B.Sc. Biochem II Biomolecule I U 2 Proteins

Proteins

Course: B.Sc. (Biochem) Sem II

Subject: Biomolecules I

Unit 2

Why We need to study About this?

Protein Engineering.

Structural Engineering.

Growth of body.

Major component of body

Curing Different Diseases.

What is Amino Acid?

• Amino acids are derivatives of carboxylic acids formed by substitution of -hydrogen for amino functional group

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What is Protein?

The word protein came from a Greek word “Proteios”

Proteins are like long necklaces with differently shaped beads. Each "bead" is a small molecule

called an amino acid.

Compounds composed of carbon, hydrogen, oxygen, and nitrogen and arranged as strands of amino acids

Structural

Movement

Transport

Storage

Hormone

Protection

Enzymes

Collagen; bones, tendons, cartilageKeratin; hair, skin, wool, nails, feathers

Myosin & Actin; muscle contractions

Hemoglobin; transports O2Lipoproteins; transports lipids

Casein; in milk. Albumin; in eggs

Insulin; regulates blood glucoseGrowth hormone; regulates growth

Immunoglobulins; stimulate immunitySnake venom; plant toxins;

Sucrase; catalyzes sucrose hydrolysisPepsin; catalyzes protein hydrolysis

Functions of Proteins

Protein Deficiency and Excess

• Protein-deficiency symptoms are always observed when either protein or energy is deficient

• Extreme food energy deficiency is marasmus

• Extreme protein deficiency is kwashiorkor

• The two diseases overlap most of the time and together are called PEM

Protein Deficiency and Excess

• Protein-energy malnutrition (PEM)

– World’s most widespread malnutrition problem

– Includes both marasmus and kwashiorkor and states of overlap

• Hunger

– Physiological craving for food

– Progressive discomfort, illness, and pain resulting from the lack of food

What do Amino Acids Do?

Amino acids are essential to life, have a role in metabolism, and are important in nutrition.

They form short polymer chains called peptides, as well as longer chains that are called polypeptides or

proteins.

About 75 percent of the human body is made up of chains of amino acids, which is why they are so vital

to how your system functions.

All the chemical reactions that occur in the body depend on amino acids and the proteins they build.

Types of Amino Acids

Amino acids are classified as

• Nonpolar (hydrophobic) with hydrocarbon side chains.

• Polar (hydrophilic) with polar or ionic side chains.

• Acidic (hydrophilic) with acidic side chains.

• Basic (hydrophilic) with

–NH2 side chains.

Nonpolar Polar

Acidic Basic

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Classification of amino acids based on structure:

C. Nutritional classification of amino acids

• 1. Essential or indispensable amino acids :

• cannot be synthesized by the body supplied through the diet

e.g., Arginine, Valine, Histidine, lsoleucine,

• Leucine, Lysine, Methionine, Phenylalanine,

• Threonine, Tryptophan.

• The two amino acids namely arginine and histidine can be synthesized by adults and not by growing children, hence these are considered as semi-essential amino Acids.

• Thus, 8 amino acids are absolutely essential hile 2 are semi-essential

• 2. Non-essential or dispensable amino acids : The body can synthesize about '10 amino acids to meet the biological needs, hence they need not be consumed in the diet.

• These are-glycine, alanine, serine, cysteine, aspartate,a sparagnie, glutamate, glutamine, tyrosine and proline.

D. Amino acid classification based on their metabolic fate :

• The carbon skeleton of amino acids can serve as a precursor for thesynthesis of glucose( glycogenico) r fat (ketogenico) r both.

• three groups:

• 1. Glycogenic amino acids : serve as precursors for the formation ofglucose or glycogen.

• e.g. alanine,aspartat

• Eg., lycine,methioninee tc.

• 2. Ketogenic amino acids : Fat can be synthesized from these amino acids.Two amino acids leucine and lysine are exclusively ketogenic

• 3. Glycogenic and ketogenic amino acids :

• The four amino acids isoleucine, phenyl -

• alanine, tryptophan, tyrosine are precursors for synthesis of glucose as well as fat.

Properties of Amino acids

• A. Physical properties:

• 1. Solubility :

• soluble in water ,

• Insoluble in organic solvents.

• 2. Melting points:

• melt at higher temperature so, often above 200˚C.

• 3. Taste: • Sweet (Cly, Ala, Val), • tasteless (Leu) or bitter (Arg, lle).• Monosodium glutamate - flavoring agent in food industry,

and Chinese foods to increase taste and flavor.

• 4. Optical properties: • except glycine, All the amino acid possesses optical isomers

due to the• presence of asymmetric carbon atom. • Some amino acids also have a second asymmetric carbon. • e.g. isoleucine, threonine.

• 5. Amino acids as ampholytes :

• contain both acidic (-COOH) and basic

• (-NH2) groups.

• donate a proton or accept a proton, hence amino acids are regarded as ampholytes.

Zwitterion or dipolar ion

• zwitter : derived from the German word which means hybrid. • Zwitter ion (or dipolar ion) : a hybrid molecule containing positive

and negative ionic groups.• Amino acids rarely : neutral form with free carboxylic (-COOH) and

free amino (-NH2) groups.• In strongly acidic pH (low pH), the amino acid : positively charged.• while in strongly alkaline pH (high pH), it is negatively charged• Each amino acid has a characteristic pH (e.g. leucine, pH 6.0) at• which it carries both positive and negative charges and exists as

zwitterion.

