Outline

Overview

The sequencing of the human genome was a landmark achievement in science and medicine, marking the 'Age of Genomics'. Now we can access the blueprints for life, but need to uncover how those blueprints work, allowing organisms to respond to internal and external environmental changes, and how we can utilise this plethora of DNA sequence information to improve human and planetary health. This unit will investigate the function of the genome by examining the proteome, metabolome and beyond. You will investigate links between the central dogma of molecular biology and the complexities of living genomes - from modifications that massively increase diversity to the dynamic metabolome. You will explore fundamental cellular processes and discover how they are shaped by the proteome via gene expression, post-translational modification and protein complex formation. These processes will be examined in the context of human health and cardiovascular and metabolic disorders (e. g. type 2 diabetes) to demonstrate how global approaches can define, diagnose and help develop treatments for disease. You will practice methods employed in the post-genome era, including the 'Multi-omics' approaches that provide a global view of living systems, and discover how they are applied to solve problems in biology, biomedicine and agriculture. Beyond the Genome (Advanced) has the same overall structure as BCMB3004 but focuses on a more advanced level of practical work, data analysis and interpretation, using cutting-edge technologies. By the end of the unit students will understand why global 'omics approaches are needed in the post-genome era and know how best to apply such tools to given biological and biomedical problems.

Unit details and rules

Academic unit	Life and Environmental Sciences Academic Operations
Credit points	6
Prerequisites ?	An average mark of 75 or above in 12 credit points from (AMED3001 or BCHM2X71 or BCHM2X72 or BCHM3XXX or BCMB2X01 or BCMB2X02 or BCMB3XXX or BIOL2X29 or BMED2401 or BMED2405 or GEGE2X01 or MBLG2X01 or MEDS2002 or MEDS2003 or PCOL2X21 or QBIO2001)
Corequisites ?	None
Prohibitions ?	BCHM3X92 or BCMB3004
Assumed knowledge ?	Biochemistry, genetics, cell and/or molecular biology concepts at 2000-level units
Available to study abroad and exchange students	Yes

Teaching staff

Coordinator	Stuart Cordwell, stuart.cordwell@sydney.edu.au

Type	Description	Weight	Due	Length
Supervised exam ?	Final exam Written exam	50%	Formal exam period	2 hours
Outcomes assessed:
Small continuous assessment	Brief Reports Submitted after specified practical	15%	Multiple weeks	5 x Brief Report, summary of practical
Outcomes assessed:
Assignment	Computational Analysis Written report	5%	Week 06 Due date: 06 Sep 2023 at 23:59	500 words
Outcomes assessed:
Tutorial quiz	Online Quiz Online MCQs	10%	Week 08 Due date: 18 Sep 2023 at 14:00	30 mins
Outcomes assessed:
Assignment	Scientific Report Written report	20%	Week 13 Due date: 30 Oct 2023 at 23:59	1500-2000 words
Outcomes assessed:

Assessment summary

Exam

Final Exam (50%) – Supervised exam with mix of MCQs, short/long answer questions that cover the material covered in the lecture and practical course. Access to written notes (open book) allowed

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.

In-Semester Exam (10%) – Online MCQ quiz examining lecture and practical material up to the end of week 6.

In-Class Assessment

Online Task (5 x Brief Reports; 5 x 3%) - Satisfactory completion and/or understanding of practical tasks; write-up of experimental work, collection of results, analysis of results, answers to practical questions as per Unit of Study Manual; and entry into ELN.

Submitted work

Assignment (Computational Analysis; 5%) - Data analysis report; finding correct computational tools to analyse a given set of problems; submission of written report via Canvas.

Assignment 3904 Advanced (Scientific Report; 20% [3904]) – Additional tutorials and laboratory work, where possible. Data analysis and interpretation of a given set of proteomics/metabolomics results in the context of a biological problem. Assignment requires Introduction and Discussion of the provided results.

Detailed information for all assessments can be found on Canvas.

Assessment criteria

Result Name	Mark Range	Description
High Distinction	85-100	Exceptional standard of work produced across multiple assessments
Distinction	75-84	Very high standard of work produced across multiple assessments
Credit	65-74	Good to very good standard of work produced across multiple assessments
Pass	50-64	Acceptable to good standard of work produced across one or more assessments
Fail	0-49	Learning outcomes of the Unit have not been met to an acceptable standard

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.

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.

Weekly schedule

WK	Topic	Learning activity
Week 01	1. Introduction 2. Global Approaches to Living Systems	Lecture (2 hr)
Week 02	1. Translating the Genome: Protein Sequences and Proteomics 2. Exploring the Proteome I	Lecture (2 hr)
Week 03	1. Exploring the Proteome II 2. Exploring the Proteome III	Lecture (2 hr)
Week 04	1. Exploring the Proteome IV 2. Biological Applications of Proteomics (Organelles and Membranes)	Lecture (2 hr)
Week 05	1. Biological Applications of Proteomics (Regulons and Stimulons 2. Introduction to Post-Translational Modification of Proteins	Lecture (2 hr)
Week 06	1. Phosphorylation and Signalling I 2. Phosphorylation and Signalling II	Lecture (2 hr)
Week 07	1. Glycosylation of Proteins I 2. Glycosylation of Proteins II	Lecture (2 hr)
Week 08	1. Redox Biochemistry I 2. Redox Biochemistry II	Lecture (2 hr)
Week 09	1. Protease Biochemistry 2. Protease Biochemistry II	Lecture (2 hr)
Week 10	1. Diagnostic and Clinical Proteomics 2. Protein-Protein Interactions / Protein Complexes	Lecture (2 hr)
Week 11	1. Validation and Integration of Multi-Omics Data 2. Introduction to the Metabolome	Lecture (2 hr)
Week 12	1. Applications of Metabolomics 2. Course Summary / Revision Lecture	Lecture (2 hr)
Weekly	Weekly Practicals - Experimental work covering large-scale protein separation (electrophoresis and chromatography), identification (sample preparation for mass spectrometry), characterization (determination of sites of protein post-translational modification, enzyme purification of assays) and data analysis (computational approaches).	Practical (3 hr)

Attendance and class requirements

See Canvas site.

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.

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. Demonstrate an understanding of key concepts in biochemistry – including translation and post-translational modification, signalling, generation and removal of oxidants, proteases, cell-cell communication etc.
LO2. Demonstrate an understanding of large-scale methodological approaches (proteomics, metabolomics) to study biochemical concepts shown in 1 (above)
LO3. Evaluate concepts in large-scale approaches to appropriately select such approaches to best solve qualitative and quantitative problems in scientific context
LO4. Identify the various ways in which proteins can be modified after translation, describe how these modifications are achieved and evaluate how they affect the physical and functional properties of proteins.
LO5. Apply appropriate analytical and computational tools to analyse scientific data
LO6. Find and analyse scientific literature and judge its reliability and significance in the context of experimental data
LO7. Explain, with examples, the difference between a qualitative and a quantitative measurement; determine which of the different measurements should be used, and implement methods to analyse various aspects of the proteome/metabolome, in an accurate and reproducible manner.
LO8. Adapt, develop and trouble-shoot experimental procedures for novel contexts and requirements at an advanced level, including self-directed data generation and research problem solving
LO9. Assess the quality of data, interpret and draw conclusions from data obtained in the laboratory at an advanced level, against a wider research context and providing evidence of hypotheses generation.
LO10. Demonstrate a sense of responsibility, understanding of WHS issues, ethical behaviour, and independence as a learner

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.

Brief Reports are now worth 3% instead of 2%, one major assignment has been removed that covers the same material as the brief reports; the value of the major advanced assignment has been increased to 20% to reflect the effort required (additional lab work and tutorials).

Additional information

Work, health and safety

See Canvas site.

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

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect

Current students

BCMB3904: Beyond The Genome (Advanced)

Semester 2, 2023 [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

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Work, health and safety

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect