Outline

Overview

Proteins are the major doing molecules in biology. Their molecular make-up gives them a much more diverse set of properties than any other biological or synthetic polymer, leading to a vast array of different structures and functions. In this unit of study, you will learn about the structure, dynamics and interactions of proteins, and how those properties influence their myriad roles in nature. You will discover how these complex molecules are thought to have evolved, how they are made and dismantled, how they fold, and drive key processes inside and outside cells. You will also explore how the properties of proteins can be modulated by other molecules, or engineered to develop proteins with new functions or properties for use in biotechnology, medicine, bioremediation and industry. Our practicals, other guided and online learning sessions will introduce you to a wide range of currently utilised techniques for protein biochemistry ranging from protein visualization, quantification, purification and enzymatic activity, to in silico and virtual reality studies. By the end of this unit you will be equipped with senior level skills and knowledge to support your studies and careers in the cellular and molecular biosciences. Protein Function and Engineering (Advanced) has the same overall structure as BCMB3002, but students enrolled in BCMB3902 participate in a partially varied practical and tutorial program that focuses on developing skills in research, critical thinking, data analysis and communication.

Unit details and rules

Academic unit	Life and Environmental Sciences Academic Operations
Credit points	6
Prerequisites ?	An average mark of 75 or above in [6 credit points from (BCMB2X02 or BCHM2X71) and 6 credit points from (BCHM2X71 or BCHM2X72 or BCMB2X01 or BCHM3XXX or BCMB3XXX or BIOL2X29 or BMED2401 or BMED2405 or GEGE2X01 or MBLG2X01 or MEDS2002 or MEDS2003 or PCOL2X21 or QBIO2001)]
Corequisites ?	None
Prohibitions ?	BCHM3X81 or BCMB3002
Assumed knowledge ?	Intermediate Biochemistry (2000 level)
Available to study abroad and exchange students	Yes

Teaching staff

Coordinator	Jacqueline Matthews, jacqueline.matthews@sydney.edu.au
Guest lecturer(s)	Toby Passioura, toby.passioura@sydney.edu.au
Lecturer(s)	Jacqueline Matthews, jacqueline.matthews@sydney.edu.au
	Joel Mackay, joel.mackay@sydney.edu.au
	Sandro Fernandes Ataide, sandro.ataide@sydney.edu.au
Tutor(s)	Ann Kwan, ann.kwan@sydney.edu.au

Assessment

The census date for this unit availability is 2 April 2024

Details
Criteria

Type	Description	Weight	Due	Length
Supervised exam ?	Final Exam MCQ and SA questions covering lecture material	40%	Formal exam period	2 hours
Outcomes assessed:
Online task	Lab book experiment short reports Participation, Revision, Notebooks, Data curation	20%	Multiple weeks	400 words plus figures
Outcomes assessed:
Tutorial quiz	Theory of lectures short quiz #1 MCQs in Lecture/Online	5%	Week 06	40 minutes
Outcomes assessed:
Tutorial quiz	Theory of lectures short quiz #2 MCQ/SAs in online.	5%	Week 10	40-45 minutes
Outcomes assessed:
Small test	Quiz / calculations Theory Of Prac Open Book exam in Lab	15%	Week 11	90-150 minutes
Outcomes assessed:
Assignment	Protein structure assignment and presentation Pymol Presentation in Week 12. Individual written report (Week 13)	15%	Week 13 Due date: 26 May 2024 at 23:59	5 minute group presentation and 300 word
Outcomes assessed:
= hurdle task ? = group assignment ?

Assessment summary

Detailed information for each assessment can be found on Canvas.

