  The frequencies of A, C, G and T in mitochondrial DNA vary among species due
to unequal rates of mutation between the bases. The frequencies of bases at
four-fold degenerate sites respond directly to mutation pressure. At 1st and
2nd positions, selection reduces the degree of frequency variation. Using a
simple evolutionary model, we show that 1st position sites are less constrained
by selection than 2nd position sites, and therefore that the frequencies of
bases at 1st position are more responsive to mutation pressure than those at
2nd position. We define a similarity measure between amino acids that is a
function of 8 measured physical properties. We define a proximity measure for
each amino acid, which is the average similarity between an amino acid and all
others that are accessible via single point mutations in the genetic code. We
also define a responsiveness for each amino acid, which measures how rapidly an
amino acid frequency changes as a result of mutation pressure acting on the
base frequencies. There is a strong correlation between responsiveness and
proximity, and both these quantities are also correlated with the mutability of
amino acids estimated from the mtREV substitution rate matrix. We also consider
the variation of base frequencies between strands and between genes on a
strand. These trends are consistent with the patterns expected from analysis of
the variation among genomes
