BCHM221 BIOCHEMISTRY A - Biomolecules and their interactions

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1 Chemistry Department General Course Information BCHM221 BIOCHEMISTRY A - Biomolecules and their interactions EFTS 15 Points First Semester 2013 Description This course runs in semester one. It counts 15 points towards a Bachelor of Science degree. It is required to major in biochemistry and preferably it should be taken in conjunction with other 200-level biochemistry, biology and chemistry courses. So what exactly is Biochemistry? Traditionally defined as the Chemistry of Life, biochemistry strives to understand the molecular nature of living organisms. Our knowledge of these biomolecules is growing at an astounding rate, with more and more being characterised in the laboratory every day. But biochemistry is more than a catalogue of chemicals that happen to make up our cells. In order to understand life at a molecular level, we must also understand how these molecules behave inside the cells, how they are organised, and how their activity is regulated. Biochemistry could equally well be defined as the Biology of Molecules. Scientists can use the tools of biochemistry to explore all aspects of an organism from basic questions about its chemical composition, through inquiries into the complexities of its metabolism, its development, to analysis of its evolution and behaviour. Biochemistry is thus a science whose boundaries now encompass all aspects of chemistry and biology, as it seeks to learn the relationships within and between molecules, cells, tissues, organisms, and even ecosystems. Society reaps huge rewards from our increased biochemical understanding. Cures for diseases, better public health, remediations for environmental pollution, and the development of cheaper and safer natural products are just a few practical benefits of this knowledge. All these research areas are active at Canterbury and all the lecturers in this course will be able to illustrate how your textbook knowledge can be put to great use in a variety of different research areas. This course aims to communicate the fundamental principles governing the structure and function of biological molecules. It is a prerequisite for several courses in Biochemistry, Chemistry and Biology and, in particular, it leads directly on to BCHM222. Students wishing to major in biochemistry must pass BCHM202, BCHM212, BCHM221, BCHM222, BCHM281 and at least one of BCHM206 and BCHM253. Those who wish to learn more including material at the frontiers of Biochemical Research can continue in BCHM301, BCHM381 and BCHM302. Course Co-ordinator Professor Ian Shaw, Department of Chemistry Room 754, ext 3105, ian.shaw@canterbury.ac.nz me if you have any queries about the course. Timetable Lectures: Two hours of lectures per week. Details to be confirmed on My Timetable and the Web. Tutorials: One hour of tutorials per week. Details to be confirmed on My Timetable and the Web. Students should note that in the Science Faculty that the average student is responsible for approximately 3.2 hours of additional study for each hour of lecture/workshop contact time at the 200-level.

2 Assessment Final Examination: 60% Assignments: 40% Examination and Formal Tests Exam: Three hours; details to be advised. Required Reading Garrett and Grisham Biochemistry: 4 th (or 3 rd ) edition. Other useful textbooks Hames and Hooper Instant Notes Biochemistry (2 nd edition) Alberts et al., Molecular Biology of the Cell (4 th edition) Buchanan et al., Biochemistry and Molecular Biology of Plants Horton et al Principles of Biochemistry Zubay Biochemistry (4 th edition) Stryer Biochemistry (4 th edition), Voet and Voet Biochemistry (2 nd edition) Mathews and Van Holde Biochemistry (3 rd edition) Lodish et al Molecular Cell Biology (3 rd edition) Dobson, Gerrard and Pratt, Foundations of Chemical Biology, Oxford Chemistry Primer Prerequisites/Restrictions P: (1) BIOL 111, (2) CHEM 112 or CHEM 115 R: BCHM 201, ENCH 323 Web-based resources Various learning resources (lecture material, reference links, quizzes, discussion forums etc.) for this course are available via the University of Canterbury s Learn web site -- This site will also be used regularly as a means of communication and information distribution for all of your Canterbury courses. You should familiarise yourself with Learn as soon as possible. Goal of the Course The course is part of a pair of 200 level 15 pt courses together they provide a fundamental grounding in Biochemistry for future study in the discipline. At the end of BCHM221 the student will understand the chemistry of important classes of biomolecules, how their molecular properties determine their biological function and how biochemists study them (with particular reference to enzymes). The course contains a significant independent research project that builds a detailed working understanding of biochemistry. Learning Outcomes Develop and demonstrate skills in critical analysis of the interconnectedness of molecular structure and biological functions. Demonstrate a knowledge of how biochemists study cells and biochemical reactions Demonstrate a knowledge of enzyme kinetics and their importance Develop and demonstrate the ability to apply biochemical principles and concepts Develop and demonstrate problem-solving and critical analysis skills Demonstrate scientific communication skills Summary of the Course Content Provides an understanding of the chemical structure and function of the major classes of biomolecules and how they interact. How biomolecules are separated from their parent organisms, tools we might use to study them in the laboratory. Particular attention will be given to enzymes and their regulation and how a study of their kinetics can give us invaluable information, for example, in drug design.

