CBG Lecture 2: Genomes Flashcards
(46 cards)
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
