Why did nature chose the twenty amino acids that she did?

[BabcockHall]

For example, why do we need both leucine and isoleucine? Does anyone know of a good book or review article that discusses (or even speculates) on this question?

[alpha2cen]

The twenty amino acid are product of evolution at the present? At the view of the information system, sixteen amino acids are efficient? 4² =16. The number 4 provides ATGC. From the basic unit 0 and 1, unit 2⁴ is sixteen. Are there any molecular distribution data of the amino acids in the living organisms?

Edited January 26, 2013 by alpha2cen

[The Flaming Goldfish]

For example, why do we need both leucine and isoleucine? Does anyone know of a good book or review article that discusses (or even speculates) on this question?

It's probably a question of protein structure. Different amino acid sequences confer different structural properties to proteins, so a change from leucine to isoleucine might result in a different 3D structure for the protein. The result would be a different protein, or one that's similar but with diminished biological activity. I don't know an article off the top of my head, but if I find one, I'll post it here.

 

 

Sixteen is reasonable? 4² =16. The number 4 provides ATGC. From the basic unit 0 and 1, unit 2⁴ is reasonable? Is a distribution of the amino acids in the body of living organisms?

Could you explain what you mean a little further? I'm not quite grasping what you're saying.

[alpha2cen]

Could you explain what you mean a little further? I'm not quite grasping what you're saying.

See #2 again.

The number 4 and 2 means a basic information transfer unit. We, living organims, use a tetrad unit(0, 1, 2, 3, or A, T, G, C) for recording.

(AA), (AT), (AG), (AC), (TA), (TT), (TG), (TC), .., (CC) Total =16

(AAA), (AAT),... Total =64

Which one is more efficient to use resources?

Edited January 26, 2013 by alpha2cen

[Ringer]

Well the codon triplets were probably preferred because it allows redundancy, so not every mutation would cause a change in amino acid sequence. Also, if you only had 16 for 16 AA there wouldn't be a stop sequence.

[alpha2cen]

Making a command codon is not difficult. We can make a special command codon by using dual codon. For example, we can set "AAAAAAAAAAAAAA" as a start command codon. Evolution and protein structure might have been more dominant for going to the way?

[John Cuthber]

If you use "AAAAAAAAAAAAAA" as the start command, how do you code what "AAAAAAAAAAAAAA" would code for?

[ewmon]

There are articles on evolution and codons (Google Scholar: codon evolution). The number of human codons is 4³ or 64, where 61 encode for 20 amino acids and 3 encode for stops. There is more than codon usage optimization to consider — for example, sufficient flexibility and subtle mutability to allow for evolution to occur. You can also read about codon usage bias.

[alpha2cen]

From protozoa to human beings, all living organisms use twenty amino acids? And, used amino acid distribution is similar?

[ewmon]

Thank you for questioning my post on genetic codes. (It's been a while.) You're right, all organisms use basically the same 20 AAs, and with similar distributions. I myself seek info on the evolution of codons because they certainly look as though they can evolve and did evolve.

[BabcockHall]

From protozoa to human beings, all living organisms use twenty amino acids? And, used amino acid distribution is similar?

Pretty much, although there is one odd extra amino acid, selenocysteine, and some residues arise from posttranslational modification of existing amino acids. The genetic code is nearly universal, although I think that there are some minor exceptions in mitochondria. I think that there must be some differences in amino acid abundance among different organisms; otherwise, there would not be the problem of consuming a complete protein that vegetarians face.

[CharonY]

The amino acid distrubution can vary quite a bit if we look at all organisms (at most one order of magnitude, usually far less). The largest differences are found with extremophiles which require specific adaptions to allow their proteins to function under extreme conditions.

[immortal]

Does anyone know of a good book or review article that discusses (or even speculates) on this question?

 

Its because she uses an algorithm, living organisms are quantum information processing systems.

 

[latex] Grover's Algorithm[/latex]

 

[latex] (2Q +1) sin^{-1} (1/ \sqrt N) = \pi / 2[/latex]

 

where,

 

N = number of elements that the algorithm can search for a given number of yes/no queries Q.

 

[latex] Q =1 => N =4[/latex]

[latex] Q =2 => N = 10.5[/latex]

[latex] Q =3 => N =20.2[/latex]

 

i.e. for three triplet codons or for three yes/no queries it can search up to 20 elements or effectively distinguish up to 20 elements.

 

The Triplet Genetic Code had a Doublet Predecessor

[Sam Viknyansky]

It's probably a question of protein structure. Different amino acid sequences confer different structural properties to proteins, so a change from leucine to isoleucine might result in a different 3D structure for the protein. The result would be a different protein, or one that's similar but with diminished biological activity. I don't know an article off the top of my head, but if I find one, I'll post it here.

 

The base tenent of chemistry and science is "Structure fits function", as you explained. Different amino acids have different functional groups in the "R" portion, which allow various interactions among nearby and faraway amino acids in the polypeptide chain. For example, insoluble hydrophobic amino acids will attract one another and seek the inner portion of an aqueous protein, while soluble hydrophilic ones will face the exterior.

 

One special case is that of the amino acid cysteine:

 

which has an "SH" group that can form strong "disulfide bridges", securing a rigid protein structure. Nature knew that disulfide bonds are very strong, so when amino acids were first forming molecules and this combination worked, she stuck with it.

[BabcockHall]

Yes, but cysteine is capable of quite a bit of chemistry apart from forming disulfide bonds.

Edited February 7, 2013 by BabcockHall

[jp255]

Since the OP's question about specific usage of similar aas has been answered, I'll add some comments to the evolution of codons. The redundancy of the code is important and has some advantages. There are also some other advantages of the codon table that evolved which have been suggested from some evidence.

http://genome.cshlp.org/content/17/4/401.long

The above link is an interesting read about codon evolution. Some important points from the paper:

 

1) Codons can be reassigned (eg. a codon coding for glyceine is switched for another aa) and variant codes exist, suggesting the "frozen accident" theory (codons evolved to carry a specific aa, and from that point onward become fixed) is not possible.

 

2) similar codons are assigned to aas with similar properties, eg. polar aas.

 

3)codons do not always result in the specific aa it codes for (eg. glyceine codon can be mistranslated and lyseine inserted). This is called mistranslation

 

4) the genetic code is optimised with respect to minimising mistranslation (actual code has been compared to other possible codes)

 

5) there is evidence to suggest codon usage is biased to codons which can read as a stop codon if read off-frame (offers some protection against frameshift mutations by faster termination than other possible codes)

 

6) the codons carry more than just amino acid sequence information. Additional information can be carried alongside aa information such as splice site sequence, RNA secondary structure and nucleosome positioning.

 

Seems to me the genetic code has been optimised by evolution somewhat.

Edited February 11, 2013 by jp255