DEAKIN UNIVERSITY Faculty of Science, Engineering and Built Environment SLE212 Biochemistry Deakin University Unit Guide Trimester 1, 2022CONTENTS WELCOME WHO IS THE UNIT TEAM? Unit chair: leads the teaching team and is responsible for overall delivery of this unit, Unit chair details (Other members of the team and how to contact them Administrative queries ‘ABOUT THIS UNIT Unit development in response to student feedback Your course and Deakin's Graduate Learning Outcomes Your Unit Learning Outcomes ASSESSING YOUR ACHIEVEMENT OF THE UNIT LEARNING OUTCOMES ‘Summative assessments - Summative assessment task 1 ~ Summative assessment task 2 - Summative assessment task 3 Formative assessment Your learning experiences in this Unit - and your expected commitment. Scheduled learning activities - campus Note (on-campus learning activities) Note UNIT LEARNING RESOURCES Essential learning resources Recommended learning resources KEY DATES FOR THIS TRIMESTER UNIT WEEKLY ACTIVITIES. 10 10 10 22 February 2022Deakin University, Faculty of Science, Engineering and Built Environment SLE212 Biochemistry - Trimester 1, 2022 WELCOME Hi and welcome to Biochemistry. Biochemistry seeks to explain the behaviour of molecules, cells and ultimately the whole organism using chemical structures and the principles of chemistry. In reality it is not quite chemistry and not quite biology, with a language of its own, Most people find Biochemistry a very challenging subject. It requires learning a lot of new material quite thoroughly. it also requires you to use chemical concepts and quantitative skills to solve problems and to understand the biochemistry. To fully Understand biochemistry you need to draw upon the principles and knowledge learnt in first year chemistry. ‘The teaching team has drawn upon their experiences of the way in which biochemistry is used in various professional settings ‘to make this unit relevant and, hopefully, easier to absorb while still including all the information necessary for students to become strong contributors in their chosen field ur goal is to produce professional scientists who are able to draw upon their fundamental knowledge of biochemical systems in varied real-life situations such as research, teaching, industrial and clinical settings. Allin all, Biochemistry is an extremely rewarding unit which we hope you will enjoy. Bernhard and the unit team This Unit Guide provides you with the key information about this unit. For the best chance of success, you should read it carefully and refer to it frequently throughout the trimester. Your Unit site (inside DeakinSync) also provides information about your rights and responsi We will assume you have read this before the Unit commences, and we expect you to refer to it throughout the trimester. In 2022, teaching will be delivered in line with the COVIDSafe health guidelines, which may change across the academic year. We appreciate your flexibility and dedication to learning. For a range of helpful services and resources, please go to study support https://www.deakin edu au/students/studying/study-support. WHO IS THE UNIT TEAM? Unit eh: leads the teaching team and is responsible for overall delivery of this unit Bernhard Dichtl Unit chair details Campus: Melbourne Burwood Campus 221 Burwood Highway BURWOOD VIC 3125, Email bernhard.dichti@deakin.edu.au Phone: +613925 17060 Other members of the team and how to contact them Geelong Campus co-ordinator: contact the campus co-ordinator for assistance at your campus Name: Erica Todd Email: e todd@deakin.edu.au 22 February 2022 Page 2 of 11Deakin University, Faculty of Science, Engineering and Built Environment SLE212 Biochemistry - Trimester 1, 2022 Phone: +61 3 52273896 ‘+ Contact your Unit Chair or Campus Leader ‘© Drop in or contact Student Central to speak with a Student Adviser For additional support information, please see the Rights and Responsibilities section under ‘Resources’ in your unit site, ‘ABOUT THIS UNIT Biochemistry is the study of biological molecules that are related to living organisms. In SLE212 students will apply their fundamental knowledge of chemistry, biology and mathematics to describe the structure, chemistry and biology of various classes of biomolecules (amino acids, proteins, enzymes, carbohydrates, fatty acids and nucleic acids). Students will lara about the structure function relationship of proteins and the principles of enzymatic catalysis. They will explore the influence of thermodynamic principles on biochemical processes that sustain lif. In practical sessions, students will learn essential skills in biochemical experimentation. They will be required to apply knowledge of chemical and physical principles to Investigate how biochemical reactions are dependent upon the chemistry of water, buffers and pH. Students will work in ‘teams and apply digital technologies to explore the structure function relationship of proteins as is done in real-world research and