BCHM3092/3992

Proteomics and Functional Genomics

Course Information

These course outlines are a guide only. They are provided for the information of prospective students. Although every effort is made to ensure the most up to date information is provided, timetables often change each semester due to the availability of rooms and resources. Content (including lecture/practical topics, assessment and textbooks) is also regularly reviewed to ensure relevance and effective learning.

Course Overview

General Information
The "Age of Genomics" has heralded a new era of high-throughput biology. The question remains, however, as to how best utilize this plethora of new DNA sequence information. Much progress has been made on two fronts: i) the use of "microarray" technology that enables monitoring of DNA expression at the transcript (RNA) level; and ii) the establishment of rapid and sensitive techniques for understanding the protein complement of the genome (the "proteome"). These techniques allow scientists to understand how the genome responds to changes in environment or genetics, and most importantly during health and disease at the organism, cell or tissue level.

This course provides a comprehensive account of the cutting-edge technologies currently being applied in the field of functional genomics – with a particular emphasis on the proteome. Technologies will be introduced with specific examples of their application in the biological and medical sciences. This knowledge will demonstrate how science is striving towards understanding the molecular and biochemical fundamentals of life.

Course Coordinator Contact Details

Assoc Prof Stuart Cordwell

Room: 713/715

Telephone: 9351 6050

E-mail: stuart.cordwell@sydney.edu.au


Mrs Jill Johnston

Room: 410

Telephone: 9351 4248

E-mail: jill.johnston@sydney.edu.au

Prerequisites

For BCHM3092
[MBLG (1001 or 1901) and 12 CP of Intermediate BCHM/MBLG units (taken from MBLG2071/2971 or BCHM2071/2971 or BCHM2072/2972)] OR [42CP of Intermediate BMedSc units (taken from BMED2801, BMED2802, BMED2803, BMED2804, BMED2805, BMED2806, BMED2807, BMED2808, but including BMED2802 and BMED2804)] OR [18CP of intermediate BMED units (taken from BMED2401, BMED2402, BMED2403, BMED2404,BMED2405, BMED2406, but including BMED2401 and BMED2405) and 6CP of Intermediate BCHM/MBLG units (taken from MBLG2071/2971 or BCHM2071/2971)

For BCHM3992
MBLG (1001 or 1901) and Distinction in 12 CP of Intermediate BCHM/MBLG units (taken from MBLG2071/2971 or BCHM2071/2971 or BCHM2072/2972)] OR [42CP of Intermediate BMedSc units (taken from BMED2801, BMED2802, BMED2803, BMED2804, BMED2805, BMED2806, BMED2807, BMED2808, with Distinction in BMED2802 and BMED2804)] OR [18CP of intermediate BMED units (taken from BMED2401, BMED2402, BMED2403, BMED2404, BMED2405, BMED2406, with Distinction in BMED2401 or BMED2405) and 6CP of Intermediate BCHM/MBLG units (taken from MBLG2071/2971 or BCHM2071/2971) with Distinction in MBLG2071/2971 or BCHM2071/2971

Timetable

1st Lecture: Wednesday 10:00am-11:00am, Chemistry Lecture Theatre 4

2nd Lecture: Thursday 9:00am-10:00am, Chemistry Lecture Theatre 4


PRACTICAL CLASS TIMES and VENUES

TIMES: 10:00am - 1:00pm Fridays, weekly, as per student timetable. *
VENUE: All practical classes will be in the Biochemistry 3 lab, Level 4, Biochemistry and Microbiology building, G08

*Note that it is possible to leave the practical class to attend a lecture in another subject, in which case the practical class will finish at 2:00pm.

Textbooks

Recommended
Kraj A. and Silberring J. Proteomics – Introduction to Methods and Applications (Wiley – Interscience 2008)

Lecture Outlines

1. An Introduction to Genomics, Functional Genomics and Proteomics (SJC)
This lecture will be a course outline, an introduction to the lecture series and background material.

Genomics and Transcriptomics
2. Systems Biology (BC)
This lecture examines how the ‘mega data’ technologies now possible through genomics, transcriptomics and proteomics can be brought together to provide a fully organismal understanding of biology.

3. Genome Sequencing (BC)
This lecture will cover the basic concepts of genome sequencing, why it is important and what there is still left to learn – a basic introduction to put the remainder of the course in context. The lecture will cover technologies for genome sequencing, conserved genes and proteins and the ‘minimal gene content’, hypothetical and unique genes and proteins.

4. Modern Genome Sequencing (BC)
Examines the technological advances made since the first full genome was sequenced. Is ‘genome-in-a-day’ possible?

5. Transcriptomics and Microarrays (BC)
This lecture will cover the use of changes in mRNA expression in different biological circumstances, including technical aspects.

