Biology Year One Handbook 2015/16 Disclaimer The timetable below was correct at the time of going to ‘press’. However, you must check your email and Blackboard regularly, as occasionally changes may have to be made. Structure of Year One 1. Year One consists of four academic courses • Biological Chemistry and Microbiology • Cell Biology and Genetics • Biology of Organisms • Ecology and Evolution 2. Year One is taught and examined in two parts • BCM and OB are taught in weeks 1 to 12, examined in week 15 (February). • EE and CBG are taught in weeks 16 to 28, examined in weeks 29/30 (June). 3. Year One provides time for structured private study • There are c. 40 lectures per course to allow time for private study. 4. Each course has small-group tutorials with academic staff • All tutorials have clear objectives and teaching materials. They are designed to support the lectured material, and improve your analytical skills. • Most tutorials are problem-oriented, with problems collated by course conveners and made available in advance of the tutorial. • Specific tutorials teach essay-writing skills, criticism of research papers, presentation skills, etc. • The Library will provide support in information literacy through lectures and hands-on sessions. 5. Every practical is designed to serve a distinct purpose • Some practicals are formatively assessed (i.e. do not contribute to your coursework grade) and some practicals are summatively assessed (i.e. for coursework grade credit). • Statistical skills and the use of R are taught in two blocks of workshops in weeks 4 and 17, and assessed by a test in spring term in week 21 that contributes to your EE coursework grade. • Formative practicals in pipetting, microscopy, etc., are timetabled, with lectures to support them. • Students will maintain a lab-book, and this will be commented upon by personal tutors. • Field-trips to Silwood are scheduled in autumn and summer terms. 6. Personal tutorials and some lectures are scheduled to develop general skills • Personal tutorials are scheduled, with rooms, times, and objectives for each. • Topics will include: o Critical review of lecture notes and lab-book early in autumn term o Revision and exams o Time management o Second year options, planning CVs and careers • Additional sessions run by the Senior Tutor and First Year Convenor will cover mental-health, resilience, revision, and general induction to College and the Department. Biological Sciences Degrees – Department of Life Sciences – Imperial College London 1 Learning objectives for Year One # 1 2 3 Objective Can navigate Blackboard and other basic ICT infrastructure Knows department's expectations and procedures for coursework, mitigating circumstances, etc. Works safely in lab 4 Is able to take usable and thorough lecture notes (or equivalent) 5 Uses databases and RefWorks to identify sources of information and cites sources in the approved Harvard style Writes confidently and competently in well-structured scientific English, and in their own words Can perform statistical tests including linear regression, t, and χ2 tests, and ANOVA (including use of R) 6 7 8 9 10 11 12 13 Is able to select and use appropriate pipettes Is capable of rearranging equations, including those involving logarithms, and can perform basic lab arithmetic Can use a compound microscope and make clear drawings Is able to critically evaluate scientific literature Is able to critically analyse methods and results of an experiment Formative development Computing induction in week 1 [Formative only] Biology introduction in week 1 Personal tuition Coursework submissions Safety induction in week 1 Lab-coats/safety specs in practicals Sterile technique practicals Second personal tutorial: review of lecture notes (or equivalent), formative tests on Blackboard Key skills lectures from Library Formative OB essay in autumn term Use of TurnItIn to detect plagiarism [Formative only] Key skills lectures from Library Feedback in academic and personal tutorials Statistics workshops, with follow-up practicals All practicals to include statistics where appropriate Quantitative skills lecture Protein estimation practical Maths for Biologists document (on Blackboard) – self-directed study Quantitative skills lecture Protein estimation, bacterial growth and pH/buffer practicals OB microscopy lecture Autumn term practicals Spring term academic tutorials Exams EE and CBG essays Formatively assessed practicals Assessed practicals, especially… BCM ion exchange practical write-up CBG bacterial growth practical test [Formative only, but underlying all material] EE conservation tutorial presentation CBG bacterial growth practical presentation BCM enzymology practical write-up (Excel) Can explain meaning and limitations of the 'scientific method' Can give clear oral account of work or ideas in presentations OB lecture Personal tutorials Autumn term tutorials EE seminar 15 Can use word-processing and spreadsheet applications 16 Be capable of working independently and in groups Essays BCM protein estimation practical write-up (Excel) Spring term tutorials Lab-partner (with rotation) 17 18 Can design experiments Reads around the lecture material Tutorials Research for essays 19 Knows and has practiced the types of question set in exams Online formative tests → MCQs Tutorials → Data interpretation Coursework essays → Essays 14 Summative assessment Exams EE and CBG essays CBG bacterial growth practical, and other practicals as required [Formative only] BCM enzymology practicals OB microscopy write-up EE and CBG essays Organisation of… EE algal growth experiment CBG bacterial growth experiment CBG bacterial growth practical CBG online assessment Exams Exams