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Biochemistry module handbook...

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Student Name: ___________________________ Tutorial group: ___________________________

Faculty of Life Sciences & Medicine

School of Bioscience Education

Department of Biochemistry

Biochemistry (4BBY1013)

Module Handbook for 2017-2018

15 Credits: Level 4

Module organiser Dr Alison Snape [email protected]

Deputy organiser Professor Paul Francis [email protected]

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Contents Introduction ..................................................................................................................................................................5 Disclaimer ..................................................................................................................................................................5 Other student handbooks ...........................................................................................................................................5 School Undergraduate Student Handbook..............................................................................................................5 King’s Student Handbook .......................................................................................................................................5 Teaching and learning....................................................................................................................................................6 Module aims and learning outcomes ..........................................................................................................................6 Aims ......................................................................................................................................................................6 Learning outcomes ................................................................................................................................................6 Online module resources ............................................................................................................................................6 Frequently Asked Questions (FAQs)........................................................................................................................6 Teaching and learning sessions...................................................................................................................................7 Timetable...................................................................................................................................................................7 Lecture capture ..........................................................................................................................................................7 Recommended reading...............................................................................................................................................7 Textbooks ..............................................................................................................................................................7 Assessment and feedback..............................................................................................................................................9 Assessment overview .................................................................................................................................................9 Formative and summative assessment .......................................................................................................................9 The components of in-course assessment ...................................................................................................................9 Provisional marks .......................................................................................................................................................9 Assessment pattern for incoming Study Abroad and Exchange Students ONLY ..........................................................10 Details of in-course assessments............................................................................................................................... 11 Assessment of Practical 1: Micropipette use.........................................................................................................11 Multiple choice test on practicals 2 and 3.............................................................................................................12 Online test on metabolic pathways via KEATS.......................................................................................................13 Online submissions .............................................................................................................................................. 15 Late submission ...................................................................................................................................................15 Midsessional exam ...................................................................................................................................................15 Midsessional exam format ...................................................................................................................................15 Example MCQ midsessional exam ........................................................................................................................15 Feedback on the midsessional exam.....................................................................................................................16 Examination ............................................................................................................................................................. 16 Format of examination......................................................................................................................................... 16 Sample examination paper...................................................................................................................................16 Feedback on your final exam ................................................................................................................................17 A note on calculators ...........................................................................................................................................17 Examination Dates ............................................................................................................................................... 17

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Examination for incoming Study Abroad and Exchange students ............................................................................... 17 Reassessment (all students)......................................................................................................................................17 Missed assessment................................................................................................................................................... 18 Mitigating circumstances .....................................................................................................................................18 What to do if you miss compulsory teaching sessions ...........................................................................................18 Lectures and learning outcomes ..................................................................................................................................20 Lectures 1 & 2 Introduction to the Biochemistry module Dr Alison Snape ...................................................................20 The Molecules of Life (Biological Macromolecules) Dr Alison Snape ...........................................................................20 Lecture 3 Energy considerations in biochemistry Dr Alison Snape ..............................................................................20 Independent reading before Lectures 7 & 8 ...............................................................................................................22 Lecture 7 & 8 DNA as genetic material, DNA Replication Dr David Chambers ........................................................... 22 Lectures 9 & 10 Protein synthesis: Transcription, the Genetic Code & Translation Dr Robert Hindges .........................23 Lecture 11 Enzymes I Professor Paul Francis..............................................................................................................23 Lecture 12 Enzymes II Professor Paul Francis.............................................................................................................23 Lecture 13 Introduction to metabolism Dr Alison Snape ............................................................................................24 Lecture 14 Glucose metabolism: glycogen and glycolysis Dr Alison Snape ..................................................................24 Lecture 15 The TCA cycle ..........................................................................................................................................25 Lecture 16 Oxidative phosphorylation Dr Alison Snape ..............................................................................................25 Lecture 17 Energy release from fat Dr Alison Snape ..................................................................................................26 Lecture 18 Lipid synthesis, Fat storage and transport Dr Despo Papachristodoulou ...................................................26 Lecture 19 Metals in Biology Professor Wolfgang Maret ...........................................................................................27 Lecture 20 The liver in metabolism: Nitrogen Dr Despo Papachristodoulou ................................................................27 Lecture 21 The liver in metabolism: glucose homeostasis Dr Despo Papachristodoulou .............................................. 28 4BBY1013 Metabolic pathways and molecular structures learning guide ...................................................................29 Practical Work ............................................................................................................................................................. 31 Practical 1:

Basic Lab Skills – Using Gilson Micropipettes...................................................................................32

Practical 2:

Molecular model building ................................................................................................................ 40

Practical 3:

Enzymes..........................................................................................................................................56

Tutorial and Problem Solving Workshop (PSW) Worksheets .......................................................................................64 Tutorial 1

Lipids and membranes, Protein structure .............................................................................................65

Tutorial 2

Enzymes ..............................................................................................................................................70

Tutorial 3

Integration of metabolism ...................................................................................................................74

Workshop PSW 1

DNA/RNA/Protein Synthesis .......................................................................................................77

Workshop PSW 2

Metabolism 1 ............................................................................................................................83

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Workshop PSW 3

Metabolism 2 ............................................................................................................................88

Week by week summary of teaching and learning.......................................................................................................93 Appendix 1: Health and safety .....................................................................................................................................95

