrogen cycle, stress responses, omics approaches, metals, and secondary metabolites.

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

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.

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.

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.

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.

Reproductive System: Male and female reproductive systems; Endocrine control of reproduction; Fertilisation; Early embryogenesis; Pregnancy and Parturition; Reproductive disorders.

Muscle: Muscle types: skeletal, smooth and cardiac; Structure of muscle; Molecular basis of contraction; Regulation of contraction including neural control; Energy requirements of muscle; Types of movement: reflex, voluntary, rhythmic; Muscle disorders.

Nervous System: Cells of the nervous system- neurons and glia; Electrical properties of neurons- action potential generation and conduction; Synaptic structure and function- transmitters and receptors; Structural organization of the central nervous system (CNS) and function of individual regions; Organization and function of the peripheral nervous system (PNS)- somatic motor, autonomic (sympathetic and parasympathetic) and sensory; Sensory systems- vision, hearing, taste, smell, pain. Disorders of the nervous system.

Endocrine System: Endocrine glands; Classes of hormones; Mechanisms of hormone action; Regulation of hormone release; Endocrine disorders.

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.

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:

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.

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.

Introduction: The ecological, medical, scientific and commercial importance of bacteria. Bacterial evolution and taxonomy.

Microbial biodiversity at the structural level: Composition of the average bacterial cell and basic bacterial cell structure. Gram positive and gram negative. Archea. Organisation of DNA. Membranes and the transport of small molecules into and out of the cell. Peptidoglycan and LPS and their importance in pathogenesis. The location and function of proteins. Capsule, flagella and adhesins.

Introduction to growth, fuelling and biosynthesis: Division by binary fission, including growth equations. Growth in batch and chemostat cultures; liquid vs. solid media. Nutritional and non-nutritional factors affecting growth (temperature, osmolarity, pH and antibiotics). Physiological state and balanced growth. Adaptation to extreme conditions.

Microbial biodiversity at the physiological and biochemical level: The diversity in bacterial metabolism (nutrient sources (particularly carbon and nitrogen)), photosynthesis, aerobic and anaerobic growth and alternative terminal electron acceptors. Fermentation. The inverse relationship between growth factor requirements and biochemical complexity. The ecological significance of bacteria.

Synthesis, localisation and assembly of macromolecular structures: DNA replication and transcription. Translational and protein localisation, assembly of flagella and adhesins. Membranes, including LPS. Peptidoglycan. Antibiotics that inhibit peptidoglycan biosynthesis. Capsules.

Microbial communities and ecology: growth and survival in the real world (e.g. soils and sediments), studying populations and individuals. Biofilms and complex communities. Diauxie and growth.

Signalling and physiological control: Introduction to bacterial genetics. The regulation of gene expression at the transcriptional and post-transcriptional level in response to environmental factors Chemotaxis.

Practical: "Antibiotics" in which students follow the growth of bacteria upon treatment with bacteriostatic and bactericidal antibiotics and answer questions about data concerning the mode of action of antibiotic resistance presented in the laboratory manual.

Workshop: "Growth and viable counts" in which the students are given numerical data + growth equations and have to define factors such as (i) dilutions needed to give specific cell numbers, (ii) generations of growth to achieve specific cells numbers (iii) growth rate/doubling time. Designed to give students the skills required to manipulate bacterial cells to achieve correct cell density and growth phase for practical work.

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?

Early in the Autumn term, projects are assigned to students by the project co-ordinator (a member of academic staff), where possible in accordance with student choice. Students then meet with their project supervisor to discuss the objectives of the project and obtain guidance on background reading. During the Autumn term students write a brief formative literature review on the project topic providing them with a good background before embarking on the project work.

The main project activities take place in the Spring term. Students taking laboratory projects spend 192 hours (24 hours per week for 8 weeks) in the lab planning, carrying out and documenting experiments. A further 108 hours are allowed for background reading and report writing. There are informal opportunities to discuss the project work and relevant literature with the supervisor and other laboratory staff. Formal meetings may be arranged at the discretion of the student and supervisor. Students undertaking non-laboratory projects are based in the library or, occasionally, in the laboratory; they are expected to dedicate 300 hours to their project work. Non-laboratory students are strongly encouraged to meet with the supervisor at least once a week to discuss progress and ideas and to resolve problems. At the end of the formal project time, students are allowed time to complete the final project report, although they are encouraged to start writing as early as possible during the Spring term. The supervisor provides feedback on content and style of a draft of the report. In addition, students are expected to deliver their findings in presentation lasting 10 minutes with 5 minutes of questions.

• 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

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.

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.

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.

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).

The module aims to develop understanding and analytical skills in oncology, 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.

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.

A synopsis of the curriculum

The module overviews the importance of studying ageing, the organisms and methods used to do so and considers how organisms age together with providing a detailed understanding of the processes and molecular mechanisms that govern ageing.

