Dental Biochemistry 1- (2)Chemistry of Proteins
Protein have different levels of structural organization; primary, secondary, tertiary and quaternary structure. 2
This refers to the number and sequence of amino acids in the polypeptide chain or chains linked by peptide bonds. Each polypeptide chain has a unique amino acid sequence decided by the genes. The following example may be taken to have a clear idea of the term "sequence". Gly – Ala – Val or Gly – Val – Ala. Both the tripeptides shown above contain the same amino acids; but their sequence is altered. When the sequence is changed, the polypeptide is also different. The primary structure is maintained by the covalent bonds of the peptide linkages.
In a polypeptide chain, at one end there will be one free alpha amino group. This end is called the amino terminal (N-terminal) end The other end of the polypeptide chain is the carboxy terminal end (C-terminal), where there is a free alpha carboxyl group which is contributed by the last amino acid.
Usually the N-terminal amino acid is written on the left hand side when the sequence of the protein is denoted. In nature, the biosynthesis of the protein also starts from the amino terminal end. Take an example of a tripeptide: Peptide bonds formed by combination of carboxyl group of Glycine with amino group of Alanine, and further combination of carboxyl group of Alanine with amino group of Valine. This tripeptide is called glycyl-alanyl-valine and abbreviated as NH2-Gly-Ala-Val-COOH or Gly-Ala- Val or GAV.
Importance of the understanding of primary structure: Many genetic diseases result in protein with abnormal amino acid sequences, which cause improper folding and loss or impairment of normal function. For example, Sickle cell anemia due to HbS, where the sixth amino acid in the beta chain, the normal hydrophilic glutamic acid is replaced by hydrophobic valine.
Coiling, folding or bending of the polypeptide chain leading to specific structure kept by interactions of amino acids close to each other in the sequence of polypeptide chain. There are two main regular forms of secondary structure; α-helix and β-pleated sheets . 8
α- Helix β- Pleated1. It is rod like structure, coiled 1. It is Sheet like structure, polypeptide chain arranged in composed of two or more spiral structure peptide chain2. All the peptide bond 2. All the peptide bond components participate in components participate in hydrogen bonding hydrogen bonding3. All hydrogen bonding are 3. Interchain between separateintrachain polypeptide chain and intrachain inEg. It is abundant in hemoglobin a single polypeptide chain foldingand myoglobin back on its self.4. The spiral of α-helix prevents 4. The chain are almost fullythe chain form being fully extended extended and relatively flat. They may be parallel or anti parallel.
3. Tertiary structure of proteins: It denotes three-dimensional structure of the whole protein Occurs when certain attraction occurs between α-helix and β-pleated sheets to gives the overall shape of the protein molecules. It is maintained by hydrophobic bonds, electrostatic bonds and Van der Waals force. There are two main forms of tertiary structure: fibrous and globular types. 13
4. Quaternary structure of proteins: Certain polypeptides will aggregate to form one functional protein. Proteins possess quaternary structure if they consist of 2 or more polypeptide chains (monomer or subunit 14
Primary structureIs determined by the sequence of amino acids Secondary structureOccurs when amino acids are linked by hydrogen bonds Tertiary structureIs formed when alpha helices and beta sheets are held together by weak interactions Quaternary structureConsists of more than one polypeptide chain
I- According to shape:1- Globular proteins: e.g. plasma albumins and globulins and many enzymes. They have spheroidal shape.2- Fibrous proteins: e.g. keratin, myosin, fibrin and collagen. 18
Catalytic proteins, e.g. enzyme. Structural proteins, e.g. collagen, elastin, keratin. Contractile proteins, e.g. myosin, actin, flagellar proteins. Transport proteins, e.g. hemoglobin, myoglobin, albumin, transferrin. Regulatory proteins or hormones, e.g. ACTH, insulin, growth hormone. Genetic proteins, e.g. histones. Protective proteins, e.g. immunoglobulins, clotting factors.
Proteins may be divided into three major groups; simple, conjugated and derived.A. Simple proteins: According to definition, they contain only amino acids. But they also contain very small quantity of carbohydrates.
