Friday, May 15, 2009

Anaerobics


In the last few ID posts, I showed some proteins from cell membranes. The point was to see that the cell needs some rather complicated structures to keep charged particles and water at a balance so the cell doesn't explode or collapse. I want to tie that into the speculations of materialistic origins of life.

To the right is a protein from a bacteria named Desulfovibrio Vulgaris (NCBI taxonomy ID 882). I show this to you because of the evolutionary story that the first creatures on Earth were anaerobes (pronounced AN-air-robes). These creatures did not need oxygen to breathe. It is maintained that atmospheric oxygen was not available at first in sufficient quantities. The materialists believe that because if oxygen were available, it would keep organic molecules from forming, and thereby life itself could not start on its own. So the first cells were supposedly anaerobic. (I have seen speculation both ways on whether there was oxygen in the very early atmosphere but will not get into it here). The oxygen was theoretically produced by the first living organisms, and then later organisms adapted to the oxygen in the atmosphere. The protein at right, from Uniprot P45574 and RCBI PDB 2v4j is part of the pathway that uses a sulfur-containing molecule instead of the ones used in oxygen-type respiration. It is made of several types of protein chains, totaling over 900 amino acids.

A paper about the very beginnings of life, "The Origins of Archaea: a state of the art," speculates on the first organisms. The paper is by Girbaldo and Brochier-Armanet, published in Philosophical Transactions of the Royal Society, May 9, 2006. It is found in full through PubMed Central here. Archaea are one of the 3 domains, or groups of life, based on cell construction. The other two are Bacteria and Eukaryotes. The article includes all three domains in its analysis (although is mostly about Archaea). It states that though a certain type of Archaea (methanogenic) were previously thought to be the first organisms, their whole-gene sequences do not bear out that theory. Now it is thought that anaerobic bacteria which have this sulfur-type respiration were among the first (see Section 3, "How Old," in the paper). So this is why I looked up this type of organism.

Interestingly, this bacteria has the complete proteome available at Uniprot here. It has 3,517 proteins listed. Some of them are not complete in themselves. They have to fit together to make the protein work. This does not diminish the effect of the number, however, since some of the types of proteins are used several times in the same protein machine. For example, ATP synthase as pictured in a previous post has several types of subunits, some used as many as 12 times in the same structure. You will notice in the complete proteome that D. vulgaris also has an ATP synthase structure.

The type of respiration in anaerobes may be different, but the first organisms still needed complex structures for energy production, cell membrane transport and other cell activities. The picture to the left is not from D. vulgaris, but shows a Sodium-hydrogen type cell membrane protein that the organism does have. This is also made up of hundreds of amino acids in specific sequence in order for them to fall into the shape they need for function.

So, you can see that even the very first types of organisms needed complex types of proteins in order to function. It doesn't really matter whether they used oxygen or not. It may sound like an organism is simpler if it doesn't use oxygen to breathe, but it still needs many metabolic pathways in order for it to manufacture its own DNA, RNA, proteins, and other structures so that it can support life and reproduce.

1 comment:

Nod said...

Wow, now that's interesting! More evidence how faith and science are not opposed: even anaerobes are very complex.