development approaches. Unit development in response to student feedback Every trimester, we ask students to tell us, through eVALUate, what helped and hindered their learning in each Unit. You are strongly encouraged to provide constructive feedback for this Unit when eVALUate opens (you will be emailed a link}. In previous versions of this unit, students have told us that these aspects of the Unit have helped them to achieve the learning outcomes: ‘* Students liked the online learning modules; these are a series of questions that are completed in class. Students are then taught rather than being lectured to. ‘+ Students appreciated the online help sessions for the worksheets. ‘The following aspects of the unit have been introduced, enhanced or retained in response to feedback from students who have undertaken this unit in previous trimesters: ‘© The content of the unit will be revised to better fit the blended on-campus and online delivery of the unit. ‘* The practical notes have been edited and revised so that the instructions are clearer. ‘* Marker moderation meetings will be held for the practical worksheet assessments. These meetings attempt to standardise the marking of these assessments among markers. ‘© Rubrics will be revised to enhance scoring consistency and feedback to student answers, I you have any concerns about the Unit during the trimester, please contact the unit teaching team - preferably early in the trimester -s0 we can discuss your concerns, and make adjustments, if appropriate. ‘Your course and Deakin's Graduate Learning Outcomes 22 February 2022 Poge 3 of 11Deakin University, Faculty of Science, Engineering and Built Environment SLE212 Biochemistry - Trimester 1, 2022 Joto4) Dscpline-specific knowledge and [appropriate to the level of study related to a discipline or profession capabilities: [communication using oral, written and interpersonal communication to inform, motivate and [oor effect change [at03) Digital literacy Using technologies to find, use and disseminate information lata critical thinking. evaluating information using critical and analytical thinking and judgment lat 05] Problem solving: creating solutions to authentic (real world and ill-defined) problems letoe| Sel management working nd learning independent, and taking responsibilty for personal lato7| Teamwork working and learning with others from different disciplines and backgrounds Keuoe| Slobal citizenship engaging ethically and productively in the professional context and with diverse communities and cultures ina global context Each Deakin course has Course Learning Outcomes which explain what the Deakin Learning Outcomes mean in your discipline. Learning in each unit builds towards the Course Learning Outcomes. Your Unit Learning Outcomes Each Unit in your course is @ building block towards these Graduate Learning Outcomes - not all Units develop and assess every Graduate Learning Outcome (GLO). “These are the Learning Outcomes (ULO) for this unit. Atthe | Deakin Graduate Learning uo completion of this unit, successful students can Qutcomes uLo1 [calculate the chemical composition of buffers; construct and | GLO2: Discipline-specific validate the buffers within the laboratory knowledge and capabilities, }GLO4: Critical thinking |GLOS: Problem solving uLo2 identify, deduce, describe and interpret the [6L02: Discipline-specific structure, chemistry and biological function of biochemical _| knowledge and capabilities molecules (amino acids, protein, carbohydrates, nucleic acids | GLO4: Critical thinking and lipids). |GLOS: Problem solving Los. [Analyse, calculate and present experimental data produced | GLO2: Discipline-specific Jduring the laboratory practicals using software packages. knowledge and capabilities, }GLO3: Digital literacy }GLO4: Critical thinking ULO4 Use biochemical knowledge to logically support conclusions _ | GLO2: Communication Jdrawn from experimental data, JGLOS: Problem solving }GL04: Discipline-specific LOS | Work collaboratively in a team to develop and present a clear | knowledge and capabilities fand informative presentation on a topic of protein structure | GLO2: Communication and function. }GLO3: Digital literacy JGLO7: Teamwork ‘These Unit Learning Outcomes are applicable for all teaching periods throughout the year ASSESSING YOUR ACHIEVEMENT OF THE UNIT LEARNING OUTCOMES Summative assessments 22 February 2022 Page 4 of 11Deakin University, Faculty of Science, Engineering and Built Environment SLE212 Biochemistry - Trimester 1, 2022 (tasks that will be graded or marked) NOTE: Its your responsibility to keep a backup copy of every assignment and the materials used to develop/complete it where possible (e.g. written/digital reports, essays, videos, Images). In the unusual event that one of your submissions becomes corrupted, is incorrectly submitted or otherwise lost, you may be asked to submit the backup copy. Any work you submit may be checked by electronic or other