Introduction

Importance and principles of ageing research

Why do organisms age and theories of ageing: e.g. Damage theory, telomeres, genetics and trade off theories.

How ageing and lifespan is measured

Overview of processes and pathways controlling ageing

Methods in ageing research

Model Organisms: Benefits and problems associated with studying ageing in model organisms. Including: Yeast, worms, flies, mice, primates.

Systems approaches to studying ageing: e.g. high throughput DNA/RNA sequencing, high throughput proteomics and, metabolomics. Pros and cons of these methods, what we have learned from them.

Signalling pathways that control ageing

Insulin signalling pathway and Target of Rapamycin (ToR) pathway

Organisation of pathways and the molecules involved, how they were discovered to be implicated in lifespan and ageing, ways of modelling and studying their molecular detail in animals e.g. genetic/ epistasis analysis

The processes downstream of these pathways that allow them to control lifespan/ageing e.g. stress resistance, autophagy, reduced translation, enhanced immunity etc…

Cross-talk between pathways.

Dietary restriction, lifespan and ageing

How dietary restriction works in different organisms, what signalling pathways and processes it affects.

Diseases of ageing

What these are e.g. Alzheimers, Huntington's

Overview of 'normal ageing’ associated processes e.g. muscle weakening.

How they can be studied in model organsims and the importance of ageing research for treating these disorders.

Ethics of ageing research

Pros and cons of studying ageing with a goal of extending human lifespan e.g. insurance, health system, social, psychological implications.

Workshop 1: Group discussion of key ageing research paper(s) (small groups).

Workshop 2: Data analysis session (whole class or 2-3 groups).

Workshop 3: Overview of the module in preparation for revision/exam (whole class).

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.

The module aims to 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.

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.

This module focuses on the endocrine system, which in conjunction with the nervous system, is responsible for monitoring changes in an animal's internal and external environments, and directing the body to make any necessary adjustments to its activities so that it adapts itself to these environmental changes.

The emphasis will be on understanding the underlying principles of endocrinology, the mechanisms involved in regulating hormone levels within tight parameters in an integrated manner and the central importance of the hypothalamic-pituitary axis.

During the lectures each major endocrine gland or functional group of glands will be explored in turn and specific clinical disorders will be used to illustrate the role of the endocrine organs in the maintenance of whole body homeostasis. The systems studied will include the following: thyroid gland, parathyroid gland and bone metabolism, adrenal gland, renal hormones (water and salt balance), pancreatic hormones, gut hormones and multiple endocrine neoplasia, gonadal function and infertility.

Consideration will be given to the methods available for the diagnosis of specific endocrine diseases, including the measurement of electrolyte and hormone levels, and the role of dynamic testing.

The role of the endocrine system in integrating metabolic pathways will be emphasised throughout the module and particular scenarios such as infertility, diabetes mellitus.

A synopsis of the curriculum

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.

Introduction:

Principles of Cell Signalling.

Cell Adhesion and Cell Communication (adhesion and gap junctions).

Signalling Molecules: Hormones, neurotransmitters, growth factors.

Receptor Types: Nuclear, G-protein coupled, Ion-channel linked, Enzyme-linked.

Nuclear Receptors:

Cellular location and molecular organisation of receptors. Structure/function/activity relationships. Receptors as sequence-specific DNA binding proteins.

G-Protein Coupled Receptors:

Receptors coupled to heterotrimeric guanine nucleotide binding proteins (G proteins). Composition and classification of G-proteins, their activation and modulation by toxins and disease.

Second Messengers and Protein Phosphorylation (kinases and phosphatases).

Cyclic Nucleotide-Dependent Systems: G proteins in regulation of adenylyl cyclase-cAMP-protein kinase A (PKA) and guanylyl cyclase-cGMP pathways. Physiological roles e.g. in visual transduction and glycogen metabolism.

Inositol lipids in signal transduction: Regulation of phospholipase C. Inositol polyphosphates (e.g. IP3) and diacylglycerol (DAG) in regulation of Ca++-dependent kinases. Roles in specific cellular responses e.g. regulation of protein kinase C.

Interactions of Signalling Pathways:

'Cross-Talk' between different pathways and messenger molecules.

Enzyme Linked Receptors:

Receptor tyrosine kinases (RTKs), e.g. epidermal growth factor receptor (EGF) family and insulin receptor, and their varied roles in cellular metabolism, cell behaviour, development and disease.

Molecular organisation of receptors, autophosphorylation of intracellular domains.

Intracellular signalling pathways: activation of monomeric G-protein Ras, leading to activation of the mitogen activated protein (MAP) kinase cascade.

Integration of signalling components: Role of adapter proteins (e.g. GRB2) and their protein-protein interaction domains (SH2, SH3 etc.) in linking ligand-receptor complexes to intracellular proteins.

Practical: Characterisation of G-protein coupled receptors using a cAMP-linked reporter gene assay.