Everything about Amino Acid Residue totally explained
In
chemistry, an
amino acid is a
molecule containing both
amine and
carboxyl functional groups. In
biochemistry, this term refers to alpha-amino acids with the general formula H
2NCHRCOOH, where R is an organic substituent. In the alpha amino acids, the amino and carboxylate groups are attached to the same
carbon, which is called the
α–carbon. The various alpha amino acids differ in which
side chain (R group) is attached to their alpha carbon. They can vary in size from just a hydrogen atom in
glycine through a
methyl group in
alanine to a large
heterocyclic group in
tryptophan.
Beyond the amino acids that are found in all forms of
life, many non-natural amino acids have vital roles in technology and industry. For example, the
chelating agents
EDTA and
nitrilotriacetic acid are alpha amino acids that are important in the
chemical industry.
Overview
Alpha-amino acids are the building blocks of
proteins. Amino acids combine in a
condensation reaction that releases water and the new "amino acid residue" that's held together by a
peptide bond. Proteins are defined by their unique sequence of amino acid residues; this sequence is the
primary structure of the protein. Just as the letters of the alphabet can be combined to form an almost endless variety of words, amino acids can be linked in varying sequences to form a vast variety of proteins.
Twenty
standard amino acids are used by
cells in
protein biosynthesis, and these are specified by the general
genetic code. These 20 amino acids are
biosynthesized from other molecules, but organisms differ in which ones they can synthesize and which ones must be provided in their diet. The ones that can't be synthesized by an organism are called
essential amino acids.
Functions in proteins
Amino acids are the basic structural building units of proteins. They form short
polymer chains called
peptides or longer chains called either
polypeptides or
proteins. The process of such formation from an
mRNA template is known as
translation, which is part of protein biosynthesis. Twenty amino acids are encoded by the standard
genetic code and are called
proteinogenic or
standard amino acids. Other amino acids contained in proteins are usually formed by
post-translational modification, which is modification after translation in protein synthesis. These modifications are often essential for the function or regulation of a protein; for example, the
carboxylation of
glutamate allows for better binding of
calcium cations, and the
hydroxylation of
proline is critical for maintaining
connective tissues and responding to
oxygen starvation. Such modifications can also determine the localization of the protein, for example, the addition of long hydrophobic groups can cause a protein to bind to a
phospholipid membrane.
Non-protein functions
The 20 standard amino acids are either used to synthesize proteins and other biomolecules or oxidized to
urea and carbon dioxide as a source of energy. The oxidation pathway starts with the removal of the amino group by a
transaminase, the amino group is then fed into the
urea cycle. The other product of transamidation is a
keto acid that enters the citric acid cycle.
Glucogenic amino acids can also be converted into glucose, through
gluconeogenesis.
Hundreds of types of non-protein amino acids have been found in nature and they've multiple functions in living organisms.
Microorganisms and plants can produce uncommon amino acids. In microbes, examples include
2-aminoisobutyric acid and
lanthionine, which is a sulfide-bridged alanine dimer. Both these amino acids are both found in peptidic
lantibiotics such as
alamethicin. While in plants,
1-aminocyclopropane-1-carboxylic acid is a small disubstituted cyclic amino acid that's a key intermediate in the production of the plant hormone
ethylene.
In humans, non-protein amino acids also have important roles, such as the
neurotransmitter gamma-aminobutyric acid. Many amino acids are used to synthesize other molecules, for example:
Hydroxyproline,
hydroxylysine, and
sarcosine are also non-protein amino acids. The
thyroid hormones are also alpha-amino acids.
Some amino acids have even been detected in
meteorites, especially in a type known as
carbonaceous chondrites. This observation has prompted the suggestion that life may have arrived on earth from an
extraterrestrial source.
General structure
In the structure shown at the right,
R represents a
side chain specific to each amino acid. The central
carbon atom, called C
α, is a
chiral central carbon atom (with the exception of glycine) to which the two termini and the R-group are attached. Amino acids are usually classified by the
properties of the side chain into four groups. The side chain can make them behave like a
weak acid, a
weak base, a
hydrophile if they're
polar, and
hydrophobe if they're
nonpolar. The chemical structures of the 20 standard amino acids, along with their chemical properties, are catalogued in the
list of standard amino acids.