means for the purposes of detecting breaches of academic integrity such as, collusion, plagiarism and contract cheating. You must understand your responsibility to act with honesty and integrity in your studies as Deakin takes all breaches very seriously. Make sure you read Your rights and responsibilities as a student in this unit to find out more about academic integrity Deakin has a universal assessment submission time of 8 pm AEDT/AEST. A late penalty will apply to assessments submitted after 11.59 pm AEDT/AEST. - Summative assessment task 1 [4 x practical worksheets Brief description of assessment task This task requires the student to work in small groups during practical sessions to perform biochemical experimentation. Students will be required to precisely implement experimental procedure, apply chemical and physical principles and use biochemical instrumentation to generate data and make experimental observations. Detail of student output This task requires individual student output in the form of 4 practical and data ]worksheets. Following practical sessions, students will be required to work individually to calculate, graph and interpret experimental data. Students may confer to discuss how the data is to be calculated and interpreted. However, students will be assessed Jon their individual ability to perform calculations and analysis, and to communicate their findings in written worksheets [Grading and weighting (26 total mark for unit) [40% - task will be marked and contributes 40% to the final mark for the unit This task assesses your Jachievement of these Unit Learning Outcome(s) ULOI - Calculate the chemical composition of buffers, construct and validate the [construction of buffers within the laboratory. ULO2 - Identify, deduce, describe and interpret the structure, chemistry and biological Function of biochemical molecules {amino acids, protein, carbohydrates, nucleic acids and lipids) ULOS - Present, calculate and analyse experimental data produced during the laboratory practicals using software packages. ULO4 - Use biochemical knowledge to logically support conclusions drawn from experimental data This task assesses your Jachievement of these Graduate Learning Outcome(s) [GLO1 — assessed through student ability to apply foundational chemical, mathematical and biological knowledge in interpreting structure, chemistry and biology of macro- molecules. }GLO2 - assessed through student ability to articulate scientific information in @ structured form to describe scientific problems, analyse evidence in order to support Jor oppose the interpretations of findings and conclusions JGLOS - assessed through student ability to identify scientific problems and use structured approaches and experimental strategies to formulate and propose solutions, How and when you will receive {feedback on your work [Within the practical, students will be provided with feedback on the quality of the data [and if they can correctly calculate, graph and interpret the data, 22 February 2022 Page 5 of 11Deakin University, Faculty of Science, Engineering and Built Environment SLE212 Biochemistry - Trimester 1, 2022 ]When and how to submit your ]work Practical worksheets A, B and C are due 8.00 pm AEDT/AEST, the DAY BEFORE practical sessions 2, 3 and 5 respectively, and practical worksheet D is due 8.00 pm AEST one teaching week after practical 5. Online submission via the dropbox on the unit site, accessed in DeakinSync. [students who miss a practical class will not receive marks for the corresponding Jquestions in a worksheet unless they have an approved application for Special [Consideration - Summative assessment task 2 [online tests Brief description [Two online tests will be conducted comprising 20 questions each, which have to be answered in 90 minutes (60 min answering time plus 30 min reading time and time for| uploading questions). The quizzes will test the knowledge of the concepts and content of the unit, the ability to transfer knowledge and understanding from a familiar to an unfamiliar situation and to solve problems. Detail of student output [Students will be required to provide answers in the form of multiple-choice questions, short answer text questions, calculations, fll n the blank and ordering questions. [Grading and weighting (26 total mark for unit) [40% (2 x 20%) - marked and graded This task assesses your Jachievement of these Unit Learning Outcome(s) ULO4 — Calculate the chemical composition and parameters of buffers. ULO2— Identify, deduce, describe and interpret the structure, chemistry and biological function of biochemical molecules (amino acids, protein, carbohydrates, nucleic acids and lipids) ULO4 - Use biochemical knowledge to logically support conclusions drawn from experimental data. This task assesses your Jachievement of these Graduate Learning Outcome(s) GLO1— assessed through student ability to apply foundational chemical, mathematical and biological knowledge in