AGRIC 2500WT - Animal and Plant Biochemistry II
Waite Campus - Semester 1 - 2016
General Course Information
Course Code AGRIC 2500WT Course Animal and Plant Biochemistry II Coordinating Unit School of Agriculture, Food and Wine Term Semester 1 Level Undergraduate Location/s Waite Campus Units 3 Contact Up to 6 hours per week Available for Study Abroad and Exchange Y Prerequisites CHEM 1100 or CHEM 1101 & CHEM 1200 or CHEM 1201 Assumed Knowledge 6 units of Level I Biology Course Description This course provides an advanced introduction to the fundamental processes of plant, animal and microbial metabolism. Topics will include protein structure and function, mechanisms and control of enzyme action, the biochemistry of carbohydrate, fat and protein metabolism, energy generation, and the fundamentals of nucleic acid biochemistry. Examples of the application and context of key biochemical concepts to areas of science including plant and animal science, viticulture and oenology, veterinary medicine and food technology will be used to highlight the importance of biochemistry to all sectors of these sciences.
Course Coordinator: Associate Professor Christopher Ford
Name Role Building/Room Assoc. Prof. Chris Ford Course Coordinator WIC 4.43, Waite Campus firstname.lastname@example.org Dr Cindy Bottema Lecturer assisting G15, JS Davies Building, Roseworthy Campus email@example.com Dr Beth Loveys Teaching G26, Charles Hawker Building, Waite Campus firstname.lastname@example.org
The full timetable of all activities for this course can be accessed from Course Planner.
Course Learning Outcomes
Describe the role of thermodynamics in the determination of biochemical reactivity and differentiate between the kinetic and thermodynamic factors influencing biochemical reactions.
Explain how protein structure and function is derived from the constituent amino acids, and compare the features of structural and globular proteins.
3 Describe the basic principles governing the rate of enzyme catalysed reactions and the forms of inhibition of enzyme-catalysed reactions. 4 Describe the major pathways of carbohydrate and lipid metabolism and demonstrate how energy is stored and released through them. 5 Explain how the functional diversity of lipids is derived from their composition. 6 Describe the basic features of the cellular metabolism of amino acids and nucleic acids. 7 At the end of this course, students will have demonstrated familiarity and competence with the practical skills and techniques used in biochemical research and analysis. This will include experimental planning, the preparation of reagents and use of basic instrumentation (spectrophotometers, centrifuges, chromatographic apparatus etc), the collection of biochemical data and its presentation, and most importantly, the analysis and interpretation of the outcomes of biochemical investigations. 8 At the end of this course, students will have demonstrated the ability to undertake the research, preparation and delivery of presentations of biochemical topics selected to reinforce and augment the material presented in lectures.
University Graduate Attributes
This course will provide students with an opportunity to develop the Graduate Attribute(s) specified below:
University Graduate Attribute Course Learning Outcome(s) Deep discipline knowledge
- informed and infused by cutting edge research, scaffolded throughout their program of studies
- acquired from personal interaction with research active educators, from year 1
- accredited or validated against national or international standards (for relevant programs)
1,2,3,4,5,6 Critical thinking and problem solving
- steeped in research methods and rigor
- based on empirical evidence and the scientific approach to knowledge development
- demonstrated through appropriate and relevant assessment
7,8 Teamwork and communication skills
- developed from, with, and via the SGDE
- honed through assessment and practice throughout the program of studies
- encouraged and valued in all aspects of learning
7,8 Career and leadership readiness
- technology savvy
- professional and, where relevant, fully accredited
- forward thinking and well informed
- tested and validated by work based experiences
7,8 Self-awareness and emotional intelligence
- a capacity for self-reflection and a willingness to engage in self-appraisal
- open to objective and constructive feedback from supervisors and peers
- able to negotiate difficult social situations, defuse conflict and engage positively in purposeful debate
There is no required textbook for this course.
The recommended text for this course is Tymoczko, Stryer and Berg (2015) Biochemistry A Short Course 3rd Edition.
Advanced treatment of topics covered during the course will be found in many of the major undergraduate biochemical textbooks. Students seeking further details and greater coverage of topics than are provided by the recommended text are encouraged to consider supplementing their study using one of these. Other good biochemistry texts include:
- Nelson and Cox (2012) Lehninger’s Principles of Biochemistry 6th Edition
- Berg, Tymoczko and Stryer (2006) Biochemistry 6th Edition
- Mathews, Van Holde and Ahern (2000) Biochemistry.
