Proteomes and Genomes

Question 1

Define genome

Answer 1

1. All genes encoded in the genetic material

2. The complete DNA sequence

Question 2

Define proteome

Answer 2

1. The entire complement of proteins expressed

2. Or sometimes the particular set of proteins expressed under specific conditions

Question 3

Describe the difference in number of chromosomes and genes in simple organisms and more complex organisms like humans. And state how this links to the complexity of an organism

Answer 3

1. Simple organisms have lower number of chromosomes and genes- 1, 4400
2. Human- 46, 20-25,000
3. Not always correlation between complexity and size of genomes- flowering plants have largest genome
4. Flowering plants- triploid and tetraploid- why they have so much genome- but not complex.

Question 4

What is the c-value

Answer 4

1. C-value is the amount of DNA contained within a haploid nucleus (e.g. a gamete) or one half the amount in a diploid somatic cell of a eukaryotic organism.

Question 5

What does c-value correlate and not correlate with?

Answer 5

1. Bears no relationship to the complexity of the organism or the number of genes contained in its genome. - Includes non-coding DNA
2. Correlates with: cell size, cell division rate, body size, metabolic rate, extinction risk

Question 6

Name 7 model systems in genomics

Answer 6

1. E. coli
2. Yeast
3. Arabidopsis
4. Drosophila
5. C. elegans
6. Mouse
7. Chimpanzee

Question 7

Why is E. coli used as a model system in genomics

Answer 7

1. Gut bacterium
2. Clone gene into bacteria so it produced the protein- easy to grow
3. No ethical problems,
4. First isolated in 1885- lots of background information
   on physiology, genetics and metabolism
5. form basis for most recent work in molecular biology

Question 8

Advantages and disadvantages of using chimpanzee as model system

Answer 8

1. Closest genome to humans so ideal
2. But ethical issues
3. And slower to reproduce

Question 9

Define proteomics

Answer 9

1. The study of the full set of proteins encoded by the genome

Question 10

What is the complexity of humans based on

Answer 10

1. The proteome not the genome

2. Posttranslational modifications (such as phosphorylation, glycosylation) can add a lot to the organisms diversity

Question 11

Define genomics

Answer 11

1. The comprehensive study of whole sets of genes and their interactions

Question 12

What is a common technique to separate proteins

Answer 12

1. Use of 2D gels to separate proteins based on their size and charge.
2. e.g. Use these gels to compare proteins from healthy and cancerous/malignant cells and look at the differences.
3. Proteins of interest can than be isolated form the gel and analysed by Mass-spectrometry.
4. And by c-terminal sequencing of a small stretch from the protein we can than identify its sequence.

Question 13

What is micro-array

Answer 13

1. single stranded DNA for genes of interest are deposited on a solid surface in a defined grid (probe)
2. Labelled target molecules (DNA or RNA) eluted over the surface and bind specifically and quantitatively
3. The DNA molecules attached to each slide act as probes to detect gene expression

Question 14

Why are proteomes more complex than genomes

Answer 14

1. Alternative splicing of pre-mRNA– 25000 genes can generate up to 100,000 proteins.
2. Post-translational modifications- proteolytic cleavage, glycosylation, phosphorylation

Question 15

What is big problem for protein biochemists

Answer 15

1. How we go from linear sequence of DNA to amino acid sequence to 3D structure and function
2. Not understood at the moment
3. Can’t tell you from genome sequence what a protein would look like in 3D
4. Can’t tell how the protein will fold up, where the active site will be or how many sub-units.

Question 16

Example of structure

Answer 16

1. Influenza Neuraminidase
2. Gene structure shows nothing about how protein functions
3. So have to look at proteome and structure of protein to understand how it works

Question 17

Describe the Influenza Neuraminidase

Answer 17

1. membrane virus
2. Haemagglutinin on surface of membrane- important for attachment of virus to our cells
3. Neuraminidase- important for release of virus after infection
4. Influenza is classified by type of Haemagglutinin
   and Neuraminidase on its surface

Question 18

Describe the proteins in influenza

Answer 18

1. When looking at gene sequence of H and N it doesn’t tell us what they do
2. So have to look at 3D protein structures
3. Found both proteins bind to sugar on surface of our cells- neuraminic acid/ sialic acid
4. Cleaves sialic acid from surface of a cell to release the virus
5. From structure can see electron density, 4 identical subunits and 4 Ligand binding sites
6. This was used to create medicine