The phrase "
branched-chain amino acids" or BCAA is sometimes used to refer to the amino acids having
aliphatic side chains that are non-linear; these are
leucine,
isoleucine, and
valine.
Proline is the only
proteinogenic amino acid whose side group links to the α-amino group and, thus, is also the only proteinogenic amino acid containing a secondary amine at this position. Proline has sometimes been termed an
imino acid, but this isn't correct in the current nomenclature.
Isomerism
Most amino acids can exist in either of two
optical isomers, called
D and
L. The
L-amino acids represent the vast majority of amino acids found in
proteins.
D-amino acids are found in some proteins produced by exotic sea-dwelling organisms, such as
cone snails. They are also abundant components of the
peptidoglycan cell walls of
bacteria.
The
L and
D conventions for amino acid configuration don't refer to the optical activity of the amino acid itself, but rather to the optical activity of the isomer of
glyceraldehyde having the same stereochemistry as the amino acid.
S-glyceraldehyde is levorotary, and
R-glyceraldehyde is dexterorotary, and so
S-amino acids are called
L-amino acids even if they're not levorotary, and
R-amino acids are likewise called
D-amino acids even if they're not dexterorotary.
There are two exceptions to these general rules of amino acid isomerism. Firstly,
glycine, where R = H, no isomerism is possible because the alpha-carbon bears two identical groups (hydrogen). Secondly, in
cysteine, the
L =
S and
D =
R assignment is reversed to
L =
R and
D =
S. Cysteine is structured in the same way as the other amino acids but the
sulfur atom alters the interpretation of the
Cahn-Ingold-Prelog priority rule.
Reactions
As amino acids have both a primary
amine group and a primary
carboxyl group, these chemicals can undergo most of the reactions associated with these functional groups. These include
nucleophilic addition,
amide bond formation and
imine formation for the amine group and
esterification,
amide bond formation and
decarboxylation for the carboxylic acid group. The multiple side chains of amino acids can also undergo chemical reactions. The types of these reactions are determined by the groups on these side chains and are discussed in the articles dealing with each specific type of amino acid.
Peptide bond formation
polymerization of amino acids is what creates proteins. This
condensation reaction yields the newly formed
peptide bond and a molecule of water. In cells, this reaction doesn't occur directly; instead the amino acid is first activated by attachment to a
transfer RNA molecule through an
ester bond. This aminoacyl-tRNA is produced in an
ATP-dependent reaction carried out by an
aminoacyl tRNA synthetase. This aminoacyl-tRNA is then a substrate for the
ribosome, which catalyzes the attack of the amino group of the elongating protein chain on the ester bond. As a result of this mechanism, all proteins made by ribosomes are synthesized starting at their N-terminus and moving towards their C-terminus.
However, not all peptide bonds are formed in this way. In a few cases, peptides are synthesized by specific enzymes. For example, the tripeptide
glutathione is an essential part of the defenses of cells against oxidative stress. This peptide is synthesized in two steps from free amino acids. In the first step
gamma-glutamylcysteine synthetase condenses
cysteine and
glutamic acid through a peptide bond formed between the side-chain carboxyl of the glutamate (the gamma carbon of this side chain) and the amino group of the cysteine. This dipeptide is then condensed with
glycine by
glutathione synthetase to form glutathione.
In chemistry, peptides are synthesized by a variety of reactions. One of the most used in
solid-phase peptide synthesis, which uses the aromatic oxime derivatives of amino acids as activated units. These are added in sequence onto the growing peptide chain, which is attached to a solid resin support.
Zwitterions
As amino acids have both the active groups of an amine and a carboxylic acid they can be considered both acid and base. At a certain pH known as the
isoelectric point, the amine group has a positive charge (is
protonated) and the acid group a negative charge (is
deprotonated). The exact value is specific to each different amino acid. This ion is known as a
zwitterion, which comes from the German word
Zwitter meaning "hybrid". A zwitterion can be extracted from the solution as a white crystalline structure with a very high melting point, due to its dipolar nature. Near-neutral physiological pH allows most free amino acids to exist as zwitterions.