6. Genome Sequencing and Transcriptomics in Disease (BC)
How have the technologies learned in the above lectures been applied, particularly to the study of human disease? This lecture examines what we have gained by taking a genomics-based approach.


Protein Separation

7. Understanding Protein Sequences (SJC)
A reminder of how proteins are made and how they work, this lecture will cover protein sequence motifs, use of databases and some information on structure, as well as how genome sequencing has made us redefine ‘traditional’ biochemical pathways.

8. Two-Dimensional Gel Electrophoresis (BC)
This lecture covers the basics of sample preparation, isoelectric focusing, SDS-PAGE, and staining of 2-DE gels, as well as Cy dye 2-D Difference In-Gel Electrophoresis with examples of biomedical applications, especially cancer.


Protein Identification

9. Principles of Mass Spectrometry (SJC)
This lecture will provide students with the necessary background to the physics and principles of mass spectrometry, how mass spectrometers work and why they have become the tool-of-choice for proteomic research.

10. Peptide Mass Fingerprinting (SJC)
This lecture will provide students with the understanding of how proteins are taken from gel to identification, via proteolytic cleavage, MALDI-TOF MS and database searching.

11. Applications of Proteomics – Cancer Proteomics (RIC)
This lecture will bring together technical concepts in the context of discovery proteomics in cancer biology.

12. Antibody Microarrays (RIC)
An introduction to antibody microarrays as an alternative technology in proteomics.

13. Tandem Mass Spectrometry (SJC)
In this lecture, students will learn the principles of MS/MS, de novo sequencing and database interrogation.

Applications in Proteomics I

15. ‘Ome is where the heart is I – Regulomes, Stimulomes and Phenomes (SJC)
This lecture describes the traditional use of proteomics technology to understand biological events in cells and tissues. It will specifically discuss – i) regulons (understanding which genes and proteins are regulated by another gene / protein; ii) stimulons – stress response; and iii) phenotype – how comparisons can be made based on two phenotypes.

16. ‘Ome is where the heart is II – Surfaceomes and Secretomes (SJC)
This lecture will introduce the concept of sub-cellular proteomics – covered topics will include technology to specifically isolate surface proteins and organelle proteomics.

17. Applications in Quantitative Proteomics (SJC)
This lecture will cover quantitative methods for comparative proteomics and show how these have been applied in the study of biological samples.

Post-Translational Modifications

18. Introduction to Post-Translational Modifications (SJC)
This lecture will describe the principles of ‘one gene, many proteins’, the size of the human proteome, and the underlying need for proteomics technologies to understand PTM complexity.

19. Phosphorylation (SJC)
This lecture will introduce the biological and medical importance of phosphorylation and signal transduction pathways and the analytical methods used to determine it. Examples used to illustrate will include the EGF and insulin signal pathways.

20. Glycosylation and Glycomics (SJC)
This lecture will introduce the biological importance of carbohydrate attachment to proteins and the analytical methods used to determine it. We will also examine how carbohydrate (glycan) structures are resolved and their importance in cancer.

21. Deamidation, Protein Cleavage, Oxidation and Oxidative Stress (SJC)
This lecture will introduce the biological importance of these PTMs and discuss their role in pathogenesis.


Applications in Proteomics II

22. Diagnostic Proteomics (SJC)
This lecture covers latest technologies for diagnostic proteomics, including SELDI-TOF MS, mass spectral tissue imaging and profiling, and understanding human plasma as the means of discovering biomarkers of disease.

23. Protein Complexes and Protein-Protein Interactions (MYW)
An introduction to the importance of proteins that function in complexes, the lecture will briefly discuss major methods used to define protein interactions, including yeast 2-hybrid system, immunoprecipitation, and tandem affinity purification.

24. Applications in Proteomics – Cardiovascular Proteomics (MYW)
This lecture will bring together technical concepts in the context of discovery proteomics in cancer biology.

25. Validation of Proteomics Data and The Human Protein Atlas (SJC)
Looks at the impact of the Human Protein Atlas and the Human Proteome Project.

26. Applications of Genomics, Functional Genomics and Proteomics (SJC)
This lecture will provide a refresher for the technical aspects of the course with an emphasis on applications in medical and biotechnological industries.

Practical Course

P1 Microarray Analysis of Murine Erythro-Leukaemia Cells During Differentiation (2 weeks)
P2 Proteome Analysis of Murine Erythro-Leukaemia Cells During Differentiation (5 weeks)
P3 Mass Spectrometric Analysis of Post-Translational Modification of Proteins (2 weeks)
P4 Affinity Chromatography: Purification of disulfide-containing proteins and analysis by mass spectrometry (2 weeks)

Assessment

Lecture course: 50% (end-of-semester examination)
Practical course: 50% (25% in-semester practical work, 25% end-of-semester examination)