A limited number of copies of some of these texts will be held on Reserve in the Waite library.
The publisher (WH Freeman and Company) offers a range of eBook options for access to the texts by Tymoczko et al., Berg et al. and Nelson & Cox. Some of these may be available for use by Australian students
A shorter biochemistry ebook suitable for Kindle readers or the Kindle App on iPads etc, Instant Notes in Biochemistry 2nd Edition, by David Hames, is available for purchase or short-term rental from the Kindle store. While this book does not cover topics in the depth provided by any of the major textbooks mentioned above, it nonetheless provides a useful background to all of the topics covered in the course.
A reading list of references relevant to topics covered in the course, which in many instances will provide the research context around these topics, is provided and can be accessed from MyUni. Individual articles contained on the reading list may be downloaded for private study. From time to time during the course, lecturing staff, tutors etc may suggest that you read additional scientific papers. These will be made available for online reading and download via MyUni; full details will be given as appropriate.
MyUni: Teaching materials and course documentation will be posted on the MyUni website (http://myuni.adelaide.edu.au/).
Course administration is accomplished using MyUni: activities will include email, Announcements, lecture handouts and recordings, an online reading list and links to past examinations. Coursework assignments may be submitted through Turnitin as directed. Coursework marks will be made available through the Gradebook. Assessment in the form of online quizzes will be offered during the semester as a part of the Formative Assessment component. All materials will be released at the relevant time during the semester.
Online activities for use before practical classes will be delivered using MyUni.
Learning & Teaching Activities
Learning & Teaching ModesLectures:
There are three lectures (each of 1 hour duration) per week; the first hour of lectures may be used to revise the previous week's lecture material.
Lecture notes may be posted to MyUni a few days in advance of the respective lecture and will not generally be provided to students in hard copy. Every attempt will be made to record lectures, and to make them available for streaming and download from MyUni.
Each student will attend one practical session per fortnight i.e., in alternate weeks. Practical sessions are of 3 hours duration. Attendance at all practical classes is compulsory.
Each student will attend compulsory tutorials each fortnight i.e., in alternate weeks to those when you will be attending a practical class.
The information below is provided as a guide to assist students in engaging appropriately with the course requirements.
A student enrolled in a 3 unit course, such as this, should expect to spend, on average 12 hours per week on the studies required. This includes both the formal contact time required to the course (e.g., lectures and practicals), as well as non-contact time (e.g., pre-class preparation, post-class assessments, reading and revision).
Learning Activities Summary
Schedule Week Type of learning activity Topic Week 1 Lecture Course introduction; Biochemistry in Context: basic principles of biochemical activity – 1 lecture. Protein structure and function - 2 lectures. Practical Analysis of nitrite. Tutorial or other activity Biochemical calculations. Protein structure and function. Week 2 Lecture Protein structure and function revisited – 1 lecture; Enzyme structure and function - 2 lectures. Practical Analysis of nitrite. Tutorial or other activity Biochemical calculations. Protein structure and function. Week 3 Lecture Online test - 1 lecture. Lipid biochemistry I and II - 2 lectures. Practical Enzyme kinetics. Tutorial or other activity Enzymes. Week 4 Lecture Lipid biochemistry III, IV and V - 3 lectures. Practical Enzyme kinetics. Tutorial or other activity Enzymes. Week 5 Lecture Lipid biochemistry VI and VII - 2 lectures. Lipids and nutritional outcomes - 1 lecture. Practical Ion exchange chromatography. Tutorial or other activity Lipids. Week 6 Lecture Carbohydrates - an introduction - 2 lectures; polysaccharides: biofuels and human health - 1 lecture. Practical Ion exchange chromatography. Tutorial or other activity Lipids. Week 7 Lecture No lectures - mid-semester assessment. Practical Glucose extraction and analysis. Tutorial or other activity No tutorial. Week 8 Lecture Carbohydrate biochemistry revisited - 1 lecture. Introduction to metabolism - 2 lectures. Practical Glucose extraction and analysis. Tutorial or other activity No tutorial. Week 9 Lecture Exam review - 1 lecture. Glycolysis - 1 lecture. Pathways to the production of low-alcohol wines - 1 lecture. Practical Starch extraction and analysis. Tutorial or other activity Carbohydrates and Metabolism. Week 10 Lecture Metabolism and the glycolysis pathway revisited - 1 lecture. Gluconeogenesis pathway; the coordinated reglation of glucose metabolism - 1 lecture. The pentose phosphate pathway - 1 lecture. Practical Starch extraction and analysis. Tutorial or other activity Carbohydrates and Metabolism. Week 11 Lecture Regulation of glucose metabolism revisited - 1 lecture. The TCA cycle and oxidative phosphorylation - 2 lectures. Practical Team Based Learning activity I (whole class). Tutorial or other activity Team Based Learning activity I (whole class). Week 12 Lecture TCA cycle and oxidative phosphorylation revisited - 1 lecture. Amino acid and nucleic acid metabolism - 2 lectures. Practical Team Based Learning activity 2 (whole class). Tutorial or other activity Team Based Learning activity 2 (whole class).