Hydrophilic and hydrophobic amino acids
Depending on the
polarity of the side chain, amino acids vary in their
hydrophilic or
hydrophobic character. These properties are important in
protein structure and
protein-protein interactions. The importance of the physical properties of the side chains comes from the influence this has on the amino acid residues' interactions with other structures, both within a single protein and between proteins. The distribution of hydrophilic and hydrophobic amino acids determines the
tertiary structure of the protein, and their physical location on the outside structure of the proteins influences their
quaternary structure. For example, soluble proteins have surfaces rich with polar amino acids like
serine and
threonine, while
integral membrane proteins tend to have outer ring of
hydrophobic amino acids that anchors them into the
lipid bilayer, and proteins anchored to the membrane have a hydrophobic end that locks into the membrane. Similarly, proteins that have to bind to positively-charged molecules have surfaces rich with negatively charged amino acids like glutamate and aspartate, while proteins binding to negatively-charged molecules have surfaces rich with positively charged chains like lysine and arginine. Recently a new scale of hydrophobicity based on the free energy of hydrophobic association has been proposed.
Hydrophilic and hydrophobic interactions of the proteins don't have to rely only on the sidechains of amino acids themselves. By various
posttranslational modifications other chains can be attached to the proteins, forming hydrophobic
lipoproteins or hydrophilic
glycoproteins.
Table of standard amino acid abbreviations and side chain properties
In addition to the normal amino acid codes, placeholders were used historically in cases where
chemical or
crystallographic analysis of a peptide or protein couldn't completely establish the identity of a certain residue in a structure. The ones they couldn't resolve between are these pairs of amino-acids:
| Ambiguous Amino Acids |
3-Letter |
1-Letter |
| Asparagine or aspartic acid |
Asx |
B |
| Glutamine or glutamic acid |
Glx |
Z |
| Leucine or Isoleucine |
Xle |
J |
| Unspecified or unknown amino acid |
Xaa |
X |
Unk is sometimes used instead of
Xaa, but is less standard.
Nonstandard amino acids
Aside from the twenty standard amino acids, there are a vast number of "non-standard" amino acids. Two of these can be specified by the genetic code, but are rather rare in proteins.
Selenocysteine is incorporated into some proteins at a UGA
codon, which is normally a stop codon.
Pyrrolysine is used by some
methanogenic
archaea in
enzymes that they use to produce
methane. It is coded for with the codon UAG.
Examples of nonstandard amino acids that are not found in proteins include
lanthionine,
2-aminoisobutyric acid,
dehydroalanine and the neurotransmitter
gamma-aminobutyric acid. Nonstandard amino acids often occur as intermediates in the
metabolic pathways for standard amino acids — for example
ornithine and
citrulline occur in the
urea cycle, part of amino acid
catabolism.
Nonstandard amino acids are usually formed through modifications to standard amino acids. For example,
homocysteine is formed through the
transsulfuration pathway or by the demethylation of methionine via the intermediate metabolite
S-adenosyl methionine, while dopamine is synthesized from l-DOPA, and
hydroxyproline is made by a
posttranslational modification of
proline.
Uses in technology
Nutritional importance
Of the 20 standard proteinogenic amino acids, 8 are called
essential amino acids because the
human body can't
synthesize them from other
compounds at the level needed for normal growth, so they must be obtained from food. However, the situation is a little more complicated since
cysteine,
tyrosine,
histidine and
arginine are semiessential amino acids in children, because the metabolic pathways that synthesize these amino acids are not fully developed. The amounts required also depend on the age and health of the individual, so it's hard to make general statements about the dietary requirement for some amino acids.
(*) Essential only in certain cases.
Several common
mnemonics have evolved for remembering the ten amino acids often described as essential. PVT TIM HALL ("
Private Tim Hall") uses the first letter of each of these amino acids. Another mnemonic that frequently occurs in student practice materials beneath "
AH TV TILL Past
Midnight", is "
These
ten
valuable
amino acids
have
long
preserved
life
in
man".
Further Information
Get more info on 'Amino Acid Residue'.
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