FUTURE TARGETS: OMICS

Question 1

Describe gene analysis.

Answer 1

Uses very homogenous samples.
Uses amplification technology (PCR).
Has small dynamic range (1-25 copies)
Gene ID methods are extensive, cheap, easy and relatively fast.
35000-40000 human genes.
Genome is relatively static (changes occur in hours as opposed to seconds)

Question 2

Describe protein analysis.

Answer 2

Very heterogenous samples.
No amplification technology available.
Huge dynamic range (1-10mil copies)
Protein ID methods are expensive and technically challenging.
up to 400k proteins in humans.
Proteome is highly dynamic, and can change within seconds.

Question 3

What is bioinformatics? What are its applications?

Answer 3

The application of computer technology to biology. Can and has been used in the human genome project, proteomics, phenotyping, medical records and toxicology.

Question 4

What is genomics?

Answer 4

Comparative study of complete genome sequence and function.

Question 5

What is functional genomics?

Answer 5

Patterns of gene expression, mechanisms for control of gene expression and interrelationships of gene expression.

Question 6

How are gene products modified?

Answer 6

• complex gene interactions
• cellular events
• environmental influences
• post translational modifications

Question 7

Define ‘proteome’ and ‘proteomics’.

Answer 7

PROTEOME: All proteins expressed by a genome, cell or tissue.
PROTEOMICS: Analysis of entire protein complement expressed by a genome, or by a cell or tissue type.

Question 8

Why is proteomics important?

Answer 8

Many changes in protein activity occur via protein modification or regulated sub cellular localisation.
Genomics and transcriptomics give no information on interactions between proteins.

Question 9

Describe the proteomics approach.

Answer 9

Search for up or down regulated proteins in cell lysates, tissue extracts, blood etc.
changes in protein levels may be due to gene deletion or over expression, pharmaceutical treatment, stimulation (thermal or chemical) or withdrawal of nutrients or oxygen.

Question 10

Describe the “ideal” proteomics experiment.

Answer 10

Is able to separate most of the expressed proteins from an organism, shows which ones are down or up regulated compared to control, identifies proteins and gives sequence info, relates findings to the literature and gives structural info for drug development and other targets.

Question 11

Describe how markers of chemotherapy resistance were identified?

Answer 11

1. sample of drug resistant and drug sensitive cancer cells
2. proteins were isolated from the cells.
3. One sample labelled red, the other green.
4. 2D gel electrophoresis used to separate and visualise proteins
5. image analysis to identify differences in expression between samples.
6. altered proteins identified by mass spec and database mining

Question 12

Describe the process of identifying proteins by mass spectrometry.

Answer 12

1. Single protein spot excised from gel.
2. tryptic digestion releases peptides and their mass is measured using mass spec.
3. protein sequence databases searched for matches with theoretical masses calculated for all trypsin-released peptides.
4. identification and isolation of corresponding gene.