Question

How do proteins act as molecular clocks?

Answer 1

The molecular clock is a figurative term for a method that deduces the time in prehistory when two or more life forms diverge using the mutation rate of biomolecules. Nucleotide sequences for DNA, RNA, or amino acid sequences for proteins are usually the biomolecular data used for such calculations.

Complete answer:
Zuckerkandl and Pauling proposed the molecular clock theory in 1965.

It states that changes in proteins and DNA occur over geological time at approximately constant rates. Therefore the number of DNA mutations and hence the number of protein substitutions is roughly the same per generation.
For the prediction of time, this molecular data can be used.

The amino acid sequence of proteins varies over time The general principle is that mutations occur at a relatively constant rate in the amino acid sequence of proteins. The longer the two species have evolved independently, the more amino acid sequence differences are predicted.

The longer two animals evolved independently, the more variations in their proteins accumulated in amino acids. Changes in amino acids are expressed in genes.

For all genes, the basic mutation rate is possibly identical, but natural filters filter out certain mutations that inhibit the function of a protein. The rate at which amino acids are substituted in a given protein is influenced by these functional restrictions.

So mutations in genes may be used as a clock for evolutionary processes, expressed in the amino acid sequence of proteins.

Note: The fact that each gene or protein is a separate clock lies in the tremendous capacity of the molecular evolutionary clock. Every clock "ticks" at a different rate, but each of the thousands and thousands of genes or proteins provides an independent indicator of the same evolutionary events, the rate of evolution characteristic of a single gene or protein.