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Energy is a central theme in biochemistry: cells and organisms depend on a constant supply of energy to oppose the inexorable tendency in nature for a system to decay to its lowest energy state. The storage and expression of information costs energy, without which structures rich in information inevitably become disordered and meaningless. The synthetic reactions that occur within cells, like the synthetic processes in any factory, require the input of energy. Energy is consumed in the motion of a bacterium or an Olympic sprinter, in the flashing of a firefly or the electrical discharge of an eel. Cells have evolved highly efficient mechanisms for coupling the energy obtained from sunlight or fuels to the many energy-consuming processes they carry out.
The above passage, a quotation from an early edition of one of our texts (Lehninger Principles of Biochemistry 2000, p.6), sets the scene for the work to be done in the Energy for Life course. We shall be concerned with the mechanisms by which organisms harness, transform and use energy for life-processes using metabolic pathways composed of controllable enzyme-catalysed reactions. At one level, this is an enormously complicated task, with much detail still to be discovered. In BI25M6, however, we shall emphasise the principles underlying the biochemical complexity. And, in fact, although we shall illustrate integration of metabolic processes by reference to human biochemistry, and consider some metabolism (photosynthesis, nitrogen fixation, glyoxylate cycle) restricted to certain, other organisms, there are relatively few fundamental metabolic pathways, and these are common to all forms of life.
The aims of the course are to enable you:
(a) to establish a knowledge of the essential features of cell metabolism and some insight into its organisation and control;
(b) to establish a knowledge of the activity and regulation of enzymes.
The subject-specific learning outcomes are such that, at the end of the course, you should be able to:
(a) describe major features of energy transformations occurring in living organisms;
(b) describe the thermodynamic principles underlying and processes of biological catalysis;
(c) describe the functions and general features of the major metabolic pathways of intermediary metabolism, including glycogen metabolism, glycolysis, gluconeogenesis, the pentose phosphate pathway, citric acid cycle, glyoxylate cycle, terminal respiratory system, oxidative phosphorylation, lipid catabolism and anabolism, photosynthesis and the metabolism of amino-acids and other nitrogen-containing molecules;
(d) describe the integration of flow through some of these metabolic processes and the ways in which intracellular flow patterns change in response to extracellular events;
(e) describe the effects on metabolic flow of controlled change in enzyme activity.
In addition, intellectual skills will comprise:
(a) recognition that much biochemical uniformity underlies biological diversity and complexity;
(b) ability to apply subject-specific knowledge and understanding to address problems (during tutorials);
practical skills will comprise:
(a) ability to obtain, record, collate and analyse information in the laboratory;
numeracy and communication skills are encouraged by opportunities to:
(a) analyse laboratory-acquired information and approach some tutorial problems;
(b) produce written laboratory reports and verbally address topics during tutorials;
interpersonal and teamwork skills are encouraged by opportunities to:
(a) work productively with others in the laboratory;
(b) recognise and respect the views and opinions of others during tutorials;
self management skills are needed in:
(a) balancing the various demands of this and other courses you are studying.
The course achieves these outcomes through a series of complementary lectures, tutorials and practical classes. The function of the lectures is to enable information to be transmitted to a large group. Most lectures are not particularly interactive, but they do provide an indication of the quality and quantity of knowledge and understanding expected to be gained by the end of the course. The tutorials provide an opportunity for small-group discussions of topics dealt with in the lecture course: there is a chance to clarify any points of doubt, and also to apply some of the information gained by discussing set tutorial questions. The practical classes enable the class to use a few of the techniques mentioned in the lectures, and to gain experience in the acquisition, recording, evaluation, interpretation and presentation of experimental results.
Subject-specific, intellectual and written communication skills are assessed in the written degree examination and in a practical report; practical and numeracy skills are assessed in this practical report; communication, interpersonal and teamwork skills, although encouraged in tutorials and practicals, are not formally assessed.
Learning to understand is not a passive process, and we encourage you to check and organise, in ways best suited to yourself, material presented in each set of lectures by referring you to the set text. In the notes on the use of the Common Assessment Scale by the School, it says that high marks are given for answers ‘showing both knowledge and comprehension’: this means that a well organised and argued response that demonstrates knowledge and understanding will attract the highest marks.
