Exam 2 Flashcards
What kind of mutation has multiple slashes through it on a dot plot?
repeats
what kind of mutation has a missing portion of the line on a dot plot?
deletion
What kind of mutation makes an X on a dot plot?
inversion
Who do you score a sequence alignment and dot plots?
matches = +1
anything else = -1
Why are 2 examples of indels?
insertion/deletion
what is an example of a subsitution?
transversion/transition
synonymous (dS) mutations means the __________ amino acid is coded for
original
non-synonymous (dN) mutations mean the _________ amino acid is coded for
incorrect
when dN/dS = 1 is means what?
neutral evolution
when dN/dS > 1 it means what?
positive/diverging evolution
when dN/dS < 1 means what?
negative/purifying evolution (conserved)
how does point mutations affect the coding sequence?
changes the amino acid = change in function
how does point mutations affect regulatory sequences?
TF binding site mutations
what is polyQ; and what disease does it cause?
polyglutamine mutation; Huntingtons
what is the mechanism of polyQ mutation?
emerges from DNA replication slippage causing amino acid repeats
What does slippage during replication cause (gene birth)?
repeats at sight of replication that are unstable
what is unequal cross over during meiosis (gene birth)?
when loci replicate and there are duplicates or portions of gene missing
what is transposible elements (gene birth)?
transient segments of DNA that remove or insert themselves
What is fusion (gene birth)?
2 genes are combined to create one gene
what is fission (gene birth)?
1 gene breaks into 2
What is horizontal gene transfer (gene birth)?
moving genetic info from one organism to another
what is de novo gene birth?
new gene comes from a DNA sequence that used to not code for a protein
what is whole genome duplication (gene birth)?
when there is 2 copies of each gene after
What are the 8 forms of gene birth?
- slippage during replication
- unequal cross over
- transposable elements
- Fision
- fussion
- horizontal gene transfer
- de novo gene birth
- whole gene duplication
What is neofunctionalizartion?
gene duplication produces a new gene with a new function
what is subfunctionalization?
gene duplication causes function to be split
what is pseudofuncationalization?
one gene does not function
Orthologs comes about from _____________
speciation event
paralogs come about from ____________
duplication event
orthologs form a ___________
clade
orthology does NOT have to be ____:____
1:1
________ usually have similar function
orthologs
What are the 4 advantages of multiple copies?
- back ups
- many functions
- increased diversity
- regulatory flexability
what is a disadvantage of multiple copies?
lots of energy
What is divergent evolution?
a common ancestor ‘radiates’ out to form sister species
what is concerted evolution?
related genes within a species undergo genetic exchange, causing their sequence evolution to be concerted over some period of time.
what is birth and death evolution?
some genes die out
Why is E. coli a good model system?
its the model bacteria
Why is yeast a good model system?
single celled eukaryote
Why is Arbidopsis a good model system?
grows fast (nicotine/tobbaco)
Why are flies a good model system?
small genome
clear genetic phenotypes
Why is C. elegans a good model system?
development
Why is sea urchin a good model system?
transparent embryo
Why is zebra fish a good model system?
toxicity screens
short life span
Why is xenopus laeu (frog) a good model system?
development
enviornmental toxicity
Why is chickens a good model system?
development
B/T cells
what 3 animals can regenerate?
- starfish
- axolotl
- planana
What has the largest neurons?
aplysia (slug)
what is organolds?
lab grown organs/ human tissue
What 2 things make us human?
- genome
- our life
what are 2 ways of studying domestication?
- archeology
- genome
What 2 ways is the genomes of domestication studied?
reference genomes
ancient genomes
What 3 things can we learn from domesticated genomes?
- differences in organism
- when
- who
how does a molecular clock work?
mutation rates are constant; relies on fossil records
on a graph of time v. mutation rate, is positive selection on the top or bottom?
top
on a graph of time v. mutation rate, is negative selection on the top or bottom?
bottom
What affect happens when domestication takes place?
bottle necking
what is gene flow?
trading of genes across other populations not near them
what happens to adrenal function after domestication?
decreased function (neural crest)
what does a divergent evolution phylogenetic tree look like?
see picture
what does a concerted evolution phylogenetic tree look like?
see picture
what is a transversion?
interchanges of purine for pyrimidine bases
(DIFFERENT TYPE)
what is a transition?
interchanges of two-ring purines (A G), or of one-ring pyrimidines (C T)
(SAME TYPE)