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Introduction Welcome to the handbook for the module 4BBY1013. This module is run by the Department of Biochemistry in the School of Bioscience Education for first year undergraduate students. Please write your name (and tutorial group) on the front of your handbook and bring it with you to lectures and other classes. The module organiser is: Dr Alison Snape [email protected] The deputy module organiser is: Professor Paul Francis [email protected] Disclaimer This handbook was published in September 2017, and reflects the information available at that time. We have endeavoured to make this information as accurate as possible. Updates to the handbook will be communicated on the module’s resource page on Keats. If there is any conflict between information on the web page and this handbook, then the web page should be taken as the authoritative source. If you should find any information that you consider to be out of date, inaccurate or misleading then please contact Alison Snape ([email protected]) with the module title and code, relevant page number(s) and your reasons for considering the information to be inaccurate. Other student handbooks If you cannot find the information you require in your module handbook it is likely to be in one of the other student handbooks. School Undergraduate Student Handbook Additional useful information relating to your programme and to student welfare can be found in the School of Bioscience Education Undergraduate Handbook https://keats.kcl.ac.uk/course/view.php?id=50620 King’s Student Handbook The university has an online student handbook, covering useful College level information about services for students: http://www.kcl.ac.uk/aboutkings/quality/academic/myhandbook/index.aspx

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Teaching and learning Module aims and learning outcomes Aims The aims of the module are:   

To provide a basic knowledge of the chemistry, structure, function and metabolism of the major classes of molecules found in living organisms. To equip students for more detailed studies of biochemistry in advanced courses, and to establish a foundation in the subject for those who may study no further biochemistry. To develop skills related to problem solving and laboratory-based practical work.

Learning outcomes After studying this module students should be able to:         

Describe the structure and function of major classes of biological macromolecules: carbohydrates, lipids, proteins and nucleic acids. Understand the importance of thermodynamic considerations in biochemical processes. Explain the function of enzymes in catalysing biochemical reactions. Describe the processes of DNA replication and protein synthesis in the cell. Outline the major pathways by which carbohydrates, fats and amino acids are metabolised to provide useful energy. Outline the biosynthetic pathway for lipids and their storage and transport. Give examples of strategies for metabolic control. Perform relevant calculations and solve problems relating to the above. Understand and carry out key experimental techniques.

Online module resources https://keats.kcl.ac.uk/course/view.php?id=46416 You will find details of assessment requirements, copies of lecture handouts, this handbook, and other learning resources such as lecture capture on the module’s KEATS page. You will also find links to information about such things as student representation, mitigating circumstances and marking criteria. Frequently Asked Questions (FAQs) If you have a question about the module that is not answered in the module handbook or on the module’s KEATS page, please check the Frequently Asked Questions (FAQ) section on the module’s KEATS page (see URL above) as it may already have been asked and answered there. If not, and you think the answer to your question will be of interest to other students, please post your question on the FAQ section, so that other students can benefit from the reply.

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If your question is about something that applies only to you (such as a mitigating circumstances query) then please email the module organisers or contact staff in the Academic Centre, but please do not send separate e-mails asking the same question to more than one person (send a single email and use the cc function to copy in multiple recipients if you are not sure who best to ask). Make sure to send any emails from your KCL email address, so that they do not get blocked by the College’s spam filters, and so that staff can be sure of who they are communicating with. Teaching and learning sessions The module consists of a variety of teaching and learning sessions throughout Semester. The main components of the module are:     

21 subject lectures 3 practicals 3 tutorials 3 problem solving workshops Private study

Please note that tutorials, practicals and workshops are an essential part of your learning as they help you to reinforce and deepen your understanding of material covered in lectures. Timetable The detailed module timetable is on the CYO timetable page and on the module’s web page (see URL above), and you should check it regularly for any changes. Corrections and updates may be necessary, so please DO NOT print or download your timetable for the whole semester at the start of term. There is a week by wee k outline of the module in the section Week by week summary of teaching and learning towards the end of this booklet. Lecture capture Currently lecture capture technology is available in all teaching rooms with a capacity of 50 or more. It is available in all lecture theatres at the Guy’s and Waterloo campuses, and in most of the classrooms. Lectures will be recorded, but sessions that include significant student participation (e.g. workshops) will generally not be recorded. https://keats.kcl.ac.uk/pluginfile.php/2018445/mod_resource/content/1/student-guidance-forlecture-capture.pdf Recommended reading The online reading list for the module can be found at: https://kcl.rl.talis.com/lists/E6E2F26A-8103-29FF-4D49-83D873DDC54F.html Textbooks The main textbook for this module is Biochemistry and Molecular Biology by Papachristodoulou, Snape, Elliott and Elliott, Fifth Edition (2014), published by Oxford University Press. You will also find useful material in the book recommended for the 4BBY1020 Chemistry module: Chemistry for

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the Biosciences by Crowe and Bradshaw, Third Edition (2014) also published by OUP . We have arranged with the publisher for KCL students to have a reduction on the price of these books if they buy both as a pack from Blackwell’s, which will be making it available on Guy’s Campus at the start of term. There are companion websites for these books with practice multiple choice questions at: http://global.oup.com/uk/orc/biosciences/molbiol/snape_biochemistry5e/ and http://global.oup.com/uk/orc/biosciences/chembio/crowe3e/ An excellent additional book that will be useful for most aspects of the course, and which is the recommended text for the 4BBY1030 Cell Biology and Neuroscience module, is: Essential Cell Biology by Alberts et al, Fourth edition (2014) Garland. You may find the introductory chapters of this book particularly helpful if you do not have one or need a quick revision of relevant A level standard Chemistry or Biology.

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Assessment and feedback The pass mark for level 4 modules is 40%. Assessment overview Your final course mark comprises an exam component and a course work component. The course work counts for 25% of the final mark for the modules and the final exam counts for 75%. Formative and summative assessment Formative assessment is designed to help you to identify strengt...