interpreting structure, chemistry and biology of macro-molecules. GLO4— assessed through student ability to use abstract and logical reasoning to evaluate problems and questions relating to biochemistry. GLOS — assessed through student capacity to apply chemical principles in solving biochemistry problems. How and when you will receive feedback on your work Feedback will be available afterall of the student cohort have completed the online test 1 or online test 2, respectively. Students will be able to review their online tests ]with a member of the Biochemistry teaching team, [When and how to submit your ]work [Ontine test 4 will ake place in week 6 (Thursday 14 April) and online test 2 will take place in week 11 (Friday 27 May). The exact details of the online tests will be communicated on the unit site. The online tests will be available as a quizzes on the unit site. The quiz will be submitted online - Summative assessment task 3 [Group assignment and presentation Brief description of assessment task [Group assignment on the structure and function of a protein, 22 February 2022 Page 6 of 11Deakin University, Faculty of Science, Engineering and Built Environment SLE212 Biochemistry - Trimester 1, 2022 Detail of student output, [Students will be assigned to teams of 4 to 6 to prepare, generate and present, biochemical knowledge about the structure and function of a protein. Students will also be required to connect the importance of protein structure to a disease, toxin or any other “real life” connection. They will relate the theory learnt in class to describe a eal word application of the knowledge and how it relates to the structure and iunction of a protein. Students will develop digital literacy/ bioinformatics skills as they interact with online biological databases to research the composition and three Jdimensional structure of a protein. They will then relate this structure back to the function and biology of the protein. This structure would then need to be analysed and a 3D model constructed using a software package. This assignment has been designed as an authentic learning Jexperience as the tasks and work processes involved may be approached in the same way by professionals in an academic or industry setting Using their research skills/problem solving skills students will meet as an online/virtual team (via Zoom) to discuss, debate and analyse the structure of the protein and form a [description of how the various parts of the structure contribute to its function. The findings of the project will be communicated in a short 5-7 minute video supported by audio visual or digital technology. A single artefact of a group presentation will be submitted. Students will be assessed on the information in the presentation and how [clearly and concisely this information is conveyed INOTE: Topics for the assignment will be prescribed by the teaching team, students are not allowed to pick a topic of their choice. [Grading and weighting (26 total mark for unit) 20% - (5% of the mark will be awarded for teamwork and 15% of the mark will be Jawarded for the quality of the presentation) Team submissions will be marked. There will be an individualised scaling factor applied based on peer and self-review to reflect your contribution and ability to work well within a team, moderated by the Unit Chair. If this self and peer review is not completed, a penalty of 25% is deducted. This task assesses your achievement of these Unit Learning Outcome(s) [UL02 - identify, deduce, describe and interpret the structure, chemistry and biological Junction of amino acids and proteins. ]ULOS - Work collaboratively in @ team to develop and present a clear and informative presentation on a topic of protein structure and function. This task assesses your Jachievement of these Graduate Learning Outcome(s) [610% - assessed through the description of structural and chemical components of a protein. 16102 - assessed through the students’ ability to prepare and present a presentation. JGLO3 - assessed through utlising digital literacy and digital technologies to research Jand present the information required for the assignment. ]GLO7 - assessed through the assessment of the teamwork skills and teamwork contribution. How and when you will receive feedback on your work The presentation will be marked by the teaching team. Students will gain feedback from the marked rubric. Students will receive feedback on their teamwork skills and [contributions via peer assessment submitted through the Feedback fruits software. [When and how to submit your ]work Feedback Fruits self and peer assessment of teamwork skills and contributions is due Friday 20 May 2022 (week 10) 8:00pm AEST. All of the listed assessment tasks are mandatory and students will receive 0 marks for the team presentation assessment if any one of the tasks has not been completed within the indicated deadlines. Please note that submission of the presentation must be done