Dental Biochemistry 1- (2)

Chemistry of Proteins

Protein have different levels of structural organization; primary, secondary, tertiary and quaternary structure.

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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 .

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α- Helix β- Pleated

1. It is rod like structure, coiled polypeptide chain arranged in

spiral structure

1. It is Sheet like structure, composed of two or more peptide chain

2. All the peptide bond components participate in hydrogen bonding

2. All the peptide bond components participate in hydrogen bonding

3. All hydrogen bonding are intrachain Eg. It is abundant in hemoglobin and myoglobin

3. Interchain between separate polypeptide chain and intrachain in a single polypeptide chain folding back on its self.

4. The spiral of α-helix prevents the chain form being fully extended

4. The chain are almost fully 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.

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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

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Primary structure

Is determined by the sequence of amino acids

Secondary structure

Occurs when amino acids are linked by hydrogen bonds

Tertiary structure

Is formed when alpha helices and beta sheets are held together by weak interactions

Quaternary structure

Consists 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.

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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.

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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.

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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.