BCHM2072/2972

Human Biochemistry

Course Information

These course outlines are a guide only. They are provided for the information of prospective students. Although every effort is made to ensure the most up to date information is provided, timetables often change each semester due to the availability of rooms and resources. Content (including lecture/practical topics, assessment and textbooks) is also regularly reviewed to ensure relevance and effective learning.

Unit of Study Overview

BCHM2072 is a 6-credit point course that consists of 24 lectures (two per week) and ten 2-3 hour practical sessions (one per week from Weeks 2 to 12 inclusive, excluding Week 9).

The major aim of the lecture course is to provide an introduction to metabolism and cell signaling within the context of whole body homeostasis.

The major function of the practical course is to nurture the technical and generic skills introduced in MBLG1001 and, perhaps, extended in BCHM2071 and MBLG2071. In addition, the experiments introduce some extended experiences: eg. working with radioactivity, preparing oral presentations, and designing assay systems. The main emphasis of the practicals is to provide students with the genuine research lab experience of gaining confidence in basic methodologies before using these to test hypotheses or make clinical diagnoses.

BCHM2972 is the Advanced version of the above course. The topics covered are generally the same but some of the practical tasks and theory assignments will be modified to encourage deeper reflection and a more challenging experience. A full comparison of the two units is provided at the end of this handout.

THERE IS NO LIMIT TO THE GRADES THAT CAN BE OBTAINED IN BCHM2072. Doing BCHM2972 does not confer a mark advantage. However, if you enroll in the advanced unit, we expect that you actually do the advanced tasks. Failure to meet a passing standard in these will result in your removal from the Advanced unit.

Course Coordinator Contact Details

A/Prof Gareth Denyer

Room: 704

Telephone: 9351 3466

E-mail: gareth.denyer@sydney.edu.au

Prerequisites

To qualify for BCHM2072 you must have achieved a full pass (>50%) in the first year course, MBLG1001. Many of the practical experiments performed this semester require you to handle basic lab equipment and perform rudimentary biochemical calculations (ie, all the things examined in the MBLG skills test).

To qualify for BCHM2972 you will have needed distinctions in one of the previous MBLG/BCHM intermediate units of study or, if you didn't do these, you need to have obtained distinctions in junior units of study, especially in MBLG1001.

Lectures

For both BCHM2072 and BCHM2972, the lectures will be in Eastern Avenue Lecture Theatre at 10:00am Monday and Chemistry Lecture Theatre 3 at 10:00am Wednesday.

Your lecturers for this semester are:

Gareth Denyer (Course Coordinator) (Room 774, Ph 9351 3466, gareth.denyer@sydney.edu.au)

Both of the lecturers are available throughout the semester for consultation but as both run research projects you should phone or email them to arrange an appointment.

It is important to remember that the examination questions relating to specific topics will be set by the lecturers who delivered the relevant lectures. Therefore, if you experience any difficulties with any part of the lecture course, discuss the matter first with the person who gave the lectures.

For other problems and inquiries, contact the Course Coordinator, Gareth Denyer.

An overview of the lectures in this course is given below. Be warned that it is not possible to capture the precise content and emphasis of each lecture in the list of bullet points. The actual notes and videos of the actual lectures will be put on Blackboard as the course progresses. It is essential that you revise from a full set of lecture notes, NOT just this overview. Similarly, the timetable is meant as a general guide to the order of material covered. Some topics may require more time than that allocated in this table while other topics may take less. USE THIS LIST AS A GUIDE ONLY!

The general strategy of the metabolism part of this lecture course is to cover the components of a standard biochemistry course by FIRST illustrating the big-picture concepts (Weeks 1-5) and ONLY THEN looking at the molecular detail of the enzymes and pathways involved (Weeks 6-8). This is in contrast to the vast majority of biochemistry courses which take the opposite approach.

Week Lecture Content

Weeks

1 - 5

Overview of Metabolic Systems and Integration  
  Principles of energy balance and fuel oxidation Anabolism and catabolism. Introduction to ATP as the energy currency of the cell. Overview of the mechanisms and pathways of ATP generation
  Oxidative Phosphorylation The molecular machinery responsible for generating ATP. The electron transport chain and the ATP synthase. The principles of coupling and uncoupling. Control of the rate of fuel oxidation and the relationship of ATP usage.
  Overview of fatty acid and glucose oxidation The pathways of glycolysis, fatty acid oxidation and the Krebs Cycle. Identification of the reaction strategies and key points of control. Regulation of each pathway by enzyme activity, cofactor availability and substrate supply.
  Fuel Selection during exercise Illustration of the regulation and integration of carbohydrate and fatty acid oxidation by reference to muscle fuel utilization during walking, jogging, running and sprinting.
  Fuel Selection during starvation The breakdown and catabolism of glycogen, fat and protein stores during the postprandial period, short-term fasting and long term food deprivation. Introducing gluconeogenesis and ketone body formation.
  Disposal of dietary carbohydrate The fate of ingested carbohydrates. The importance of the regulation of blood glucose by insulin. The glycemic index as a measure of the post-prandial glucose response. The formation of glycogen in muscle and liver (glycogenesis). The formation of fat in adipose tissue and liver (lipogenesis). Supporting pathways and alternative fates of glucose, such as the pentose phosphate pathway.
  Disposal of dietary fat and storage The fate of ingested fats and cholesterol. Digestion of fat and repackaging as chylomicrons in the gut. Processing of lipoproteins by the liver. Transport of fats and cholesterol to the peripheral tissues. Endogenous formation of cholesterol. Strategies to regulate blood cholesterol concentration.
  Protein and nucleic acid metabolism Overview of nitrogen metabolism. The processing of amino acids and formation of urea. Pathways of amino acid backbone synthesis and degradation. Overview of nucleotide formation and degradation.

Weeks

6 - 9

Details of Pathways and Case Studies  
  ATP generation The molecular detail of electron transport and oxidative phosphorylation. Details of protons pumps and electron transfer reactions. Inhibitors of electron transport. The generation of free radicals. Uncoupling Proteins. Thermogenesis.
  Carbohydrate metabolism Carbohydrate structure. Details of the reactions of glycolysis. Regulation of the pathway. Glycolysis in tumor cells and targets for chemotherapy. Feeder pathways for glycolysis and fate of non-glucose mono-saccharides. Fates of pyruvate under different conditions. Production of acetyl CoA, lactate and ethanol. Details of the Pentose Phosphate Pathway (PPP). Oxidative phase producing NADPH and recycling phase to produce glycolytic intermediates. Physiological significance of the PPP.
  Gluconeogenesis The major 'glycolysis bypass' reactions of gluconeogenesis. Regulation of gluconeogensis, reciprocal regulation with glycolysis. Precursors of gluconeogenesis and relationship to other pathways.
  Glycogen metabolism Molecular mechanisms involved in glycogen synthesis and breakdown. Role of glycogenin. Regulation of glycogen phosphorylase and synthase by reversible phosphorylation. Allosteric and hormonal signals regulating glycogen formation and mobilization. Glycogen loading regimes.
  The Citric Acid Cycle The eight steps of the cycle. Important cofactors. Regulation of the pathway. Substrate channeling. Anaplerotic reactions and relationship to other pathways.
  Fatty acid catabolism Regulation of lipolysis. The pathway of beta-oxidation. Oxidation of unsaturated fatty acids. Regulation of the pathway. Genetic defects in the process. Peroxisomal fatty acid oxidation. Ketone body formation.
  Fatty acid biosynthesis Shuttling of acetyl-CoA from mitochondria. Formation of malonyl CoA. Repeating reaction sequence of fatty acyl synthase. Regulation of fatty acid synthesis. Formation of very long chain and unsaturated fatty acids. Formation of triacylglycerol. Glyceroneogenesis.
Mid Semester Break  Case study and Revision  Integration of above themes using metabolic case study and Revision sessions.
Week 10   Introduction to signaling: general principles of specificity, sensitivity, affinity, integration and adaptation. Control of blood pressure: Guanylyl cyclase receptors for atrial natriuretic factor and nitric oxide. Glucagon signaling via G-protein coupled receptors and cyclic AMP. Coordinated regulation of glycogen levels. Cross talk between other G-protein coupled receptors (e.g. adrenalin) in glycogen regulation pathways. Receptors of taste (gustation) and smell. Termination of signaling by GTPases.
Week 11   Insulin signaling via Receptor Tyrosine Kinases. Cross talk between pathways: interaction with β-adrenergic receptor. Other receptors that use tyrosine kinases including cytokine receptors. Other second messenger pathways. The Phospholipase C pathway, Ca2+ signaling and calmodulin.
Week 12   Altering gene expression via steroid and thyroid hormones. Regulation of carbohydrate metabolism by cortisol.
Week 13   When good signaling goes bad! How disorders of signaling can lead to disease, and how drug treatments can interfere with aberrant pathways at a number of levels.

