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WHAT ARE PROTEINS ?

Proteins are biochemical compounds consisting of one ormore polypeptides typically folded into a globular or fibrousform, facilitating a biological function.

It takes part in maintaining the structural Integrity of thecell, transport and storage of small molecules , catalysis,regulation, immune system.

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Functions:

Enzymes: Accelerate biochemical reactions Structural: Form biological structures

Transport: Carry biochemically important substances

Defense: Protect the body from foreign invaders

Structural definition:

Globular: Complex folds, irregularly shaped tertiarystructures

Fibrous: Extended, simple folds -- generally structuralproteins

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Fibrous Proteins

Little or no tertiary structure.

Long parallel polypeptide chains. Cross linkages at intervals forming long fibres or sheets.

Usually insoluble.

Many have structural roles.

E.g. keratin in hair and the outer layer of skin, collagen (aconnective tissue).

Globular Proteins

Have complex tertiary and sometimes quaternary structures.

Folded into spherical (globular) shapes. Usually soluble as hydrophobic side chains in centre of structure.

Roles in metabolic reactions.

E.g. enzymes, haemoglobin in blood.

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AMINO ACIDS PROPERTIES

Amino acids have backbone (successive bonds constituteand repeating amino-acid units)

They differ in size, shape, charge, H bonding capacity,hydrophobicity and reactivity.

Amino acids serve as the building blocks of proteins,which are linear chains of amino acids

20 amino acids can be grouped in 4 categories:

A). Hydrophobic or non polar

B). Polar (hydrophillic) but uncharged

C). Negatively charged

D). Positively charged

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On the basis of nutritional value they have been

categorized as essential and nonessential amino acids Essential: which cannot be synthesized by the body

or cannot be synthesized at an adequate rate or are ininsufficient quantity and are obtained through diet.

Adults require 9 (Phenylalanine Valine TryptophanThreonine Isoleucine Methionine Histidine LeucineLysine) while infants and children require 10 (arginine)

The remaining amino acids are Non essential, i.ethose that can be synthesized by the body and aredifferent from essential amino acids that are obtainedfrom food

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Anatomy of an amino acid

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Majority of amino acids has amphoteric character functional group COOH is the reason of acidity and NH2 group causes basic properties.

In basic environment AA dissociate proton to form carboxyl anion COO-.Basic surround defends NH2 against dissociation.

In acidic environment AA accept proton to form amonium cation NH3+.

Acidic environment defends COOH against dissociation.

AMPHOTERIC CHARACTER OF AMINO ACID

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Non-polar amino acids

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Polar, non-charged amino acids

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Negatively-charged amino acids

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Positively-charged amino acids

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Amino Acids Are Joined By

Peptide Bonds In Peptides

- a-carboxyl of one amino acid is joined to a-amino

of a second amino acid (with removal of water)

- only a-carboxyl and a-amino groups are used, not

R-group carboxyl or amino groups

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Chemistry of peptide bond formation

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Levels of Protein Structure

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Primary structure = order of amino

acids in the protein chain

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1. Primary Structure:

Linear chain of amino acids.

Held together by covalent or peptide

Bonds.

The two ends of the polypeptide chain

are referred to as the carboxyl terminus(C-terminus) and the amino terminus

(N-terminus) based on the nature of

the free group on each extremity.

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Secondary structure = local folding

of residues into regular patterns

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2. SECONDARY STRUCTURE: local ordered structure via H- Bonds , mainly

within backbone.

Includes the alpha helix and the beta strand

or beta sheets

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Alpha helix (-helix) is a right-handed coiled or spiralconformation, in which every backbone N-H group

donates a hydrogen bond to the backbone C=O group ofthe amino acid four residues earlier.

Three-dimensional arrangement of amino acids with thepolypeptide chain in a corkscrew shape

Looks like a coiled telephonecord

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Beta sheets consist ofbeta strands connected laterally by at least twoor three backbone hydrogen bonds, forming a generally twisted,pleated sheet.

A beta strand (also strand) is a stretch of polypeptide chain typically3 to 10 amino acids long with backbone in an almost fully extendedconformation.

Hydrogen bonds form between chains

The beta sheets could be arranged either parallel or antiparalleldirection

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In an antiparallelarrangement, the successive

strands alternate directions sothat the N-terminus of onestrand is adjacent to the C-terminus of the next.

Produces the strongest inter-

strand stability because it allowsthe inter-strand hydrogen bondsbetween carbonyls and aminesto be planar

In a parallel arrangement, allof the N-termini of successive

strands are oriented in the samedirection;

Slightly less stable because itintroduces nonplanarity in theinter-strand hydrogen bonding

pattern.

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Tertiary structure = global folding of

a protein chain

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3. TERTIARY STRUCTURE:

3D structure of protein, results by large number

of non-covalent interactions b/w amino acids.

The alpha-helices and beta-sheets are folded

into a compact globule

structure is stable only when the parts of a proteindomain are locked into place byspecific tertiary

interactions, such as salt bridges, hydrogen bonds,

and the tight packing of side chains and disulfide bonds

This shape is held in place by bonds such as

weak Hydrogen bonds between amino acids that lie close to eachother,

strong ionic bonds between R groups with positive and negativecharges, and

disulfide bridges (strong covalent S-S bonds)

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Quaternary structure = Higher-order

assembly of proteins

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Levels of Protein Structure

4. QUATERNARY STRUCTURE

It is the non-covalent interactions that bindmultiple polypeptides into a single, larger protein

Eg: Haemoglobin

2 -globin and 2 -globin polypeptides

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Disruption of secondary, tertiary and quaternaryprotein structure by

Heat/organics :

Break apart H bonds and disrupt hydrophobic attractions

Acids/ bases:Break H bonds between polar R groups and ionic bonds

Heavy metal ions :

React with S-S bonds to form solids

Agitation :Stretches chains until bonds break

DENATURATION:

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Protein Functions

Antibodies - are specialized proteins involved in defending the body

from antigens (foreign invaders). They travel through the blood streamand are utilized by the immune system to identify and defend againstbacteria, viruses, and other foreign intruders. One way antibodiesdestroy antigens is by immobilizing them so that they can be destroyedby white blood cells.

Contractile Proteins - are responsible for movement. Examplesinclude actin and myosin. These proteins are involved in musclecontraction and movement.

Enzymes - are proteins that facilitate biochemical reactions. They areoften referred to as catalysts because they speed up chemical reactions.

Examples include the enzymes lactase and pepsin. Lactase breaksdown the sugar lactose found in milk. Pepsin is a digestive enzyme thatworks in the stomach to break down proteins in food.

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Hormonal Proteins - are messenger proteins which help tocoordinate certain bodily activities. Examples include insulin, oxytocin,and somatotropin. Insulin regulates glucose metabolism by controlling

the blood-sugar concentration. Oxytocin stimulates contractions infemales during childbirth. Somatotropin is a growth hormone thatstimulates protein production in muscle cells.

Structural Proteins - are fibrous and stringy and provide support.Examples include keratin, collagen, and elastin. Keratins strengthen

protective coverings such as hair, quills, feathers, horns, and beaks.Collagens and elastin provide support for connective tissues such astendons and ligaments.

Storage Proteins - store amino acids. Examples include ovalbuminand casein. Ovalbumin is found in egg whites and casein is a milk-

based protein. Transport Proteins - are carrier proteins which move molecules from

one place to another around the body. Examples include hemoglobinand cytochromes. Hemoglobin transports oxygen through the blood.Cytochromes operate in the electron transport chain as electron carrier

proteins