20221202F Day -19: Amino Acid A is for Alanine

20221202F-1111-AustinTX

It’s been a while since I have regularly posted and I would like to document daily the exit of the wormhole that I’m feeling in my own timeline. To increase the probability of doing this, today I’m going to talk about Alanine, one of the amino acids encoded by the genetic code that has a heritage shared by all life forms known to exist.

Amino acids are fundamental to all known life. Through their amine and carboxyl ends, they link together to form a chain of amino acids that folds up into a dynamic 3-D functional shape called a protein. These proteins can be enzymatic and catalyze reactions or they can be structural.

In bioinformatics, latin letters have been assigned to each of the common amino acids for standardization of storing protein sequence data. The Latin alphabet becomes then a reasonable choice for ordering the amino acids.

A is for Alanine. Alanine has a very simple side chain, or residue, of a single methyl group (CH3). It is the second smallest amino acid after Glycine, which has no residue. The methyl group results in it being non-polar and aliphatic. It is ambivalent, meaning it does not have a strong preference for being inside or on the surface of a protein. It is non-essential in humans and can be synthesized from pyruvate or branched chain amino acids such as Leucine, Isoleucine, and Valine. The largest common amino acid, Tryptophan, is a derivative of Alanine.

Alanine is the second most popular amino acid, used almost 9% of the time in a diverse set of proteins and taxa. Second only to Leucine at almost 10%. See https://proteopedia.org/wiki/index.php/Amino_acid_composition for details.

Alanine is encoded by all codons starting with GC (GCA, GCC, GCG, and GCU).

The “Alanine World” hypothesis (ref: https://doi.org/10.3390/ijms20215507) proposes that ancestral proteins predominantly relied on Alanine to provide the basic scaffold and secondary structure of the protein.

I haven’t heard of the Alanine World hypothesis before today. I do remember reading about the RNA World hypothesis. It makes sense to me that some amino acids were here along with RNA in the beginning. I imagine that future computer simulations will provide convincing evidence for how and when our unique genetic code came into existence.

Another death in my circle today – my friend just texted that her mother passed away this morning. I am grateful that I was able to visit her and her Mom earlier this year.