Title: Bioenergetics
No of lectures: 3
Lecturer: Dr Michael Scholz
• Review of thermodynamic principles: conservation of energy, Enthalpy and Entropy, free energy and chemical equilibrium, standard free energy, biochemical catalysis, thermodynamics of life, equilibrium versus non-equilibrium thermodynamics
• Review of organic reaction mechanisms: nucleophiles and electrophiles , Group transfer reactions, isomerisation and elimination, reactions that make or break C-C bonds
• Catabolism and Anabolism, oxidation and reduction in the metabolism, Nernst equation and redox potentials, thermodynamics of phosphate compounds, the role of ATP
Title: Enzymes
No of lectures: 3
Lecturer: Dr Donna MacCallum
Enzymes are often referred to as the “engines” or “robots” of the cell, as they perform all major functions from catalysis of metabolites through to building important structures within cells. These 3 lectures aim to give an overview of enzyme properties, and using specific examples, the mechanisms of common enzymes prior to in depth study of metabolic pathways. Areas that will be covered are:
• General enzyme characteristics
• How catalysis occurs through enzymes
• How rates of enzyme activity can be studied
• How cells are able to control enzymes within specific pathways
Title: Photosynthesis
No of lectures: 2
Lecturer: Dr Donna MacCallum
Photosynthesis is the main route by which energy enters biological systems. The light reactions of photosynthesis take place in biological membranes in chloroplasts. These membranes contain pigments that absorb light very efficiently and channel the energy from the light to reaction centres in the photosystems. This causes electrons to become excited and transported through a photosynthetic electron transport chain leading to production of ATP and NADPH. In the photosynthetic dark reactions, ATP and NADPH are used to bring about reduction of carbon dioxide resulting in the production of triose phosphates. These may be converted to sugars and other assimilates which are transported to sinks throughout the plant. In C4 plants and CAM plants, adaptations have occurred which have increased the efficiency of photosynthesis and/or water use. Topics covered in these lectures will include:
• Processes by which energy is trapped in photosynthetic systems;
• Biochemical pathways which allow for the synthesis of carbohydrates during photosynthesis
• Differences in the photosynthetic mechanisms used by different plants
• Factors which regulate rates of photosynthesis.
Title: Carbohydrates and Intermediary Metabolism
No of Lectures: 4
Lecturer: Dr John Barrow
Without carbohydrates we would have little energy to survive, so this very important aspect of biochemistry will be given some in depth analysis and thought in these 4 lectures. Topics to be covered will be:
• Carbohydrate structure and function
• Dietary carbohydrate metabolism
• Overviews of the major catabolic and anabolic pathways of carbohydrates;
o Glycolysis
o Gluconeogenesis
o Glycogen metabolism
o Pentose phosphate pathway
Title: The Citric Acid Cycle
No of Lectures: 2
Lecturer: Dr John Barrow
Oxygen is used by the body to oxidise food molecules. These 2 lectures will cover the citric acid cycle as follows:
• The reactions of the citric acid cycle
• How the cycle fits into other metabolic pathways
• The cycle in catabolism
Title: Terminal Respiration
No of Lectures: 2
Lecturer: Dr John Barrow
This process utilises compounds that are generated in the citric acid cycle to fuel the final stage in the full breakdown of fuel molecules to provide us with the energy we need. Areas covered will be:
• The role of the mitochondria in terminal respiration
• The energetics of terminal respiration
• The components of the terminal respiratory system
• Production of ATP through ATP synthase
Title: Lipid Metabolism
No of lectures: 3
Lecturer: Dr Michael Scholz
Lipids are water-insoluble molecules found in all living cells and tissues. Most are esters of long hydrocarbon-chain carboxylic (‘fatty’) acids. As triacylglycerols, they are dietary fuel molecules, act as fuel stores in the body, and provide insulation. Structurally related but amphipathic phospholipids are membrane components. Prostaglandins, thromboxanes and leukotrienes are specialised fatty acids, with potent physiological activities. The sterol cholesterol is also classed as a lipid; it is a component of cell membranes, and a precursor of bile acids, steroid hormones and vitamin D. Topics to be covered in these lectures will include:
• Structural diversity of lipids.
• Structure and properties of lipids.
• Biochemical synthesis of fatty acids, triglycerides and phospholipids.
• Transport of lipids through the body
• Process of fatty acid oxidation
• Fatty acids as signalling molecules.
Title: Metabolic Retrospective
No of lectures: 4
Lecturer: Prof Kevin Docherty
To appreciate fully the significance of individual metabolic pathways and their regulation it is important to view these pathways in the context of the whole organism. The specialised functions of tissues and organs of complex organisms such as humans impose characteristic fuel requirements and patterns of metabolism. Hormonal signals integrate and coordinate the metabolic activities of different tissues and optimise the allocation of fuels and precursors to each organ. The body must also adapt to stressful situations and periods of starvation and we will learn how failure of these processes leads to metabolic disturbances including obesity and diabetes.