The laboratory course is an essential part of the unit of study and students must pass the laboratory component in order to pass the unit. In order to pass students must attend 80% of practical sessions, demonstrate engagement, and submit satisfactory lab notebooks for assessment (minimum of 4/5 indicative and marked reports/notebooks). This is a hurdle task. If technical issues, illness, a requirement to isolate etc. prevent attendance at a specific class, students should discuss the problem with the coordinator to find out how to make up the missed attendance. Notebooks to be completed in Lab classes. One revision session and three graded notebook submissions plus one indicative submission throughout the lab series.
Presentation. Pairs of students will select a topic and carry out research and prepare a 5 minute presentation to subsets of students and assessors using a structural visulisation platform. Students will prepare an individual written report on the same topic (1000 Words). Details to be provided by Week 7.
Tutorial quizzes will be held in Lectures or as take home quizzes. These will include MCQs relating to lecture material (covering specific modules) and some short answer questions.
Short Test. In Lab Theory of Prac exam. This will be open book and include calculations and analysis of the type done in lab classes, plus questions from the Lab Manual (format of the question may change).
Final Exam. Covers lecture material (all modules). MCQ and short answer questions. This assessment is compulsory and failure to attend, attempt or submit will result in the awards of an AF grade. If a second replacement exam is required, this exam may be delivered via an alternative assessment method, such as a viva voce (oral exam). The alternative assessment will meet the same learning outcomes as the original exam. The format of the alternative assessment will be determined by the unit coordinator.

Assessment criteria

The University awards common result grades, set out in the Coursework Policy 2014 (Schedule 1).

As a general guide, a high distinction indicates work of an exceptional standard, a distinction a very high standard, a credit a good standard, and a pass an acceptable standard.

Result name	Mark range	Description
High distinction	85 - 100	factual information of an outstanding standard with a sophisticated grasp of the principles and interpretation clear evidence of critical analysis, understanding of experimental design and statistical analysis, integration of knowledge and application to the experimental situation, evidence of originality of thought
Distinction	75 - 84	factual information of a superior standard with a sophisticated grasp of the principles and interpretation good evidence of critical analysis, understanding of experimental design and statistical analysis and integration of knowledge; good understanding of the application of knowledge; some evidence of application to the experimental situation
Credit	65 - 74	factual information of a high standard, but some information may be incorrect or missing, with sound grasp of the principles and interpretation critical analysis is mainly superficial and relevance of knowledge not always clear, understanding of experimental design and statistical analysis is sufficient and applied to the experimental situation
Pass	50 - 64	factual information is of an acceptable standard but basic and contains gaps, errors or inconsistencies/contradictions critical analysis is relatively poor, material may be correct but not entirely relevant; surface understanding of experimental design and statistical analysis with limited application to the experimental situation and limited interpretation
Fail	0 - 49	a significant amount of factual information is incorrect misses the point, fundamental misunderstandings evident evidence of plagiarism

For more information see guide to grades.

Late submission

In accordance with University policy, these penalties apply when written work is submitted after 11:59pm on the due date:

Deduction of 5% of the maximum mark for each calendar day after the due date.
After ten calendar days late, a mark of zero will be awarded.

This unit has an exception to the standard University policy or supplementary information has been provided by the unit coordinator. This information is displayed below:

Reports marked in class must be completed by the stipulated time. Late submissions will lose 5% per day or part thereof up until marks and comments are released to the class or 10 days late (if marks have not yet been released) after which time a mark of 0 will be recorded.

Academic integrity

The Current Student website provides information on academic integrity and the resources available to all students. The University expects students and staff to act ethically and honestly and will treat all allegations of academic integrity breaches seriously.

We use similarity detection software to detect potential instances of plagiarism or other forms of academic integrity breach. If such matches indicate evidence of plagiarism or other forms of academic integrity breaches, your teacher is required to report your work for further investigation.

Use of generative artificial intelligence (AI) and automated writing tools

You may only use generative AI and automated writing tools in assessment tasks if you are permitted to by your unit coordinator. If you do use these tools, you must acknowledge this in your work, either in a footnote or an acknowledgement section. The assessment instructions or unit outline will give guidance of the types of tools that are permitted and how the tools should be used.

Your final submitted work must be your own, original work. You must acknowledge any use of generative AI tools that have been used in the assessment, and any material that forms part of your submission must be appropriately referenced. For guidance on how to acknowledge the use of AI, please refer to the AI in Education Canvas site.