Specific Course RequirementsPRACTICAL SESSION CODE OF CONDUCT All students must follow these rules in practical exercises:
- Our students are from many countries, and speak in many different languages. The language of tuition and assessment of all courses at the University of Adelaide is English. Our teaching and demonstrating staff work exclusively in English and it is vital therefore that all discussion and communication between students in all class situations is in English ONLY. This is of particular importance with respect to laboratory classes, in which the Health, Safety and Wellbeing of all participants are at all times the most important consideration. It is expected that ALL students will be respectful and understanding of the diversity of language skills possessed by class members, and where appropriate will provide explanation and guidance to peers.
- No eating, drinking, application of makeup, etc in laboratories; no water bottles or items of food or drink may be visible in laboratories; mobile phone calls to be taken and made outside the laboratory only.
- Closed shoes must be worn at all times in all practical exercises, wherever they are held.
- Lab coats and other personal protective equipment must be worn at all times in laboratories or other areas whenever students are instructed to wear them; these should be removed when leaving the laboratory.
- Bags, coats, etc. that are brought into a lab must be placed under the bench to avoid causing obstructions.
- All containers used during a practical session must be labelled, including water and other common non-toxic substances.
- Report all accidents, personal or involving experimental materials, to the person in charge.
- Playing around in a laboratory and many other work areas is dangerous; participants in improper behaviour will be asked to leave.
- Students must dispose of materials as directed.
- Students must wash their hands upon departing the labs and other work areas.
- Students must clean and tidy their bench and/or work area before departure; benches and/or work areas will be inspected at the end of each practical session.
- Students not complying with the rules will not receive credit for the practical session in which the breach occurred.
The University's policy on Assessment for Coursework Programs is based on the following four principles:
- Assessment must encourage and reinforce learning.
- Assessment must enable robust and fair judgements about student performance.
- Assessment practices must be fair and equitable to students and give them the opportunity to demonstrate what they have learned.
- Assessment must maintain academic standards.
Assessment SummaryNo elements of the course have a formal exemption from the requirements of the Assessment for Coursework Programs Policy.
Assessment task Task type Due Weighting Learning Outcome Practical report - ion-exchange chromatography Summative/Formative Week 6 or end first week mid-semester break 5% 7 Practical report - starch extraction Summative/Formative Week 11 or 12 10% 7 Practical skills and biochemical calculations - Online test Summative/Formative Week 3 7.5% 7 Laboratory notebook Summative/Formative Week 12 or 13 5% 7 Online quizzes Summative/Formative Ongoing during semester 7.5% 1,2,3,4,5,6 Tutorials Summative/Formative Weeks 1 or 2, 3 or 4, 5 or 6 and 9 or 10 10% 1 to 6; 8 Team-Based-Learning Summative/Formative Weeks 11 and 12 5% 2,3,4,8 Mid-semester assessment Summative/Formative Week 7 25% 1,2,3,5 Exam Summative 25% 4,6
Assessment Related Requirements
Attendance at practicals and tutorials is compulsory; it is not acceptable to leave part-way through classes.
To pass the course students must gain an overall scaled mark of at least 50% when the marks for the Summative and Formative components are added together.
Students must achieve at least 40% of the total marks for the Summative Assessment component, i.e. a combined mark of not less than 72/180 for the mid-semester assessment and the end of semester examinations.
Summative (examination-based) Assessment - details:
The mid-semester assessment in week 7 will consist of a 2-hour paper containing questions based on lecture material covered in weeks 1 to 5 and in the tutorials associated with these lectures in weeks 1 to 6. All questions must be answered. Note that the Carbohydrate topic covered in lectures in week 6 will be assessed in the end-of-semester examination.
The examination in the Semester 1 exam period ( the 'final exam') will consist of a 2-hour paper, containing questions derived from lectures delivered in week 6, and weeks 8 to 12, and the tutorials associated with these lecture topics, in weeks 9 or 10. All questions must be answered. Note: TBL tutorial topics will NOT be re-examined in the final exam.
