Genome Structure

Question 1

As a recap, what is DNA?

Answer 1

DNA is deoxyribonucleic acid. It is a macromolecule consisting of a linear strand of nucleotides.
Single linear strands bind to complementary strands to form double-stranded DNA.

Question 2

How does DNA exist in 3D?

Answer 2

• there are two antiparallel strands of DNA
• the bases are ‘stacked’
• there are two grooves: major and minor

Question 3

What is the order in which DNA is packed?

Answer 3

• DNA basic helix
• nucleosomes
• chromatin fibre
• extended section of chromosome
• loops of chromatin fibre
• chromosome

Question 4

As a recap, describe histones.

Answer 4

They are basic proteins that bind DNA.

Eight histones in total form the nucleosome unit; histone 1 binds the linker DNA.

Question 5

What is the relation between DNA and genes?

Answer 5

The primary DNA sequence encodes all the gene products necessary for an organism.
The primary DNA sequence also includes a large number of regulatory signals.

Much of the DNA sequence does not have an assigned function as of yet.

Question 6

What is a gene?

Answer 6

A gene is: all of the DNA that is transcribed into RNA, plus all of the cis-linked (local) control regions that are required to ensure quantitatively appropriate tissue-specific expression of the final protein.

(ie. it is not just the bits that code for the final protein, regulation of the gene is very important)

Question 7

How is the genome organised?

Answer 7

Genes often cluster in families - eg. globin clusters

This:

• allows for coordinate gene regulation
• may just reflect evolutionary history

Question 8

What are the intergenic regions in the genome?

Answer 8

Intergenic regions contain sequences of no known function, such as repetitive DNA, endogenous retroviruses, pseudogenes, etc.

Question 9

How does RNA polymerase bind to the strand?

Answer 9

• promoters recruit RNA polymerase to a DNA template

- RNA polymerase binds asymmetrically and can only move 5’ to 3’.

Question 10

List the functions of the three RNA polymerases.

Answer 10

• RNA Polymerase I - needed to transcribe rRNA genes
• RNA Polymerase II - needed to transcribe mRNA
• RNA Polmerase III - needed to transcribe tRNA an other small RNAs

Question 11

Very briefly, describe the steps of transcription.

Answer 11

1) RNA Polymerase recruited (closed complex)
2) DNA helix locally unwound (open compex)
3) RNA synthesis begins
4) Elongation
5) Termination
6) RNA Polymerase dissociates

Question 12

List some other regulatory regions and their functions.

Answer 12

• ENHANCERS upregulate gene expression - they are short sequences that can be in the gene or many kilobases distant. They are targets for transcription factors (activators).
• SILENCERS downregulate gene expression. They are also position-independent and are also targets for transcription factors (repressors).
• INSULATORS are short sequences that act to prevent enhancers/silencers influencing other genes.

Question 13

How is eukaryotic mRNA modified after transcription?

Answer 13

• capped at the 5’ end
• polyadenylated at the 3’ end
• intervening sequences (introns) are removed

Question 14

Recap, what is alternative splicing?

Answer 14

Exons can be skipped or added, so variations of a protein (called isoforms) can be produced from the same gene.

Question 15

Describe pseudogenes.

Answer 15

These are genes that have been at least partially inactivated by the loss or gain of sequence that disrupts their correct transcription and/or translation.

Processed pseudogenes have no promoter or exons as they are copied from mRNA by retrotransposition.