BIOCHEM 3125 - Advanced Molecular Biology IIIA (Biochemistry)

North Terrace Campus - Semester 1 - 2017

This course aims to extend the discussions of protein structure and function beyond Biochemistry Level II courses to gain a better understanding of the essential processes of molecular biology. Two principle themes are covered. 1. Protein Structure and Function: topics include structure and function of different classes of proteins, protein folding, targeted protein degradation, development of new therapies, molecular interactions and recognition. 2. Control of Gene Expression: topics include genetic circuits and synthetic biology; chromatin structure and remodelling during transcription; recruitment and assembly of transcription factors and the RNA polymerase complex; manipulating gene expression using "designer genes" and synthetic transcription factors; eukaryote mRNA synthesis, processing, modification, stability and translation, and manipulation of these processes to effect selective gene expression. This course combines lectures and tutorials from Molecular and Structural Biology III with molecular biology focussed laboratory placements in professional research laboratories or practical exercises in the first six weeks of the semester. The final six weeks include specialised Problem Based Learning (PBL) exercises designed to provide a perspective of how cutting edge biochemical principles and techniques are applied to major research questions in molecular biology. The importance of cross disciplinary approaches in modern biomedical research will be illustrated.

  • General Course Information
    Course Details
    Course Code BIOCHEM 3125
    Course Advanced Molecular Biology IIIA (Biochemistry)
    Coordinating Unit School of Biological Sciences
    Term Semester 1
    Level Undergraduate
    Location/s North Terrace Campus
    Units 6
    Contact Up to 14 hours per week
    Available for Study Abroad and Exchange N
    Prerequisites BIOCHEM 2510, BIOCHEM 2520, BIOCHEM 2504 & BIOCHEM 2505
    Incompatible BIOCHEM 3000 & BIOCHEM 3230
    Restrictions Available to BSc(MolBiol) students only
    Course Description This course aims to extend the discussions of protein structure and function beyond Biochemistry Level II courses to gain a better understanding of the essential processes of molecular biology. Two principle themes are covered. 1. Protein Structure and Function: topics include structure and function of different classes of proteins, protein folding, targeted protein degradation, development of new therapies, molecular interactions and recognition. 2. Control of Gene Expression: topics include genetic circuits and synthetic biology; chromatin structure and remodelling during transcription; recruitment and assembly of transcription factors and the RNA polymerase complex; manipulating gene expression using "designer genes" and synthetic transcription factors; eukaryote mRNA synthesis, processing, modification, stability and translation, and manipulation of these processes to effect selective gene expression. This course combines lectures and tutorials from Molecular and Structural Biology III with molecular biology focussed laboratory placements in professional research laboratories or practical exercises in the first six weeks of the semester. The final six weeks include specialised Problem Based Learning (PBL) exercises designed to provide a perspective of how cutting edge biochemical principles and techniques are applied to major research questions in molecular biology. The importance of cross disciplinary approaches in modern biomedical research will be illustrated.
    Course Staff

    Course Coordinator: Dr John Bruning

    Course Timetable

    The full timetable of all activities for this course can be accessed from Course Planner.

  • Learning Outcomes
    Course Learning Outcomes
    1 Understanding aspects of protein structure and function including protein folding, degradation, development of new therapies, molecular interactions and recognition.
    2 Understanding aspects of the control of gene expression including genetic circuits, chromatinstructure and remodelling, gene promoter assembly, eukaryotic mRNA synthesis, processing and translation.
    3 Understanding key experimental processes required to evaluate protein structure, functionand gene expression, and knowledge of how to apply them to solve specific biochemical problems.
    4 Specific skills in planning, performing, interpreting, quantitatively analysing and communicatingbiochemical research using a variety of modern experimental techniques.
    5 Ability to find, read, interpret and critically analyse relevant scientific literature.
    6 Ability to work in teams and communicate scientific outcomes.
    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 - 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
    1 - 6
    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
    1 - 6
    Career and leadership readiness
    • technology savvy
    • professional and, where relevant, fully accredited
    • forward thinking and well informed
    • tested and validated by work based experiences
    1 - 6
    Intercultural and ethical competency
    • adept at operating in other cultures
    • comfortable with different nationalities and social contexts
    • Able to determine and contribute to desirable social outcomes
    • demonstrated by study abroad or with an understanding of indigenous knowledges
    1 - 6
    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
    1 - 6
  • Learning Resources
    Required Resources
    Laboratory coat, safety glasses and closed shoes
    Recommended Resources
    Text book: Molecular Biology of the Cell (5th Edn) by Alberts et al., 2008, Published by Garland Science
    Online Learning
    Resource material such as lecture, tutorial, practical and past exams will be available on Myuni.

    Online assessment will be conducted via Myuni.
  • Learning & Teaching Activities
    Learning & Teaching Modes
    This course will be delivered by the following means:

    3 Lectures of 1 hour each per week. (same lectures as Molecular and Structural Biology III (BIOCHEM 3000)).

    1 Tutorial of 1 hour per week.

    1 Laboratory based research project (45 hours) or MSB III Practical (15 hours per fortnight, odd weeks = 5 hours & Even weeks = 10 hour duration) in  weeks 1-6. Includes oral presentation in week 6 with immediate feedback provided.

    1 x 2 hour problem-based learning (PBL) exercise per week for weeks 6-12. Involves two different PBLs based on current research, each assessed by 10-15 minute presentation in small groups

    3 online multiple choice tests of 1 hour duration (weeks 4, 8 and 12, with immediate feedback provided), to be done during non contact hours.