Albumins:They are soluble in water and coagulated by heat. Globulins: These are insoluble in pure water, but soluble in dilute salt solutions. They are also coagulated by heat. E.g. egg globulin and serum globulins.
Protamines: These are soluble in water, dilute acid and alkalies. They are not coagulated by heating. They contain large number of arginine and lysine residues, and so are strongly basic. Hence they can combine with other acidic proteins.
Scleroproteins: They are insoluble in water, salt solutions, organic solvents and soluble only in hot strong acids. They form supporting tissues. E.g. collagen of bone, cartilage and tendon; keratin of hair, horn, nail and hoof.
B- Conjugated proteins:They are combinations of protein with a non-protein part, called prosthetic group. Conjugated proteins may be classified as follows: Glycoproteins: These are proteins combined with carbohydrates. Hydroxyl groups of serine or threonine and amide groups of asparagines and glutamine form linkages with carbohydrate residues. When the carbohydrate content is more than 10% of the molecule, the viscosity is correspondingly increased; they are sometimes known as mucoproteins or proteoglycans. Blood group antigens and many serum proteins are glycoproteins.
Lipoproteins: These are proteins loosely combined with lipid components. They occur in blood and cell membranes. Nucleoproteins: These are proteins attached to nucleic acids, e.g. Histones. The DNA carries negative charges, which combines with positively-charged proteins. Chromoproteins: These are proteins with coloured prosthetic groups. Hemoglobin (Heme, red); Flavoproteins (Riboflavin, yellow), Visual purple (Vitamin A, purple) are some examples of chromoproteins.
Phosphoproteins: These contain phosphorus. Ex. Casein of milk and vitellin of egg yolk. The phosphoric acid is added to the hydroxyl groups of serine and threonine residues of proteins. Mettaloproteins: They contain metal ions. Ex. Hemoglobin (iron), cytochrome (iron), tyrosinase (copper) and carbonic anhydrase (zinc).
C- Derived proteins: They are degradation products of native proteins. Denaturation is the first step. Progressive hydrolysis of protein results in smaller and smaller chains: Protein → Peptones → Peptides → Amino acids.
A. Nutritionally rich proteins: They are also called as complete proteins or first class proteins. They contain all the essential amino acids in the required proportion. On supplying these proteins in the diet, the young individuals will grow satisfactorily. A good example is casein of milk.
B. Incomplete proteins: They lack one essential amino acid. They cannot promote body growth in young individuals; but may be able to sustain the body weight in adults. Proteins from pulses are deficient in methionine, while proteins of cereals lack in lysine. If both of them are combined in the diet, good growth could be obtained.
C. Poor proteins: They lack in many essential amino acids and a diet based on these proteins will not even sustain the original body weight. Zein from corn lacks tryptophan and lysine.
1- Protein solutions exhibit colloidal properties and therefore scatter light.2- Shape of proteins vary. Thus insulin is globular, albumin is oval, fibrinogen molecule is elongated.3- As the protein molecule become bigger and elongated, the viscosity of the solution increase.
It is loss of native structure (natural conformation) of protein by many physical or chemical agents leading to nonspecific alterations in the secondary, tertiary and quaternary structure of proteins. due to rupture of the non-covalent bonds (hydrogen bonds, hydrophobic bonds and electrostatic bonds and may be disulphide, but not peptide bonds), with loss of biological activity. 32
N.B. The primary structure of proteins is not altered in denaturation since there is no hydrolysis of peptide bonds. Native proteins are often resistant to proteolytic enzymes, but denatured proteins will have more exposed sites for enzyme action. Since cooking leads to denaturation of proteins, cooked foods are more easily digested. Agents caused denaturation:Brief heating, urea, salicylate, X-ray, ultraviolet rays, high-pressure and vigorous shaking. 33
When heated at iso-electric point, some protein denature irreversibly to produce thick conglomerates called coagulum. This process called heat coagulation. Albumin is easily coagulated, globulins is lesser extent. Some proteins when heated, though denatured, are still soluble, they may be precipitated by bringing to iso-electric pH. This is the basis of “heat and acetic acid test”, very commonly employed to detect the presence of albumin in urine.