Genome Structure Flashcards
DNA is
Deoxyribonucleic acid
What type of molecule is DNA?
Macromolecule consisting of a linear strand of nucleotides
Nucleotide
What the difference between deoxyribose sugar and ribose sugar
Deoxyribose doesn’t have the 2’- hydroxy group
What charge is the phosphate group?
Negative charge
DNA in 3D
2 groves (major and minor)
2 antiparallel strands
bases stacked
How to pack DNA
Histones
Histones
Basic (positively charged) proteins that bind DNA
8 Histones form a nucleosome
Histone 1 binds the linker DNA
DNA packing
DNA double strand helix -> Nucleosomes -> chromatin -> loops of chromatin fiber -> metaphase chromosome
How many chromosomes in a human?
23 pairs (human karyotype)
What do gene contain?
CAAT box TATA box Transcription initiation Translation initiation Translation termination Transcription termination
The exome
• The exome is made up of gene sequences
What is a gene?
Gene promoter, the coding sequences, stop codon
Globin gene size
1.8 kb
Dystrophin gene size
2.4 Mb
Gene clusters
An example of clusters globin clusters
- allows for co-ordinated gene regulation
- may just reflect evolutionary history
Introns within a gene
- Vary in number from 0 to at least 311
- Vary in size - 30 bp to 1 Mbp
- Some introns contain other genes
What do promoters do?
Recruit RNA polymerase
Regulation of RNA synthesis
Regulation occurs via transcription factors
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
Short sequences that act to prevent enhancers/silencers influencing other genes
Transcription
Catalysed by RNA Polymerase II
• Transcribes in 5’ to 3’ direction
• Transcribes everything after the transcription start site (exons and introns)
• mRNA is post-transcriptionally modified
RNA polymerase 2
Recognise promoters efficiently with the assistance of many other transcription factors
Post transcriptional modification of mRNA
- Capped at 5’ end
- Spliced - introns removed
- Polyadenylated at 3’ end
5’ cap
After 25-30nts are synthesised, a methylated cap is added to the 5’ end by three enzyme activities:
• RNA 5’-triphosphatase
• Guanylyltransferase
• N7G-methyltransferase
What other enzyme is needed for 5’ capping?
The first two activities are carried out by a bifunctional capping enzyme (CE)
RNA Pol II is also required
What is the TREX complex?
Transcription-EXport.
mRNA alsohas the 5’ cap, poly A tail and exon junction complexes.
3’ Poly A tail
- CPSF recognise the PAS and acts on cleavage site.
- CSTF recognises GU-rich downstram elements
- PAP is requited and adds multiple A bases after cleavage site
- PAB is Poly A Binding protein. Other proteins appear to be required for this process - CFlm and simplekin
CPSF
Cleavage and Polyadenylation Stimulating Factor
PAS
Polyadenylation Signal
CSTF
Cleavage Stimulating Factor
DSE
Downstream Elements
PAP
Poly-A polymerase
PAB
Poly A binding protein
CFlm
Cleavage Factor lm
Alternative splicing
Produces different proteins due to exon splicing
Isoform
Variations of proteins from the same gene
