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Amino acid

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Balls-and-sticks representation of aspartic acid, an amino acid.
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This article is only a brief description of the subject and is not intended to give a full explanation.
Check out the "see also" or "references" sections, or Wikipedia's article for more detail.

Amino acids are substances formed from molecules that consist of atoms from specific functional groups. They are the building blocks of protein molecules. Amino acids can be found inside all known organisms, and unique varieties can be created artificially.

Chemistry[edit]

The name "amino acid" comes from the presence of two functional groups: an amine-group (-NH2) and a carboxylic acid (-COOH). Any molecule containing both these groups is technically an amino acid, but the term is generally used for a selection of organic molecules of biological importance, such as glycine (H2N-CH2-COOH). These molecules differ by their side chains, which give each of them different chemical properties such as, for example, polarity (the property that governs whether the molecule is attractive to water or not; this property is important in protein folding as described below).

The amine group of an amino acid can chemically join to the acid group of another amino acid to form an amide bond. This enables long chains of amino acids to form. These amino acid based short polymers (chemical chains) are known as peptides and can vary in length from just two to several hundred or thousands (like proteins).

Stereochemistry[edit]

An important property of the natural occurring amino acids is their stereochemistry (the chemistry concerning space and the occupation thereof). The central carbon atom in the naturally occurring amino acids is chiral with four different groups attached to it.[1] These four different groups can be arranged differently in space to produce mirror images of each other, described in lay terms as left or right-handed in reference to how hands are essentially identical but mirror images that cannot be superimposed.

Implications of Stereochemistry[edit]

Almost all amino acids have the same absolute stereochemical configuration, the (S) configuration.[2] This is at odds with intuition that would suggest a 50:50 mixture of each, as both forms are of equal energy and with equal chemical properties, there is no way to distinguish between them without another chiral source.

Although stereochemistry can be conserved from chemical precursors, this doesn't fully explain where it initially came from, leading some people to conclude that there must be some form of design or creation going on. The naturalistic explanation of why one form was favoured over another is not fully formed, although creationists do neglect the presence of diastereoisomers (which occur when two stereoisomers interact and are not chemically or energetically equivalent) or the presence of other chiral agents such as polarised light.

Biology[edit]

In the genetic code made of DNA, a group of three nucleotides (a codon) encodes for a specific amino acid. As a ribosome moves along the DNA strand, a collection of codons will be read to produce a polypeptide. Sufficiently long chains, with the assistance of other enzymes, then fold up to become active proteins or other enzymes.

List of amino acids[edit]

Of the 20 amino acids existing (plus one special rare amino acid usually not counted), the human body can naturally synthesize 12 of them. This means the other 9 must be obtained from outside sources, i.e. by eating protein and then breaking those down in their components (namely the amino acids). Just about any protein source will have at least some amount of the essential amino acids in it; but if you subsist entirely on fats and carbohydrates (sugars) with no protein intake, you'll eventually get a protein deficiency condition such as KwashiorkorWikipedia (a protein malnutrition).

The 20 amino acids used in the translation (synthesis of proteins):

Graphical representation of how to read the genetic code via codons (the nucleotide triplets): You start from the middle (5') — the larger letters — and move away from it (3'). Notice that multiple codons codify for the same amino acid but there is no overlap to what amino acid it codifies; this is important, since that prevents ambiguity within the genetic code i.e. a codon codifying for multiple amino acids. That would be catastrophic!
▶ Start codon: The amino acid methionine (Met/M) starts every protein sequence (via the AUG codon).
Stop codon: This is not codified by an amino acid, but signals to the biologic machine to end the synthesis of the protein.
Amino acid Three letter
(one letter) abbr.
Chemical structure Codons Essential?
[note 1]
Chiral?
[note 2]
Alanine Ala   (A) Amminoacido alanina formula.svg
GCU GCC GCA GCG
No Yes
Arginine Arg   (R) Amminoacido arginina formula.svg
CGU CGC CGA CGG
AGA AGG
No
[note 3]
Yes
Asparagine Asn   (N) Amminoacido asparagina formula.svg
AAU AAC
No Yes
Aspartic acid Asp   (D) Amminoacido acido aspartico formula.svg
GAU GAC
No Yes
Cysteine Cys   (C) Amminoacido cisteina formula.svg
UGU UGC
No
[note 4]
Yes
Glutamine Gln   (Q) Amminoacido glutammina formula.svg
CAA CAG
No Yes
Glutamic acid Glu   (E) Amminoacido acido glutammico formula.svg
GAA GAG
No Yes
Glycine Gly   (G) Amminoacido glicina formula.svg
GGU GGC GGA GGG
No No
Histidine His   (H) Amminoacido istidina formula.svg
CAU CAC
Yes Yes
Isoleucine Ile   (I) Amminoacido isoleucina formula.svg
AUU AUC AUA
Yes Yes
Leucine Leu   (L) Amminoacido leucina formula.svg
UUA UUG
CUU CUC CUA CUG
Yes Yes
Lysine Lys   (K) Amminoacido lisina formula.svg
AAA AAG
Yes Yes
Methionine Met   (M) Amminoacido metionina formula.svg
AUG
Yes Yes
Phenylalanine Phe   (F) Amminoacido fenilalanina formula.svg
UUC UUU
Yes Yes
Proline Pro   (P) Amminoacido prolina formula.svg
CCU CCC CCA CCG
No Yes
Serine Ser   (S) Amminoacido serina formula.svg
UCU UCC UCA UCG
AGC AGU
No Yes
Threonine Thr   (T) Amminoacido treonina formula.svg
ACU ACC ACA ACG
Yes Yes
Tryptophan Trp   (W) Amminoacido triptofano formula.svg
UGG
Yes Yes
Tyrosine Tyr   (Y) Amminoacido tirosina formula.svg
UAC UAU
No Yes
Valine Val   (V) Amminoacido valina formula.svg
GUU GUC GUA GUG
Yes Yes

Two special amino acids:

Amino acid Codons (nucleotide triplets) Essential? Chiral?
Selenocysteine UGA No[note 5] Yes
Pyrrolysine UAG[note 6] N/A Yes

External links[edit]

Notes[edit]

  1. Essential in this context means that the amino acids must be consumed as part of the human diet, they cannot be made (in humans) by converting one amino acid into another.
  2. Technical word for "looks like a pair of gloves" (chiral molecules are like gloves in that they are made from all the same parts, but are mirror images of each other)
  3. If you're an adult, it is not essential.
  4. Cysteine can be essential in rare cases, but is usually not.
  5. Selenocysteine is produced in humans. Normally, UGA means "stop", but through a complicated process, it will code for selenocysteine.
  6. No, this isn't a mistake. Pyrrolysine is used in bacteria, not humans, where it is coded for using UAG.

References[edit]

  1. With the exception of glycine, which is achiral due to having two identical groups attached to the central carbon atom.
  2. With the exception of glycine because it is achiral and cysteine because its groups have a different priority in the system used to identify them.