Genome Structure Flashcards
how many base pairs is the human genome
3 x 10^9
is genome size strongly related to complexity of an organism?
no
what are the problems related to DNA length
2m of DNA in a nucleated cell
average cell is 50um
how do we overcome the problem with DNA length in our cells?
histone proteins which are basic positively charged proteins that bind DNA
what are the different levels of DNA packaging
DNA double helix nucleosomes chromatin fibre extended section of chromosome loops of chromatin fibre metaphase chromosome
what does the primary DNA do?
encodes all the gene products necessary for a human
includes many regulatory signals
what is the exome
made up of gene sequences
some use all coding sequences or whole gene sequence
what is a gene
all the DNA that is transcribed into RNA and all the cis-linked control regions required to ensure quantitatively appropriate tissue specific expression of the final protein
describe the gene structure
98% of the genome
contain sequence of no known function, repetitive DNA, endogenous retroviruses, pseudogenes
cluster into families
describe introns in genes
vary in number 0-311
vary in size 30bp-1Mbp
describe the structure of a gene
coding regions/exons
introns
promoter at 5’ end
Transcriptor factor binding sites
what is the promoter
recruit RNA polymerase to a DNA template
RNA p binds asymmetrically and only moves 5’-3’
what are enhancers
up-regulate gene expression, short sequences that can be in the gene or many kilo bases distant.
targets for transcription factors
what are silencers?
down regulate gene expression
position independent and targets for TFs
what are insulators?
short sequences that act to prevent enhancers/silencers influencing other genes
7 steps of transcription
- promoter and transcription unit region
- RNA polymerase recruited
- DNA helix locally unwound
- RNA synthesis begins
- elongation of strand
- termination
- RNA polymerase dissociates
post-transcriptional modification of mRNA
capped at 5’ end
spliced = introns removed
polyadenylated at 3’ end
3 enzymes involved in 5’ cap
RNA 5’ triphosphatase
guanylyl transferase
N7G- methyltransferase
what do spliceosomes do
help remove introns
what is a lariat
the joining of two axons, intron spliced out
what is the TREX complex
transcription export complex
what is CPSF
cleavage and polyadenylation simulating factor
recognises Polyadenylation signal and acts on cleavage site
what is CSTF
cleavage stimulating factor
recognises GU rich downstream elements
what is PAP
poly A polymerase
recruited and adds multiple A bases after cleavage site
what is PAB
poly B binding protein
cleavage factor Im, CFIIm, simpleton
the purpose of splicing?
allows variations of a proteins to be produced from the same gene
how is DNA arranged in somatic cells
non-randomly
how has organisation of DNA been identified
Hi-c (detects genomic DNA sequences in proximity)
high-throughput microscopy
genomes can be separated into compartments.
describe compartment A and B
A = transcriptionally active with active histone modifications
B= transcriptionally repressed with repressive histone modifications
what are TADs
topologically associated domains
- individual compartments made up of several non-interacting sub-compartments
usually separated by transcriptional repressor CTCF protein
what is 3D transcription control
loop extrusion model for enhancer control of transcription