Biological Sciences Degrees – Department of Life Sciences – Imperial College London 2 Biological Chemistry and Microbiology (BCM) Convenor • Dr Steve Cook (s.cook@imperial.ac.uk) Course aims • To ground an understanding of living systems in terms of their underlying physics and chemistry. • To appreciate the diversity of metabolic processes, their regulation, and their importance. • To explore how mathematics can be used to model biochemical systems. • To confidently use lab equipment, prepare and dilute solutions, and quantitatively analyse data. Course syllabus • Chemistry of biomolecules: atomic and molecular structure, bonding, acids and bases, reactions, nucleophiles and electrophiles, oxidation/reduction reactions, functional groups. • Monomers & polymers and the biochemical techniques used to analyse them: amino acids and proteins, carbohydrates, nucleotides and nucleic acids; spectroscopy, electrophoresis, chromatography. • Thermodynamics and enzymology: energy, entropy, free energy, Gibbs and Nernst equations; Arrhenius reaction kinetics, catalysis, Michaelis-Menten model, enzyme inhibition and regulation. • Central metabolism and its regulation: respiration, glycolysis, Krebs cycle, PPP, β-oxidation, excretion. • Membranes and their role in metabolism: lipids, structure, transport across membranes, chemiosmosis, oxidative phosphorylation. • Bacteriology: cell structure, sporulation, growth, metabolic diversity, metabolic diversity, phototrophy, chemolithotrophy, heterotrophy. Learning outcomes • Perform lab calculations involving moles, masses, concentrations, relative masses, densities, volumes, molarities, dilutions, pH, etc., both by hand, and using Excel. • Recall and apply the Michaelis-Menten, Gibbs, Nernst, and Arrhenius equations, and recall their limitations and assumptions. • Accurately select and use pipettes, spectrophotometers, microscopes, pH probes, and simple chromatography equipment. • Analyse the structure of macromolecules in terms of the interactions of their constituent monomers, and analyse the properties of those monomers in terms of their functional groups, bonding and atoms. • Interpret simple chromatograms, electropherograms and spectra. • Propose suitable combinations of techniques for purification and analysis of macromolecules. • Know the overall structure of the 'core' metabolic pathways, and how they interact. • Distinguish between metabolic flux and homeostatic regulation, and explain how and why enzymes are regulated in metabolic pathways. • Explain what is meant by the term 'entropy', and appreciate its fundamental importance in science. • Explain how model refinement in science occurs, e.g. in terms of models of membrane structure. • Propose how a given molecule would cross a membrane, and relate this to the underlying thermodynamics and chemistry. • Explain quantitatively how respiration generates ATP through substrate level phosphorylation and through chemiosmosis; perform simple proton-motive force calculations. • Recall the structure of Gram positive and Gram negative bacterial cells. • Quantitatively analyse bacterial growth; calculate doubling-times from exponential phase data. • Relate bacterial nutritional modes such as phototrophy, chemo-organotrophy and chemolithotrophy to their underlying redox thermodynamics. Biological Sciences Degrees – Department of Life Sciences – Imperial College London 3 Teaching methods • 45 lectures. • 6 practicals. • 4 tutorials. Assessment • 25% coursework. One formative item (Excel based protein estimation practical write-up). Three summative items: Excel-based enzymology practical write-up (33%); online test on quantitative aspects of biochemistry lectures and associated practicals (33%); conventional ion-exchange practical write-up (34%). • 75% exam, taken in week 15 (February): 40 MCQs (40%), 1 data interpretation question (20%), 1 essay from choice of 5 (40%). Reading list • Voet, D. & Voet, J. G. (2011) Biochemistry. 4th edition. New York, John Wiley and Sons, Inc. [A similar book, Berg/Stryer, is available in an older edition through NCBI http://www.ncbi.nlm.nih.gov/books/NBK21154/] • Fisher, J. & Arnold, J. R. P. (2013) Chemistry for biologists. BIOS Instant Notes, 3rd edition. Abingdon, Taylor and Francis. [Useful for students without A-level chemistry]. • Aitken, M., Broadhurst, B. & Hladky, S. (2009) Mathematics for Biological Sciences. New York, Garland Science. [Useful for students without A-level maths]. Biological Sciences Degrees – Department of Life Sciences – Imperial College London 4 Cell Biology and Genetics (CBG) Convener • Dr Steve Cook (s.cook@imperial.ac.uk) Course aims • To understand how genetic information is expressed as phenotype, and how this is regulated. • To know the components from which eukaryotic cells are constructed and how proteins are targeted to them. • To understand how cells communicate with their environment and with each other. • To understand how viruses and the vertebrate immune system behave and interact. • To confidently use microscopes, sterile technique, and quantitatively analyse data. • To work as a team to design experiments to investigate simple hypotheses. Course syllabus • Cells and their molecular biology: prokaryotes, eukaryotes, endosymbiosis, Three Domains hypothesis, structure of eukaryotic genomes; replication, transcription, RNA processing, and translation and regulation of these processes (lac, trp, etc.) • Cell structure and communication: import into the nucleus, secretory pathway, protein targeting and its study; ion channels, cell junctions, enzyme- and G-protein linked receptors, adhesion to the ECM; cell cycle, cyclins and CDKs, cancer, and stem-cells. • Genetics: Mendelian principles, linkage, epistasis, units