only by the team leader or nominee. Since this is a team assignment all team members must proactively ensure that the submission of presentations can be done by the team leader in a timely manner; applicable late penalties will be applied to the entire team. 22 February 2022 Poge 7 of 11Deakin University, Faculty of Science, Engineering and Built Environment SLE212 Biochemistry - Trimester 1, 2022 Formative assessment (for practice and feedback rather than marks and grades) In addition to the above, you will have a better chance of success in this Unit if you complete these tasks — you will get valuable experience and feedback peta Pre-prac questions [at the beginning of the practical sessions students will formulate answers jabout the theory, mechanics of the practical and the analysis of the data They will then provide an oral report to the class and be prepared to ldefend their answer. lbrief description [UL03— Analyse, calculate and present experimental data produced during the laboratory practicals using software packages. [This task assesses your ]ULO4— Use biochemical knowledge to draw conclusions about the data, lachievement of these Unit, lLearning Outcome(s) This task assesses your achievement of these Graduate Learning JOutcome(s) GLO7 - work in teams to prepare an answer, GLO2 orally |communicate the answer to the class JWhen and howto submit your [oral group report atthe end of the class hwork How and when you will receive _ |The oral reports given by the students will be discussed immediately by the feedback on your work group, Your learning experiences in this Unit - and your expected commitment ‘To be successful in this unit, you must: ‘+ Read all materials in preparation for your classes or seminars, and follow up each with further study and research on the topic; ‘* Start your assessment tasks well ahead of the due date; ‘= Read or listen to all feedback carefully, and use it in your future work; ‘= Attend and engage in al timetabled learning experiences as follows: Scheduled learning activities - campus 2x1 hour classes per week, 1x1 hour online class per week, 5 x 3 hour practicals per trimester. Note (on-campus learning activities) Teaching will continue to be delivered inline with the most current COVIDSafe health guidelines and may be subject to change across the teaching period in response to government guidelines. Please refer to the details provided in your unit site for announcements and updates. Students will on average spend 150 hours over the trimester undertaking the learning, practical and assessment activities for this unit. This includes class time, designated activities in the practical sessions (five 3-hour sessions), assessment tasks, readings and study time. Participation in the practical sessions is compulsory unless students are sick or have another valid reason for not attending the practicals. Students should spend at least three hours of each week working on the online learning modules prior to class. Preparing practical worksheets take a considerable amount of time. Students should allow at least 3-5 hours following practical sessions for completing the required analyses for reporting. Students should also allocate 22 February 2022 Poge 8 of 11Deakin University, Faculty of Science, Engineering and Built Environment SLE212 Biochemistry - Trimester 1, 2022 time to work on the protein assignment. This includes, meeting with the team, researching the protein and preparing the materials for the presentation. Biochemistry will be taught using in class online learning modules and tutorial questions online. Before class, students should work through these modules. This requires students to watch videos, read and then identify, deduce, describe, debate and interpret the structure, chemistry and biological function of biochemical molecules (amino acids, protein, carbohydrates, nucleic acids and lipids) to answer questions in the learning modules, tests, exams and practicals. Class time involves an active learning process whereas, as a group, we will answer the questions in the OLMs together. This allows the students to identify and correct any misconceptions. It also allows the students to form a group understanding of the material, and to actively solve problems using deduction, description, debating and interpretation. Tutorial style questions are then worked through in the online sessions after the students have had a period to reflect on the material ‘taught in class. This allows consolidation of the theory and to identify and correct for any further misconceptions. The unit utilises the language, and chemical concepts taught in first year chemistry. Accordingly, students may need to review these concepts. Mathematics in the form of problem solving, algebra and log properties are required to answer the tutorial, theory and worksheet questions. Students may need to seek help via the maths mentors for the understanding of these concepts. Within the laboratories