Amino acids and proteins are the intermediates passing from the mineral world to living matter.
As their name indicates, amino acids are bifunctional organic substances: that is, they consist of the amino function (-NH2) and the carboxylic function (-COOH); they can be α, β, γ, etc., depending on the position occupied by the amino group with respect to the carboxyl group:
 |  |  |
| α-amino acid | β-amino acid | γ-amino acid |
Biologically important amino acids are all α-amino acids.
Protein structures consist of twenty amino acids.
As can be seen from the generic structures shown above, the amino acids all have a common part and a different part that characterizes them (represented generically with R) .
Of the twenty amino acids, nineteen are optically active (deviate the plane of polarized light).
Most amino acids have only one amino group and one carboxyl so they are called neutral amino acids ; those that have an extra carboxyl are called acid amino acids while those with an extra amino group are basic amino acids .
Amino acids are crystalline solid substances and have a good solubility in water.
The lack of some amino acids in the diet determines serious alterations in the development; in fact, the human organism is not able to synthesize some amino acids that are precisely called essential (they must be introduced with the diet), while it can produce by itself only some amino acids (the non essential ones).
One of the diseases due to the lack of essential amino acids is the one known as kwashiorkor (word that derives from an African dialect that translated means "first and second"); this disease affects the firstborn but after the birth of the second child because the first one misses the mother's milk which contains the correct protein intake. This disease, therefore, is widespread among undernourished populations and leads to diarrhea, a lack of appetite that leads to a progressive weakening of the organism.
As already mentioned, natural amino acids, with the exception of glycine (it is an a-amino acid with a hydrogen instead of the R group and is the smallest of the winds), possess optical activity due to the presence of at least one asymmetric carbon. In natural amino acids the absolute configuration of the asymmetric carbon on which only the amino group and the carboxyl group belong belong to the L series;
D-amino acids never enter the structure of a protein.
We remember that:
DNA ---- transcription → m-RNA ---- translation → protein
Transcription is capable of coding as L-amino acids; D-amino acids can be contained in non-protein structures (eg in the lining wall of bacteria: in bacteria there is no genetic information to have D-amino acids for a protective role, however, there is genetic information for enzymes which take care of the bacterial coating wall).
Let's go back to the amino acids: the different structure of the R group defines the individual characteristics of each amino acid and makes a specific contribution to the characteristics of the proteins.
It was therefore thought to divide amino acids according to the nature of the R group:
Polar but not charged amino acids (7):
Glycine (R = H-)
Serina (R = HO-CH2-)
threonine
Threonine has two centers of symmetry: in nature only threonine 2S, 3R exists.
Threonine is an essential amino acid (not to be confused with indispensable: all amino acids are indispensable), so it must be taken with the diet, that is eating foods that contain it because, as already said, in the cells of human beings there is no genetic heritage able to produce this amino acid (this heritage is present in many plants and betteri).
The hydroxyl group of serine and threonine can be esterified with a phosphoryl group (obtaining phosphoserine and phosphotreonine), this process is called phosphorylation ; phosphorylation is used in nature for the translation of signals between the inside and the outside of the cell.
Cysteine (R = HS-CH2-)
Cysteine sulfhydryl is more easily protonable than serine hydroxyl: sulfur and oxygen are both from the sixth group but sulfur is more easily oxidizable because it is larger.
Tyrosine [R = HO- (C6H4) -CH2-]
NB
(C6H4) = di-substituted benzene ring
As for serine and threonine, the hydroxyl can be esterified (phosphorylated).
Asparagine (R = NH2-CO-CH2-)
Glutamine (R = NH2-CO-CH2-CH2-)
Non-polar amino acids (8)
have hydrophobic lateral groups; within this class we distinguish:
Aliphatics :
Alanine (R = CH3-)
Valine (R = (CH3) 2-CH-) essential
Leucine (R = (CH3) 2-CH-CH2-) essential
Isoleucine (R =
Methionine (R = CH3-S-CH2-CH2-) essential
The cell membranes consist of a lipid bilayer with proteins anchored thanks to their hydrophobic character therefore they contain alanine, valine, isoleucine and leucine. Methionine, on the other hand, is an amino acid almost always present in small quantities (about 1%).
Proline
Aromatics :
Phenylalanine (R = Ph-CH2-) Ph = phenyl: essential monosubstituted benzene
Tryptophan (R =
These two amino acids, being aromatic, absorb the radiation of the near ultraviolet (about 300 nm); therefore it is possible to exploit the UV spectrophotometry technique to determine the concentration of a known protein that contains these amino acids.
Amino acids with charge (5)
In turn they are distinguished in:
Acid amino acids (having polar residues with negative charge at pH 7) are such because they are able to yield a positive charge H +:
Glutamic acid (R =
These amino acids derive respectively from asparagine and glutamine; all four exist in nature and this means that there is a specific information for each of them, that is, there is a triplet of bases in the DNA that codes for each of them.
Basic amino acids (having polar residues with positive charge at pH 7) are such because they can accept a positive charge H +:
Lysine (R =
Arginine (R =
Histidine (R =
There are proteins in which there are derivatives of amino acids in the side chains: for example, a phosphoserine may be present (there is no genetic information that codes for phosphoserine, only that for serine); phosphoserine is a post-translational modification: after protein synthesis has occurred
DNA ---- transcription → m-RNA ---- translation → protein
such post-translational modifications can occur on the side chains of the protein.
See also: Protein, a look at chemistry