of heredity vs. DNA sequences, sex determination, bacterial genetics (transformation, transduction, conjugation), mapping. • Infection and immunity: animal, plant and bacterial viruses, innate and adaptive immunity. Learning outcomes • Apply understanding of chemistry and of biochemical techniques from the BCM course to the behaviour and analysis of DNA, RNA and protein in the cell. • Recall how DNA is replicated, how DNA is transcribed to RNA, and how mRNA is translated to protein; and explain the mathematical and evolutionary underpinnings of these three processes. • Relate the contents of the human and bacterial (Escherichia coli) genomes to their evolutionary origins. • Know the main compartments of the eukaryotic cell, and explain how proteins are targeted to them; be able to apply this to novel situations where targeting sequences have been manipulated. • Explain how cells communicate chemically and electrically; be able to apply this to novel situations in which communication pathways have been manipulated. • Analyse cancer in terms of mutations in cell cycle regulation and cell communication/adhesion loci. • Apply Mendelian principles to genetic data; propose explanations (linkage, epistasis, etc.) to account for them, and test them quantitatively. • Recall the general principles of viral infection, and relate this to viral structure and genome replication. • Recall the general principles of immunology, and explain how pathogens and immune systems interact. • Design a safe, logistically sensible and statistically valid experiment on the growth of bacterial cells in culture, and execute, analyse and present that experiment in a seminar. Biological Sciences Degrees – Department of Life Sciences – Imperial College London 5 Teaching methods • 38 lectures. • 5 practicals (one is a part of a fortnight-long experimental-design and execution exercise). • 4 tutorials. Assessment • 25% coursework. Several formative items (peer-assessed practical work). Three summative items: essay (33%); online conceptual test with MCQs (33%); presentation, peer assessment, and online Team Based Learning tests on bacterial growth practical (34%). • 75% exam, taken in week 30 (June): 40 MCQs (40%), 1 data interpretation question (20%), 1 essay from choice of 5 (40%). Reading list • Alberts, B., Johnson, A., Lewis, J., Raff, M., Roberts, K. & Walter, P. (2015) Molecular biology of the cell. 6th edition. New York, Garland Science. [An older edition is available through NCBI http://www.ncbi.nlm.nih.gov/books/NBK21054]. • Griffiths, A. J. F., Wessler, S. R., Lewontin, R. C., Gelbart, W. M., Suzuki, D. T. & Miller, J. H. (2015) Introduction to genetic analysis. 11th edition. New York, W. H. Freeman. . [An older edition is available through NCBI http://www.ncbi.nlm.nih.gov/books/NBK21766; this book is very useful for its worked problem sets, which are an excellent way to test your understanding]. Biological Sciences Degrees – Department of Life Sciences – Imperial College London 6 Biology of Organisms (OB) Convener • Dr Martin Brazeau (m.brazeau@imperial.ac.uk) Course aims • To gain an overall understanding of the tree of life, especially in regards to animals, plants and fungi. • To understand how the complexity of eukaryotic life has changed both in terms of timescales and evolutionary novelty. • To gain a more detailed knowledge of the relationships and evolution of certain groups of organisms and how these groups have changed over time. • To understand how the evolution of photosynthesis has profoundly shaped the diversity of life. • To understand how phylogenetics is central to our analysis of the relationships between organisms. Course syllabus • The tree of life. • Phylogenetic theory and practice. • Overview of primate variation and evolution. • Evolution of hominins and the origin of modern humans. • Vertebrate evolution and diversity. • Invertebrate evolution, especially insects and arthropods. • Developmental evolution of animals. • The reactions of photosynthesis. • Algae, ferns, conifers and flowering plants. • Fungal diversity and symbiosis. Learning outcomes • Be able to interpret a phylogenetic tree and distinguish monophyletic, paraphyletic and polyphyletic groups. • Be able to construct a phylogenetic tree from a morphological or DNA character state matrix, using the principle of parsimony. • Know the problems, such as homoplasy, that can lead to the construction of inaccurate phylogenies. • Know how modern humans originated and explain the subsequent variation and adaptation of different individuals or populations since that time. • Know how fossils inform our understanding of modern groups. • Explain the key features behind the development of the animal body plan and how this has helped in our understanding of modern groups. • Know the major features of vertebrates, insects, plants and fungi. • Explain the principles behind plant physiology. • Recall the light and dark reactions of photosynthesis; compare and contrast the former with oxidative phosphorylation; explain the problem caused by RuBisCO's lack of specificity quantitatively, and explain how this is solved under different ecological conditions (C4, CAM, etc.) • Perform basic dissection and produce high quality microscope drawings. Biological Sciences Degrees – Department of Life Sciences – Imperial College London 7 Teaching methods • 40 lectures. • 5 practicals. • 4 tutorials. Assessment • 25% coursework. Several formative items (essay, peer assessment of practicals). Three summative items: microscopy practical images (33%); plant bioinformatics and phylogenies practical write-up (33%); plant lightstress practical write-up (34%). • 75% exam, taken in week 15 (February): 