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genes and genomes ii > Genome Evolution > Flashcards

Genome Evolution Flashcards

1
Q

what is a genome?

A

genetic material of an organism

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2
Q

describe the features of a genome.

A
  • variable and change over time
  • can drive speciation
  • Coding DNA - genetic code
  • Non – coding DNA - regulatory
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3
Q

describe the relationship between genome size and organism?

A

in simple organisms - genome size correlates with complexity

- when you go beyond bacteria eukaryotes show pretty much no correlation

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4
Q

what is the c value paradox?

A

eukaryotes show no correlation - compelxity and genome size dont link

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5
Q

outline the key features of prokaryotic genomes.

A
  • contain a single circular chromosome
  • chromosomes condensed in the nucleoid
  • transcription and translation occur simultaneously
  • haploid (one copy)
  • non essential genes are encoded on extrachromosomal plasmids
  • genomes are efficient and compact
  • contain little repetitive DNA
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6
Q

outline the key features of eukaryotic genomes.

A
  • multiple linear chromosomes
  • chromosomes condensed in a membrane bound nucleus via histones
  • transcription = nucleus
  • translation = cytoplasm
  • most two copies = diploid
  • some in operons
  • large amounts of non coding and repetitive DNA
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7
Q

what else does proaryote genome size correlate with?

A

lifestyle

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8
Q

what has larger genomes, free living or obligate symbionts?

A

free living

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9
Q

what is the minimum genome size of a free living bacteria?

A

1Mbp genes for lviing DNA replication and energy

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10
Q

describe Prokaryote Genome Evolution of • Symbiotic or parasitic organisms

A
  • Can allow their genomes to degrade
  • Use host metabolites for instance
  • These genes can be lost
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11
Q

describe Prokaryote Genome Evolution of • Free living

A
  • Mostly under purifying selection

- Repetitive or junk DNA is lost from the genome  genome streamlining

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12
Q

describe Prokaryote Genome Evolution of • Innovation

A
  • Duplication, HGT, replicon fusion
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13
Q

what are prokaryotes genomes balancng?

A

benefits of a compact genome with benefits of genome innovation

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14
Q

how do innovations happen through mutation?

A
  • mutation rate is slow but bacterial proliferation is high
  • new mutations impact genetic diversity
  • eg vertical inheritance
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15
Q

what are the different types of horizontal inheritance (HGT)?

A

transduction, conjugation and transformation

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16
Q

what is transduction?

A

phages transfer genetic material between hosts

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17
Q

what is conjugation?

A

material passed between in close contact, produce pilus structure

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18
Q

what is transformation?

A

bacteria can absorb material from the environment

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19
Q

how do we know that genetic material can cross domains?

A
  • occurred at least twice
  • evolution of eukaryotes (mitochondria)
  • evolution of land plants (chloroplasts)
  • organelles from an endosymbiotic relationship
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20
Q

what did mitochondria evolve from?

A

aerobic bacteria

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21
Q

what did chloroplasts evolve from?

A

photosynthetic bacteria eg cyanobacteria

22
Q

what does a larger genome in eukaryotes allow for?

A

variation

23
Q

what makes up a large part of the human genome?

A

transposable elements

- make up almost half the genome

24
Q

what are transposable elemetns?

A

vast array of DNA sequences that can move around in genomes

25
Q

what are the 2 categories of transposable elements?

A
  1. Transposons - cut and paste mechanism

2. Retrotransposons - copy and paste, move their genomes around and can acquire a large amount

26
Q

what are the functions of transposable elements?

A
  • move
  • disrupt gene functions
  • most are actually silent
  • DNA methylation occurs around transposons (prevents damaging effects)
  • use as a method for regulating genes
27
Q

how do transposable elements drive diversity?

A
  • lots of them
    • Cleavage and resection of DNA by transposases virtually guarantees sequence variation, genome scrambling and the appearance of transposases at rearrangement breakpoints
28
Q

what else can transposable elements facilitte?

A

adaptation

29
Q

what are • Spliceosomal Introns?

A
  • introns that splice
30
Q

what is alternative splicing?

A

 Allows you to produce a vast array of gene products

31
Q

what is cassette exon splicing?

A

splicing involves either skipping or retaining specific exons to give different products

32
Q

what is mutually exclusive splicing?

A

when a gene contains exons which are specifically retained in different gene products

33
Q

what is intron retention?

A

includes the intron sequence in the product

34
Q

what are alternative 5’ or 3’ splice sites?

A

provide expandable exons

35
Q

what are alternative promoters?

A

provide products which are differentially regulated

36
Q

what is alternative splicing and polyadenylation?

A

provides different stop sites

37
Q

what is intron mediated enhancement?

A

the ability of an intron sequence to enhance the expression of a gene

38
Q

what do introns enable?

A

enable protein diversification and fine tuning expression

39
Q

why is the Dscam1 gene important?

A
  • the most extensively spliced gene

- 115 exons with 95 alterantalively spliced

40
Q

what is the origin of splicesomal introns?

A
  • bacterial have a type on intron, group II self-splicing introns
  • they have also been found in mitochondria and chloroplast genomes of fungi, plants, protists and annid worm
  • spliceosomal introns are transferred to the eukaryotic genome from mitochondria/chloroplast (then proliferated before losing their ability to self-splice)
41
Q

what are group II self-splicing introns?

A

splice themselves in and out of precursor RNA and invade new genomic DNA

42
Q

what is whole genome duplication?

A

when the whole genome is accidentally duplicated and becomes part of the genome structure

43
Q

what does whole genome duplication cause?

A

autopolyploidy

44
Q

how else can polyploidy occur?

A

by hybridisation which can produce allopolyploidy

- eg brassica

45
Q

what is the result of polyploidy?

A
  • polyploidy creates new species
  • provides additional genome complexity
  • spawns large multigene families
46
Q

how did Y and X chromosomes evolve to be very different?

A
  • evolved from a common set of autosomal sex chromosome pairs
    1. pair of autosomes recombine
    2. at some point the gene confers sex occurs on these autosomes
    3. get other sex specific genes, its advantageous these to be inherited alongside and so end up being clustered
    4. dont want these clusters to be broken up so evolution has stopped recombination (large inversion in the chromosome which fixes the genes)
    5. recombination helps removes deleterious alleles
47
Q

why is the Y chromosome so small?

A
  • big pieces of the chromosome gets lost or removed and the chromosome shrinks
48
Q

how many inversion events have there been on the X chromosome?

A

5

49
Q

how can sex chromosomes become heteromorphic?

A

Accumulation of additional sexually antagonistic genes can lead to cessation of recombination in additional regions

50
Q

how can genome evolution shape behaviour?

A

there is a bird with 4 sexes. first set for females and males and the second element fixed for other autosomal pairs for different traits.

51
Q

when can transposable elements spread easily?

A

they can spread easily in species that sexually reproduce

genes and genomes ii (8 decks)

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