Biochemistry IBIOCA2301

Topics

• Carbohydrates• Lipids• Proteins• Nucleic acids• Enzymes• Metabolism

The Remaining Part..

• Proteins- Classification- Properties of proteins- Denaturing Factors of proteins

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The isoelectric Point (pI)

• If placed in an electric field, the amino acid will therefore migrate toward the cathode (negative electrode) at low pH

• and toward the anode (positive electrode) at high pH.

• At some intermediate pH, called the isoelectric point (pI), the amino acid will have a net charge of zero.

• It will be unable to move toward either electrode.• Each of the amino acids has a characteristic

isoelectric points

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Secondary Structure

• Review• Polypeptide chains can fold into regular

structures.• Two types of secondary structure elements:

1. α-helix

2. β-sheet

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1. α-helix

• Is a coiled structure stabilized by intrachain hydrogen bonds.

• Each turn of the helix contains a bout 3.6 amino acids.

• Hair & wool are examplesof protein with helicalstructure, both contain keratin.

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β-sheet

• Beta sheets are stabilized by hydrogen bonding between polypeptide strands.

• The β-sheet is composed of 2 or more polypeptide chains called β-strands.

• A β-strand is almost fully extended rather than being tightly coiled as in the α-helix.

• The distance between adjacent amino acids along a β-strand is approximately 3.5 Å, in contrast with a distance of 1.5 Å along an α-helix.

• The side chains of adjacent amino acids point in opposite directions.

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The structure of a β-strand. The side chains (green) are alternatively above and below the plane of the strand. The bar shows the distance between two residues

Examples of proteins with β-sheet are protein in silk (fibroin), and proteins that bind fatty acids

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Classification of Proteins

• Proteins can be classified into three classes:1. Simple protein2. Conjugated proteins3. Derived proteins

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Simple proteinsthey give amino acids or their derivative (polypeptides) upon hydrolysis

Conjugated proteins they give amino acids and other compounds (non protein compound) upon hydrolysis

Derived proteinsAre produced from simple or conjugated proteins upon chemical or enzymatic action on proteins.

As derived proteins one can consider proteoses, peptones, polypeptides, tripeptides, and dipeptides.

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Classification Of Proteins According To Solubility

• Simple proteins are classified according to their solubility in various solvents and also as to whether they are coagulated by heat.

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Classification Of Proteins According To Composition

• Conjugated proteins can be classified into different types:

1. Nucleoproteins: (nucleic acid/ chromosomes)2. Glycoproteins: (carbohydrates/ mucin in

saliva)3. Phosphoproteins: (Phosphate/ casein in milk)4. Chromoproteins: (Chromophore/ hemoglubin,

cytochrome)5. Lipoproteins: (lipids/ fibrin in blood)6. Metalloproteins: Metals/ ceruloplasmin

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Classification Of Proteins According To Function

1. Structural proteins:Collagen (in connective tissues), keratin (in hair).

2. Contractile proteins:Myosin, actin (muscle contraction)

3. Storage proteins: Ferritin (storage of iron)

4. Transport proteins:Hemoglobin (transfers oxygen)

5. Hormones:Insulin ( metabolism of carbohydrates)

6. Enzymes:Pepsin (digestion of proteins)

7. Protective proteins:γ-globulin (antibody formation)

8. Toxin:Venoms (poisons)

According to their biological function, proteins can be classified into various classes:

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Classification Of Proteins According To Shape

1. Globular proteins:• Folded into a shape of ball.• Are soluble in water or form colloidal dispersions.• Examples: Hemoglobin, Albumin, globulins• Enzymes are globular

2. Fibrous proteins• Consist of parallel polypeptide chains that are coiled

and stretch out.• Are insoluble in water.• Examples: collagen, elastin, myosin.

Collagen and Collagen and ElastinElastin

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Properties of Proteins

• Proteins have two characteristic properties:1. Colloidal Nature2. Denaturation

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1. Colloidal Nature

• When proteins are in water, they form a colloidal dispersion.

• Due to this property, proteins will not pass through a membrane.

• This is very important because proteins present in bloodstream can not pass through the capillaries & should remain in blood-stream.

• Therefore there should be no protein in the urine.• So if there is a protein in urine, it indicates that there

is a damage in the kidney membranes-possibly nephritis.

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2. Denaturation

• Unfolding & rearrangement of secondary and tertiary structure of a protein without breaking the peptide bonds.

• A denatured protein loses its activity• If denaturing conditions are mild, protein will

restore their active structure if these conditions of denaturing are reversed.

• If denaturation is drastic, the process is irreversible; the protein will coagulate or precipitate from solution.

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Factors or Reagents Causing Denaturation

1. Alcohol (ethanol)- It causes irreversible denaturation.

- Alcohols form hydrogen bonds, that compete with original hydrogen bonds

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2. Salts of heavy metalsHgCl2 (mercuric chloride) and AgNO3 (silver

nitrate) cause irreversible denaturation by disrupting salt bridges & disulfide bridges.

3. Heat- If heat is gentle, protein will denature

reversibly.- If heat is vigorous, protein will denature

irreversibly by disrupting several types of bonds.

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• Examples:1.Egg-white coagulates on heating.2. In bacteria heat destroys & coagulates proteins, hence in hospitals, the sterilization of instruments and clothing for use, need high temperature.3. Determination of proteins present in urine can be done by heating a sample of urine which will cause the coagulation of any protein present.

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4. Alkaloidal Reagents (tannic acid & picric acid)- Both form insoluble compounds with proteins.

They denature proteins irreversibly by dis-rupting salt bridges and hydrogen bonds.

5. RadiationUV & X-ray cause coagulation of proteins. They denature proteins irreversibly by disrupting the hydrogen bonds and hydropho-bic bonds.

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6. pHChanging the pH will disrupt hydrogen bonds and salt bridges causing irreversible denaturing. (H2SO4, HCl, HNO3).

7. Oxidizing & reducing agents- Bleach (chlorine), nitric acid, both oxidizing agents.- SO3

2- (sulfites) & oxalates are reducing agents. Both denature proteins by disrupting disulfide bridges.

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8. Salting out:- The vast majority of proteins are insoluble in

saturated salt solutions and precipitate out unchanged.

- It is possible to separate proteins from other proteins in a mixture by placing the mixture in a saturated solution of (NH4)2SO4, Na2SO4 or NaCl.

- The protein is precipitated out and removed by filtration.