students will work in teams and use biochemical instrumentation to make measurements and observations. Using these measurements, observations, biochemical theory and digital technology, students will present, calculate and analyse experimental data. Students will communicate these measurements and analytical process through written practical reports. Note At Deakin, 1 Lectures are referred to as classes (definition: a general meeting forall students, for which students do not need to register and where students are engaged through presentations and learning activities) ‘* Tutorials, workshops and seminars are referred to as seminars (definition: more interactive meetings for smaller groups of students). ‘= For the complete list of agreed definitions for learning experiences, see the Course Design and Delivery Procedure. UNIT LEARNING RESOURCES Your unit learning resources are available in your unit site accessed in Deakinsync. Prescribed text(s): Moran & Horton, 2013, Principles Of Biochemistry, Sth (Pearson New International) Ed, Pearson Education, Harlow, United Kingdom. ‘The texts and reading list for the unit can be found on the University Library via the link below: SLE212 Note: Select the relevant trimester reading list. Please note that a future teaching period’s reading list may not be available until a month prior to the start of that teaching period so you may wish to use the relevant trimester's prior year reading list as @ guide only. Essential learning resources This unit has a prescribed text listed above) Pymol Educational software ‘This software package is require for preparation of the 3D protein structure required for the assignment. (httos://oymol.org/edu/2q=educational), Please note that you should use the free educational version of this software. 22 February 2022 Page 9 of 11Deakin University, Faculty of Science, Engineering and Built Environment SLE212 Biochemistry - Trimester 1, 2022 Textbooks, reference books, general books and software may be ordered from the bookshop: ‘© phone 1800 686 681 (Freecall); ‘¢ email to DUSA-Bookshop@deakin.edu.au; or ‘© order online from the University bookshop web site at http://www dusabookshop.com.au/ Recommended learning resources Recommended texts: ‘© Berg, Tymoczko, Stryer and Gatto (2019) Biochemistry Sth Ed. Freeman, New York. ‘© Tymoczko, Berg and Stryer (2015) Biochemistry: A Short Course, Macmillian ‘# Nelson and Cox (2013) Lehninger Principles of Biochemistry, Macmillan You do not need to buy more than one textho ‘There are numerous Biochemistry books available with different teaching approaches that suit different learning preferences. Although Moran et al is the prescribed text for biochemistry, students may want to use other biochemical publications (for example — Berg et al is another good, clear, easy to read text book) referring to the relevant sections each week and using the class slides to help navigate through the appropriate topics. Relevant chapters in the textbook should be read each week in conjunction with the online learning module. This will allow you to focus on the important information required to be learnt in this unit. Which textbook you buy should also depend on your learning preference. Borrow the text from the library first to see if you find it to be easily understood. KEY DATES FOR THIS TRIMESTER [Trimester begins (classes bet Monday 7 March 2022 lintra-trimester break (a short break di i trimester) [Friday 15 April - Sunday 24 April 2022 [Trimester ends (classes cease) Friday 27 May 2022 [study period (examination preparation period) Monday 30 May - Friday 3 June 2022 lExaminations begin Monday 6 June 2022 [Examinations end Friday 47 June 2022 linter-trimester break (the period between trimesters]] Monday 20 June - Friday 8 July 2022 lunit results released Thursday 7 July 2022 (6pm) UNIT WEEKLY ACTIVITIES [Week [Commencing [Topic [Special learning activities [Assessment activity 1 [7 March 2022 [introduction, critical Concepts, water 2¢ [aamarch [Buffers Thermodynamics 3 [2imarch [Amino Acids | Worksheet Ahelp session fa [2smarch [Protein structure 22 February 2022 Page 10 of 11Deakin University, Faculty of Science, Engineering and Built Environment SLE212 Biochemistry - Trimester 1, 2022 5 [4 April Protein Function | Worksheet B help session 68 [at April Revision [Team Assignment workshop Online test 1 (Thu April 14) 7 [25 April Enzymes 8 [zmay [carbohydrates 2 [omay Nucleic Acids [Submission of protein assignment video and presentation 10 |ieMay Lipids [Worksheet C help session [Summative self and peer assessment of Membranes teamwork skills and contributions 1 [23 may Revision [Worksheet D help session Online test 2 (Fri May 27) ‘Victorian Labour Day public holiday: Monday 44 March 2022 - University open ‘Easter vacation/Intra-trimester break: F lay 15 Apr *ANZAC Day observed, Monday 25 April 2022 - University closed Sunday 24 April 2022 (between weeks 6 and 7) 22 February 2022 Page 1 of 11