Lec 6. Molecular Evolution Flashcards
What does Divergent Evolution mean?
Homologs are derived from a common ancestor
What are two types of homologs?
Paralogs and orthologs
What does paralog mean?
Within a species (Gene Duplication)
What does Ortholog mean?
Between species
What does Convergent Evolution mean?
Same end point, different start point.
Pertaining to convergent evolution, what is similar and not similar?
Phenotypes structures similar but nucleotide/amino acid identity not similar
What are four reasons why a phylogenetic Trees can disagree?
When comparing phenotypic/molecular info, convergent evolution or horizontal gene transfer has occurred, sequence info has been lost through purifying selection
What is assumption 1 in Zuckerkandl and Linus Pauling’s 1965 hypothesis?
Spontaneous DNA mutation is random throughout the genome
What is assumption 2 in Zuckerkandl and Linus Pauling’s 1965 hypothesis?
Mutation of each gene is that genome is equally random
What is the observation in Zuckerkandl and Linus Pauling’s 1965 hypothesis?
Mutation rates are consistent amongst several mammalian lineages
What is the conclusion in Zuckerkandl and Linus Pauling’s 1965 hypothesis?
The rate of molecular evolution is constant over time in all lineages
Was Zuckerkandl and Linus Pauling’s 1965 hypothesis conclusion true or false? why
False, within lineages, molecular clocks are roughly constant over time and UNIVERSAL molecular evolutionary clock most definitely does NOT exists.
What are three ways to classify mutations?
The cause, phenotypic effects and genotype descriptions
What are the two subtypes of genotype descriptions when pertaining to classifying mutations?
Positional and molecular change
What are the three subtypes for molecular change?
substitution mutation, Insertions/deletions and transposition.
What are substitution mutations?
point mutations
Define substitution mutations
A single base pair changed indentity
What causes substitution mutations?
Pol error that was not proofread and error-prone DNA damage repair
During substitution mutations what changes occur?
Transition and transversion
What is transition?
Purine to purine or pyrimidine to pyrimidine
What is transversion?
purine to pyrimidine and vice versa
What are the effects of substitution mutations?
silent mutations, Missense mutations, Neutral mutation and Nonsense mutation
Define a silent mutation
No change in amino acid
Define Missense mutation
Change in amino acid
Define Neutral mutation
Change to a chemically similar amino acid
Define Nonsense mutation
change to a stop codon
Neutral mutation falls under what other mutation?
Missense mutation
Which of the three mutations pertaining to substitution mutation are synonymous?
Silent mutation
Which of the three mutations pertaining to substitution mutation are nonsynonymous?
Missense and nonsense
With Codon degeneracy, what two rules do you need to keep in mind?
Changes in the 1st and 2nd codon position are usually nonsynonymous. Transitions in the 3rd codon position are usually silent
Consider every position of every codon, and mutate each to ever other possible nucleotide. What NS:S ratio would we see?
3:1:1
In the absense of selection, what NS:S ratio do we expect?
3:1:1
If positive selection (mutations are good) is present, what do we expect from the NS:S ratio?
To be larger
If purifying selection is present (mutation is bad), what do we expect from the NS:S ratio?
to be smaller
What is the definition for insertion or deletion?
1-1000s of base pairs are added or removed
What causes insertions or deletions?
Transposon cut/paste, pol slippage, unequal crossing over.
What are the effects of insertions or deletions in a coding region?
No much if the number of base pairs was a multiple of 3 but FRAMESHIFT mutation if not a multiple of 3
What are the effects of insertions or deletions in a noncoding region?
Can alter regulation, deposition of a new/duplicate exon or gene
What is another effect of insertions or deletions?
Creation of a fragile site on the chromosome
What is the definition of Transposition?
Movement of a transposon within the genome
What are two characteristics of Transposition?
Excision is not precise, so host sequences go along for the ride to the next destination. Removal leaves behind a scar
What are the effects of Transposition?
In general the same as insertions and deletions.
What is one thing to note about Transposition?
This is the second way to make a gene duplication
What are two ways to duplicate all/part of the gene?
Transposition or crossing over
Duplicate all/part of the chromosome
aneuploidy
Duplicate the whole genome
polyploidy
What are two outcomes after gene duplication occurs?
Gene inactivation or change of gene function
True or False? Mutations are more likely to be advantageous than detrimental
False. Are more likely to be detrimental
Why do most duplicate genes become inactive?
Mutations are more likely to be detrimental
What are pseudogenes?
Non-functional genes
What is a pseudoexon?
Non-functional exon
True or False? Some genes that become active can become active once more
True
Do single-copy genes become pseudogenes?
Rarely
What is one single-copy gene that became a pseudogene in vertebrates?
L-gulono-γ-lactone oxidase
How did we lose L-gulono-γ-lactone oxidase?
Via diet. Not having enough vitamin C
What are two reasons for a duplicate gene to be retained?
Extra expression is needed or a new function is created
What are two ways the function of a gene can change?
Addition of function by protein elongation or mutation accumulation tinkers with protein function
What are 4 ways of adding function by protein elongation?
duplicate a protein domain, remove the stop codon, remove a splice site, and transposon/viral insertion into an exon
What are gene terms?
Exon, intron
What are protein terms?
Domain
Can domain boundaries by different than exons?
Yes. Moving an exon does not mean moving a domain
What is an example of domain repeats?
Immunoglobulins
What are three ways mutation accumulation tinkers with protein function
Subfunctionalization, Neofunctionalization and gene rearrangements
Define subfunctionalization
Fine-tuning the exsisting function
Define Neofunctionalization
A brand new function emerges
Define gene rearrangements
Shuffle of the deck
What are three ways to exon shuffle?
Exon duplication (protein elongation, Exon deletion (protein shortening) and exon Insertion (protein domain swapping)
What are the 5 types of gene rearrangements?
Exon shuffling, alternative splicing, overlapping genes, intron sliding, genes within introns
What are mosaic/chimeric proteins?
Pieces of one protein mixed with another protein usually resulting from Exon insertion.
What is a good example of mosaic/chimeric proteins?
Blood clotting agents
What is alternative splicing?
Temporary domain swapping
Define overlapping genes
Constrains mutation
What is an example of how overlapping genes can occur?
Frameshift mutation
What does intron sliding do?
Expose/cover protein coding regions
What are Intron-encoded protein genes?
Translated gene within excised intron
What is a nested gene?
gene in antisense strand of an intron
