A look at chemistry
Proteins can be placed in the first place in the "biological world" since, given their many functions, there would be no life without them.
Elemental analysis of proteins gives the following average values: 55% of carbon, 7% of hydrogen and 16% of nitrogen; it is clear that proteins differ from one another, but their average elemental composition deviates little from the values indicated above.
Constitutionally, proteins are macromolecules formed from natural α-amino acids; The amino acids combine through the amide bond that is established by reaction between an amino group of an a-amino acid and the carboxyl of another a-amino acid. This bond (-CO-NH-) is also called peptide bond because it binds peptides (amino acids in combination):
the one obtained is a dipeptide because it is formed by two amino acids. Since a dipeptide contains a free amino group at one end (NH2) and a carboxyl at the other (COOH), it can react with one or more amino acids and stretch the chain both from the right and from the left, with the same reaction seen above.
The sequence of reactions (which, in any case, are not really so simple) can continue indefinitely: until there is a polymer called polypeptide or protein . The distinction between peptides and proteins is linked to molecular weight: usually for molecular weights greater than 10, 000 it is called protein.
Binding together amino acids to obtain even small proteins is a difficult operation, although recently an automatic method for producing proteins from amino acids has been developed that gives excellent results.
The simplest protein, therefore, is made up of 2 amino acids: by international convention, the ordered numbering of amino acids in a protein structure starts from the amino acid with the free a-amino group.
Protein structure
The protein molecules are shaped so that we can see up to four distinct organizations: they are generally distinguished, a primary structure, a secondary one, a tertiary one and a quaternary one.
Primary and secondary structures are essential for proteins, while tertiary and quaternary structures are "accessory" (in the sense that not all proteins can be equipped with them).
The primary structure is determined by the number, type and sequence of amino acids in the protein chain; it is therefore necessary to determine the ordered sequence of the amino acids that make up the protein (to know this means to know the exact sequence of DNA bases that codify for this protein) which encounters non-negligible chemical difficulties.
It was possible to determine the ordered sequence of amino acids through Edman degradation: the protein is reacted with phenylisothiocyanate (FITC); initially the doublet of the α-amino nitrogen attacks the phenylisothiocyanate forming the thiocarbamyl derivative; subsequently, the obtained product cyclises giving the phenyltioidantoin derivative which is fluorescent.
Edman has devised a machine called sequencer that automatically adjusts the parameters (time, reagents, pH etc.) for degradation and provides the primary structure of proteins (for this he received the Nobel prize).
The primary structure is not sufficient to completely interpret the properties of protein molecules; it is believed that these properties depend, in an essential way, on the spatial configuration that the molecules of proteins tend to assume, bending in various ways: that is, assuming what has been defined as a secondary structure of proteins. The secondary structure of proteins is tremolabile, ie it tends to discard due to heating; then the proteins are denatured, losing many of their characteristic properties. In addition to heating above 70 ° C, denaturation can also be caused by irradiation or by the action of reagents (for example strong acids).
The denaturation of proteins by thermal effect is observed, for example, by heating the egg whites: it is seen losing its gelatinous appearance and turning into an insoluble white substance. However, the denaturation of the proteins leads to the destruction of their secondary structure, but leaves the primary structure (the concatenation of the various amino acids) unchanged.
Proteins take on the tertiary structure when their chain, while still flexible despite the folding of the secondary structure, folds up so as to create a twisted three-dimensional arrangement in the form of a solid body. The disulphide bonds that can be established between the cysteine -SH scattered along the molecule are mainly responsible for the tertiary structure.
The quaternary structure, on the other hand, competes only for proteins formed by two or more subunits. Hemoglobin, for example, is composed of two pairs of proteins (that is, in all of four protein chains) located at the vertices of a tetrahedron in such a way as to give rise to a structure of spherical shape; the four protein chains are held together by ionic forces and not by covalent bonds.
Another example of a quaternary structure is that of insulin, which appears to consist of as many as six protein subunits arranged in pairs at the vertices of a triangle at the center of which two zinc atoms are located.
PROTEINS FIBROSE: they are proteins endowed with a certain rigidity and having an axis much longer than the other; the most abundant fibrous protein in nature is collagen (or collagen).
A fibrous protein can take several secondary structures: α-helix, β-leaflet and, in the case of collagen, triple helix; α-helix is the most stable structure, followed by the β-leaflet, while the least stable of the three is the triple helix.
α-helix
The propeller is said to be right-handed if, following the main skeleton (oriented from the bottom upwards), a movement similar to the screwing of a right-handed screw is performed; while the propeller is of the left hand if the movement is analogous to the screwing of a left-handed screw. In the right-hand α-helices the -R substituents of the amino acids are perpendicular to the main axis of the protein and face outwards, whereas in the left hand a-helices the substituents -R face inwards. The right-hand a-helices are more stable than those of the left hand because between the vats -R there is less interaction and less steric hindrance. All the α-helix found in proteins are dextroginous.
The structure of the α-helix is stabilized by hydrogen bonds (hydrogen bridges) which is formed between the carboxyl group (-C = O) of each amino acid and the amino group (-NH) which is four residues later in the linear sequence.
An example of a protein having an α-helix structure is hair keratin.
β-sheet
In the β-leaflet structure, hydrogen bonds can be formed between amino acids belonging to different but parallel polypeptide chains or between amino acids of the same protein even numerically distant from each other but flowing in antiparallel directions. However, hydrogen bonds are weaker than those that stabilize the α-helix form.
