in what way do proteins behave like molecular clocks?

Question

can you explain it please?

Answer 1

A protein (such as hemoglobin or insulin in your blood) is a very long molecule consisting of a long string of amino acids. You can think of a protein as a long word, and the amino acids as the letters in that word. The exact sequence of letters (amino acids) in, say, a hemoglobin molecule, is expressly spelled out in the DNA of the organism ... every hemoglobin molecule is letter-by-letter identical in your body.

When an organism makes offspring, the instructions for making that protein (that hemoglobin molecule) are passed to the offspring in DNA. For the most part, the child will get the the DNA from one of its two parents ... and its hemoglobin molecules will be letter-by-letter identical to that parent.

However, every once and a while a small mutation in one or two letters will appear ... like a typo in the word. Sometimes this will harm the function of the protein, sometimes it will improve it slightly, but usually the change of a couple of letters will have little effect and the offspring will survive just fine and pass that new mutation onto its offspring.

So in this way, little differences ("typos") accumulate in the protein.

It turns out that we can measure the rate at which these differences accumulate. I.e. how many tiny differences happen over the course of, say, 1000 years.

This is the "molecular clock." We can look at two individuals, count the differences in the letters (amino acids) in the protein (like hemoglobin), and estimate that these two individuals are separated by 3,000 years ... or 30,000 years ... or 300,000 years, etc. This works with two members of the same species, or between members of different species. For example, by looking at hemoglobin or insulin betwen a human and chimp, and counting the differences, we estimate that humans and chimps are separated by about 4.6 to 6.2 million years. And humans and gorillas are separated by about 6.2 to 8.4 million years. These dates correspond with when these organisms appeared in the fossil record.

Answer 2

Well, they can build-up their concentration over time until they reach a threshold above which they perform their function, such as a transcription factor regulating gene expression through it's moderate to low binding affinity for either it's protein interaction partner or the sequence-specific DNA element it binds to, at a high enough concentration it will bind enough to exert it's function in a meaningful way. This can occur in cycles, say every twelve hours until the right concentration or only when there is light is the protein produced. Look up circadian rhythms and the genetics and molecular biology behind them, interesting stuff.

Answer 3

The previous answers are very good.

I'd like to add one more aspect of molecular clocks.

There are proteins which are in the active form only when they bind GTP. Upon hydrolysis to GDP and Pi the protein is inactivated or dissociates from the active complex rendering it inactive. An example is the elongation factor EF-Tu.
EF-Tu-GTP binds to aminoacyl-tRNAs (tRNAs carrying their respective amino acid). This complex can pair with the mRNA but cannot be used by the ribosome for adding the amino acid to the growing polypeptide chain. When the complex pairs to the mRNA through the tRNA anticodon, GTP hydrolysis is triggered and EF-Tu-GDP dissociates, allowing the tRNA to participate in that translation step.
This delay ensures that only tRNAs with the proper anticodon will stay long enough to be used by the ribosome; other tRNAs will dissociate before GTP is hyrolysed. It is a crucial mechanism for increasing the fidelity of translation.