Textbooks

Any up-to-date Biochemistry text-book that gives a fundamental coverage of metabolism and cell signaling will be sufficient for this course - especially as materials will be provided during the semester. However, the strongly recommended text for this course is by Devlin and is called "Textbook of Biochemistry with Clinical Correlations" 7th Edition. It is published by Wiley. We have chosen this book because a) it will serve you well in future studies (especially Medicine) b) it has an appropriately extensive cell signaling component that fits our course nicely and, most importantly, c) we have negotiated with the publisher to make the book available as an eCopy, and specifically, have arranged for you to be able to download individual chapters at $6 per chapter (not much more than a coffee and cake from one of the more hip cafes on campus). When you purchase the text, you also get access to some of the accompanying on-line materials. We will link the learning objectives and lectures to this book.

Internet Resources
The Blackboard site will be updated regularly as the course progresses Please note, that the laboratory printers are NOT to be used for printing out course files. Whenever you log on to the printers in SMB, your usage is recorded. Any abuse of the printers will be reported to A/Prof Denyer! Scary hey!

Practical Course

General Arrangements
The practicals are NOT specifically designed to complement the material taught in the lectures. Although they do somewhat dove-tail with the lectures, they are mainly designed to teach you a wide range of scientific and generic skills (ie, the sorts of skills much loved by employers).

Laboratory classes run from 1.00 pm to between 3:00pm and 4:00pm from Monday to Thursday. The classes are in Room 380.

There will be no practical classes in the first week of the semester. Attendance at EVERY practical session is compulsory. Absence from a session needs to be made up by arrangement. Do not take it upon yourselves to swap sessions or assume that this will be possible.

You may have the same demonstrator as in MBLG1001/2071 or BCHM2072 although we endeavor to minimize this. If you feel disadvantaged by having the same demonstrator twice see A/Prof Denyer. This is a courtesy that might also be extended to the demonstrators!

Late work penalties are specific to each assessment task as described in the practical manual – the rule of thumb is the loss of 20% of available marks per day.

How do I change my practical day?
It should be possible for you to change your schedule via the central timetabling unit. If it is not, then it means that your proposed change will either adversely affect your own timetable, or that the session that you are trying to transfer to is already fully subscribed. Generally this means that you cannot change your day. However, if you believe that you have exceptional reasons for needing to change and you encounter a problem THAT CANNOT BE SOLVED WITH CENTRAL TIMETABLING UNIT, please channel your request to A/Prof Denyer. All requests must be made by email.

When can I use the Computer Facility?
You may use the computer facility on any day from 9:30am to 5:00pm. Computers may ONLY be used for Biochemistry-specific work. In particular, the printers must NOT be used to print out any material that is not directly connected with your practical class. Students undertaking a practical have priority during class times.

What happens if I miss some Practical Classes?
As mentioned above you MUST attend ALL of the practical classes. If you miss a class, you cannot expect to pass the practical course. It is, however, possible to make up classes and this can be arranged with A/Prof Denyer or the lab class supervisor. DO NOT TAKE IT UPON YOURSELF TO OMIT AND/OR ENTER SPECIFIC SESSIONS. You must get permission in writing to attend make-up classes.

Where do I get a Practical Manual?
A practical manual will be given to you by your demonstrator in your first practical. This has been done so that you do not have to pay (or queue!) for the manuals. A small number of replacement manuals may be on sale in the Co-Op bookshop.

