BIOCHEM 3000 - Molecular and Structural Biology III

North Terrace Campus - Semester 1 - 2020

This course aims to extend the discussions of protein structure and function presented in the Biochemistry Level II courses and to use this knowledge to gain an understanding of some of the essential processes of molecular biology. The course covers two principle themes: Protein Structure and Function: topics include - structure and function of different classes of proteins, protein folding, targeted protein degradation, the development of new therapies, molecular interactions and recognition. The Control of Gene Expression: topics include; genetic circuits and synthetic biology; chromatin structure and its remodelling during transcription; the recruitment and assembly of transcription factors and the RNA polymerase complex on a gene promoter; artificially manipulating gene expression with the use of "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 with cutting edge research-based practical exercises to complement the lecture material.

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Course Details

Course Code	BIOCHEM 3000
Course	Molecular and Structural Biology III
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	Y
Prerequisites	BIOCHEM 2500 & BIOCHEM 2501 or BIOCHEM 2502
Incompatible	BIOCHEM 3230 and BIOCHEM 3125
Assessment	Exam on lecture material, practical reports, written and online assessments

Course Staff

Course Coordinator: Dr John Bruning

Course Timetable

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

Course Learning Outcomes

1	Understand aspects of protein structure and function including protein folding, degradation, development of new therapies, molecular interactions and recognition.
2	Understand aspects of the control of gene expression including genetic circuits, chromatin structure and remodelling, gene promoter assembly, eukaryotic mRNA synthesis, processing and translation.
3	Understand key experimental processes required to evaluate protein structure, function and gene expression, and knowledge of how to apply them to solve specific biochemical problems.
4	Acquire specific skills in planning, performing, interpreting, quantitatively analysing and communicating biochemical research using a variety of modern experimental techniques.
5	Find, read, interpret and critically analyse relevant scientific literature.
6	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 Modes

This course will be delivered by the following means:

3 Lectures of 1 hour each per week.

1 Tutorial of 1 hour per week.

1 Practical of 15 hours per fortnight. (Odd weeks = 5 hours & Even weeks = 10 hour duration) Includes 2 oral presentations in weeks 6, 12/13, with immediate feedback provided.

3 online multiple choice tests of 1 hour duration per semester (weeks 4, 8 and 12, with immediate feedback provided).

1 hour written test in week 7.

The course content will include the following:
·      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 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.

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	Topic	Lecture
1	Protein Life Cycle	Lecture
2	Introduction to Macromolecular X-ray Crystallography	Lecture
3	Applications of Structural Biology	Lecture
4	Protein-nucleic Acid Interactions	Lecture
5	Genetic Circuts and Synthetic Biology	Lecture
6	Proteomics	Lecture
7	Chromatin Remodelling and Transcriptional Control	Lecture
8	Chromatin Remodelling and Transcriptional Control	Lecture
9	How Transcription Factors are Regulated to Control Complex Promoters	Lecture
10	How Transcription Factors are Regulated to Control Complex Promoters	Lecture
11	RNA Processing	Lecture
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.

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 Summary

Assessment Task	Task Type	Due	Weighting	Learning Outcome	Approximate Timing of Assessment
Written exam on lecture material	Summative	examination week	40%	1, 2, 3	Exam Period
Practical write up on research project	Formative and Summative	week 6 and 12	30%	4, 5	Week 12
Online assessments	Formative and Summative	weeks 4, 8 and 12	5%	1, 2, 3	Weeks 4, 8, 12
Written Test	Summative/Formative	Week 7	25%	1,2,4	Week 7

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 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.

Practical (30% of total course grade). The semester long practical exercise will include experimental work, keeping an up to date laboratory notebook, 2 oral presentations and the submission of a final practical report. The two oral presentations are each 10-15 minutes, cover the research performed in the practical, and performed in small groups in weeks 6, 12/13. Students receive feedback throughout the semester on laboratory performance and keeping of laboratory notebooks immediately after each oral presentation, and on the final report. Outstanding students may have the option of a laboratory-based research project in place of the practical exercise.

Online exercises: 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. This is done outside of contact time.

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
This section contains links to relevant assessment-related policies and guidelines - all university policies.
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.

Authorised by:	Deputy Vice-Chancellor and Vice-President (Academic)
Maintained by:	Course Outlines Administrator