Lecture 16 Flashcards
What is MHC?
The major histocompatibility complex(MHC)-the name is involved with the idea that transplants fail when different species are involed. The MHS genotypes has an unusually large amount of variation
What does the MHC proteins do?
Explain photo 10
they bind to petides generated inside the cell then displays them outside the cell. If the petides are weird then they are killed
This is a MHC class 1 protein. All of this encodes for one gene. Your genome has three copies of this gen
Explain photo 11
Heterozygosity in humans ranges from 80 to 90% so most of us have six alleles and generate six different MHC class 1 proteins
Overdominance refers to…
selection that favours heterozygotes. If a mutation changes a AA sequences it will be favoured since it makes heater. This is called positive selection. This is weird becuase creating a mutation in a protein usually breaks it. Usually we see purifying selection.
On photo 10 where is the ARS and what is it?
ARS is at the top between a1 and a2 it is the antigen recognition site
Photo 12
Where are the codons that that code ARS(N=?), codons that do not(n=?). Codons that code non ARS regions(codons?)of the MHC protein
a1 and a2 ARS is in the middle n=57, do not on the outside n=125
the whole thing of a3 92 codons-no changing
Explain the dn/ds in photo 12.
The dn in ARS site is larger then the ds- positive selection. When there is an mutation that changes the AA diversity goes up..mutation is good in this region
What’s the difference between BLASTn and BLASTx
Why do we use AA?
BLASTn the alignment would be DNA
BLASTx Amino acids
So we can have less unobserved mutations
Potential problem with p-distance?
What can we do to decrease this?
unobserved mutations
higher the p-distance the more inaccurate
The Jukes and Cantor formula
-3/4In(1-1 1/3p)
Neighbor-joining and Bootstrap method
photo 13
Bootstrap is sample with replacement
sp.1 and 2 are most common but position 3 goes against this