To pass the summative assessment component of the course, a student must achieve a total score for the two papers of at least 72/180 marks.
Formative (coursework) Assessment - details:
Formative assessment for the course will be covered by the following items:
1. Practical class reports, laboratory book presentation and online test:
a. There will be five practical classes conducted per student over the course of the semester. Each of these will incorporate assessment of work, submitted as a formal write-up no later than 1 week after the class (ion-exchange and carbohydrate analysis practical classes only) or by submission of the laboratory notebook in weeks 12 or 13. All submitted work will be returned with feedback within 2 weeks of submission.
b. You will be supplied with a laboratory notebook and detailed instructions on its use. The notebooks will be checked at intervals during the course and assessed in weeks 12 or 13. The marks awarded for the laboratory notebook will be added to those for the practical assessments.
c. An online test will be held during the first lecture period in week 3 (0910-1000). The test will comprise questions covering the biochemical calculations and basic practical skills encountered in weeks 1 and 2.
2. Tutorial assessments: Tutorial classes will be held in weeks 1 or 2, 3 or 4, 5 or 6 and 9 or 10. You will attend tutorials in the weeks when you are not scheduled for practical classes. The tutorial classes will comprise two one-hour sessions. In the first of these ('reinforcement tutorials') you will be required to provide answers to questions, provided through MyUni a week before your class, based on material covered in the relevant earlier lectures. Full details will be provided in week 1 or 2 as appropriate. The second session ('extension tutorials') will seek to guide you to an in-depth undertstanding of the topic, through a series of short class-based discussion questions designed to extend the knowledge gained in the lectures.
There will also be two whole-class Team Based Learning (TBL) exercises during the semester, in which you will be provided with some learning materials prior to the class that will provide you with the background knowledge for the TBL topic under consideration. The TBL class itself will begin with a series of 'single-best-answer' questions based on the pre-class learning material, which will be answered individually by each of you. You will then join your team members, and working together, provide answers to the same SBA questions. The answers will be revealed and an opportunity for discussion and clarification of any areas of confusion will occur. Subsequently, still working in your teams, you will be presented with a series of SBA questions based on one or more scenarios developed from the topics under study, and will provide answers to these in a class-based settting.
3. Online quizzes: During the semester, 5 online quizzes will be set from within MyUni/Assessments. Each quiz will contain between 10 and 20 questions, which will comprise a number of formats including but not limited to multiple choice, missing words, ordering and calculations. Quizzes will normally be available for a four-day period including weekends, which will be announced via a MyUni Announcement and email to each student.
The quizzes are intended to provide each student with a brief assessment of their knowledge of topics covered in recent and past lectures and tutorials. Each quiz may be attempted only once; you will receive full answers upon completion of the quiz.
Late submission of assessments
If an extension is not applied for, or not granted then a penalty for late submission will apply. A penalty of 10% of the value of the assignment for each calendar day that is late (i.e. weekends count as 2 days), up to a maximum of 50% of the available marks will be applied. This means that an assignment that is 5 days or more late without an approved extension can only receive a maximum of 50% of the mark.
Grades for your performance in this course will be awarded in accordance with the following scheme:
M10 (Coursework Mark Scheme) Grade Mark Description FNS Fail No Submission F 1-49 Fail P 50-64 Pass C 65-74 Credit D 75-84 Distinction HD 85-100 High Distinction CN Continuing NFE No Formal Examination RP Result Pending
Further details of the grades/results can be obtained from Examinations.
Grade Descriptors are available which provide a general guide to the standard of work that is expected at each grade level. More information at Assessment for Coursework Programs.
Final results for this course will be made available through Access Adelaide.
The University places a high priority on approaches to learning and teaching that enhance the student experience. Feedback is sought from students in a variety of ways including on-going engagement with staff, the use of online discussion boards and the use of Student Experience of Learning and Teaching (SELT) surveys as well as GOS surveys and Program reviews.
SELTs are an important source of information to inform individual teaching practice, decisions about teaching duties, and course and program curriculum design. They enable the University to assess how effectively its learning environments and teaching practices facilitate student engagement and learning outcomes. Under the current SELT Policy (http://www.adelaide.edu.au/policies/101/) course SELTs are mandated and must be conducted at the conclusion of each term/semester/trimester for every course offering. Feedback on issues raised through course SELT surveys is made available to enrolled students through various resources (e.g. MyUni). In addition aggregated course SELT data is available.
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