The unapproved use of these tools or unacknowledged use will be considered a breach of the Academic Integrity Policy and penalties may apply.

Studiosity is permitted unless otherwise indicated by the unit coordinator. The use of this service must be acknowledged in your submission as detailed on the Learning Hub’s Canvas page.

Outside assessment tasks, generative AI tools may be used to support your learning. The AI in Education Canvas site contains a number of productive ways that students are using AI to improve their learning.

Learning support

Simple extensions

If you encounter a problem submitting your work on time, you may be able to apply for an extension of five calendar days through a simple extension.  The application process will be different depending on the type of assessment and extensions cannot be granted for some assessment types like exams.

Special consideration

If exceptional circumstances mean you can’t complete an assessment, you need consideration for a longer period of time, or if you have essential commitments which impact your performance in an assessment, you may be eligible for special consideration or special arrangements.

Special consideration applications will not be affected by a simple extension application.

Using AI responsibly

Co-created with students, AI in Education includes lots of helpful examples of how students use generative AI tools to support their learning. It explains how generative AI works, the different tools available and how to use them responsibly and productively.

Support for students

The Support for Students Policy 2023 reflects the University’s commitment to supporting students in their academic journey and making the University safe for students. It is important that you read and understand this policy so that you are familiar with the range of support services available to you and understand how to engage with them.

The University uses email as its primary source of communication with students who need support under the Support for Students Policy 2023. Make sure you check your University email regularly and respond to any communications received from the University.

Learning resources and detailed information about weekly assessment and learning activities can be accessed via Canvas. It is essential that you visit your unit of study Canvas site to ensure you are up to date with all of your tasks.

If you are having difficulties completing your studies, or are feeling unsure about your progress, we are here to help. You can access the support services offered by the University at any time:

Support and Services (including health and wellbeing services, financial support and learning support)
Course planning and administration
Meet with an Academic Adviser

Weekly schedule

WK	Topic	Learning activity
Multiple weeks	Module 1 - Evolution, Making and Breaking Proteins	Lecture (4 hr)
	Module 2 - Protein Function	Lecture (6 hr)
	Module 3 - Interactions and Disorder	Lecture (4 hr)
	Module 4 - Protein Folding	Lecture (4 hr)
	Module 5 - Protein Engineering and Design	Lecture (6 hr)
	Practical Laboratory Classes	Practical (36 hr)
	Presentation assignment	Tutorial (3 hr)

Attendance and class requirements

The laboratory course is an essential part of the unit of study and students must pass the laboratory component in order to pass the unit. In order to pass students must attend 80% of practical sessions, demonstrate engagement, and submit lab notebooks for assessment (minimum of 4/5 indicative and marked reports/notebooks).

Failure to submit this material will result in AF for the Unit.

If technical issues, illness, a requirement to isolate etc. prevent attendance at a specific class, students should discuss the problem with the coordinator to find out how to make up the missed attendance.

Study commitment

Typically, there is a minimum expectation of 1.5-2 hours of student effort per week per credit point for units of study offered over a full semester. For a 6 credit point unit, this equates to roughly 120-150 hours of student effort in total.

Required readings

This Course draws material from a range of different sources that will be advised by the lecturers. We don’t have a single textbook for the course, but recommend you have access to a comprehensive Biochemistry text book such as Lehninger - The Principles of Biochemistry. The following Reference texts may be useful for parts of the course.

Williamson M How Proteins Work Mike Garland, 2012

Cooper et al The Cell A Molecular Approach (7th edition, Sinauer, 2018)

Lodish H et al Molecular Cell Biology (8th edition, W H Freeman 2016)

Learning outcomes

Learning outcomes are what students know, understand and are able to do on completion of a unit of study. They are aligned with the University's graduate qualities and are assessed as part of the curriculum.

