fundamental molecular lecture 3 genomes Flashcards
how do species share homologous genes?
by orthologs and paralogs
what are orthologs?
-by common descent, probably same function/ role
-hence study role in one species (ethically and costs allowed)
-and thus infer role in other species (where ethics, cost and practicalities might be an issue)
47% identity in protein sequence
(»>5%)Between yeast & Human gene
how do orthologs do the same job?
A human gene (CDC2) can take the place of a missing yeast gene (cdc2)
After ~1 billion years of evolution (since last common ancestor)
Look similar (encode a key cell cycle regulatory protein)
Really DO DO the SAME job: are interchangeable … Nobel Prize 2001
what are paralogs?
by duplication, probably diverged function/ role
what are between the spaces?
Brightly-coloured bits below line are repeated elements:
LINES (long interspersed nuclear elements)
SINES (short interspersed nuclear elements)
Transposons
LTRs (Long terminal repeats)
what are indels?
-they are insertions and deletions. they can be very small like 1-2bp and are surprisingly common
-can affect the protein product of a gene, if they occur in the protein coding region of a protein coding gene.
-can affect function of a ncRNA
-can affect regulatory regions
-most do not affect gene function, occur outside genes and in introns
what are micro and mini satellites?
Micro- ~1bp to 9bp repeating (“short tandem repeats” FORENSICS)
Mini- ~10bp to 100bp repeating
Relatively STABLE (generation to next) but highly variable in LENGTH (i.e., NUMBER of repeats) across alleles in the population
what is evolution?
a change in allele frequency in a gene pool / the change in allele frequency with time
what are CNVs (copy number variants)
there are a very surprising amount of CNVs variation in number of a segment of a chromosome, typically 500bp to 1 million bp segments.
what are SNPs (single nucleotide polymorphisms)?
rare snps= between 1-4.9% allele frequency
common snps= 5% allele frequency or more
Can affect the protein product of a gene if they occur in the protein-coding region (Open Reading Frame – ORF) of a protein-coding gene: silent, missense, nonsense
(MOST) do not cause a phenotype… occur outside genes, in introns etc…
Surprisingly common:A common SNP occurs approximately EVERY 1,000 bps in Human genome
how do point mutations/ variants range?
PRIVATE (to YOU): the ~200 de novo point mutations
FAIRLY COMMON (allele frequency of <1%) – call “VARIANT”
VERY COMMON (allele frequency of >1%) – “POLYMORPHISM”: Typically only 2 versions at a LOCUS (site in the genome) across the population(s):
how do you calculate allele frequency?
eg for allele frequency of A = no of A / total
what is the hardy-weinberg theory?
measuring the population at one timepoint = now.
For a given pair of allele frequencies, p and q: it predicts the GENOTYPE frequencies of diploids (humans, animals, plants..) assuming alleles are stable, a large homogeneous population, random mating and all genotypes are equally ‘fit’
what is the hardy-weinberg equation?
p2 + Ppq + q2 = 1
p2 = Frequency of AA homozygotes IF NO evolution
2pq = Frequency of Aa heterozygotes IF NO evolution
q2 = Frequency of aa homozygotes IF NO evolution
what does the hardy Weinberg equation find?
For a given pair of allele frequencies, p and q: it predicts the GENOTYPE frequencies that will keep that allele frequency constant from one generation to the next ie no evolution
