G25-26 Flashcards
how many base pairs and genes in the human genome
3.2 x 10^9 bp, 21,000 genes roughly
what is the stanley miller
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
what can a purely geochemical process lead to?
the synthesis of polymerase biomolecules
what could have been the first coding RNA
a ribozyme with duel catalytic and coding function.
what are viroids
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.
what is the smaulhausen threshold
threshold between life and non life
how many genes are universally present in all organisms? what does this info combined with knockouts suggest
65 genes
knockouts have shown that minimum set of genes is 200, luca genes must have been lost from some organisms
what are COGS
clusters of orthologos genes - subset of COGs probably represent minimum LUCA genome.
what are type of genes are the overlaps between archea and eukaryotes
mostly involved in dna replication
what type of genes are in the overlap between bacteria and archea
those that have been transfered by horizontal transfer (so share more gens that E/A)
what types of genes are shared between eukaryotes and bacteria
endosymbiont genes - chloropast and mitchochondria
What do the number of genes and protein coding genes show in many viruses and bacteria
mosst genes are protein coding.
how many of yeasts genes are protein coding
roughly half.
what was used to analyse how many of yeasts genes were protein coding and what were the resutls
disruption analysis
40% have no phenotype
what is disruption analysis
when a transposon is added to knockout a gene.
what could be the issues with results from disruption analysis
some genes might be required under different growth conditions.
and duplications of genes = redundency
what is the genomic organisation of a typical eukaryotic genome
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%
where do the highest proportion of new genes arise from?
already exisisting genes (exons)
which type of selfish genetic element is more likely to produce new genes
LINEs
SINES arent that useful for new genes
what are the simplist retroelements
lines with no LTRs or ENV genes (envelope genes)
what is an example of a gene family that is related by sequence but not function
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
how did globin genes evolve?
via unequal crossing over events - occurs when chromosomes misalign at recombination.
- becausse they are simialr they misalign
what do multigene globin allow the production of
different types of heamoglobin embryonic foetal and adult
what is vpr?
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
How are paralogous genes within one species more closely related to each other than to members of the same gene family
due to homologous recombination events that elad to gene conversion, effecitvely copying some sequence from one and overwriting the homolgous region in the other.
what are orthologs adn paralogs
orthologs = genes in different species that evolved from common ancesteral gene by speciation paralogs = related genes in the same species
what is concerted evoltion?
the tendency of different genes in a gene family or cluster to evolve in concert.
what is responsible for 40% of new genes being formed?
gene duplication
what is responsible for 60% of new genes being formed
de novo
how many new protein genes do humans have compared to chimps
27
expression highest in cerebral cortex and testes
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
- 548 genes without protein orthologs
- 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
what was discovered from the genome wide de novo gene substitution rates for humans and chimps
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
Give an example of a transposition causing the formation of a new gene
- 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.
what is an example of a eukaryotic gene dervied from a virus
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
what does new gene formation via lateral transfer usually occur in
unicellular organisms
eg antibiotic resistance in bacteria
what causes disease in vibrio cholerae
the CTX phage it is infected with
how did CTX phage infect V. cholerae
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
what causes cholerae
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