    1 hour written test in week 7.

     
    Lectures are from the existing Molecular and Structural Biology III (BIOCHEM 3000) course and will include the following topics:

     ·     Protein Life Cycle
     ·     Protein-Protein Interactions
     ·     Protein-carbohydrate / small molecule interactions     
     ·     Proteins and Drug Design
     .     Protein-nucleic Acid Interactions
     ·     Genetic Circuits and Synthetic Biology 
     ·     Chromatin Remodelling and Transcriptional Control
     ·     How Transcription Factors are Regulated to Control Complex Promoters
     ·     RNA-processing

     The laboratory-based research projects or research-based practicals are run by the Biochemistry Academic staff as well as PhD students.

    The tutorials are based around the lecture content as well as current relevant research papers

    The online tests reinforce the lecture material.

     The PBL exercises in term 2 will be conducted by academics who will select current molecular biology research areas of interest.

    Workload

    The information below is provided as a guide to assist students in engaging appropriately with the course requirements.


    A student enrolled in a 6 unit course, such as this, should expect to spend, on average 24 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., reading and revision).
    Learning Activities Summary
    Schedule
    Week 1 Protein Life Cycle Lecture
    Week 2 Introduction to Macromolecular X-ray Crystallography Lecture
    Week 3 Applications of Structural Biology/Proteomics Lecture
    Week 4 Proteomics/Protein-Nucleic Acid Interactions Lecture
    Week 5 Genetic Circuts and Synthetic Biology Lecture
    Week 6 Genetic Circuts and Synthetic Biology Lecture
    Week 7 Chromatin Remodelling and Transcriptional Control Lecture
    Week 8 Chromatin Remodelling and Transcriptional Control Lecture
    Week 9 How TranscriptionFactors are Regulated to Control Complex Promoters Lecture
    Week 10 How TranscriptionFactors are Regulated to Control Complex Promoters Lecture
    Week 11 RNA Processing Lecture
    Week 12 RNA Processing Lecture
    Small Group Discovery Experience
    Students perform small group discovery in their practical sessions in which they work together in small groups of approximately 12. 
    Students also perform small group discovery in their PBL sessions in which they work in small groups (~4) to solve problems together.
  • Assessment

    The University's policy on Assessment for Coursework Programs is based on the following four principles:

    1. Assessment must encourage and reinforce learning.
    2. Assessment must enable robust and fair judgements about student performance.
    3. Assessment practices must be fair and equitable to students and give them the opportunity to demonstrate what they have learned.
    4. Assessment must maintain academic standards.

    Assessment Summary
    Assessment Task Task Type Due Weighting Learning Outcome
    Written exam on lecture material

    Summative examination week 40% 1, 2, 3
    Practical write up on research project Summative/Formative week 12 15% 4, 5
    PBL exercises Summative/Formative weeks 7 -  12 15% 4, 5, 6
    Online assessment Summative/Formative weeks 4, 8 and 12 5% 1, 2, 3
    Written Test Summative/Formative Week 7 25% 1,2,4
    Assessment Related Requirements
    Attendance and active participation at all practicals is mandatory
    Assessment Detail
    End of term Exam (40% of total course grade) – A 2 hour examination covering the lecture material. It is made up of a mixture
    of short and long answer type questions.

     Mid-term written test (25% of total course grade) – A 1 hour examination covering the lecture material. It is made up of short and long answer type questions.

     Laboratory placement/Practical (15% of total course grade). The half semester research project (students can choose a laboratory placement or MSBIII practical) will include experimental work, keeping an up to date laboratory notebook, 1 oral presentation and the submission of a final practical report.  The oral presentation is 10-15 minutes, covers the research performed in the practical and performed individually (research placement) or small groups (MSB III practical) in week 7.Students receive feedback throughout the semester on laboratory performance and keeping of laboratory notebooks, as well as immediately after  the oral presentation, and on the final report.

     PBL exercises, weeks 7-12: Involves two different PBLs based on current research, each assessed by 10-15 minute presentation in small groups.  (15% of total course grade).

     Online exercises (3 per semester): Three multiple choice tests in weeks 4, 8 and 12 (5% of total course grade). Encourages revision of the material soon after the relevant lectures and immediate feedback provided to students.

    Submission
    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 the assignment 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 late or more without an approved extension can only receive a maximum of 50% of the marks available for that assignment.
    Course Grading

    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.

  • Student Feedback

    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.

    Provision of Feedback to Students
    The assessor usually provides appropriate feedback of assessment tasks to the student by means of written comments. The student has the opportunity to directly liaise with the assessor to obtain additional feedback and clarification if required.
  • Student Support
  • Policies & Guidelines
  • Fraud Awareness

    Students are reminded that in order to maintain the academic integrity of all programs and courses, the university has a zero-tolerance approach to students offering money or significant value goods or services to any staff member who is involved in their teaching or assessment. Students offering lecturers or tutors or professional staff anything more than a small token of appreciation is totally unacceptable, in any circumstances. Staff members are obliged to report all such incidents to their supervisor/manager, who will refer them for action under the university's student’s disciplinary procedures.

The University of Adelaide is committed to regular reviews of the courses and programs it offers to students. The University of Adelaide therefore reserves the right to discontinue or vary programs and courses without notice. Please read the important information contained in the disclaimer.