Dayhoff paper

What is an accepted point mutation?

The replacement of one amino acid for another, accepted by natural selection.

What are the two processes resulting in accepted point mutations?

Occurrence of mutation in the gene template and acceptance of the mutation by the species.

Why must the new amino acid must function similarly to the old one?

Because it must have similar physiochemical properties to be accepted.

What is the basis for the assumptions made about amino acid replacement in mutations?

The likelihood of amino acid X replacing Y is the same as Y replacing X, based on their frequencies and chemical similarity.

How many amino acid exchanges were observed in the study?

1572 exchanges.

Which amino acids had the most exchanges according to the study?

Asp and Glu.

Approximately what percent of amino acid interchanges involved codons differing by more than one nucleotide?

About 20%.

What is relative mutability?

The probability that each amino acid will change in a given small evolutionary interval.

How is relative mutability calculated?

By dividing the number of changes of each amino acid by its occurrence in sequences subject to mutation.

Which amino acids are the most mutable?

Asn, Ser, Asp, and Glu.

Which amino acids are the least mutable?

Trp and Cys.

What does the mutation probability matrix represent?

A distance-dependent matrix that combines individual kinds of mutation and relative mutability of amino acids.

How are the nondiagonal elements of the mutation probability matrix calculated?

By using the formula $M_{ij} = \frac{\lambda m_j A_{ij}}{\sum_i A_{ij}}$.

What do the columns of the mutation probability matrix represent?

The original amino acid and the probability that it will change.

What is the formula to calculate the percentage of amino acids that will change on average?

$100(1-\sum_i f_i M_{ii})$.

What do scores greater than 1 in the relatedness odds matrix indicate?

That the amino acids replace each other more often in related sequences than in random sequences.

Why do hydrophobic and aromatic amino acids tend to replace one another more often?

Due to natural selection and genetic code constraints reflecting similarities in function.