Connected With Each Other By Peptide Bond Biology Essay

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The smallest unit of protein is amino acid and these amino acids are connected with each other by peptide bond, when it forms long chain then it is called polypeptide chain.

The clustering and connection between two or more different or same polypeptide will give rise to different 3D structure of protein; this 3D structure will have their own function.

Peptide Bond.

When the amine group of one amino acid reacts with carboxylic group of another amino acid, the water molecules will be lost and product formed is joined by the "CONH", this connection is called peptide bond. E.g.: (Structure of peptide bond, (n. d))

Peptide.

When the two or more amino acids are linked each other by the peptide bond (-CONH-), this compound formed is called peptide compound. E.g.:

(Source: structure of peptide bond, (n. d))

Factors.

The sequence of polypeptides gives rise to structure of the proteins; formation of protein structure solely depends on the following factors.

Bond formation

Ionic bond:

The bond formed between the amine and the carboxylic group of two different amino acid is called ionic bond.

Disulphide bond:

Bond formed between two residues of cysteine this will be in same peptide chain or in different chain.

Hydrogen bond:

The bond formed between the CO and NH of the peptide linkages. E.g.:

Figure A. Details of intra-molecular hydrogen bonds in a protein.

(Source: Kratz, 2009)

(Source: Kratz, 2009)

Hydrophobic bond:

Alanine, valine, leucine, isoleucine and phenylalanine has a non-polar hydrophobic side chain, these side chains helps in bringing the hydrophobic group together because it will not reacts with the water molecules which is polar in nature.

Figure A. How a protein folds into a globular conformation. The polar amino acid side chains tend to gather on the outside of the protein, where they can interact with water. The non-polar amino acid side chains are buried inside to form a hydrophobic core that is "hidden" from water.

(Source: Kratz, 2009)

Φ and Ψ angle:

Phi is the angle between the alpha carbon and nitrogen; psi is the angle between the alpha carbon and carbonyl. These angles play an important role in protein folding; if these angles are not correct, then the protein will not fold due to steric hindrance. (Source: Weil, 2008)

Types of protein structure.

The protein can be classified into four groups and these are as follow;

Primary structure,

Secondary structure,

Tertiary structure and

Quaternary structure.

Primary structure.

When the amino acids are arranged in linear form or if they are in sequence then the structure is collectively called primary structure.

In this structure the phi and psi angles should be approximately -120â-¦.

(Source: Lodish et al, 1986)

The backbone of the polypeptide chain of primary structure will be in zigzag pattern.

E.g.:

(SOURCE: Kratz, 2009)

Secondary structure.

When the two or more primary structures come closer to each other and held together by the hydrogen bond, forming a structure collectively called secondary structure.

According to the arrangement of the primary structure in the secondary structure the secondary structure can be divided into two;

Alpha helix and

Beta sheet.

(Source: Nelson, 2008)

Alpha helix. When the polypeptide chain is twisted, the carbonyl oxygen atom of the peptide bond will form the hydrogen bond with the amine hydrogen atom of the amino acid of four residues towards the C-terminus. The bond arrangement is periodic and this helps in conferring the directionality on the alpha helix because orientations in all the hydrogen bond donors are same. There will be three to four hydrogen bond which will hold the two successive turns, combination of all hydrogen gives the whole helical structure considerable structure.(Source: Nelson, 2008)

In this structure the hydrogen bond plays an important role in joining two same or different polypeptide chains. Phi (ɸ) and psi (Ψ) angles should be approximately -60â-¦ and if these angles are not approximately -60â-¦ then the structure will be unstable because of steric hindrance.

(Source: Nelson, 2001)

Fig: Alpha helix. (Source: Kratz, 2009)

Beta sheet.

This is another type of structure of the protein found in the secondary structure of the protein which is predicted by Pauling and Corey. This structure is confirmed by the X-rays analysis.

(Source: Nelson, 2008)

In this structure the backbones of the structure of the structure will be in the zigzag conformation. This zigzag polypeptide chains are arranged side by side and finally form a series of pleats and this particular structure is collectively called Beta-sheet.(Source: Nelson, 2008)

According to the arrangement or position of N-terminals and C-terminals, the Beta sheet is divided in to two;

Parallel beta sheet and

Anti-parallel beta sheet

Parallel beta sheet.