An example of a β-leaflet structure is silk fibrin (it is also found in cobwebs).
By extending the α-helix structure, the transition from α-helix to β-leaflet is performed; also the heat or the mechanical stress allow to pass from the α-helix structure to the β-sheet structure.
Usually, in a protein, the β-leaflet structures are close to each other because hydrogen bonds between the portions of the protein can be established.
In fibrous proteins most of the protein structure is organized as α-helix or β-leaflet.
GLOBULAR PROTEINS: they have an almost spherical spatial structure (due to the numerous changes of direction of the polypeptide chain); some portions of being can be traced back to an α-helix or β-leaflet structure and other portions are not, instead, attributable to these forms: the arrangement is not random but organized and repetitive.
The proteins referred to so far are substances of a completely homogeneous constitution: that is, pure sequences of combined amino acids; these proteins are called simple ; there are proteins made up of a protein part and a non-protein part (prostate group) called conjugated proteins.
Collagen
It is the most abundant protein in nature: it is present in the bones, nails, cornea and lens of the eye, between the interstitial spaces of some organs (eg liver), etc.
Its structure gives it particular mechanical capabilities; it has great mechanical resistance associated with high elasticity (eg in tendons) or high rigidity (eg in the bones) depending on the function it has to perform.
One of the most curious properties of collagen is its constitutive simplicity: it is formed for about 30% by proline and for about 30% by glycine ; the other 18 amino acids must be divided only the remaining 40% of the protein structure. The amino acid sequence of collagen is remarkably regular: every third residue, the third is glycine.
Proline is a cyclic amino acid in which the R group binds to α-amino nitrogen and this gives it a certain rigidity.
The final structure is a repetitive chain having the shape of a helix; within the collagen chain, hydrogen bonds are absent. Collagen is a left-hand helix with a step (length corresponding to a revolution of the helix) greater than the α-helix; the helix of collagen is so loose that three protein chains are able to wrap between them forming a single rope: triple helix structure.
The triple helix of collagen is, however, less stable than both the α-helix structure and the β-leaflet structure.
Let us now see the mechanism by which collagen is produced ; consider, for example, the rupture of a blood vessel: this rupture is accompanied by a myriad of signals in order to close the vessel, thus forming the clot. Coagulation requires at least thirty specialized enzymes. After the clot it is necessary to continue with the repair of the tissue; the cells close to the wound also produce collagen. To do this, first the expression of a gene is induced, that is, organisms that start from the information of a gene are able to produce the protein (genetic information is transcribed on the mRNA which comes from the nucleus and reaches the ribosomes in the cytoplasm where the genetic information is translated into protein). Then the collagen is synthesized in the ribosomes (it appears as a left hand helix composed of about 1200 amino acids and having a molecular weight of about 150000 d) and then accumulates in the lumens where it becomes substrate for enzymes capable of making post modifications -traditional (language modifications translated by mRNA); in collagen, these modifications consist of the oxidation of some side chains, especially proline and lysine.
The failure of the enzymes that lead to these modifications causes scurvy: it is a disease that causes, initially the rupture of blood vessels, rupture of the teeth which can be followed by interintestinal bleeding and death; it can be caused by the continuous use of long-life food.
Subsequently, by the action of other enzymes, other modifications occur which consist in the glycosidation of the hydroxyl groups of proline and lysine (a sugar is bound to oxygen by OH); these enzymes are found in areas other than the lumen therefore, while the protein undergoes modifications, it migrates inside the endoplasmic reticulum to end up in sacs (vesicles) which close up on themselves and detach from the lattice: inside they are contained the glycosidated pro-collagen monomer; the latter reaches the Golgi apparatus where particular enzymes recognize the cysteine present in the carboxy part of the glycosidated pro-collagen and cause the different chains to approach each other and form disulfide bridges: three chains of pro glycosidated collagen linked together and this is the starting point of which the three chains, interpenetrating, then, spontaneously, give rise to the triple helix. The three glycidoxidated pro-collagen chains linked to each other reach, then a vesicle which, choking on itself, detaches itself from the Golgi apparatus, transporting the three chains towards the periphery of the cell where, through the fusion with the plasma membrane, the trimetro is expelled from the cell.
In the extra cellular space, there are particular enzymes, the pro-collagen peptidases, which remove from the species expelled from the cell, three fragments (one for each helix) of 300 amino acids each, on the carboxy terminal side and three fragments (one for each helix) of about 100 amino acids each, from the amino-terminal part: a triple helix remains, consisting of about 800 amino acids for the helix known as tropocollagen .
The tropocollagen has the appearance of a fairly rigid stick; the different trimers are associated with covalent bonds to give larger structures: the microfibrils . In the microfibrils, the various trimers are arranged in a staggered manner; so many microfibrils are tropocollagen bundles.
In the bones, among the collagen fibers, there are interstitial spaces in which calcium and magnesium sulphates and phosphates are deposited: these salts also cover all the fibers; this makes the bones stiff.
In the tendons, the interstitial spaces are less rich in crystals than the bones while smaller proteins are present compared to the tropocollagen: this gives elasticity to the tendons.
Osteoporosis is a disease caused by a deficiency of calcium and magnesium which makes it impossible to fix salts in the interstitial areas of tropocollagen fibers.