Isoelectric pH

• Isoelectric pH (pl) : pH at which a molecule exists as a zwitterion or dipolar ion and carries no net charge.

• molecule : electrically neutral

• For instance, leucine has two ionizable

• groups/ and its pl can be calculated as follows.

• Leucine - cation at pH below 6 and anion at pH above 6.

• At the isoelectric pH (pl = 6.0), leucine is found as zwitterion.

• pH of the medium determines the ionic nature of amino acids.

• For the calculation of pl of amino acids with more than two ionizable groups, the pKas for all the groups have to be taken into account.

Titration of amino acids :

• At low pH, leucine : protonated form as cation.

• As the titration proceeds with NaOH, leucine loses its protons and at isoelectric pH (pl), it becomes a zwitterion.

• Further titration results in the formation of anionic form of leucine.

• Some more details on isoelectric pH are

• discussed under the properties of proteins.

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Chemical properties of Amino Acids

• carboxyl (-COOH) group and amino (-NH2) group.

Reactions due to -COOH group:

• 1. Amino acids form salts (-COONa) with bases and esters (-COOR') with alcohols.

2. Decarboxylation: produce corresponding Amines.

• This react ion assumes significance in the living cells due to the formation of many biologically important amines.

3. Reaction with ammonia: The carboxyl group of dicarboxylic amino acids reacts with NH3 to form amide.

Reactions due to -NH2 group

• 4. The amino groups behave as bases and combine with acids (e.g. HCI) to form salts (-NH3+Cl-).

5. Reaction with ninhydrin : The α-amino acids react with ninhydrin to form a purple, blue or pink colour complex (Ruhemann's purple)

Ninhydrin reaction is effectively used for the quantitative determination of amino acids and proteins. (Note : Proline and hydroxyproline give yellow colour with ninhydrin)

6. Colour reactions of amino acids : Amino acids can be identified by specific colour reactions.

7. Transamination: Transfer of an amino group from an amino acid to a keto acid to form a new amino acid is a very important reaction in amino acid metabolism.

8. Oxidative deamination : The amino acids undergo oxidative deamination to liberate free ammonia.

Formation of Peptide Bond

• When the amino group of an amino acid combines with the carboxyl group of another amino acid, a peptide bond is formed.

Formation of Peptide bond:

• rigid and planar with partial double bond in character.

• lt generally exists in trans configuration.

• Both -C=O and –NH groups of peptide bonds are polar and are involved in hydrogen bond formation.

Nomenclature of peptides

Short peptides are often given a general name according to how many residues

(amino acids) are linked together.

Glycyl-alanyl-tyrosyl-glycine is a "TETRAPEPTIDE"

Alanyl-valyl-tryptophane is a "TRIPEPTIDE"

A general name for a long peptide is oligopeptide or POLYPEPTIDE.

The Structure of Proteins

• Side chain

– The unique chemical structure attached to the backbone of each amino acid that differentiates one amino acid from another

• Essential amino acids

– Amino acids that either cannot be synthesized at all by the body or cannot be synthesized in amounts sufficient to meet physiological needs

The Structure of Proteins

• Conditionally essential amino acid

– Amino acid that is normally nonessential, but must be supplied by the diet in special circumstances when the need for it exceeds the body’s ability to produce it

• Peptide bond

– Bond that connects one amino acid with another, forming a link in a protein chain

• Amino acids link into long strands that coil and fold to make a wide variety of different proteins

Essential AA Nonessential AA• Valin

• Leucin

• Isoleucine

• Threonine

• Lysin

• Methionin

• Phenylalanine

• Tryptophan

• Arginine

• Histidine

• Alanine

• Asparagine

• Aspartate

• Cysteine

• Glutamate

• Glutamine

• Glycine

• Proline

• Serine

• Tyrosine

Peptide Linkages

• Two dipeptides can result from reaction between A and S, depending on which COOH reacts with which NH2 we get AS or SA

• The long, repetitive sequence of NCHCO atoms that make up a continuous chain is called the protein’s backbone

• Peptides are always written with the N-terminal amino acid (the one with the free NH2

group) on the left and the C-terminal amino acid (the one with the free CO2H group) on the right

• Alanylserine is abbreviated Ala-Ser (or A-S), and serylalanine is abbreviated Ser-Ala (or S-A)

Peptides and Proteins

• Proteins and peptides are amino acid polymers in which the individual amino acid units, called residues, are linked together by amide bonds, or peptide bonds

• An amino group from one residue forms an amide bond with the carboxyl of a second residue

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References:

Image 1: http://postimg.org/image/yq74xmbtz/

Image 2: http://postimg.org/image/yq74xmbtz/

Image 3: Biochemistry, U. Satyanarayan, Elsevier India publication

Image 4: Biochemistry, U. Satyanarayan, Elsevier India publication

Image 5: http://postimg.org/image/61ys84z1j/

Table : Biochemistry, U. Satyanarayan, Elsevier India publication

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