In this type of structure the N-terminal polypeptide chain will aliened with another N-terminal polypeptide chain, which means all the N-terminal, will be in one side and C-terminal will be in another side. (Lodish et al, 2004)

The hydrogen bond will formed between carbonyl group of one polypeptide chain with the amine group of another polypeptide chain. The hydrogen bond formed will be in "A" shape or diagonal direction. (Source: Lodish et al, 2004)

In this structure the phi and psi angle should be approximately if the angles are not matching then the structure will become unstable because of steric hindrance. (Source: Rawn, 1983)

E.g.: Diagram

(Source: Kratz, 2009)

Fig: Parallel Beta sheet.(Source: Kratz, 2009)

Anti-parallel beta sheet.

In this type of structure the N-terminal of one polypeptide chains will aliened with the C-terminal of another polypeptide chain. Hence, N and C-terminal will be arranged alternatively in each side. The hydrogen bond between the carbonyl and amine will be in parallel direction. (Source: Lodish et al, 2004)

The structure should have accurate the phi and psi angle that will help the structure to attain equilibrium. (Source: Rawn, 1983)

E.g.:

Fig: Anti parallel beta sheet.

As in the b sheet, every peptide bond in a a helix is hydrogen-bonded to a neighboring peptide bond. (Source: Kratz, 2009)

Tertiary structure.

In this type the secondary structure is stabilized by the hydrophobic interaction between the non-polar side chains. This hydrophobic interaction will bring the secondary structure together by clumping all the hydrophobic side inside the structure and hydrophilic side outside the structure.(Source: Lodish et al, 2004)

E.g.:

Fig: The tertiary structure of Protein. (Source: Kratz, 2009)

Quaternary structure.

When the two or more subunits are joining together by a non-covalent bond and this structure is collectively called quaternary structure.

(Source: Lodish et al, 2004)

E.g.:

(Source: Kratz, 2009)

The fibrous proteins are adapted for a structural function.

Alpha keratin.

The alpha keratin is found in mammals and the entire weight of hair, wool, claw, nail, horn, hooves and other layer of skin are made up of alpha keratin. Proteins which have alpha keratin will have structural features and have a structural functions, which is oriented in parallel and two strands of alpha keratin are wrapped to form a coil. The right hand alpha helix is used but the helical path is left handed. The quaternary structure of alpha keratin is more complex. The intermediate filament of hair is formed due to the assemble of alpha keratin. Because of covalent bond fibrous protein has high strength and it is also strengthen by the disulphide bond formation.

E.g.: In Rhinoceros horn, 18% of cysteine residues from disulphide bonds.

Silk fibroin.

The silk fibroin has a polypeptide chain and the beta conformation is more, it is produced by insects and spiders. It has greater strength due to the presence of hydrogen bond, but it is flexible due to the lack of strong bond such as covalent, disulphide, etc. (Source: Nelson, 2008)

Globular protein.

The folding and binding of tertiary and quaternary structure gives the globular proteins. Hence, folding and binding helps the protein to carry out their respective functions such as transportation, movement, signaling, etc.

Types of globular protein;

Myoglobin

The myoglobin contains eight alpha helices and each alpha helix is joining together by bends. There are 153 amino acids in a single polypeptide chain. These alpha helices will make the myoglobin adaptable to store oxygen.

The 93rd amino acid is histone and it is amino terminus, this histone will bond with the heme and this particular heme will acts as binding sites for oxygen. Finally helps in storage of oxygen. (Source: Nelson, 2008)E.g.:

Fig: Myoglobin

(Source: Tertiary protein structures, (n. d))

. Fig: Myoglobin.

(Source: Tertiary protein structures, (n. d))

Hemoglobin.

Oxygen is carried by hemoglobin in all mammals. Subunits of myoglobin and subunits of hemoglobin are structurally similar to each other.

