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 the material is discussed in greater detail and at a more advanced level. Students enrolled in BCMB3902 participate in a partially varied practical and tutorial program that focuses on developing skills in experimental design, critical thinking, data analysis and communication.

Unit details and rules

Unit code	BCMB3902
Academic unit	Life and Environmental Sciences Academic Operations
Credit points	6
Prohibitions ?	BCHM3X81 or BCMB3002
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
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
	Sandro Fernandes Ataide, sandro.ataide@sydney.edu.au
	Joel Mackay, joel.mackay@sydney.edu.au
Tutor(s)	Ann Kwan, ann.kwan@sydney.edu.au

Type	Description	Weight	Due	Length
Final exam (Record+)	Final Exam MCQ and short answer questions covering lectures and practical classes	50%	Formal exam period	2 hours
Outcomes assessed:
Assignment	Protein structure assignment and presentation Pymol Presentation in Week 12. Individual written report (Week 13)	10%	Multiple weeks	See Canvas for more detail
Outcomes assessed:
Assignment	Lab book experiment short reports Data curation and short report	7.5%	Multiple weeks	400 words plus figures
Outcomes assessed:
Assignment	Lab worksheets Week 1 Lab work sheets and revision exercises	2.5%	Week 01	120-150 min
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 MCQs in Lecture/Online	5%	Week 10	40 minutes
Outcomes assessed:
Assignment	Short paper format lab report RTP laboratory practicals written up in format of a short scientific paper	10%	Week 10	1000 words plus figures
Outcomes assessed:
Small test	Quiz / calculations Theory Of Prac Open Book exam in Lab	10%	Week 11	90-120 minutes
Outcomes assessed:
= group assignment ? = Type B final exam ?

Assessment summary

Detailed information for each assessment can be found on Canvas.

Lab Revision Week 1 – work through online and in lab revision exercises in Lab Class.

Lab Book Experiment Short Reports – eLN lab reporting and data analysis of experimental labs. To be completed in Lab classes. Additional time may be allowed to finalise reports depending on the complexity or timing of the task. One short sample lab write up (not graded but indicative marks and feedback given). Three graded reports throughout the lab series.

Detailed Lab report. Short paper format report of continuing series of labs up to end of Week 7 will draw on on-going lab reporting. Specific details provided by Week 7.

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 in Week 7.

Tutorial quizzes will be held in Lectures. These will include MCQs relating to lecture material (covering specific modules).

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) and theory of prac. MCQ and short answer questions.

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.

High Distinction

85-100

As for the criteria for ‘Distinction’, however the work also shows a high degree of originality and creativity. There is evidence that the view of teaching and learning in professional, vocational and/or higher education and their application in practice, have contributed to personal learning. There is good evidence of critical reflection on academic practice and identification of strategies for development. There is evidence of the ability to generalise the subject content to areas not covered in formal class session.

Distinction

75-84

The work shows a good appreciation of the general purpose of the topic. There is good coverage of the topic with relevant and accurate support and a well developed scholarly argument. The work demonstrates a clear view of how the various aspects of the topic integrate to meet the purpose. There is good evidence of application of assignment content to a relevant context.

Credit

65-74

The work is relevant, accurate and addresses several aspects of the topic. There is demonstration of understanding in relation to a reasonable amount of the content and a scholarly argument has been advanced. There is emerging evidence of an overall integrative view of the topic, and growing awareness of application or integration.

Pass

50-64

The information in the various aspects of the work is relevant and accurate but is not integrated and only covers core aspects of the topic. There is an attempt at a scholarly argument and the work indicates a limited understanding of the topic.

Fail

0-49

The information in the work is irrelevant, inaccurate or has missed the point. The work is insufficient; there is a lack of engagement with learning tasks or a failure to submit in the agreed timeframe.

For more information see sydney.edu.au/students/guide-to-grades.

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.

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.

You may only use artificial intelligence and writing assistance tools in assessment tasks if you are permitted to by your unit coordinator, and if you do use them, you must also acknowledge this in your work, either in a footnote or an acknowledgement section.

Studiosity is permitted for postgraduate units unless otherwise indicated by the unit coordinator. The use of this service must be acknowledged in your submission.

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.

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 (72 hr)
	Presentation assignment	Tutorial (3 hr)

Attendance and class requirements

Due to the exceptional circumstances caused by the COVID-19 pandemic, attendance requirements for this unit of study have been amended. Where online tutorials/workshops/virtual laboratories have been scheduled, students should make every effort to attend and participate at the scheduled time. Penalties will not be applied if technical issues, etc. prevent attendance at a specific online class. In that case, students should discuss the problem with the coordinator, and attend another session, if available.

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.

Changes have been made to this units to facilitate remote and in person lab classes

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 and mask (3-layer) 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.

Please note that masks must be worn in Laboratory Classes for this course.

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

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, 2021 [Normal day] - Remote

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

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