BG3

Question 1

gene no. association with complexity

Answer 1

rough association between metazoans and unicells
humans 25000, e.coli = 4000
however relationship breaks down in metazoans
c. elegans = 19000
amphioxous = 21,900

Question 2

orthologues

Answer 2

gene or proteins in different species that are more closely related to each other than genes present in those species
example: six3/6 and optix

Question 3

paralogues

Answer 3

genes or proteins within a single species that are closely related to each other
example: six3 and six6

Question 4

what are 4 main mechanisms of genome evolution

Answer 4

1. gene duplication
2. polyploidisation
3. exon and domain shuffling.
4. non-coding regulatory element
   5, gene loss

Question 5

susumu ohno 1970 hypothesis

Answer 5

gene no. could increase by duplication or polyploid

Question 6

how does gene duplication occur

Answer 6

unequal crossing over
chromatid pairs align incorrectly so that after crosing over, one chromatid will have two copies ad other will lack *usually lethal.

• one gene tends to conserve ancestral function

Question 7

gene duplication in humans

Answer 7

resequencing shows most genes seem to be diploid
but high vairation in copy no. in humans
implies gene duplication is continuous and common.

Question 8

what are many of the genes duplicated in humans compared to other apes

Answer 8

involved in brain development
GPRIN2 and SRGAP2 - implicated in neurite outgrowth and branching.
HYDIN2: associated with micro and macrocephaly.
DRD-5 dopamine receptor.

Question 9

gene duplication among ethnic groups

Answer 9

as many as 2/10/11 gene duplications.

Question 10

Polyploidy leading to vertebrates

Answer 10

seems to be two rounds of whole genome duplication leading to vertebrates.

• first in branch from amphioxous to tunicates
• second in the branch diverging from jawless fish (hagfish)

Question 11

what is synteny

- why may is not be the case

Answer 11

conservation of large scale genomic architecture.

• gene function is independent of gene location so shuffling can break up synteny, however this is sufficiently slow for synteny to occur generallly.

Question 12

describe the synteny of amphioxous and higher vertebrates

Answer 12

basic structure sufficiently conserved that can be aligned with genome of higher vertebrates.
- amphioxous genome shows large regions where genes correspond more or less ot those of particualr human chromosomes.

Question 13

what is the direct evidence of vertebrate polyploidsation

Answer 13

amphioxous genome can be reduced to 17 linkage chromosomes (ancestral linkage groups)
these are found to be distributed across the vertebrate genome.
in general in any given component there are usually four different places where it has been distributed across vertebrate genome, usually adds up to no more than 4 of those genes.
suggests two whole genome duplication

Question 14

implication of duplication on genome size of amphioxous compared to humans

Answer 14

would expect 4x as many genes in humans
however, humans = 25,000, amphioxous = 20,000
suggests widespread polyploidisation followed by mass reduction.

Question 15

what is exon shuffling

Answer 15

exons from two or more differnet genes can be brought together ectopically or the same exon can be duplicated.

• important common mechanism by which new classes of proteins are made.
• an exon contains a no. of functional domains

Question 16

what is domain shuffling

Answer 16

gene segment coding for functional domains are shuffled between different genes during evolution
- boundaries between domains may or may not correspond to exon boundaries, occasioanlly a single domain is encoded by more than one exon.

Question 17

what causes domain and exon shuffling

Answer 17

unequal crossing over within introns can cause new domains to be added or lost or new exons to be put together

Question 18

how do vertebrate domains compare to other metazoans

Answer 18

have few new domains but many proteins with more complex combos of domains

Question 19

what is gene regulation often accomplished by, how can these evolve

Answer 19

cis acting reg elements. - can be duplicated and diverged to acquire more complex functions

Question 20

Give an example of importance of cis acting regulatory elements

Answer 20

drosophila - initial embryo is a syncytia.
concentration gradients of TFs cause different levels of gene expression.
each stripe on drosophila is determined by precide levels of TF binding to particualr cis acting reg element.

Question 21

how is second stripe of dorophila formed

Answer 21

cis acting reg for second stripe is bound by repressors such as Giant, kruppel and activators such as bicoid and hunchback in different regions at precise levels

Question 22

evo history of non coding reg elements in vertebrates

Answer 22

the reg regions of genes involved in post translational modification have become more complex late in vertebrate evolution
** suggests how we can get away with fewer genes: more post translation reg,
those of transcription factors became complex early

Question 23

yeast mating

Answer 23

fusion of partner cells stimulated by pheromones
responses mediated by signalling moelcules heterotimeric G protein ste2 and mitogen activated protein MAP kinase cascades

Question 24

describe experiment of genome evolution

Answer 24

constructs with duplicated genes, duplicated domains and co-expressed domains and new combos of domain (domain shuffling) were made and put back into yeast.
matting efficieny was assayed and recombinate relative to WT.

Question 25

results of experiment of genome evolution

Answer 25

gene duplication, domain duplication and domain co-expression had little effect.
some duplicated domain constructs were less efficient.
but making proteins with new combos of domains changed mating efficiency greatly - in some cases increased (may not occur naturally due to pleiotropy)
domain shuffling can therefore bring about major phenotypic effects.
explains freq in evo

Question 26

gene loss in vertebares

Answer 26

with polyploid expect humans to have 80,000 genes.

vertebrate gene loss

Question 27

Gene loss in platypus,

Answer 27

monotremes lay eggs, plesiomorph share with amphibians, reptiles and birds.
monotremes like these^ have yolk proteins vitellogenins
marsupials have 1
eutherian mammals have none.

Question 28

describe vitellogenin evolution in vertebrates

Answer 28

`1. duplication of yolk proteins leading to amphibians who lay gelatinous eggs (x2 vtgA/B), X2 vtgA1/A2

2. monotremes have lost VIT1 but maintained VIT.
3. VIT2 extinction in eutherians.
4. inactivating mutations in vitellogenin genes in platypis and opposum can be seen, stop codons and indels.

Question 29

Bdelloid rotifer genome evolution

Answer 29

1. polyploidy
2. gene duplication, alpah tubulin (antarctic fish), lea-1.
3. gene conversion - mutation accumulation deal.
4. HGT, 10%

Question 30

exon shuffling in defensins

Answer 30

arhtopods and molluscs compared to scorpian defensin
found aside from exon encoding mature protein differ widely in no., size and seq.
variability suggests exon encoding mature defensin has undegone exon shuffling and integrated downstream of unrelated leader seq.