The hemoglobin is tetrameric protein because it has four binding sites or four prosthetic group. It has two globins such as two alpha helices and two beta helices. Each alpha helix contains 141 residues and beta chain contains 146 residues, these helices will make hemoglobin more adaptable to carry the oxygen. (Source: Nelson, 1982)

Relaxed state and tense state are the two major structures of hemoglobin. R-state has more affinities than the T-state towards oxygen.( Source: Nelson, 1982)

Hemoglobin will be in either state(R or T) when it bind with oxygen, as soon as the oxygen binds with the hemoglobin, the R-state stabilize. The T-state will helps in triggering the change in the conformation of the R-state, as a result it will promote the oxygen binding capacity. (Source: Nelson, 1982)E.g.:

(Source: Tertiary protein structures, (n. d))

(Source: Tertiary protein structures, (n. d))

Hemoglobin also transports H+ and carbon dioxide, carbon dioxide is excreted in form of carbonate. Hydrogen will binds with to any amino acids of several residues of the protein. (Source: Nelson, 2001)

Immunoglobin.

It consists of two heavy polypeptide and two light polypeptide chain and they are linked together by disulphide bond. (Source: Nelson, 1982)

There are two identical antigen binding site. When the heavy and light chain interacts then it will form a Y-shaped molecule.( Source: Nelson, 1982)

When this molecule reacts with protease, there will be liberation of basal fragments such as Fc and Fab (antigen-binding site) and each fragment has single binding site. (Source: Nelson, 2001)

E.g.:

Fig: Immnoglobin. (Source: Tertiary protein structures, (n. d))

Motor proteins -Actins and Myosin.

There are two major components of the muscles.

Myosin.

It consists of four heavy subunits and two light subunits, former four will for the much of overall structure.

It has extended alpha helices at the C-terminus and amino terminus has globular domain where the ATP can hydrolyze. The thick filament is the aggregate form of myosin and it acts as contractile unit.

(Source: Nelson, 2008)

Actins.

It consists of monomer called S-actins and polymer called F-actins. Polymers are formed by the binding of monomer, it also binds with the ATP and it hydrolyzes to form ADP. This ATP hydrolysis indirectly contributes energy for muscle contraction.

The muscle fiber has alternating region of high and low electron density, called A and I-band. The A-band will have thick bundle of filament but I-band will have thin bundle of filament.

A-band and I-band is dissected by Z-band, the structure which have alternating thin and thick band is called sarcomeme.

Thin filament is made up of alpha helix, other large polypeptide chain called titans and this helps in linking the thick filament to Z-band.

The actins myosin interaction between proteins involves weak bonds. Myosin will binds with actins when ATP is not bound with myosin.

When ATP is binds with myosin, ATP is hydrolyzed to ADP and phosphate. This helps in releasing F-actins subunits and binds other subunits along the thin filament. This accounts for muscle contraction mechanism. (Source: Nelson, 2008)

Fig: Actins and Myosin Filament. (Source: Kratz, 2009)

The sequence of amino acids in polypeptide chain will determine the final 3D structure of the proteins like primary, secondary, tertiary and quaternary structure. The 3D structure will determine the function of that particular protein.

References

Kratz, R.F (2009). Molecular and cell biology for Dummies .Canada: Wiley publishing,

Inc.

Lodis, H, Berk, A, Matsadaira, p, Kaiser, C.A, Krieger, M, Scott, M.P, Zipursky, S.L and Darnell, J

(2004).Molecular cell biology (8th edition).New York: W.H freeman and company.

Nelson, D.L and Cox, M.M (2008) Principles of biochemistry (4th edition) India: Replika press pvt.

ltd.

Nelson, D.L and Cox, M.M (2001) Principles of biochemistry (3rd edition) New Delhi: Replika press

pvt. ltd.

Weil, J.H. (2008) General biochemistry. New Delhi: New age international pvt.ltd.

Tertiary protein structures, (n. d). Retrieved on 29th March 2010 from

http://images.google.com/imgres?imgurl.

Tertiary protein structures, (n. d). Retrieve on 29th March 2010 from

http://themedicalbiochemistrypage.org/hemoglobin-myoglobin.html

Structure of peptide bond, (n. d). Retrieve on 29th March 2010 from

http//www.elmhurst.edu/~chm/vchembook/images/568heme.gif.

Table of Contents

Serial No.

Contents

Page No.

1

Peptide bond and peptide.

1

2

Factor (Helps in protein folding).

2-3

3

Types of protein structure.

3-7

4

Fibrous and globular proteins are adapted for structural function.

12-13

5

Globular protein (function)

8-12

6

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