3 The topics covered by this course are: Overview of cell structure and function Structure and function of lipids, nucleic acids, carbohydrates and proteins Methods of studying cellular biochemistry Enzyme kinetics There are 20 lectures in the course they will be given by Professor Ian Shaw (Rutherford, room 754, ext 3105, and Dr Ren Dobson (von Haast, room 620, ext 7646, They cover the following (number of lectures in brackets): Studying biochemistry [1] breaking the cell up into its biochemical components. Lipids [2] - why is water insolubility so important? Their role in membranes and cell compartmentalisation. Other important lipids (e.g. sex hormones). Nucleic acids [2] - information storage and retrieval. What happens when the information gets corrupted? How is it protected and controlled? Carbohydrates [3] - their key functions, e.g. energy storage and supply. How are they involved in cell recognition? Proteins [4] - why is shape so important in their function? How can shape control function and activity? Enzymes [8] protein catalysts. Mechanisms of catalysis. Enzyme kinetics, mechanisms and the role of enzyme inhibitors. Finally we will explore how this all fits together to make a functioning cell. Professor Shaw will give the lectures on Studying Biochemistry, Lipids, Nucleic Acids, Carbohydrates and Proteins, and Dr Dobson will give the lectures on Enzymes.

4 GENERAL INFORMATION (200-LEVEL) 2013 Chemistry Department Policy on Dishonest Practice The University has strict guidelines regarding dishonest practice and breach of instructions in relation to the completion and submission of examinable material. In cases where dishonest practice is involved in tests or other work submitted for credit a department may choose to not mark such work (p 52 of the 2013 University Calendar under the headings Breach of Instructions and Dishonest Practice ). The Department of Chemistry upholds this policy. It considers plagiarism, collusion, copying, and ghost writing to be unacceptable and dishonest practices: Plagiarism is the presentation of any material (text, data or figures, on any medium including computer files) from any other source without clear and adequate acknowledgement of the source. Collusion is the presentation of work performed in whole, or in part, in conjunction with another person or persons, but submitted as if it has been completed by the named author alone. This interpretation is not intended to discourage students from having discussions about how to approach an assigned task and incorporating general ideas that come from those discussions into their own individual submissions, but acknowledgement is necessary. Copying is the use of material (in any medium, including computer files) produced by another person or persons with or without their knowledge and approval. Ghost writing is the use of other person(s) (with, or without payment) to prepare all or part of an item of work submitted for assessment. Additional Information Aegrotat applications: If you feel that illness, injury, bereavement or other critical circumstances has prevented you from completing an item of assessment or affected your performance, you should complete an aegrotat application form, available from the Registry or the Student Health and Counselling Service. This should be within seven days of the due date for the required work or the date of the examination. In the case of illness or injury, medical consultation should normally have taken place shortly before or within 24 hours after the due date for the required work, or the date of the test or examination. For further details on aegrotat applications, please refer to page 47 of the 2012 University Calendar. You have the right to appeal any decision made, including aegrotat decisions. Missing of tests: In rare cases a student will not be able to sit a test. In such cases, the student should consult with the course co-ordinator to arrange alternative procedures. This must be done well in advance of the set date for the test. Past tests and exams: these can be found on our website using the link below: Submission of reports and assignments: Reports and assignments should be handed in on time. Extensions will be granted only in exceptional circumstances (such as illness or bereavement). If an extension is required, as early as possible you should request it from the lecturer concerned. Note: If you do not submit an assignment for assessment, you will be allotted zero marks, which will affect your final result. You should ensure that you pick up marked assignments and keep them until the end of the course as evidence that the work was completed and marked in the case that either is disputed. To guard against accidental loss, it would be prudent to keep photocopies or electronic copies of anything submitted. Late Work: Late work is not usually accepted. If you have significant extenuating circumstances please submit your late work with a detailed explanation of why the work is late. Depending on the severity of your circumstances the work will either be accepted and marked or it will be marked and 10% of the total marks will be subtracted for each day the work is late. Days late include weekends and holidays.

5 Marks and Grades: The following numbers should be considered as a guide to the expected grades under normal circumstances. The Department reserves the right to adjust mark/grade conversions, if necessary. This will occur only where statistical analysis of marks indicates that the numerical distribution, and subsequently arising grades, is anomalous. Any such adjustments will not be made to the detriment of students grades. Grade: A+ A A B+ B B C+ C C- D E Minimum mark %: Reconsideration of Grades: Students should, in the first instance, speak to the course co-ordinator about their marks. If they cannot reach an agreeable solution, or have questions about their grade in a course, students should then speak to the Director of Undergraduate Studies (Richard Hartshorn, room 830, ext 6874, richard.hartshorn@canterbury.ac.nz). Students can appeal any decision made on their final grade. You can apply at the Registry for reconsideration of the final grade within four weeks of the date of publication of final results. Be aware that there are time limits for each step of the appeals process. Students with Disabilities: Students with disabilities should speak with someone at Disability Resource Service ( phone: (or ext. 6350), disabilities@canterbury.ac.nz). Academic Advice: Dr Richard Hartshorn (richard.hartshorn@canterbury.ac.nz, Room 830, phone ) is the coordinator of 200-level chemistry courses. His interest is in the academic performance and well-being of all such students. Anyone experiencing problems with their 200-level chemistry courses or requiring guidance about their B.Sc. in Chemistry should get in contact with Richard. Staff-Class Rep Liaison: Dr Richard Hartshorn (richard.hartshorn@canterbury.ac.nz, Room 830, phone ) is in charge of liaison with students in science courses. Your class will appoint a student representative to the liaison committee at the start of the semester. Please feel free to talk to the Academic Liaison or the student rep about any problems or concerns that you might have. Computer equipment: The University provides several student computer facilities. There is a suite of PCs in Room 540 on the 5th floor of the Chemistry Department which 200-level chemistry students are welcome to use OUTSIDE THE TIMES WHEN THESE COMPUTERS ARE NEEDED FOR CLASSES. Commonly used programs such as Word and Excel have been loaded onto these PCs. Richard Hartshorn Director of Undergraduate Studies Department of Chemistry February 2013