4- Genome Structure Flashcards
define the structure of DNA from single base to the grooves of the helix
two anti-parallel polynucleotide strands with sugar-phosphate backbones bonded by phosphodiester bonds. run in opposite orientation (5’ to 3’ and vice versa) forming a right-handed helix
held together by H bonds between complementary bases - AT and CG
phosphate groups give nucleic acids and thus DNA an overall negative charge
major and minor grooves with internal base stacking - van der Waals between them depending on how close the molecules are
describe histones. how do they solve the DNA packaging problem?
histones are basic, positively charged proteins that bind DNA = as DNA is neg. charged, opposites attract.
solve the DNA packaging problem by forming nucleosomes:
eight histones - two each of H2A, H2B, H3 and H4 form the core optima, with H1 binding the linker DNA and 146 base pairs of DNA winding around the nucleosome.
nucleosomes condense into several other forms before forming chromosomes.
define the exome
EXOME is a portion of a genome with protein-coding genes = exons and their associated splicing junctions
what are the regulatory regions of a gene? what do they do?
REGULATORY REGIONS are non-coding segments of DNA that allow genes to be turned on or off in response to cellular signals or the external environment
include the promoter, enhancer, silencers and insulators
PROMOTERS recruit RNA polymerase to a DNA template - recruitment is affected by activator or depressor transcription factors binding to the promoter’s TF binding sites. TATA box is especially involved in recruitment of transcriptional machinery.
ENHANCERS upregulate gene expression when bound to TFs
SILENCERS downregulate gene expression when bound to TFs
INSULATORS are sequences that prevent enhancers and silencers influencing other genes
describe the process of transcription
transcription is the production of mRNA from a gene
catalysed by RNA polymerase II which is recruited to the promoter along with TFs, also involves co-factors
- RNA polymerase is recruited to the promoter along with TFs – DNA is a closed complex
- DNA helix is locally unwound forming an open complex
- RNA synthesis begins in 5’ to 3’ direction
- RNA polymerase II moves along the DNA template strand, synthesising a longer complementary RNA strand
- once the transcriptional termination site is reached – RNA poly. dissociates from DNA with the primary transcript of mRNA attached
what is alternative splicing? how does it work and why is it useful?
when splicing doesn’t happen the same way and different exons are selected for inclusion in the final mRNA transcript
useful as it allows variations of a protein - isoforms - from the same gene
different proteins may be needed for different stages of development
how it works:
alternative promoters induce alternative splicing
mRNA editing creates many different transcripts
post-translational modification of a protein – e.g. glycosylation
what’s the difference between enhancers and silencers?
ENHANCERS upregulate gene expression when bound to TFs
SILENCERS downregulate gene expression when bound to TFs
what are the two nucleus compartments?
compartment A is transcriptionally active with active histone modification
compartment B is transcriptionally repressed with repressive histone modifications
how do nucleus compartments and TADs contribute to the 3D arrangement of DNA?
same compartment types are brought together in the 3D genome and interact with one another - genes in A are more likely to be transcribed and may co-regulate one another
genes being in gene rich (A) or gene poor (B) affects their expression patterns, and their accessibility to regulatory elements
TADs are smaller, self-interacting sub-compartments within the genome - DNA sequences within the same TAD interact with one another, and not with other TADs. TADs are usually separated by the transcriptional repressor CTCF protein which prevents inappropriate interactions between genes and reg. elements in adjacent TADs as opposed to their own TADs.
define a gene
GENE is a fundamental unit of hereditary information separated by intergenic regions
what is a transcription factor?
protein that enhances/represses interaction with RNA Poly II with the promoter
TFs recognise different signals given by the promoters
what are the three post-transcriptional modifications made to the mRNA primary transcript?
capping
polyadenylation
splicing
describe the process capping
a 5’ methyl guanosine cap is added to the 5’ end of mRNA - protects it from being degraded by nuclease activity, stimulates splicing and allows it to be exported from the nucleus
four enzymes are involved:
RNA 5’ triphosphatase = forms 5’-5’ triphosphate bridge
guanylyl transferase = adds guanosine
N7G methyltransferase = methylation at N7 position
RNA polymerase II = positions enzymes
describe polydenylation
poly A tail added to 3’ end of pre-mRNA
added for stability to protect 3’ end from nuclease activity, transcript is checked for 3’ poly A tail before being exported