• Tissue specific metabolism: the liver as the powerhouse of metabolism, the adipocyte and its role in the storage of fat, muscle and its role in preserving blood glucose through the use of fatty acids, and the brain as a major consumer of ATP fuelled through metabolism of glucose
• Hormonal regulation of fuel metabolism: the key role of insulin and glucagon in the maintenance of glucose homeostasis
• Adaptation to starvation: changes in fuel metabolism during short and prolonged periods of starvation. Implications for the present-day epidemic of obesity
• Diabetes mellitus: emphasis on metabolic derangements
Title: Protein metabolism
No of Lectures: 3
Lecturer: Dr John Barrow
Proteins, and the amino acids that make up this macromolecule, are an important source of metabolic energy. Since amino acids cannot be stored, an excess of amino acids, either from dietary sources or from the breakdown of the body’s own protein, results in their oxidative degradation. This involves the breakdown of amino acids to a carbon skeleton (which can enter the citric acid cycle) and an amino group which can be used for the synthesis of amino acids and nucleotides. The nitrogen in amino acids and nucleotides ultimately comes from atmospheric N2. N2 is very unreactive, and only a few, mainly soil-living micro-organisms, can reduce it and ‘fix’ it in the biosphere. In this series of lectures we will look at:
• The nitrogen cycle: nitrogen is fixed from the atmosphere and, ultimately, transferred to an amino acid (glutamate). From there, by the process of transamination, other amino acids can be formed.
• Amino acid degradation: What happens to the carbon skeleton of amino acids? The carbon skeletons of some amino acids are converted into pyruvate or intermediates of the citric acid cycle and hence could be converted to glucose (i.e. they are glucogenic) whereas others are converted into acetyl CoA or acetoacetyl CoA and can then form ketone bodies (i.e. they are ketogenic).
• Amino acid degradation: What happens to the amino group of amino acids? The amino group is transferred to α-ketoglutarate to form glutamate which can then be transported to the liver. Glutamate plays a central role in biosynthetic pathways (formation of other amino acids or nucleotides) or in excretion pathways (to remove excess ammonia from the body).
Lectures: Metabolic Regulation
No of lectures: 3
Lecturer: Dr Kath Shennan
All metabolic pathways need to be tightly regulated to maintain balance. Much metabolic regulation involves changes in metabolic flow caused by changes in concentrations and activities of enzymes. This set of lectures will consider different ways in which this regulation is achieved, e.g.
• changing the concentration of an enzyme by changing gene expression (lac operon) or by zymogen activation (pepsinogen)
• changing the activity of the enzyme (covalent modification and allosteric regulation)
• “fight or flight” response; use as an example of the control systems discussed previously
Information on the practical classes (and relevant safety information) will be available on the course webCT site from the beginning of the course and will be given to you in hard copy at your practical class. You are required to read the appropriate practical manual in advance of the class to ensure efficient running of the class.
See details of tutorials in accompanying hand-out
The required texts for the course are:
Lehninger Principles of Biochemistry by D.L. Nelson & M.M. Cox (2008); Fifth Edition, Worth Publishers Inc., New York. ISBN 1429208929. Price £49.99. This provides a more than adequate supplementation for most of the course, and lecturers will refer to it specifically. It is also the recommended text for a companion course to BI25M6: BI20M3 (Molecular Biology of the Gene).
Or the shorter, less detailed:
Bios Instant Notes: Biochemistry by B.D. Hames & N.M. Hooper. (2011); Fourth Edition, Taylor & Francis, Oxford. ISBN 0415608457. Price £20.00.
The Queen Mother Library holds multiple copies of these texts.
There are several other very good Biochemistry textbooks available, many of which are also in the Library for you to refer to. It is NOT expected that you should buy these.
Molecular Biology of the Cell
by B. Alberts et al. (2008), Fifth Edition, (Garland).
Biochemistry
by J.M. Berg et al. (2006), Sixth Edition, (Freeman).
Molecular Cell Biology
by H. Lodish et al. (2007), Sixth Edition, (Freeman). This is the major recommended textbook for the first half-session level 3 Molecular and Cell Biology courses run by the School of Medical Sciences.
