W1 - Genome Structure Flashcards
What is DNA?
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
What does a single strand of DNA consist of?
5’ and 3’ carbons are indicated – numbering starts at the carbon
closest to the base.
* Sequence is 5’->3’ by convention
What does a double stranded DNA consist of?
Antiparallel, complementary base pairing.
The 5’ and 3’ go in diagonal and opposite directions making it antiparallel.
How can DNA be seen in a 3D format?
- Two antiparallel strands of DNA
- Bases “stacked”
- Two grooves
- Major
- Minor
How is there genome variation?
- Human genome is 3 x 10^9 base pairs – 3Gbp
- It contains ~20 000 genes.
- There is a trend for simpler organisms to have fewer genes,
for example, flies have 10,000, yeast 4,000, bacteria 1,000 - However, genome size is not strongly related to complexity of an organism - marbled lungfish is 130Gbp and Paris japonica is 149Gbp
What is the solution to the DNA packing problem?
Nuclear DNA = 2m per cell
Solution to packing:
* Basic (+vely charged) proteins that binds the negatively charged DNA
* Eight histones 2x(H2A+H2B+H3+H4) form the nucleosome
* Histone 1 binds the linker DNA
What is the nucleosome structure with the DNA packed?
After being packed into histones, the DNA then wound around themselves to form fibres. They then wound further to form an extended chromosome. This is again wound to form loops of chromatin fibre to then produce the metaphase chromosome - the densest form of DNA.
What is the definition of an exome?
- The exome is made up of gene sequences
- Some definitions use all of the coding sequences (~37 Mbp – 1.2% of genome)
- Some definitions use all of the gene sequences (~60Mbp – 2% of genome)
What is a gene?
- 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
- It is NOT just the bits that encode the final protein, regulation of the gene is
very important.
What is the structure of a gene?
Structure of chromosome is: Genes, Intergenic region (98%), Genes.
These genes can be very different sizes.
Intergenic regions contain sequences of unknown function, such as repetitive DNA, endogenous retroviruses, pseudogenes. They may contain many regulatory elements.
Genes often cluster in families – e.g. globin clusters:
- allows for co-ordinated gene regulation
- may just reflect evolutionary history
Structure of a gene: Promotor (CAATboxes and TATA boxes) and within the transcriptional unit, multiple exons and introns. Transcriptional initiation and termination. There are also 5’ UTR and 3’ UTR (untranslated region).
What are introns and what is their purpose?
- Vary in number – from 0 to over 300
- Vary in size - 30bp to 1Mbp
- Some introns contain other genes
There is always one less intron than exons - none exist after final exon.
Purpose: Allow for splicing - multiple different forms of the same gene.
They do not exist in the matured RNA
What is a promoter?
- Promoters recruit RNA polymerase to a DNA template
- RNA polymerase binds asymmetrically and can only move 5’ to 3’
- Regulation occurs via transcription factors
What is a regulatory element?
Regulatory element
(needed to regulate recruitment
of RNA polymerase)
What is a TATA box?
“TATA box”
(needed to recruit general
transcription factors and RNA
polymerase)
What are enhancers?
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).
