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CBG PANT Replication, transcription and translation > CBG Lecture 2: Genomes > Flashcards

CBG Lecture 2: Genomes Flashcards

1
Q

define genome

A

the complete haploid set of genetic material in an organism

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2
Q

what is the common core of genes also known as? what does it imply

A

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

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3
Q

why is it not necessarily helpful to look for genes found in all organisms to infer presence of LUCA?

A

because gene loss is common, particularly in parasites, so because this is probably limited to just some tiny subset (ribosomal genes)

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4
Q

what are informational genes involved in

A

replication, repair, transcription,translation

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5
Q

what are metabolic genes involved in

A

energy transduction, aa/carb/nucleotide metabolism and transport, coenzyme metabolism and lipid metabolism

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6
Q

what are three main classes of genes

A

metabolic
cellular
informational

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7
Q

what are cellular genes involved in

A

protein folding, cell division, membrane construction, motility and secretion, ion transport, signalling

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8
Q

which 2 domains share informational genes - why?

exceptions?

A

eukarya and archaea due to common descent but DNA may have evolved differently in bacteria
LUCA may have had an RNA genome

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9
Q

which 2 domains share metabolic genes - why?

exceptions

A

eukarya and bacteria

due to HGT from proto-mitochondrion (but HGT between bacteria and archaea too)

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10
Q

which 2 domains share cellular genes - why?

A

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

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11
Q

what does the prokaryotic genome normally include

A

a single circular chromosome plus extra chromosomal plasmids

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12
Q

why/how do prokaryotes have extra chromosomal plasmids

A

due to HGT between bacteria and archaea

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13
Q

whats the difference between the proteins associated in DNA of prokaryotes and eukaryotes

A

the DNA associated with prokaryotic DNA is non-structural and involved in transcription, unlike that of eukaryotes

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14
Q

what does eukaryotic genome normally include

A

several larger linear chromosomes plus mitochondrial/plastid genomes in matrix/stroma
extensive packaging - centromeres and telomeres bind to nuclear lamins

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15
Q

what is the C value paradox

give exception/anomaly

A

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

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16
Q

how much % of human DNA codes for proteins?

A

1%
90% is non coding:SINEs and LINEs
10% of known utility
junk DNA is mostly dead parasites (60%)

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17
Q

how would you work out average size of polypeptide

A

average gene length (BP) / 3

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18
Q

how would you work out size of genome

A

approx number of genes*average gene size (BP)

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19
Q

how is the C value paradox explained

A

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

20
Q

what does L/SINEs stand for

A

Long/Short INterspersed Elements

21
Q

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?

A

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

22
Q

what are SINEs - what size are they

give example

A

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

23
Q

how large is a human nucleus?

how much DNA is packaged into it?

A

human cell contains 2m of DNA packed into a 5 micrometre nucleus

24
Q

what is the length of a chromosome in metaphase

A

2 micrometres

25
Q

what are histones

A

basic proteins which bind DNA to form nucleosomes in euks and archaea
histone becomes octamer which DNA wraps round

26
Q

how are nucleosomes formed?
what is packaging ratio?
what does this confer?

A

fromed by histones binding DNA which wraps round an octamer twice every 200bp
packing ratio is 1/3
could confer heat stability

27
Q

what is an octamer?

how often does DNA wrap around this

A

histone proteins:
H2B,H2A,H3,H4 used twice
DNA wraps round this twice every c.200bp

28
Q

what is the primary level of DNA packaging?

A

nucleosomes forming the 11nm (wide) fibre “beads on a string” form of chromatin
this is readily expressed

29
Q

what is the second level of packaging

A

histone H1 packs 11nm fibre into the poorly expressed 30nm fibre

30
Q

why/how is 11nm fibre readily expressed

A

RNAP can run around the nucleosome without disrupting it too much

31
Q

why do we think histones evolved for thermostability?

A

because bacteria dont have but archaea which are thermophiles could have evolved histones for heat stability

32
Q

what is the significance of histone tails in eukaryotes?

A

can be modified to affect gene expression, then these modifications can be epigenetically inherited

33
Q

in what ways can histone tails be modified?

A

affefct gene expression eg.
when ON: Acetylation by histone acetyltransferases reduce binding of tails to DNA
OFF: Gene silencing and heterochromatinisation by methylation

34
Q

what does epigenetic inheritance mean

A

functinally relevant changes to the genome that do not involve a change in the nucleotide sequence
eg. histone modification
DNA methylation

35
Q

give some examples of epigenetic inheritance

A

histone modification
DNA methylation
happens in the form of epigenetic tags

36
Q

why do histone tails exist

what are they made of

A

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

37
Q

what can be methylated on the histone tail to get further DNA packaging

A

lysine

38
Q

what are higher levels of DNA packaging

A

looped domain

chromatin

39
Q

what is packaging ratio of 11nm fibre nucleosomes

A

1:3

40
Q

what is packaging ratio of 30nm fibre nucleosomes

A

1:12

41
Q

what is packaging ratio of looped domain

A

1:25

42
Q

what is packaging ratio of chromatid

A

1:25

43
Q

what is a chromatid structure made of

A

rosettes of looped domains around nuclear scaffold

44
Q

what is a polytene chromosome

A

oversized chromosomes which have developed from standard chromosomes

45
Q

where does 11nm to 30nm puffing exist

-> how do you see this down a microscope

A

in polytene chromosomes from Drosophila larva salivary glands
have a banding pattern with 30nm and 11nm fibres due to different C+G density

46
Q

which level of DNA packaging makes the DNA completely inactive

A

the second stage of 30nm fibre

CBG PANT Replication, transcription and translation (10 decks)

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