Proteins do much of the work of the cell, the basic biological unit. Proteins are made of sub-units called amino acids, which in turn are made of atoms.
There are thousands of different kinds of proteins. I have posted previously about a set of proteins that work together, called ATP Synthase (ATPS, pronounced ATP sin-thase). The set acts together in this energy production machine. All organisms have ATPS (with the exception of viruses which are parasites and so benefit from ATPS indirectly).
Though I have pictures of ATPS elsewhere, I am putting this picture in my blog because it shows in one view the detail from three levels. The one on the upper left is the whole machine, a picture by David Goodsell at PDB-101 Molecule of the Month, under ATP Synthase HERE.
One of the proteins of ATP Synthase is circled and an arrow points to the box to the right. It shows the makeup of the amino acids in just one part of the machine (represented by their single letter symbols). The sequence for E. coli bacteria can be found at protein database Uniprot entry P0ABB4. As you can see, it is made up of 460 amino acids which have to be in correct order for the ATPS machine to work. (For humans the entry is P06576. Though the number of amino acids is different in humans from E. coli, they still have to be in an arrangement that is functional.) The next box to the left is an image of the atomic arrangement of one amino acid (atoms are represented by their own letters which can be determined by the context).
If you are interested, you can see in a video at a previous post HERE how ATPS operates when protons flow through it because of an electrochemical gradient. The video lasts less than 4 minutes. The molecule that it makes is called ATP, or adenosine triphosphate (ah-den-oh-seen try-fos-fate). This molecule is used to make proteins and DNA among other uses. Here is a picture of it:
Beyond the ATPS, other molecules are needed to set up the proton gradient that makes it work (seen at the same link HERE).
Some proteins can handle a few changes of amino acids, but some positions can't be changed or the protein will not work.
These proteins did not come about by chance, even in billions of years.