Biochemistry
by D. Voet & J.G. Voet. (2011), Fourth Edition, (Wiley).
The University has strict regulations on plagiarism. If you are unsure about what constitutes plagiarism read the University guide on plagiarism at: http://www.abdn.ac.uk/writing
Copying or plagiarising another persons work, either from other students or published material in books or papers and submitted as your own for assessment is considered a form of cheating. This is considered by the University to be a serious offence and will be penalised according to the extent involved and whether it is decided there was an attempt at deliberate deception, or whether bad practice was involved. If you do use information or ideas obtained from textbooks or other published material you must give a precise reference to the source both at the appropriate point in your narrative and in a list of references at the end of your work. Direct quotations from published material should be indicated by quotation marks and referenced in the text as above.
Assessment in BI25M6 consists of:
(i) assessment of classes (contributing 30% towards total degree assessment);
(ii) a Written Examination (contributing 70% towards total degree assessment).
(a) The Examination paper is divided into three sections (A, B, C). There are 4 questions in A, 6 questions in B and 4 questions in C. 1, 2 and 1 questions are to be answered from sections A, B and C respectively. All questions carry equal marks. The Course Co-ordinator will give more information about material examined in the different sections of the paper during the course and in the Examination Preparation session at the end of the course (see Course Timetable).
(b) Criteria used in assessing Practical Reports and in marking Examination answers are set out in the table which is included in this Course Guide, and which gives details of the version of the University Common Assessment Scale (CAS) used by the School.
(c) Examination results will be posted through Student Portals. They are likely to be posted no later than ten and no earlier than five working days after the Written Examination.
(d) Oral Examinations may be arranged for students who, although failing, have marks that fall close to the pass/fail borderline. These examinations normally last for 15-20 minutes. In the examination, any aspect of the course may be examined. Those students invited to Oral Examination will be e-mailed directly, after the Written Examination. Please make sure to check your e-mail regularly.
Please note that it is your responsibility to check whether or not you are invited to attend an Oral Examination. If you are invited to attend and fail to do so you will be assigned your pre-oral (failing) mark. It is important, therefore, that you do not arrange to go away from Aberdeen after the written exam and before the end of term, unless you can be sure that you will not require to attend an Oral Examination. Please note also that times and locations of Oral Examinations are NOT negotiable.
(e) Re-sit Written Examination papers follow the same format as those used in the first diet of examination. For re-sit candidates, marks for Practical Reports are normally taken into account when this is advantageous to the student. Re-sit candidates may be invited to attend an Oral Examination, according to the criteria and arrangements set out in Section (d) above.
(f) The External Examiner in Biochemistry is an overall arbiter in all matters connected with the assessment of students in this course.
Dr Kath Shennan
Dr Trevor Stuchbury, School of Biological Sciences External Examiner: Professor J Ian Mason, Biochemistry and Immunology, Clinical Biochemistry Section, Uiversity of Edinburgh
The University is keen to help you successfully complete your studies. If at any time you feel you need assistance, there is a range of support services available to help you. These include support to help with unexpected and/or exceptional financial difficulty, support for disabled students and academic learning support through the Student Learning Service. Further details about all these services are available at http://www.abdn.ac.uk/studenthelpguide/.
We value student’s opinions in regard to enhancing the quality of teaching and its delivery; therefore in conjunction with the Students Association we support the operation of a Class representative system. The students within each course, year, or programme elect representatives by the end of the fourth week of teaching within each half-session. In this course we operate a system of course representatives. Any students registered within a course that wishes to represent a given group of students can stand for election as a class representative. You will be informed when the elections for class representative will take place.
What will it involve?
It will involve speaking to your fellow students about the course you represent. This can include any comments that they may have. You will attend a Staff Student Liaison Committee and you should represent the views and concerns of the students within this meeting. As a representative you will also be able to contribute to the agenda. You then feedback to the students after this meeting with any actions that are being taken.
Training
Training for class representatives will be run by the Students Association in conjunction with SPARQS (Student Participation in Quality Scotland). Training will take place in the fourth or fifth week of teaching each semester. For more information about the Class representative system visit www.ausa.org.uk or email the VP Education & Employability vped@abdn.ac.uk. For further information on class representation and student involvement in Quality, visit www.sparqs.org.uk.
