How do proteins create chemical bonds?

Question

I have a fascination in biology and have wondered how proteins designed to make certain molecules like DNA or ATP, etc., create the chemical bonds between the atoms when making it.

I understand that they don’t make them from scratch, they usual just “smash” two different molecules together, but still how are the bonds created?

In: 2

Answer 1

Proteins are [mostly] stitched together by a molecule called a ribosome.

Ribosomes add amino acids one by one to a long chain called a polypeptide. Proteins are made of one or more polypeptides, sometimes with modifications made later.

The ribosome grabs the appropriate amino acid from the cytoplasm (“stuff inside the cell”) and adds it through a condensation reaction involving the -OH off of the carboxylic acid end of one amino acid and the hydrogen off of the nitrogen end of the other.

The actual mechanism by which this happens is complicated, but, yeah, mostly the ribosome brings the ends close together. What probably happens is something like:

The oxygen in the -OH group is close to one of the hydrogens hanging off of the nitrogen. If they’re close enough, the oxygen will start to grab at the hydrogen more than the nitrogen does. Once the oxygen grabs that hydrogen, it now has two hydrogens and decides that it would rather be a water molecule by itself than hang around with the lame amino acid. This leaves the carbon that oxygen used to be bonded to sad and alone. Meanwhile, the nitrogen that just lost its hydrogen is also sad and alone. The carbon and nitrogen find comfort in each other, and form a lasting bond. Meanwhile, the water goes away, maybe to find itself in Bali or something.

I’m just now realizing you asked how proteins make DNA, not how DNA makes proteins.

Anyway, it’s similar: the protein grabs the two molecules to be bonded, and put them close to each other. If they’re placed close to each other at the right orientation, then they’ll start to reaction and form a bond. Sometimes the protein may also change shape while the reaction proceeds, helping force it in a particular direction, and sometimes the protein might include a metal atom which sort of helps the electrons move from one place to another as the bond forms.