CBG Lecture 2: Genomes Flashcards
define genome
the complete haploid set of genetic material in an organism
what is the common core of genes also known as? what does it imply
COGs - clusters of orthologous groups of proteins ie. families of related proteins of similar function)
shared in most organisms and may be representative of LUCAs genome
include 250 COGs like: ribosome, RNAPs, glycolysis/kreps, ATPase
why is it not necessarily helpful to look for genes found in all organisms to infer presence of LUCA?
because gene loss is common, particularly in parasites, so because this is probably limited to just some tiny subset (ribosomal genes)
what are informational genes involved in
replication, repair, transcription,translation
what are metabolic genes involved in
energy transduction, aa/carb/nucleotide metabolism and transport, coenzyme metabolism and lipid metabolism
what are three main classes of genes
metabolic
cellular
informational
what are cellular genes involved in
protein folding, cell division, membrane construction, motility and secretion, ion transport, signalling
which 2 domains share informational genes - why?
exceptions?
eukarya and archaea due to common descent but DNA may have evolved differently in bacteria
LUCA may have had an RNA genome
which 2 domains share metabolic genes - why?
exceptions
eukarya and bacteria
due to HGT from proto-mitochondrion (but HGT between bacteria and archaea too)
which 2 domains share cellular genes - why?
archaea and bacteria share many structural genes - MreB and FtsZ and eukarya show divergence from this FtsZ (tubulin) and MreB (actin)
chaperonins among all domains are well conserved
what does the prokaryotic genome normally include
a single circular chromosome plus extra chromosomal plasmids
why/how do prokaryotes have extra chromosomal plasmids
due to HGT between bacteria and archaea
whats the difference between the proteins associated in DNA of prokaryotes and eukaryotes
the DNA associated with prokaryotic DNA is non-structural and involved in transcription, unlike that of eukaryotes
what does eukaryotic genome normally include
several larger linear chromosomes plus mitochondrial/plastid genomes in matrix/stroma
extensive packaging - centromeres and telomeres bind to nuclear lamins
what is the C value paradox
give exception/anomaly
lower end of group’s genome size ≈ apparent complexity of the group, but upper end has no such relationship
AMOEBA has a genome 100x larger than humans
how much % of human DNA codes for proteins?
1%
90% is non coding:SINEs and LINEs
10% of known utility
junk DNA is mostly dead parasites (60%)
how would you work out average size of polypeptide
average gene length (BP) / 3
how would you work out size of genome
approx number of genes*average gene size (BP)
how is the C value paradox explained
eukaryotic genomes are full of noncoding DNA
1% protein, 10% of known utility, >60% is dead parasites
amount of junk can be, and is highly variable
what does L/SINEs stand for
Long/Short INterspersed Elements
what are LINEs? what size are they
give example
what do they function as
why do LINEs still exist? why havent they died out due to natural selection?
LINE-1 : >5kb
-parasitic jumping genes
-function as endonucleases
-transcribe DNA to ssRNA which gets translated, makes reverse transcriptase and integrase, which puts the new LINE DNA strand into DNA
“copy+paste” (copy with RT, paste with integrase”
NO selection pressure to get rid of it
what are SINEs - what size are they
give example
eg. Alu
hyperparasites
get transcribed but dont encode anything
instead use LINEs RT to make new dsDNA to get integrated back into genome via LINEs integrase
how large is a human nucleus?
how much DNA is packaged into it?
human cell contains 2m of DNA packed into a 5 micrometre nucleus
what is the length of a chromosome in metaphase
2 micrometres
what are histones
basic proteins which bind DNA to form nucleosomes in euks and archaea
histone becomes octamer which DNA wraps round
how are nucleosomes formed?
what is packaging ratio?
what does this confer?
fromed by histones binding DNA which wraps round an octamer twice every 200bp
packing ratio is 1/3
could confer heat stability
what is an octamer?
how often does DNA wrap around this
histone proteins:
H2B,H2A,H3,H4 used twice
DNA wraps round this twice every c.200bp
what is the primary level of DNA packaging?
nucleosomes forming the 11nm (wide) fibre “beads on a string” form of chromatin
this is readily expressed
what is the second level of packaging
histone H1 packs 11nm fibre into the poorly expressed 30nm fibre
why/how is 11nm fibre readily expressed
RNAP can run around the nucleosome without disrupting it too much
why do we think histones evolved for thermostability?
because bacteria dont have but archaea which are thermophiles could have evolved histones for heat stability
what is the significance of histone tails in eukaryotes?
can be modified to affect gene expression, then these modifications can be epigenetically inherited
in what ways can histone tails be modified?
affefct gene expression eg.
when ON: Acetylation by histone acetyltransferases reduce binding of tails to DNA
OFF: Gene silencing and heterochromatinisation by methylation
what does epigenetic inheritance mean
functinally relevant changes to the genome that do not involve a change in the nucleotide sequence
eg. histone modification
DNA methylation
give some examples of epigenetic inheritance
histone modification
DNA methylation
happens in the form of epigenetic tags
why do histone tails exist
what are they made of
because the N-terminus of the protein sticks out a bit
tails have serine and lysine and can be modified to (in)activate
methylation of lysine results in further packaging of DNA
what can be methylated on the histone tail to get further DNA packaging
lysine
what are higher levels of DNA packaging
looped domain
chromatin
what is packaging ratio of 11nm fibre nucleosomes
1:3
what is packaging ratio of 30nm fibre nucleosomes
1:12
what is packaging ratio of looped domain
1:25
what is packaging ratio of chromatid
1:25
what is a chromatid structure made of
rosettes of looped domains around nuclear scaffold
what is a polytene chromosome
oversized chromosomes which have developed from standard chromosomes
where does 11nm to 30nm puffing exist
-> how do you see this down a microscope
in polytene chromosomes from Drosophila larva salivary glands
have a banding pattern with 30nm and 11nm fibres due to different C+G density
which level of DNA packaging makes the DNA completely inactive
the second stage of 30nm fibre