40 MCQs (40%), 1 data interpretation question (20%), 1 essay from choice of 5 (40%). Reading list • Wolpert, L. (1992) The unnatural nature of science. Harvard, University Press. [Later editions are also available] • Dawkins, R. (2004) The ancestor's tale. Boston, Houghton Mifflin. • Evert, R. F. & Eichhorn, S. E. (2013) Raven biology of plants, 8th edition. New York, Freeman & Co. • Lecointre, G. & Le Guyader, H. (2006). The Tree of Life: A phylogenetic classification. London, Belknap Press. • Moore, D., Robson, G. D. & Trinci, A. P. J. (2011) 21st Century guidebook to fungi. Cambridge, Cambridge University Press. Biological Sciences Degrees – Department of Life Sciences – Imperial College London 8 Ecology and Evolution (EE) Convener • Dr Jason Hodgson (j.hodgson@imperial.ac.uk) Course aims • To understand the processes by which the diversity of life on earth has arisen and is maintained. • To recognize the different processes underpinning evolutionary change, including genetic mutation, drift, and natural selection. • To explore how the planet’s biological diversity is organized by ecological processes into ecosystems, communities, and populations, and to appreciate the interactions that bind and define these. • To understand the roles of observation, experimentation, and theory in building our knowledge base about the natural world. Course syllabus • Natural selection and its different forms, including purifying, balancing, and directional selection. • How natural selection fits among a suite of evolutionary processes driving phenotypic change. • Genome evolution and evolutionary analysis. • Speciation and diversification. • Coevolution. • The evolution of sex, and sexual selection. • Describing and categorizing the natural world. • Climate and the biosphere. • Ecological interactions and the niche. • Ecological theory and the mathematics of ecological interactions and population dynamics. • Ecological science and environmental challenges. • Biodiversity and conservation biology. • Species-area relationships, adaptive radiations, and diversity gradients through space and time. Learning outcomes • Recall the general principle of evolution, and explain how mutation, natural selection, and drift lead to phenotypic change through time. • Explain how and why phenotypic change leads to speciation. • Calculate allele frequencies under Hardy-Weinberg equilibrium. • Formulate and test a hypothesis about some aspect of the organization of the natural world, based on observed patterns. • Recall and apply equations for population growth under no constraints and under constraints of limiting resources, competition, and predation. • Calculate slopes for species-area relationships, and apply those relationships toward predicting the consequences of habitat loss. • Explain the Equilibrium Theory of Island Biogeography, and how island diversity is further affected by isolation and habitat complexity. • Explain how global climate change could impact on each of the above. • Classify a species according to the IUCN Red List criteria as endangered, vulnerable, etc., based on data on that species' range, population size, etc. Biological Sciences Degrees – Department of Life Sciences – Imperial College London 9 Teaching methods • 40 lectures. • 2 practicals (one is a week-long sampling exercise) plus 2 field course trips to Silwood. • 3 tutorials. • 2 one-day fields trips to Silwood (October, May) Assessment • 25% coursework. Four summative items: essay (25%); IUCN species plan presentation (25%); evolution of salt tolerance practical write-up (25%); online test on statistics taught throughout all four first-year courses (25%). • 75% exam, taken in week 30 (June): 40 MCQs (40%), 1 data interpretation question (20%), 1 essay from choice of 5 (40%). Reading list • Cain, M. L., Bowman, W. D. & Hacker, S. D. (2014) Ecology. 3rd edition. Sunderland, Massachusetts, Sinauer. • Dawkins, R. (2006) The selfish gene. 30th Anniversary edition. Oxford, Oxford University Press. • Coyne, J. A. (2010) Why evolution is true. Oxford, Oxford University Press. • Zimmer C., & Emlen D. J. (2012) Evolution: making sense of life. Greenwood Village, Colorado USA, Roberts and Company Publishers. Biological Sciences Degrees – Department of Life Sciences – Imperial College London 10 Statistics (STATS) Convener • Dr Samraat Pawar (s.pawar@imperial.ac.uk) Course aims • Understand the underlying principles of statistics. • Use the statistical programming language R. • Select appropriate tests for particular kinds of data, and interpret their results critically. Course syllabus • Describing data as continuous, discrete, numerical, count, categorical, etc. • Manipulating data, producing graphics, and performing statistical tests in R. • The t, F, and χ2 tests, analysis of variance (ANOVA), and linear regression. • Experimental design: designing experiments around statistics (rather than the other way round!) Learning outcomes • Format data for import into R; import that data, and manipulate numbers, vectors and data frames using R. • Classify data as continuous, discrete, numerical, count, categorical, etc, and then select suitable tests for different combinations of those kinds of data. • Be able to perform t, F, and χ2 tests, analysis of variance (ANOVA), and linear regression on suitable data sets in R. • Know the limitations of these tests, and be able to test whether data meet their assumptions. • Interpret the results of these tests (P values) critically, in the light of the tests' limitations. • Design an experiment that will produce data that should be analysable using the tests above. Teaching methods • 6 workshops. Assessment • Online test on statistics contributes 25% to EE coursework. • Skills in R cannot be directly tested in an exam; however, data interpretation, and simple statistics (mean, standard deviation, linear regression) on exam calculators may be assessed in any exam. Reading list • Beckerman, A. P. & Petchey, O. L. (2012) Getting started with R: an introduction for biologists. Oxford, Oxford University Press. [Good, short, general introduction] • Crawley, R. (2013) The R book. 2nd edition. Chichester, Wiley. [excellent but enormous reference book, scripts and data available from http://www.bio.ic.ac.uk/research/mjcraw/therbook/index.htm] Biological Sciences Degrees – Department of Life Sciences – Imperial College London 11 Autumn 2015 Lecture 1 (0900, Read Lecture 2 (1100, Read Afternoon session Afternoon session lecture theatre in Sherfield) lecture theatre in Sherfield) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) Mon 5 Oct 1030 Biology intro (HDW, SRC, MC, SNC, AD) 1150 College intro [Great Hall] Tue 6 Oct Freshers' fair Freshers' fair Wed 7 Oct Computing intro (MS) Safety briefing (SH) Thu 8 Oct First-year course structure , intro to lab-books (SRC) ob.01 The Tree-of-Life (MDB) ob.03 The scientific method (MDB) Set OB essay titles 1000 Imperial expectations (AD, PS, SRC) ob.05 Vertebrate origins (MDB) ob.07 Tetrapods: amphibians and the conquest of land (MDB) ob.09 Mammals (MDB) ob.04 Evolution in deep time: rocks, clocks and fossils (MDB) [Group A] 1 Fri 9 Oct 2 Mon 12 Oct Tue 13 Oct Wed 14 Oct Thu 15 Oct Fri 16 Oct 3 Mon 19 Oct Tue 20 Oct Wed 21 Oct Thu 22 Oct PAL session: 1400-1300 [121, Barber]] Fri 23 Oct ob.11 Origin of the bilateria (AML) Commemoration day [Group B] 1400-1700 Intro to RCSU, BioSoc & DepReps. Meet "mums & dads" Freshers' fair 1400-1700 Intro to RCSU, BioSoc & DepReps. Meet "mums & dads" 1630 Intro for Language for Science students [315 Sherfield] Study skills (SNC) pt.01 Meet personal tutors ob.02 Phylogenetics (MDB) Library visit (EK) [G27→Library] Library visit (EK) [G27→Library] pt.01 ob.t01 Thinking about trees [Seminar rooms] Pick up labcoats [Barber, RCS1] (DF) ob.10 Origin of the metazoa (AML) ob.12 Body plans (AML) ob.p01 Mammal skulls (MDB /SRC) [Barber, RCS1] Commemoration day Commemoration day ob.13 Primates (JH) ob.14 Hominins (JH) ob.15 Humans (JH) ob.16 Cnidaria & porifera (RG) ob.17 Platyhelminthes & nematodes (RG) Complete English test on Blackboard Complete English test on Blackboard ob.t01 ob.06 Jaws, teeth and fins: the proliferation of fish (MDB) ob.08 Amniotes (MDB) Silwood trip. Depart from South Ken at 0900 (RG, SRC) Plagiarism (EK) Submission deadline Submission deadline (1300) [Group A] (1300) [Group B] Pick up labcoats [Barber, RCS1] (DF) ob.p01 Commemoration day Return to South Ken at 1800. Bring your own lunch 1500-1700 Literature searching and RefWorks hands-on session (EK) [310/311 SEC] ob.t02 Constructing phylogenies [Seminar rooms] ob.t02 1500-1700 Literature searching and RefWorks hands-on session (EK) [310/311 SEC] Biology Degrees – Department of Life Sciences – Imperial College London 12 Autumn 2015 4 Afternoon session Afternoon session lecture theatre in Sherfield) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) [Group A] [Group B] ob.18 Annelids & molluscs (RG) ob.19 Arthropods 1 (RG) Tue 27 Oct ob.20 Arthropods 2 (RG) Wed 28 Oct stats.01 Fundamentals of statistics, intro to R (SP) [G27: Group A, 0900] stats.02 Describing data, t and F tests (SP) [G27: Group A, 0900] stats.03 Linear regression (SP) [G27: Group A, 0900] Essay writing skills (BH) ob.21 Parasitic protists: malaria, sleeping sickness (TN) stats.01 Fundamentals of statistics, intro to R (SP) [G27: Group B, 1030] stats.02 Describing data, t and F tests (SP) [G27: Group B, 1030] stats.03 Linear regression (SP) [G27: Group B, 1030] Quantitative skills and Excel (SRC) Fri 30 Oct Mon 2 Nov Tue 3 Nov bcm.01 Atoms, nuclei, moles, radioactivity, orbitals (SRC) Wed 4 Nov bcm.03 Bonds, electronegativity, Lewis structures, formal charge (SRC) bcm.05 Reactions, nucleophiles, electrophiles, curly arrows (SRC) Thu 5 Nov PAL session: 12001400 [119, 560] Fri 6 Nov 6 Lecture 2 (1100, Read lecture theatre in Sherfield) Mon 26 Oct Thu 29 Oct 5 Lecture 1 (0900, Read Mon 9 Nov bcm.07 Redox, oxidation state, OILRIG, redox cofactors (SRC) bcm.09 Amino acids (SNC) bcm.08 Functional groups, overview of organic nomenclature (SRC) bcm.10 Protein structure (SNC) bcm.12 Polysaccharides (SNC) Tue 10 Nov bcm.11 Monosaccharides (SNC) Wed 11 Nov bcm.13 Nucleotides (SNC) bcm.14 Nucleic acids (SNC) bcm.15 Spectroscopy, fluorescence (SNC) bcm.16 Electrophoresis (SNC) bcm.17 Chromatography (SNC) 1100-1300 Revision, exam essay practice (SRC) Thu 12 Nov PAL session: 12001400 [122, 560] Fri 13 Nov ob.p02 Male and female squid dissections (SRC) [Barber, RCS1] ob.p02 pt.02 Meet personal tutors, review lab-book and lecture notes [Seminar rooms] pt.02 bcm.p01 Protein estimation Gilsons & specs, lab-book review (SRC) [Barber, RCS1] bcm.02 Orbitals, electrons, periodicity, waves and particles (SRC) bcm.04 Molecules, VSEPR, MOs, hybridisation, resonance (SRC) bcm.06 Acids and bases, pH, buffers (SRC) Submission deadline Submission deadline (1300) [Group A] (1300) [Group B] bcm.p01 bcm.p02 pH and buffers (SRC) [Barber, RCS1] Submit protein estimation practical to Blackboard only (Excel) for formative assessment bcm.p02 Submit protein estimation practical bcm.t01 bcm.t01 Purification of enzymes, lab arithmetic [Seminar rooms] bcm.p03 Enzyme assay (SRC) [Barber, RCS1] Submit OB essay, 1500 words maximum, in both hard-copy to EO and to Blackboard (referencing) for formative assessment Submit OB essay bcm.p03 Biological Sciences Degrees – Department of Life Sciences – Imperial College London 13 Autumn 2015 Lecture 1 (0900, Read Lecture 2 (1100, Read Afternoon session Afternoon session lecture theatre in Sherfield) lecture theatre in Sherfield) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) [Group A] 7 Mon 16 Nov Tue 17 Nov Wed 18 Nov Thu 19 Nov Fri 20 Nov 8 Mon 23 Nov Tue 24 Nov Wed 25 Nov Thu 26 Nov PAL session: 12001400 [120, 122] Fri 27 Nov 9 Mon 30 Nov Tue 1 Dec Wed 2 Dec bcm.18 Energy and entropy, limits of explanation (SRC) bcm.20 Free energy, ATP, Gibbs and Nernst (SRC) bcm.19 Thermodynamics: you'll never win (SRC) bcm.21 Reaction kinetics (SRC) bcm.22 Catalysis, enzymes, AChE (SRC) bcm.24 Enzyme inhibitors, medical slant (SRC) bcm.23 Michaelis Menten, analysing assumptions (SRC) bcm.25 What happens to your breakfast? Respiration, NADH, zymogen regulation (SRC) bcm.27 Krebs, competitive feedback inhibition, what happens to protein? (SRC) bcm.29 Pentose phosphate, plasticity of PPP (SRC) bcm.26 Glycolysis, allosteric and kinase regulation what happens to sugar? (SRC) bcm.28 Krebs as an evolved amphibolic cycle, beta oxidation, what happens to fat? (SRC) bcm.30 Excretion and its ecological implications, uric acid and purine metabolism (SRC) bcm.32 Lipids, specialisation of membranes, archaeal membranes (SRC) bcm.34 Chemiosmotic systems (SRC) Submission deadline Submission deadline (1300) [Group A] (1300) [Group B] [Group B] bcm.t02 bcm.t02 Is the looking glass milk good to drink? [Seminar rooms] bcm.p04 Enzyme inhibition (SRC) [Barber, RCS1] bcm.p04 bcm.p05 Ion exchange chromatography (SRC) [Barber, RCS1] bcm.31 History of membranes (SRC) Submit enzymology write-up to Blackboard only (Excel formulae) for summative assessment bcm.p05 Submit enzymology write-up bcm.33 Transport across membranes (SRC) bcm.35 Oxidative phosphorylation (SRC) bcm.t03 ob.22 Plant-like protists, the algae - seaweeds aren't plants. (SRC) bcm.q01 Online summative test (SRC) [G27: Group A, 0900-1000] ob.23 Evolution of eukaryotic photosynthesis, origins, losses and retooling of plastids (SRC) bcm.q01 Online summative test (SRC) [G27: Group B & extra-time, 1030-1230] bcm.t03 Integration of metabolism [Seminar rooms] ob.24 Green algae and mosses (MB) ob.26 Flowering plants (MB) ob.25 Ferns and conifers (MB) ob.t03 Discussion of OB essays Thu 3 Dec ob.28 Life as a tree: water potential, vascular elements (CT) ob.27 Principles of microscopy, plagiarism (SRC) ob.29 Life under a tree: photoperception and phytochrome (CT) Fri 4 Dec ob.30 Plants under stress (CT) ob.31 Plants under attack(CT) ob.t03 ob.p03 Angiosperm bioinformatics and phylogenies (MB) [Barber, RCS1] Submit BCM online test (quantitative skills) to Blackboard for summative assessment Submit BCM online test Submit IEC write-up to Blackboard only (analysis of methods) for summative assessment ob.p03 Submit IEC write-up Biological Sciences Degrees – Department of Life Sciences – Imperial College London 14 Autumn 2015 10 Lecture 2 (1100, Read Afternoon session Afternoon session lecture theatre in Sherfield) lecture theatre in Sherfield) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) [Group A] [Group B] Mon 7 Dec ob.32 Fungal overview (MB) ob.33 Ascomycete lichens and pathogens (MB) Tue 8 Dec ob.34 Glomeromycota, mycorrhizal symbioses (MB) ob.36 Fungus-like organisms (MB) Plagiarism wash-up (BH) ob.35 Basidiomycetes and recycling (MB) Coursework feedback sessions by appointment (SNC, SC) bcm.36 Introduction to the prokaryotic world, Archaea are not bacteria (HDW) bcm.38 Prokaryotic cell structure 2, envelopes and appendages, antibiotics (HDW) bcm.40 Physiology of bacterial growth, growth of cell and populations and how we measure it (HDW) bcm.42 Bacterial metabolic diversity 2, chemolithotrophy, life in extreme environments(HDW) bcm.44 Prokaryotic diversity 1, making order out of diversity, Pseudomonas the generalist (HDW) Coursework feedback sessions by appointment (SNC, SC) bcm.37 Prokaryotic cell structure 1, the cell interior (HDW) bcm.39 Making a bacterial cell, bacterial nutrition, the framework of growth metabolism (HDW) bcm.41 Bacterial metabolic diversity 1, heterotrophic metabolism, the role of oxygen (HDW) bcm.43 Bacterial metabolic diversity 3, phototrophs, the ultimate in metabolic flexibility (HDW) bcm.45 Prokaryotic diversity 2, differentiation and development, bacterial sporulation (HDW) Wed 9 Dec Thu 10 Dec PAL session: 12001400 [120, 122] Fri 11 Dec 11 Lecture 1 (0900, Read Mon 14 Dec Tue 15 Dec Wed 16 Dec Thu 17 Dec Fri 18 Dec Mental health and resilience (SNC, ICHC, SCS) ob.p04 Microscopy (SRC) [Barber, RCS1] Submission deadline Submission deadline (1300) [Group A] (1300) [Group B] Submit microscopy write-up in hard-copy at end of lab for summative assessment ob.p04 Submit microscopy write-up ob.p05 Light stress (CT) [Barber, RCS1] Submit bioinformatics writeup, in both hard-copy to EO and to Blackboard for summative assessment ob.p05 Submit bioinformatics writeup bcm.p06 Gram staining (PS) [Barber, RCS1] bcm.p06 bcm.t04 bcm.t04 Succinate dehydrogenase [Seminar rooms] Submit light stress write-up, in both hard-copy to EO and to Blackboard for summative assessment Submit light stress write-up Biological Sciences Degrees – Department of Life Sciences – Imperial College London 15 Spring 2016 Lecture 1 (0900, Read Lecture 2 (1100, Read Afternoon session Afternoon session lecture theatre in Sherfield) lecture theatre in Sherfield) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) [Group A] 12 Mon 11 Jan Tue 12 Jan ob.37 Light reactions of photosynthesis, comparison with oxphos and chemolithotrophy (SRC) ob.39 Photorespiration, importance of historical contingency in evolution of biochemical pathways (SRC) ob.38 Dark reactions of photosynthesis, Calvin & Benson’s work: how are pathways elucidated? (SRC) ob.40 C4 metabolism and CAM (SRC) Submission deadline Submission deadline (1300) [Group A] (1300) [Group B] [Group B] ob.t04 ob.t04 Plants and phylogenies tutorial [Seminar rooms] Wed 13 Jan Thu 14 Jan pt.03 Pre-exam tutorial Fri 15 Jan 13 pt.03 Pre-exam tutorial Mon 18 Jan Tue 19 Jan Wed 20 Jan Thu 21 Jan PAL session: 12001400 [121] Fri 22 Jan 14 Mon 25 Jan Tue 26 Jan Wed 27 Jan Thu 28 Jan Fri 29 Jan 15 Mon 1 Feb Tue 2 Feb BCM exam [460/560, 10001300] Wed 3 Feb Thu 4 Feb OB exam [460/560, 10001300] Fri 5 Feb Biological Sciences Degrees – Department of Life Sciences – Imperial College London 16 Spring 2016 16 Lecture 1 (0900, Read Lecture 2 (1100, Read Afternoon session Afternoon session lecture theatre in Sherfield) lecture theatre in Sherfield) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) [Group A] [Group B] Mon 8 Feb cbg.01 Prokaryotes and eukaryotes (SRC) cbg.02 Genomes (SRC) Tue 9 Feb cbg.03 DNA replication (SRC) cbg.04 Transcription (SRC) cbg.05 Regulation of transcription, lac, trp (SRC) cbg.06 RNA processing (SRC) Wed 10 Feb Thu 11 Feb PAL session: 12001400 [121, RCS1 labs] Fri 12 Feb 17 Mon 15 Feb cbg.p01 cbg.07 Translation (SRC) cbg.09 Cell cycle (SRC) cbg.08 Mutation and repair (SRC) cbg.10 Cell signalling (SRC) cbg.p02 cbg.t01 cbg.t01 Molecular biology (critical reading) [Seminar rooms] stats.04 ANOVA (SP) [G27: Group A, 0900] stats.05 Experimental design (SP) [G27: Group A, 0900] stats.06 Count data, χ2 tests (SP) [G27: Group A, 0900] ee.01 Intro to evolution and evolutionary thinking (TB) stats.04 ANOVA (SP) [G27: Group B, 1030] stats.05 Experimental design (SP) [G27: Group B, 1030] stats.06 Count data, χ2 tests (SP) [G27: Group B, 1030] ee.02 Genetics and neutral evolution (JH) Tue 23 Feb ee.03 Genetic variation (JH) ee.04 Natural selection (JH) Wed 24 Feb cbg.q01 Online summative test (SRC) [G27: Group A, 0900-1000] ee.05 Phenotype and genome evolution (JH) cbg.q01 Online summative test (SRC) [G27: Group B & extra-time, 1030-1230] ee.06 Sexual selection (JH) ee.p01 [continued] (1300) Subculture #1 ee.07 Social evolution (JH) ee.08 Evolution in action (JH) ee.p01 [continued] (1300) Subculture #2 Thu 18 Feb Fri 19 Feb 18 cbg.p01 Sterile technique (SRC) , lab-book review [Barber, RCS1] cbg.p02 Bacterial transformation and inducibility of operons (SRC) [Barber, RCS1] Tue 16 Feb Wed 17 Feb Mon 22 Feb Thu 25 Feb PAL session: 12001300 [121, 122] Fri 26 Feb Submission deadline Submission deadline (1300) [Group A] (1300) [Group B] ee.p01 (1400) Evolution of halotolerance practical (TB) [Barber, RCS1]: This practical is long-term and will require sampling and subculturing over the following weeks ee.p01 (1530) Evolution of halotolerance practical (TB) [Barber, RCS1]: This practical is long-term and will require sampling and subculturing over the following weeks Submit CBG online assessment (concepts) to Blackboard for summative assessment Submit CBG online assessment Biological Sciences Degrees – Department of Life Sciences – Imperial College London 17 Spring 2016 19 Mon 29 Feb Tue 1 Mar Lecture 1 (0900, Read Lecture 2 (1100, Read Afternoon session Afternoon session lecture theatre in Sherfield) lecture theatre in Sherfield) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) [Group A] [Group B] ee.09 Molecular ecology and evolution (TB) ee.11 Speciation (TB) Wed 2 Mar Thu 3 Mar PAL session: 12001400 [120, 122] Fri 4 Mar 20 21 Mon 7 Mar ee.13 Evolution of sex (TB) ee.p01 [continued] (1000) Sample #4 ee.15 EE seminar (human evolution) #1 (TB) ee.p01 [continued] (1000) Sample #6 ee.17 Intro to ecology (JL) ee.10 Genome evolution(TB) ee.12 Coevolution (TB) ee.p01 [continued] (1000) Sample #2 ee.14 What is life (TB) ee.p01 [continued] (1600) Sample #3 ee.p01 [continued] (1600) Sample #5 ee.16 EE seminar (human evolution) #2 (TB) ee.p01 [continued] (1400) Data analysis (TB) [G27] ee.18 Climate on a rotating Earth (JL) ee.20 Biomes (JL) Tue 8 Mar ee.19 Succession, plants and soils (JL) Wed 9 Mar Thu 10 Mar stats.q01 Online summative test (SP) [G27: Group A, 09001000] ee.21 The niche (JL) stats.q01 Online summative test (SP) [G27: Group B & extra time, 1030-1230] ee.22 Carbon (JL) Fri 11 Mar ee.23 Nitrogen (JL) ee.24 Climate change (JL) Mon 14 Mar ee.25 Intro to population biology (???) ee.26 Density dependence, regulation and management (???) Tue 15 Mar ee.27 Intra-specific competition (???) ee.29 Predation 1 (???) ee.28 Inter-specific competition (???) ee.30 Predation 2 (???) ee.31 Metapopulations (???) ee.32 Population management and harvesting (???) ee.34 State of biodiversity (TB) Wed 16 Mar Thu 17 Mar PAL session: 12001400 [121, 122] Fri 18 Mar ee.33 Intro to biodiversity and conservation biology (TB) ee.p01 [continued] (1400) Subculture #3 ee.p01 [continued] (1300) Set up growth assay, sample #1 (TB) [Barber, RCS1] Submission deadline Submission deadline (1300) [Group A] (1300) [Group B] Submit CBG essay ee.p01 [continued] (1430) Set up growth assay, sample #1 (TB) [Barber, RCS1] Submit CBG essay, 1500 words maximum, in both hard-copy to EO and to Blackboard (referencing) for summative assessment ee.p01 [continued] (1530) Data analysis (TB) [G27] ee.t01 ee.t01 Evolutionary biology [Seminar rooms] Students to select essay topic ee.t02 Submit STATS online assessment (R) to Blackboard… …for summative assessment (contributes to EE c/w grade) Submit evolution experiment write-up in both hard-copy to EO and to Blackboard (statistics) for summative assessment Submit evolution experiment write-up ee.t02 Experimental design in ecology [Seminar rooms] ee.p02 ee.p02 IUCN Red List criteria. Students work in small groups to apply the criteria to collated information on a set of species. (TB) [Barber, RCS1] Submit EE essay