Outcomes
Graduate qualities

At the completion of this unit, you should be able to:

LO1. outline the basic principles and describe in detail the constituent elements of protein structure; attribute these properties to protein and cell function.
LO2. describe the physical principles and chemical properties that drive protein structure, function, folding and biomolecular interactions
LO3. understand and predict how changes in protein sequence can aﬀect structure and function and contribute to disease.
LO4. compare the various ways in which proteins can be designed or engineered; assess which properties of proteins and protein machines can be adapted to achieve a range of diﬀerent activities or speciﬁcities
LO5. describe how the processes of protein synthesis, folding and degradation contribute to homeostasis in the cell; evaluate how disruptions to these processes are regulated.
LO6. examine the mechanisms through which enzymes can be regulated through naturally occurring and synthetic modulators.
LO7. explain, with examples, the diﬀerence between qualitative and quantitative measurements; determine which of the diﬀerent techniques should be used; implement methods to visualize and characterise the properties of proteins in an accurate and reproducible manner.
LO8. collect experimental data and adapt, develop and trouble-shoot experimental procedures for novel contexts.
LO9. assess the quality of data, critically interpret and draw conclusions from data obtained in the laboratory.
LO10. summarise and identify the key points from biochemical data from a range of published sources; synthesise, analyse and communicate the ﬁndings. Judge its reliability and signiﬁcance in the context of experimental data.

Graduate qualities

The graduate qualities are the qualities and skills that all University of Sydney graduates must demonstrate on successful completion of an award course. As a future Sydney graduate, the set of qualities have been designed to equip you for the contemporary world.

GQ1	Depth of disciplinary expertise Deep disciplinary expertise is the ability to integrate and rigorously apply knowledge, understanding and skills of a recognised discipline defined by scholarly activity, as well as familiarity with evolving practice of the discipline.
GQ2	Critical thinking and problem solving Critical thinking and problem solving are the questioning of ideas, evidence and assumptions in order to propose and evaluate hypotheses or alternative arguments before formulating a conclusion or a solution to an identified problem.
GQ3	Oral and written communication Effective communication, in both oral and written form, is the clear exchange of meaning in a manner that is appropriate to audience and context.
GQ4	Information and digital literacy Information and digital literacy is the ability to locate, interpret, evaluate, manage, adapt, integrate, create and convey information using appropriate resources, tools and strategies.
GQ5	Inventiveness Generating novel ideas and solutions.
GQ6	Cultural competence Cultural Competence is the ability to actively, ethically, respectfully, and successfully engage across and between cultures. In the Australian context, this includes and celebrates Aboriginal and Torres Strait Islander cultures, knowledge systems, and a mature understanding of contemporary issues.
GQ7	Interdisciplinary effectiveness Interdisciplinary effectiveness is the integration and synthesis of multiple viewpoints and practices, working effectively across disciplinary boundaries.
GQ8	Integrated professional, ethical, and personal identity An integrated professional, ethical and personal identity is understanding the interaction between one’s personal and professional selves in an ethical context.
GQ9	Influence Engaging others in a process, idea or vision.

Outcome map

Learning outcomes	Graduate qualities
Learning outcomes

Responding to student feedback

This section outlines changes made to this unit following staff and student reviews.

No significant changes.

Additional information

Please bring at least one waterproof marking pen for labelling tubes/plates in laboratory classes.

Additional costs

Students must have their own lab coat, safety glasses for use in lab classes.

Work, health and safety

Personal and communal safety is of the highest importance. Students must familiarize themselves with and observe the safety procedures outlined in the WHS guidelines (see Canvas site). For this Unit of Study, you are required to submit a Safety Awareness Statement. This form and submission details are available from Canvas.

Disclaimer

The University reserves the right to amend units of study or no longer offer certain units, including where there are low enrolment numbers.

To help you understand common terms that we use at the University, we offer an online glossary.

Current students

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Support for students

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Required readings

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Additional costs

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect

Current students

BCMB3902: Protein Function and Engineering (Advanced)

Semester 1, 2024 [Normal day] - Camperdown/Darlington, Sydney

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Support for students

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Required readings

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Additional costs

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect