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Unit of study_

BCMB3904: Beyond The Genome (Advanced)

Semester 2, 2021 [Normal day] - Camperdown/Darlington, Sydney

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

Unit code BCMB3904
Academic unit Life and Environmental Sciences Academic Operations
Credit points 6
Prohibitions
? 
BCHM3X92 or BCMB3004
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
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
Final exam (Record+) Type B final exam Final exam
Written exam
50% Formal exam period 2 hours
Outcomes assessed: LO1 LO2 LO3 LO4 LO5
Online task Brief Reports
Submitted after specified practical
10% Multiple weeks 4 x report
Outcomes assessed: LO7 LO10 LO9 LO8
Assignment Scientific Report
Written with non-written elements
15% STUVAC 1500-2000 words
Outcomes assessed: LO1 LO2 LO3 LO7 LO9 LO10
Assignment Computational Analysis
Written report
5% Week 07 500 words
Outcomes assessed: LO4 LO5 LO7 LO9
Assignment Laboratory paper
Scientific Report
10% Week 08 1000-1500 words
Outcomes assessed: LO5 LO6 LO7 LO8 LO9 LO10
Tutorial quiz In-Semester Quiz
Online MCQs
10% Week 10 1 hour
Outcomes assessed: LO1 LO5 LO4 LO3 LO2
Type B final exam = Type B final exam ?

Assessment summary

Exam

Final Exam (50%) – Mix of MCQs, short/long answer questions that cover the material covered in the lecture and practical course.

In-Semester Exam (10%) – Online MCQ quiz examining lecture and practical material up to the end of week 9.

In-Class Assessment

Online Task (4 x Brief Reports; 4 x 2.5%) -  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 (Laboratory Paper; 10%) - Formal report of Practical work in Experiment 2 (Protein separation and identification) in the form of a scientific paper.

Assignment 3904 Advanced (Scientific Report; 15% [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.

 

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.

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.

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.

WK Topic Learning activity Learning outcomes
Week 01 1. Introduction 2. Global Approaches to Living Systems Lecture (2 hr) LO1 LO2
Week 02 1. Translating the Genome: Protein Sequences and Proteomics 2. Exploring the Proteome I Lecture (2 hr) LO1 LO2 LO3 LO5
Week 03 1. Exploring the Proteome II 2. Exploring the Proteome III Lecture (2 hr) LO1 LO2 LO3 LO5
Week 04 1. Exploring the Proteome IV 2. Biological Applications of Proteomics (Organelles and Membranes) Lecture (2 hr) LO1 LO5
Week 05 1. Biological Applications of Proteomics (Regulons and Stimulons 2. Introduction to Post-Translational Modification of Proteins Lecture (2 hr) LO1 LO5
Week 06 1. Phosphorylation and Signalling I 2. Phosphorylation and Signalling II Lecture (2 hr) LO1 LO2 LO4 LO5 LO7
Week 07 1. Glycosylation of Proteins I 2. Glycosylation of Proteins II Lecture (2 hr) LO1 LO2 LO4 LO5 LO7
Week 08 1. Redox Biochemistry I 2. Redox Biochemistry II Lecture (2 hr) LO1 LO2 LO3 LO4
Week 09 1. Protease Biochemistry 2. Protease Biochemistry II Lecture (2 hr) LO1 LO2 LO3 LO4 LO5
Week 10 1. Diagnostic and Clinical Proteomics 2. Protein-Protein Interactions / Protein Complexes Lecture (2 hr) LO1 LO2 LO3 LO5 LO6 LO8
Week 11 1. Validation and Integration of Multi-Omics Data 2. Introduction to the Metabolome Lecture (2 hr) LO1 LO2 LO3 LO5
Week 12 1. Applications of Metabolomics 2. Course Summary / Revision Lecture Lecture (2 hr) LO1 LO2 LO3 LO5 LO6 LO7
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) LO5 LO6 LO7 LO8 LO9 LO10

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 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.

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
GQ1 GQ2 GQ3 GQ4 GQ5 GQ6 GQ7 GQ8 GQ9

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

This is the first time this unit has been offered.

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.