Teaching
Junior Freshman Biology
Click here for details of all Junior Freshman Biology Modules available in the academic year 2012-13.
Senior Freshman Biology
Click here for details of all Senior Freshman Biology Modules available in the academic year 2012-13.
Timetables
Michaelmas Term 2012
JUNIOR FRESHMAN
BY1101 - Introduction to Molecular and Cellular Biology
SENIOR FRESHMAN
BY2201 - Cell Structure and Function
BY2202 - Vertebrate Form and Function
BY2203 - Metabolism
BY2204 - Evolution
Hilary Term 2013
JUNIOR FRESHMAN
BY1102 - Introduction to Evolution, Biodiversity and the Environment
SENIOR FRESHMAN
BY2205 - Microbiology
BY2206 - Ecosystem Biology and Global Change
BY2207 - Behaviour
BY2208 - Genetics
BY2209 - Infection and Immunity
BY2210 - Animal and Plant Bioresources
Foundation Scholarship 2012-13
This year’s Foundation Scholarship exams will take place in January 2013, and will follow the same format as in 2011/12. General information of the Foundation Scholarship may be found on the Senior Lecturer’s website (click here), and the Science Course Office website (click here)
Each of the four Biology modules (BY2201, BY2202, BY2203 and BY2204) will form one section of a two section, three hour examination.
The modules will be arranged as follows:
Paper 1 (XID 3078): BY2201 and BY2203 (three questions each, students answer three questions, the compulsory question from each section and one other). The 2011-12 paper may be accessed here: XID 3078.
(Students of the course in "Human Health and Disease", taking modules BY2201 and BY2203, will also sit this paper).
Paper 2 (XID 3153): BY2202 and BY2204 (three questions each, students answer three questions, the compulsory question from each section and one other). The 2011-12 paper may be accessed here: XID 3153.
In addition, modules BY2201, BY2202 and BY2204 (different questions) will appear as sections on a Science (Combined Subjects) paper (XID 3192), together with modules from Maths. The 2011-12 paper may be accessed here: XID 3192.
Human Genetics students taking BY2204 will be examined on this in a section on a separate ‘Human Genetics’ paper (XID 3126), which will also contain questions on the Human Genetics tutorials. The 2011-12 paper may be accessed here: XID 3126.
Details of the special topics and reading, associated with each module, is given below, together with contact information for the Special Topic Coordinators.
All of the speacial readings marked with an asterick (below) are available to download as PDFs from the Trinity College Library website (http://www.tcd.ie/Library/). Under 'Search Collections' select E-Journals Only. Enter the full title of the Journal and click on 'Search'. Select the appropriate source (usually the first one listed) and then select the volume number (and part, if appropriate) and search for the article by author, title or page number.
BY2201: Cell Structure and Function
Module Coordinator: Dr Emma Creagh (ecreagh@tcd.ie)
Special Topic: Signal Transductions and 2nd Messengers
Special Topic Coordinator: Dr Danny Zisterer (dzistrer@tcd.ie)
Special Reading:
The following three reviews constitute the specific extra reading for this special topic.
* Lefkowitz, R.J. 2000. The superfamily of heptahelical receptors. Nature Cell Biology. 2(7):E133-136.
* Burgess, A.W., Cho, H-S., Eigenbrot, C., Ferguson, K.M., Garrett, T.P.J., Leahy, D.J., Lemmon, M.A., Sliwkowski, M.X., Ward, C.W. and Yokoyama, S. 2003. An open-and-shut case? Recent insights into the activation of EGF/ErbB receptors. Molecular Cell. 12(3):541-552.
* De Luca, A., Maiello, M.R., D’Alessio, A., Pergameno, M. and Normanno, N. 2012. The RAS/RAF/MEK/ERK and the PI3K/AKT signalling pathways: role in cancer pathogenesis and implications for therapeutic approaches. Expert Opinion on Therapeutic Targets. 16 (S2):17-27.
BY2202: Vertebrate Form and Function
Module Coordinator: Dr Aine Kelly (aikelly@tcd.ie)
Special Topic: Hypertension
Special Topic Coordinator: Dr Aine Kelly (aikelly@tcd.ie)
Study guide:
The special topic for the BY2202 scholarship examination this year is Hypertension and the compulsory examination question will be on the pathophysiology of hypertension. In your answer, you may be required to demonstrate that you understand the physiology underlying the causes and progression of hypertension and its potential physiological consequences. You should also be familiar with the physiological rationale underlying the treatment of hypertension. To aid you in understanding the physiology of hypertension, you have been provided with additional reading consisting of a book chapter and three review articles published in Volume 380 (August 11, 2012) of The Lancet. I have given a brief study guide to each below. Please note that you will not be required to reproduce figures or tables from these papers.
Book:
Sherwood, Lauralee. 2010. Human Physiology: From Cells to Systems (7th edition)
publisher - Cengage Learning-Brooks/Cole
ISBN 9780495826293 / 0495826294 (International Edition)
(Hamilton Counter Reserve - 5 copies - 612 M98*6;19 - 6;23)
(Hamilton Lending - 15 copies - S-LEN 612 M98*6;4 - 6;18)
Chapter 10 gives an excellent overview of the fundamental physiology of the blood vessels. Pages 381-383 give a concise summary of the physiology of hypertension.
Review Articles:
* Laurent, S., Schlaich, M. and Esler, M. 2012. New drugs, procedures, and devices for hypertension. The Lancet 380: 591-600.
This review article highlights the current classes of antihypertensive pharmacological drugs currently used in the clinic, with brief discussion of their effectiveness. It also discusses potential novel drug and non-drug antihypertensive therapies. Please pay particular attention to the mechanisms of action of these therapies, as they illustrate the underlying pathophysiology of the disease.
* Ferrannini, E. and Cushman, W.C. 2012. Diabetes and hypertension: the bad companions. The Lancet 380: 601-610.
Diabetes and hypertension are frequent comorbidities, as discussed in this review article. You should pay particular attention to the descriptions of the complex pathophysiology linking these diseases.
* Ibrahim, M.M. and Damasceno, A. 2012. Hypertension in developing countries. The Lancet 380: 611-619.
This article highlights the high prevalence of hypertension in developing countries. The discussion of the potential reasons for this provides insight into the pathogenesis and progression of the disease.
Dr Kelly will meet with students to discuss details of the Scholarship paper and special reading towards the end of the BY2202 module.
BY2203: Metabolism
Module Coordinator: Dr Emma Creagh (ecreagh@tcd.ie)
Special Topic: Bioenergetics and Photosynthesis
Special Topic Coordinator: Dr Derek Nolan (denolan@tcd.ie)
General Texts:
Harold, Franklin M. 1986. The Vital Force: A Study of Bioenergetics
publisher – W.H. Freeman & Co.
ISBN 0716717344
(Hamilton Open Access - 1 copy – 574.191 M6)
(Hamilton Lending - 2 copies - S-LEN 574.191 M6;1, M6;4)
Harold’s book gives an excellent overview of the diversity of applications of chemiosmotic principles including, energy transduction, transport and photosynthesis. The style is exemplary for its clarity and simplicity. Although 25 years have passed since publication and sections of the text are dated (e.g the description of the electron transport chain complexes), this text still remains unsurpassed in its description and discussion of the key concepts that underlie energy coupling and transduction involving ion gradients.
Recommended chapters:
Chapter 2 The metabolic web
Chapter 3 Energy coupling by Ion Currents
Chapter 7 Mitochondria and oxidative phosphorylation
Chapter 8 Harvesting the light
Chapter 9 Carriers, channels and pumps.
Nicholls, David G. and Ferguson, Stuart J. 2002. Bioenergetics 3
publisher – Academic Press, Amsterdam/London.
ISBN 0125181213
(Hamilton Open Access - 1 copy – 574.191 M2*2;12)
(Hamilton Counter Reserve - 4 copies – 574.191 M2*2 – M2*2;3)
(Hamilton Lending - 8 copies - S-LEN 574.191 M2*2;4 – M2*2;11)
Possibly the standard textbook on Bioenergetics covering the basic concepts and the structures involved in energy transduction the focus is primarily on how cells make ATP and less so about the role of ion gradients in transport.
Chapter 1 Chemiosmotic energy transduction
Chapter 4 The chemiosmotic proton circuit
Chatper 5 Respiratory Chains
Chapter 6 Photosynthetic generators of protonmotive force
Chapter 7 The ATP synthase
These two texts are extremely informative and will provide you with a substantial foundation in the field. These are more than just basic texts. The extra reading and reviews are intended to back up this information but there is little point in trying to wade through reviews if you have not covered these texts first.
Further Reading and Reviews:
The chemiosmotic idea:
* Mitchell, P. 2011. Chemiosmotic coupling in oxidative and photosynthetic phosphorylation. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1807(12): 1507–1538.
(A special edition of BBA. Special Section: Peter Mitchell - 50th anniversary of the chemiosmotic theory.)
* Prebble J. 2002. Peter Mitchell and the ox phos wars. Trends in Biochemical Sciences. 27: 209–212.
(John Prebble gives an accurate account of the controversies involving Michell and chemiosmosis and their resolution.)
* Rich, P. 2011. Chemiosmotic coupling summarised. Biochimica et Biophysica Acta (BBA) – Bioenergetics. 1807(12): 1505-1506.
(Pete Rich gives a history of Mitchell’s work on chemiosmosis.)
* Harold, F.M. 2001. Gleanings of a chemiosmotic eye. BioEssays, 23: 848-855.
(A good summary.)
ATPase:
* Stock, D., Gibbons, C., Arechaga, I., Leslie, A.G.W. and Walker, J. 2000. The rotary mechanism of ATP synthase. Current Opinion in Structural Biology. 10: 672–679.
(A description of rotary catalysis by the group who did much of the work to solve the mechanism.)
* Arechaga, I. and Jones, P.C. 2001. Quick guide: ATP synthase. Current Biology. 11: R117
(FAQ on the F1F0-ATPase.)
Electron transport chains:
Note electron transport chain complexes: how they transfer electrons and pump protons has become a major area of research in structural biology. There are multiple reviews and papers on individual complexes but these are very specialized and intended for the well informed reader/researcher. What is important is to be able to give an overview of the major features of electron transport and proton pumping by the electron transport chain complexes rather than to dig into the details of the structure of individual complexes. For example, what do the individual complexes catalyse, how complex are they, how was electron transport /oxidation investigated, what have inhibitors told us about the complexes, which complexes pump protons, how is the Q cycle proposed to transfer electrons and protons?
* Schultz, B.E. and Chan, S.I. 2001. Structures and proton-pumping strategies of mitochondrial respiratory enzymes. Annual Review of Biophysics and Biomolecular Structures. 30: 23-65.
(Review. Decsription of H+ pumping by the various complexes. This review is an overview of the mechanisms but details of individual complexes has advanced considerably in the past few years. However, this is a good overview of an area that is quite complex.)
* Cape, J.L., Bowman, M.K. and Kramer, D.M. 2006. Understanding the cytochrome bc complexes by what they don’t do. The Q-cycle at 30. Trends in Plant Science. 11(1): 46-55.
(A review of the Q cycle 30 years after the original proposal.)
Finazzi, G., Rappaport, F. and Goldschmidt-Clermont, M. 2003. From light to life: an interdisciplinary journey into photosynthetic activity. EMBO reports. 4(8): 752-756.
Download free at http://www.nature.com.elib.tcd.ie/embor/journal/v4/n8/index.html
(An overview of various approaches used to investigate photosynthesis by several leading workers in the field.)
After the material covered in the lecture course and practical session combined with the reading outlined above you should be able to say something about the following:
- What does the concept of displacement from equilibrium mean and why is it important in cells?
- What does the term “redox potential” mean and why is it important.
- In oxidative phosphorylation: where is the energy input coming from? What is displaced from equilibrium here?
- What do you understand by the concept of energy transduction by ionic gradients, which is the very heart of bioenergetics and chemiosmosis.
- What contributions did the following biochemists make to the field of bioenergetics:
Peter Michell; David keilin, Ephariam Racker; John Walker, Robert Emerson; Hartmut Michel
- What does energy transduction by ionic gradients mean?
- What do we mean by coupled and uncoupled mitochondria?
- How does it work?
- How can an oxygen electrode be used to demonstrate oxidative phosphorylation?
- Why do we believe the chemiosmotic view of how cells make ATP is correct? What evidence do we have that it is the way cells make ATP?
- What features of the process are shared between mitochondria, bacteria and chloroplasts?
- Where do they differ?
- Why are ionic gradients so central to life?
BY2204: Evolution
Module Coordinator: Dr Trevor Hodkinson (hodkinst@tcd.ie)
Special Topic: Evolutionary Radiations
Special Topic Coordinator: Dr Trevor Hodkinson (hodkinst@tcd.ie)
Evolutionary radiations have occurred since life began and have generated extraordinary biodiversity. Some are called adaptive radiations. Reading material is based around this theme, and particularly the patterns and processes of radiations and the methods used to study them. Famous examples, include the Cambrian explosion, placental mammals, Darwin's finches, angiosperms, insects, cichlid fish, orchids and grasses.
Reference Material:
Reece, Jane B. 2011. Campbell Biology (9th edition)
publisher - Pearson/Benjamin Cummings, San Francisco, CA
ISBN 9781408277379
(Hamilton Counter Reserve - 5 copies - 574 M84*8;1 - 8;5)
(Hamilton Lending - 30 copies S-LEN 574 M84*8;6 - 8;35)
* Baldwin, B.G. and Wagner, W.L. 2010. Hawaiian angiosperm radiations of North American origin. Annals of Botany. 105(6): 849-879.
Hodkinson, T.R. and Parnell, J.A.N. 2007. Introduction to the Systematics of Species Rich Groups.
pp3-20 in Hodkinson, T.R. and Parnell, J.A.N. (eds). Reconstructing the tree of life: taxonomy and systematics of species rich taxa. Systematics Association Special Volume 72.
publisher - Boca Raton, FL, USA/Taylor and Francis, CRC Press, London.
ISBN 0849395798
(Hamilton Open Access - 1 copy – BM 574 L194.72;6)
(Hamilton Lending - 4 copies - S-LEN BM 574 L194.72;2 – 72;5)
Stiassny, M.L.J. and Meyer, A. 1999. Cichlids of the Rift Lakes. Scientific American. 280(2): 64-69
Download free at http://www.nature.com.elib.tcd.ie/scientificamerican/journal/v280/n2/index.html
(The extraordinary diversity of cichlid fishes challenges entrenched ideas of how quickly new species can arise.)
* Salzburger, W. and Meyer, A. 2004. The species flocks of East African cichlid fishes: recent advances in molecular phylogenetics and population genetics. Naturwissenschaften. 91(6): 277-290.
There are lots of references (internet or text books) on the adaptive radiation of Darwin's Finches. Likewise, you may wish to explore the literature on the Burgess shales and Cambrian explosion.