Midterm 2 - Notes 3 (Part 3) Flashcards
What is important in protein coding genes?
The protein function
- not the sequences
What is the assumption of purifying and positive selection?
Natural selection acts on protein, not on genes
Silent mutation
No change in protein sequence
- their frequency should be the same regardless of selective pressures on the protein
What do amino acid changing mutations likely change?
Properties of proteins
- if there is selection pressure to maintain the function these will be selected against (purifying selection)
- if there is selection to optimize a novel function changes should be selected for (positive selection)
How do you test for purifying, neutral or positive selection?
Compare number of silent mutations with number of amino acid changing mutations
Ka
Amino acid changing mutations
What is the ratio Ka/Ks called?
ω
What does it mean if ω is 1?
Neutral evolution
- both silent mutation and amino acid changing mutation occur at the same frequency
What does it mean if ω < 1?
Purifying selection
- silent mutations are made more frequent than animo acid changing mutations
What does it mean if ω > 1?
Positive selection
- amino acid changing mutations are made more frequent than silent mutations
What is ω3?
The average of ω1 and ω2
Why do retro copies change expression?
Because they move around
What are expression levels based on?
RT-PCR
Why are parental genes broadly expressed?
Because they contain house keeping genes and is in all cells
- transcription, poly A tail functions, etc
What was striking in the retro-copies experiment?
Common expression in the male germ line (testis)
Where are parent genes of successful retro-copies over represented?
On the X-chromosome
What happens to the genes on the X-chromosome during haploid stages of spermatogenesis?
They are silenced
What do retroposons on autosomes do?
Take over functions of house keeping genes on the X-chromosome
What does silencing of the genes on the X-chromosomes explain? (2)
- There coding region is under purifying selection
- They are expressed in the testis
- need to compensate for the lack of parental function
What may transposons and/or transposition lead to? (4)
- Gene inactivation
- Exon-shuffling
- Gene translocation
- Gene duplication
What are 3 things duplicated genes may do?
- Lose in function
- Divide function with other copy (sub-functionalization)
- Gain a new function (neo-functionalization)
What are 3 duplication types?
- Duplication as a passenger of a DNA-transposon or retrotransposons
- either complete of parts of the genome - Duplication as retroposon (retro-copy)
- duplication of complete open reading frame
- without regulatory elements - Duplications not involving transposons
What does duplication as a passenger of a DNA-transposon or retrotransposons depend on?
Integration site of transposons
Poly-ploidy
3 or more chromosomes
How do you get a poly-ploidy chromosome?
During mitosis the organisms can have irregular amount of chromosomes (either too many or not enough)
WGD
Whole genome duplication
How can WGD be identified? (2)
- Analysis of compete genome
2. Re-diploidization
Re-diploidization
The repeated loss of chromosome by a tetraploid organism to become diploid
What is an example of a re-diploidization?
Populus Trichocarpa
What are 2 forms of analysis of the complete genome?
- Sequence analysis
2. Micro-colinerity of genes (synteny)
Synteny
The physical co-localization of genetic loci on the same chromosome within an individual or species
