G25-26

Question 1

how many base pairs and genes in the human genome

Answer 1

3.2 x 10^9 bp, 21,000 genes roughly

Question 2

what is the stanley miller

Answer 2

reproducing environment of early earth
proposed constituents H2O, CH4, NH3, H2
no O2
produced 17/20 of the AA used in protein synthesis and all the purines and pyrimidines used in NA synthesis

Question 3

what can a purely geochemical process lead to?

Answer 3

the synthesis of polymerase biomolecules

Question 4

what could have been the first coding RNA

Answer 4

a ribozyme with duel catalytic and coding function.

Question 5

what are viroids

Answer 5

200bp rna - too simple to be viruses
often complex secondary loops
often non coding
some ribozyme properties - can interact with proteins and replicate
move between plant cellsa nd case disease. through plasmodestmata.

Question 6

what is the smaulhausen threshold

Answer 6

threshold between life and non life

Question 7

how many genes are universally present in all organisms? what does this info combined with knockouts suggest

Answer 7

65 genes

knockouts have shown that minimum set of genes is 200, luca genes must have been lost from some organisms

Question 8

what are COGS

Answer 8

clusters of orthologos genes - subset of COGs probably represent minimum LUCA genome.

Question 9

what are type of genes are the overlaps between archea and eukaryotes

Answer 9

mostly involved in dna replication

Question 10

what type of genes are in the overlap between bacteria and archea

Answer 10

those that have been transfered by horizontal transfer (so share more gens that E/A)

Question 11

what types of genes are shared between eukaryotes and bacteria

Answer 11

endosymbiont genes - chloropast and mitchochondria

Question 12

What do the number of genes and protein coding genes show in many viruses and bacteria

Answer 12

mosst genes are protein coding.

Question 13

how many of yeasts genes are protein coding

Answer 13

roughly half.

Question 14

what was used to analyse how many of yeasts genes were protein coding and what were the resutls

Answer 14

disruption analysis

40% have no phenotype

Question 15

what is disruption analysis

Answer 15

when a transposon is added to knockout a gene.

Question 16

what could be the issues with results from disruption analysis

Answer 16

some genes might be required under different growth conditions.
and duplications of genes = redundency

Question 17

what is the genomic organisation of a typical eukaryotic genome

Answer 17

introns and reg seqs = 24%
repetitive DNA that includes transposable elements - 44%
reperative dna unrelated to transpoable elements - 15%
unique non coding = 15%
exons = 1.5%

Question 18

where do the highest proportion of new genes arise from?

Answer 18

already exisisting genes (exons)

Question 19

which type of selfish genetic element is more likely to produce new genes

Answer 19

LINEs

SINES arent that useful for new genes

Question 20

what are the simplist retroelements

Answer 20

lines with no LTRs or ENV genes (envelope genes)

Question 21

what is an example of a gene family that is related by sequence but not function

Answer 21

serpins serine protease inhibitors
dont all have serine protease inhibitor function othersa re hormones for example antithrombin. or ovalbumin
* may only need one AA change to dramatically change gene function

Question 22

how did globin genes evolve?

Answer 22

via unequal crossing over events - occurs when chromosomes misalign at recombination.
- becausse they are simialr they misalign

Question 23

what do multigene globin allow the production of

Answer 23

different types of heamoglobin embryonic foetal and adult

Question 24

what is vpr?

Answer 24

an example of a gene in primate lentivirus - in HIV 2 the virus has duplicated and has both the vpr gene and the related vpx gene

Question 25

How are paralogous genes within one species more closely related to each other than to members of the same gene family

Answer 25

due to homologous recombination events that elad to gene conversion, effecitvely copying some sequence from one and overwriting the homolgous region in the other.

Question 26

what are orthologs adn paralogs

Answer 26

orthologs = genes in different species that evolved from common ancesteral gene by speciation
paralogs = related genes in the same species

Question 27

what is concerted evoltion?

Answer 27

the tendency of different genes in a gene family or cluster to evolve in concert.

Question 28

what is responsible for 40% of new genes being formed?

Answer 28

gene duplication

Question 29

what is responsible for 60% of new genes being formed

Answer 29

de novo

Question 30

how many new protein genes do humans have compared to chimps

Answer 30

27

expression highest in cerebral cortex and testes

Question 31

how many different genes (not nex protein coding) do humans have compared to chimps
1. not exlcuding those without start/stop codons
2/ excluding those without start/stop codons

Answer 31

1. 548 genes without protein orthologs
2. 352 orf looked for orthologs in chimps
   found 66 disrupted open reading frames in chimps which were examined to identify those human specific mutations that generate intact open reaading frames = 46 candidates.
   27 genes confirmed via transcription and tranasaltion

Question 32

what was discovered from the genome wide de novo gene substitution rates for humans and chimps

Answer 32

de novo had a higher than genome wide average rates of mutation
chimps de novo evolving at a faster rate
de novo genes evolving faster than other genes

Question 33

Give an example of a transposition causing the formation of a new gene

Answer 33

• hibernating mammals do so by limiting carb catabolism and using triacylglycerols stored in white adipose tissues as fuel.
• hormone sensitive lipase is typically responsible for hydrolysis of tiacyglycerols in white adipose tissue
• lipolytic enzyme normally found in the gut (pancreatic triacyglycerol lipase PTL) is expressed in white adipose tissue in 13 lines ground squirrels
• PTL duplicated by non homologous recombination - insertion of ERC alters regulation elements of PTL allowing expression in white adipose, stnadard PTL remains inactive in WAT but chimeric is active.

Question 34

what is an example of a eukaryotic gene dervied from a virus

Answer 34

Fv1 gene in mice, encodes a restriction factor which blocks infection by some retrovirses
this comes from part of the gag gene from another virus

Question 35

what does new gene formation via lateral transfer usually occur in

Answer 35

unicellular organisms

eg antibiotic resistance in bacteria

Question 36

what causes disease in vibrio cholerae

Answer 36

the CTX phage it is infected with

Question 37

how did CTX phage infect V. cholerae

Answer 37

recognises pilus on surface and uses it to enter cell

once inside the cell the CTX phage integrates into the chromosome and the bacteria then expresses cholera toxin

Question 38

what causes cholerae

Answer 38

released cholera toxin into infected intestine binds to enterocytes (intestinal wall cells) through interaction of the patameric B subunit of the toxin with GM1 ganglioside receptor on the intestinal cell triggering endocytosis of toxin
toxin then undergoes cleavage to become an active enzyme
then activates G protein through ADP ribosylation reaction that acts to lock G protein in its GTP bound form thereby continually stimualating adenylcylase to produce cAMP
rise in cAMP levels in CFTR ccause dramatic influx of ions adn water from infected entericytes leading to watery diarrrhoa