What else do I need?
You should attend your first practical class with a signed copy of the Academic Honesty declaration sheet (available from Blackboard), a laboratory coat, something to write in and a waterproof/permanent-ink marking pen.

What if I need help with some part of the practical course?
Your first port of call should be your demonstrator. If they are not available, A/Prof Denyer.

BE VERY SURE to read the section in your MBLG1001 Resource Manual on Laboratory SAFETY. Attendance in the labs is conditional on your doing this. Since you must have done MBLG1001 to enter this course, the information is not duplicated here. However, if for some reason you do not have a copy, please ask A/Prof Denyer.

Assessment

The lecture (theory) component of the course is worth 50% of the final assessment with the practical components also contributing 50% to the final mark. A mark of at least 40% in the theory component is required to obtain a pass.

The lecture (theory) component of the course will be assessed: a) by two hours of questions in the end of semester exam b) by short quizzes on WebCT. These will differ in content and style for BCHM2972.

The practical component of the course will be assessed: a) by your laboratory work (including your eNotebook, presentations, and assay design assignments). This part of the course is strongly based on achievement of basic standards. By arriving punctually, actively participating in the experimental sessions, adequately recording the results and showing respect to others, you can expect to score well on this section. b) One hours worth of questions in the end of semester exam.

In summary, your final BCHM2072/2972 mark is calculated as;

- Theory part of the examination (2 hours) 40%
- Theory quizzes/assignments during semester 10%
- Exam questions relating to practical course (1 hour) 25%
- Practical work (lab work, reports, associated assignments, etc) 25%

This table summarises the commonality and differences between the Advanced and Regular units. Approximately 20% of the assessment is different.

Note that if you score badly (<50%) in the advanced components, we will not submit a mark for you under the BCHM2972 code.

Task

Notes

% Total Marks

Theory exam

Same for both units

40

Theory of practical exam

Same for both units

25

In-semester, on-line assignments

2972 have different assignments

10

Colorimetric assignment

2972 have a longer, more challenging assignment

3

Radioactivity presentation

Same for both, although 2972 expected to perform a more challenging investigation

4

Enzyme-linked metabolite assay

Ethanol kit development and instructions the same for both. Advanced students have individual live kit design test in final week

7

Other laboratory work, eNotebook

Same for both units

14

Policies

Academic Honesty

Any submitted work that appears to have been copied or otherwise plagiarised may be seen as evidence of academic misconduct and may be subject to an investigation by the University Registrar. Further information on the Academic Policy of the University of Sydney is available on the University Website. Of particular relevance here is the section concerning the responsibilities of students.

The School Website also has links to important documents describing our policy regarding Academic Honesty. It is a condition of enrolment in this Unit of Study that you read these documents. http://sydney.edu.au/science/molecular_bioscience/current_students/

The University requires that each submitted assessment is accompanied by a declaration that you have complied with the Universities Academic honesty regulations. However, we try and make this less torturous by getting you to complete a single coversheet to cover all assessment tasks. This must be completed and submitted to your demonstrator during the first practical class. In fact, you must complete this sheet to obtain your free practical manual.

Special Consideration

It is Faculty of Science policy that there are no Supplementary Examinations for courses which are only studied for one semester. However, we recognize that sickness or other misadventures can have an adverse effect on your performance. A copy of the Illness and Misadventure Policy for the School of Molecular Bioscience is located on the School website (http://sydney.edu.au/science/molecular_bioscience/current_students/ )

If you are granted Special Consideration, you may be permitted to sit for a postponed examination. It will be held during the week after the regular examination period (usually on the Friday of this week). DO NOT BOOK OVERSEAS TRAVEL DURING THIS TIME. Although this exam will cover the same lecture and practical material as the original exam, it will contain new questions and may be in a different format. It will MOST ASSUREDLY NOT BE THE SAME EXAM. Let’s say that again, shall we….. IT WILL NOT BE THE SAME EXAM. There will be no further testing after this date.

SIDs of those students eligible to sit this deferred exam will be posted on WebCT. IT IS YOUR RESPONSIBILITY TO FIND OUT IF YOU ARE ELIGIBLE TO SIT THE DEFERRED EXAM.