How do proteins behave like molecular clocks?
The amino acid sequence of proteins changes over time.
Note that here is still a lot of debate about the theory of molecular clocks. The general idea is that mutations in the amino acid sequence of proteins occur at a relatively constant rate . The longer two species have been evolving seperately, the more differences in amino acid sequence is expected.
Mutation is a chance process and the basic mutation rate is probably the same for all genes, but natural selection filters proteins out that are not functional; only the functional mutations remain.
So mutations in genes, reflected in the amino acid sequence of proteins, can be used as a clock for evolutionary processes . However, research has shown that different proteins have different mutation rates, making it a lot more difficult to put the theory into practice.