Amino acid

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 H2NCHRCOOH, 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 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.

General structure
The general structure of an -amino acid, with the amino group

on the left and the carboxyl group on the right. In the structure shown at the right, R represents a side chain specific to each amino acid. The central carbon atom, called C, is a chiral central carbon atom (with the exception of glycine) to which the two termini and the R-group are attached.

Isomerism
L-isomer

In proteins, only the L-isomer is found normally. As you travel onward (from the carbonyl carbon to the amino group), the R group of L-amino acids will be on the left as shown in the molecular graphic on the right The L-amino acids represent the vast majority of amino acids found in proteins.

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.

Zwitterions
An amino acid, in its (1) unionized and (2) zwitterionic forms. 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.

Twenty Amino Acids

Such as

Acidic Amino Acids and their Amides

Atoms in Amino Acids

Atoms in Amino Acids

Aliphatic Amino Acids

Aliphatic R groups are nonpolar and hydrophobic. Hydrophobicity increases with increasing number of C atoms in the hydrocarbon chain

Less hydrophobic

Less hydrophobic

More hydrophobic

Aromatic Amino Acids

Aromatic amino acids are relatively nonpolar.

Least hydrophobic

Least hydrophobic

Very hydrophobic

Basic Amino Acids

Basic amino acids are polar and positively charged at pH

values below their pKa's, and are very hydrophilic.

Cyclic Amino Acid

Proline is the only cyclic amino acid. It is nonpolar and

shares many properties with the aliphatic group.

Hydroxyl Amino Acids

Hydroxyl amino acids are polar, uncharged at physiological pH, and hydrophilic. The phenolic hydroxyl ionizes with a pKa of 10 to yield the phenolate anion. The hydroxyl groups of serine and threonine are so high that they are generally regarded as nonionizing.

Sulfur-Containing Amino Acids

The sulfur-containing amino acids

(cysteine and methionine) are generally considered to be nonpolar and hydrophobic

Essential amino acids

Humans can produce 10 of the 20 amino acids. The others must

be supplied in the food. Unlike fat and starch, the human body does not store excess amino acids for later usethe amino acids must be in the food every day. The 10 amino acids that we can produce are alanine, asparagine, aspartic acid, cysteine, glutamic acid, glutamine, glycine, proline, serine and tyrosine. Tyrosine is produced from phenylalanine, so if the diet is deficient in phenylalanine, tyrosine will be required as well. The essential amino acids are arginine (required for the young, but not for adults), histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. These amino acids are required in the diet. Plants, of course, must be able to make all the amino acids. Humans, on the other hand, do not have all the the enzymes required for the biosynthesis of all of the amino acids.

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.

Essential Isoleucine

Nonessential Alanine Leucine Asparagine Lysine Aspartate Methionine Cysteine* Phenylalanine Glutamate Threonine Glutamine* Tryptophan Glycine* Valine Proline* Arginine* Serine* Histidine* Tyrosine* (*) Essential only in certain cases

Peptide bond
A peptide bond is a chemical bond formed between two

molecules when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water (H2O). This is a dehydration synthesis reaction (also known as a condensation reaction), and usually occurs between amino acids. The resulting CO-NH bond is called a peptide bond, and the resulting molecule is an amide. The four-atom functional group -C(=O)NH- is called an amide group or (in the context of proteins) a peptide group.

Peptide bond formation

As both the amine and carboxylic acid groups of amino acids can react to form amide bonds, one amino acid molecule can react with another and become joined through an amide linkage.

Globular proteins
Globular proteins, or spheroproteins are one of the two main

protein classes, comprising globelike proteins that are more or less soluble in aqueous solutions (where they form colloidal solutions). This main characteristic helps distinguishing them from fibrous proteins (the other class), which are practically insoluble.

3-dimensional structure of hemoglobin, a globular protein.

Fibrous protein
Fibrous proteins, also called scleroproteins, are one of the

two main classes of protein quaternary structure (the other being globular proteins). Fibrous proteins are only found in animals.proteins are usually used to construct connective tissues, Fibrous tendons, bone matrix and muscle fiber. Examples of fibrous proteins include keratins, collagens and elastins. Structure of collagen

primary structure
In biochemistry, the primary structure of a biological molecule

is the exact specification of its atomic composition and the chemical bonds connecting those atoms (including stereochemistry). For a typical unbranched, un-crosslinked biopolymer (such as a molecule of DNA, RNA or typical intracellular protein), the primary structure is equivalent to specifying the sequence of its monomeric subunits, e.g., the nucleotide or peptide sequence.

secondary structure
secondary structure is the general three-dimensional form of

local segments of biopolymers such as proteins and nucleic acids (DNA/RNA). It does not, however, describe specific atomic positions in three-dimensional space, which are considered to be tertiary structure.

A representation of the 3D structure of the myoglobin protein. Alpha helices are shown in colour, and random coil in white, there are no beta sheets shown.

Tertiary structure
In biochemistry and chemistry, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.

Quaternary structure
Many proteins are actually assemblies of more than

one polypeptide chain, which in the context of the larger assemblage are known as protein subunits. In addition to the tertiary structure of the subunits, multiple-subunit proteins possess a quaternary structure, which is the arrangement into which the subunits assemble. Enzymes composed of subunits with diverse functions are sometimes called holoenzymes, in which some parts may be known as regulatory subunits and the functional core is known as the catalytic subunit. Examples of proteins with quaternary structure include hemoglobin, DNA polymerase, and ion channels.