Submit EE essay, 1500 words maximum in both hard-copy to EO and to Blackboard for summative assessment Biological Sciences Degrees – Department of Life Sciences – Imperial College London 18 Spring 2016 Lecture 1 (0900, Read Lecture 2 (1100, Read Afternoon session Afternoon session lecture theatre in Sherfield) lecture theatre in Sherfield) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) pt.04 Personal tuition, discuss BCM and OB exams [Seminar rooms] ee.t03 Conservation status presentations. Students work in pairs through the week to prepare 10-minute presentations on the conservation status of a species of their choice [Seminar rooms] ee.t03 [Group A] 22 Submission deadline Submission deadline (1300) [Group A] (1300) [Group B] [Group B] Mon 21 Mar ee.35 Drivers of biodiversity decline (TB) ee.36 Conservation strategies and practice (TB) IUCN presentation Tue 22 Mar ee.37 Simple biodiversity models (TB) ee.38 Adaptive radiation (TB) Wed 23 Mar Thu 24 Mar ee.39 Diversity gradients and hotspots (TB) College closed ee.40 Diversity through time (TB) College closed College closed College closed Fri 25 Mar Bank holiday Bank holiday Bank holiday Bank holiday pt.04 IUCN presentation in tutorial Biological Sciences Degrees – Department of Life Sciences – Imperial College London 19 Summer 2016 23 Mon 25 Apr Tue 26 Apr Wed 27 Apr Lecture 1 (0900, Read lecture theatre in Sherfield) cbg.11 Mendelian genetics (MC) cbg.13 Meiosis and linkage (MC) cbg.15 Chromosome aberrations, ploidy (MC) Thu 28 Apr Afternoon session Afternoon session lecture theatre in Sherfield) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) [Group A] [Group B] cbg.12 Extensions toMendelian genetics (MC) cbg.14 Mapping(MC) cbg.18 Bacterial genetics conjugation (AF) Bank holiday Wed 4 May Careers guidance (SNC) 1100-1300 Y2 option adverts Thu 5 May Silwood trip. Depart from South Ken at 0900 (RG) Coursework feedback sessions by appointment (SNC, SC) cbg.20 Viral diversity (MT) Mon 2 May Submission deadline (1300) [Group A] Submission deadline (1300) [Group B] Complete TBL in afternoon session (teamwork) Complete TBL Submit requirements for bacterial growth practical to Blackboard by 1300 Submit requirements cbg.p03 Drosophila salivary glands (MC) [Barber, RCS1] cbg.p03 cbg.16 Sex determination (MC) cbg.17 Bacterial genetics transformation (AF) cbg.19 Bacterial genetics transduction (AF) Bank holiday Fri 29 Apr 24 Lecture 2 (1100, Read cbg.t02 cbg.t02 Genetics problem sets [Seminar rooms] Bank holiday Bank holiday Tue 3 May Fri 6 May 25 26 Mon 9 May Return at 2000. Bring your own lunch, but dinner provided Coursework feedback sessions by appointment (SNC, SC) cbg.21 Viral replication (MT) Tue 10 May cbg.22 Virus/cell interactions (MT) cbg.23 Animal viruses (MT) Wed 11 May cbg.24 Bacteriophage (MT) Thu 12 May [Discuss bacterial growth plans] cbg.25 Immune system (HB) Fri 13 May cbg.27 T&B cells (HB) cbg.28 Effector mechanisms (HB) cbg.29 Communicating junctions (MBAD) cbg.31 Membrane electrogenesis 1 (MBAD) cbg.33 Cell architecture (DB) cbg.30 Noncommunicating junctions (MBAD) cbg.32 Membrane electrogenesis 2 (MBAD) cbg.34 Protein sorting and the nucleus (DB) cbg.36 Vesicular traffic (DB) cbg.p04 Cell cycle practical (SRC) [Barber, RCS1] cbg.38 Extracellular matrix (DB) cbg.t04 Immunology/virology tutorial [Seminar rooms] Mon 16 May Tue 17 May Wed 18 May Thu 19 May Fri 20 May cbg.35 Endomembranes and the secretory pathway (DB) cbg.37 Cytoskeleton (DB) cbg.26 Types of immunity (HB) cbg.t03 Design bacterial growth experiments: team based learning session (SRC, PS) [G27+G29] cbg.t03 Both groups do this on the same day [Discuss bacterial growth plans] [Discuss bacterial growth plans] cbg.p04 cbg.t04 Biological Sciences Degrees – Department of Life Sciences – Imperial College London 20 Summer 2016 27 Lecture 1 (0900, Read lecture theatre in Sherfield) Lecture 2 (1100, Read Afternoon session Afternoon session lecture theatre in Sherfield) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) (1300-1600 Tue 1400-1700 Mon/Thu/Fri) [Group A] [Group B] Mon 23 May Submission deadline (1300) [Group A] Submission deadline (1300) [Group B] pt.05 Personal tuition, Y2 options [Seminar rooms] Tue 24 May pt.05 Personal tuition, Y2 options [Seminar rooms] Wed 25 May Thu 26 May Fri 27 May 28 Mon 30 May cbg.p05 Bacterial growth curves [Barber, RCS1+G27, Group B, 0900-1500; Read 1500-1700] (PS/SRC) cbg.p05 [Barber, RCS1+G27, Group A, 0900-1500; Read 1500-1700] (PS/SRC) Bank holiday Give presentations for summative assessment; combined with cbg.t03 TBL grade for overall grade Presentations Bank holiday Bank holiday Bank holiday Tue 31 May Wed 1 Jun Thu 2 Jun Fri 3 Jun 29 Mon 6 Jun Tue 7 Jun EE exam [460/560, 10001300] Wed 8 Jun Thu 9 Jun Fri 10 Jun 30 Mon 13 Jun CBG exam [460/560, 10001300] Tue 14 Jun Wed 15 Jun Thu 16 Jun Fri 17 Jun 31 Mon 20 Jun Tue 21 Jun Wed 22 Jun Thu 23 Jun Fri 24 Jun Biological Sciences Degrees – Department of Life Sciences – Imperial College London 21 Key to teaching staff • AD: Prof Anne Dell • AF: Prof Alain Filloux • AML: Prof Armand Leroi • BH: Brett Harmony • CT: Dr Colin Turnbull • DB: Dr Doryen Bubeck • DF: David Featherbe • EK: Elizabeth Killeen • HB: Dr Hugh Brady • HDW: Dr Huw Williams • JH: Dr Jason Hodgson • JL: Prof Jon Lloyd • MB: Dr Martin Bidartondo • MBAD: Prof Mustafa Djamgoz • MDB: Dr Martin Brazeau • MC: Dr Magda Charalambous • MS: Moira Sarsfield • MT: Dr Mike Tristem • PS: Prof Pietro Spanu • RG: Dr Richard Gill • SH: Stefan Hoyle • SNC: Dr Steve Connolly • SP: Dr Samraat Pawar • SRC: Dr Steve Cook • TB: Prof Tim Barraclough • TN: Dr Tony Nolan • ???: Dr Toby Confirmed Biological Sciences Degrees – Department of Life Sciences – Imperial College London 22