The University operates a system for monitoring students' progress to identify students who may be experiencing difficulties in a particular course and who may be at risk of losing their class certificate. If the Course Co-ordinator has concerns about your attendance and/or performance, the Registry will be informed. The Registry will then write to you (by e-mail in term-time) to ask you to contact their office in the first instance. Depending on your reason for absence, the Registry will either deal directly with your case or will refer you to your Adviser of Studies or a relevant Support Service. This system is operated to provide support for students who may be experiencing difficulties with their studies. Students are required to attend such meetings with their Adviser of Studies in accordance with General Regulation 8.
Set criteria are used to determine when a student should be reported in the monitoring system. You will be asked to meet your Adviser if any of the following criteria apply for this course:-
either (i) if you are absent for a continuous period of two weeks or 25% of the course (whichever is less) without good cause being reported;
or (ii) if you are absent from two small group teaching sessions (e.g. tutorial, laboratory class) without good cause;
or (iii) if you fail to submit a piece of summative or a substantial piece of formative in-course assessment by the stated deadline'
If you fail to respond within the prescribed timescale (as set out in the e-mail or letter), you will be deemed to have withdrawn from the course concerned and will accordingly be ineligible to take the end-of-course assessment or to enter for the resit. The Registry will write to you (by e-mail in term-time) to inform you of this decision. If you wish consideration to be given to reinstating you in the course you will require to meet with the Convener of the Students' Progress Committee.
Students who attend and complete the work required for a course are considered to have been awarded a ‘Class Certificate’. Being in possession of a valid Class Certificate for a course entitles a student to sit degree examinations for that course. From 2010/11 class certificates will be valid for two years and permit a total of three attempts at the required assessment within that two year period i.e. the first attempt plus up to two resits.
You will receive a University e-mail account when you register with the University Computing Centre. The University will normally use e-mail to communicate with you during term-time. These e-mails will be sent to your University e-mail account.
It is your responsibility;
• to check your e-mail on a regular (at least weekly) basis
• to tidy the contents of your e-mail inbox to ensure that it does not go over quota
NB. failure to check your e-mail or failure to receive e-mail due to being over quota or due to non-delivery of an e-mail forwarded to a non-University e-mail account would not be accepted as a ground for appeal (for further information on appeals procedures, please refer to http://www.abdn.ac.uk/registry/quality/appendix5x18a.pdf)
[If you already have a non-University e-mail account that you use for personal correspondence, it is possible to set up automatic forwarding of messages from your University e-mail account to your personal e-mail address but, should you do so, it is your responsibility to ensure that this is done correctly. The University takes no responsibility for delivery of e-mails to non-University accounts.]
Additional
1. Instructions for four Tutorial Classes. These are available as a separate manual.
2. Instructions for two Practical Classes, Practical Report templates and Laboratory Safety Notes will be available on the course webCT site from the beginning of the course but will only be handed out in hard copy at the practical classes. You must have read the practical instructions from the course webCT site in advance of the practicals
3. BI25M6 WebCT Site:
There is a WebCT site for the course containing information and resources.
To log in, go to: http://webct.abdn.ac.uk/
Click on 'Log in to my WebCT' and log in using your University username as your WebCT ID, and your University password as your password.
If you have any problems accessing the WebCT site, please contact the helpdesk by telephoning 01224 273636 or e-mailing: helpdesk@abdn.ac.uk
ON-LINE SELF-TESTS
There are a number of online formative self-tests in Questionmark Perception that have been designed to help you improve your knowledge and understanding of the central topics of the course. There is a link to the self-tests within each topic section within the 'Lecture Synopses, Notes and Self Tests 2006-2007' section of the BI25Ml WebCT site.
You can also access the self-tests directly by going to: http://question.abdn.ac.uk/q/perception.dll
Log in by following the instructions on the Questionmark Perception Login Screen.
If you have any problems accessing the Questionmark Perception self-tests, please contact the helpdesk by telephoning 01224 273636 or e-mailing: helpdesk@abdn.ac.uk
SUPPORT AVAILABLE TO STUDENTS
The University is keen to help you successfully complete your studies. If at any time you feel you need assistance, there is a range of support services available to help you. These include support to help with unexpected and/or exceptional financial difficulty, support for disabled students and academic learning support through the Student Learning Service. Further details about all these services are available at http://www.abdn.ac.uk/studenthelpguide/.
PERSONAL DEVELOPMENTAL PLANNING (PDP)
Level 1 and 2 students are encouraged to develop a Personal Development Plan (PDP) to help them learn more effectively, make the most of their University time and plan for their future. Further details on PDP can be accessed from the School website at http://www.abdn.ac.uk/sms - click on "Undergraduate Teaching".
