The 3D Structure Of Amino Acids Biology Essay


Amino acids are the building blocks of the proteins. A protein consists of a polypeptide backbone with attached side chains. Each type of protein differs in its sequence and number of amino acids. Polypeptide chains consist of sequences of amino acid that determine the three dimensional structure. Proteins have 20 types of amino acid, each with different chemical properties. The different amino acids differ from each other in their side chains or R groups, which vary in structure, size and electric charges. Proteins are also known as polypeptides as they consists of long chain of amino acid linked by covalent peptide bonds. Out of 20 amino acids, 9 amino acids ( Gly, Ala,Val, Leu, Ile, Met, Phe, Trp, Pro ) are hydrophobic (non polar) and the remaining 11 ( Ser, Thr, Cys, Asn, Gln, Asp, Gln, Asp, Glu, Lys, Arg, His) are hydrophilic. The hydrophobic tends to be interior of the molecules while the hydrophilic lie on the surface of protein.

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Proteins are the most abundant biological macromolecules, occurring in all parts of body. The folding of the protein is limited by many non covalent bonds like hydrogen bond, electrostatic attractions, vander waals force etc. proteins exists in two forms; fibrous proteins including keratin, collagen etc and globular proteins including enzymes, receptor proteins, transport proteins etc. The structural diversity is necessary for the proteins to carry out various biological functions.

The sequence of amino acids in a polypeptide chain is referred to as the primary structures. The term secondary structure refers to the local conformation of some part of the polypeptide. The 3D arrangement of all the atom in the protein is called tertiary structure and the arrangement of the protein subunits in 3 dimensional complex constitutes quaternary structure.

(Nelson and Cox, 2005)

How does the sequence of amino acids in polypeptide determines the final 3D structure of the proteins?

Different proteins have different sequences of amino acids in their polypeptide chain. each amino acid differs in their side chains and has its unique properties. The atom in the polypeptide backbone as well as the atoms in the amino acids side chains contributes formation of many weak non covalent bonds. Side chain may be polar, non polar, hydrophobic, uncharged or negatively or positively charged helps in the formation the 3D structures of the protein.

3D conformation of the protein is maintained by folding of proteins due to many non covalent and covalent bonds.

Hydrogen bond

Hydrogen bond forms between a weakly acidic donor group and an acceptor atom that bears lone pair of electron. In proteins hydrogen bond usually formed between hydrogen atom and nitrogen atom or oxygen atom of different amino acid of the polypeptide chain. H bonding can be intrachain or interchain interaction where intrachain maintains the helicoidal conformation of polypeptide chain. The Hydrogen bond is weaker than covalent bond but stronger than Vander Waals force, thus play important role in 3D conformation of the protein.

Hydrophobic Force:

3D conformation maintained by hydrophobic character. Some amino acid are polar like Asn, Gln, Ser, Thr etc and some are non polar like Ala, Gly, Val, Leu etc.., thus the distribution of the non polar and polar amino acid in the polypeptides chain affects the 3D conformation of the proteins. The non polar amino and which are normally hydrophobic, always hide from the water and minimize their contact with water by clustering in the interior of the molecule whereas the polar amino acids to the outside forming hydrogen with water.

Disulphide bond

The stability of the proteins is also maintained by the disulphide bridges. Disulphide bond usually formed between the two cysteine residues of same or different polypeptide chain of the proteins.

Renaturation of unfolded, denatured ribonuclease

The classic experiment carried out Christian Anfinsen in the 1950s, proved that the amino acids sequence determines tertiary structures. This experiment explains that the denaturations of some proteins are reversible. The purified ribonuclease was exposed to concentrated urea solution in presence of reducing agent and was denatured completely. The four disulphide bond were broken to yield eight Cys residue and the stability of the hydrophobic interactions was disturbed. When the urea and the reducing agent are removed, the denatured ribonuclease refolds into normal tertiary structure. This proves that the amino acids sequence of a polypeptide chain contain all the information required to fold the chain into native, 3D structure.

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(Nelson and Cox, 2005)

Diversity of proteins structure and its function

According to the structure of the proteins, proteins are classified into two major groups: fibrous proteins, having polypeptide chains arranged in long strands or sheets, and globular proteins, having polypeptides chains folded into a spherical shape or globular shape.

Globular proteins

It has globular structure formed by the folding of the polypeptide chain upon each other. This folding provides structural diversity necessary for the proteins to carry out various biological functions.

Some of the globular proteins are signaling proteins, receptor proteins, transport proteins, receptor proteins etc… (Alberts et al, 2008)


Myosin are the types of motor proteins which generate moment in cells. Myosin consists of six polypeptides chain and is considered as a large protein. The six polypeptides involves two heavy chain

and 4 light chains. Myosin consists of long rod to which double headed globular region was joined. Rod is alpha helical coiled coil of two heavy chain while the globular region is part of each heavy chain with four light chain attached to it.

Function of myosin;

Myosin is the ATPase i.e. hydrolyze ATP

Myosin binds the polymerized form of actin

Myosin molecules spontaneously assembled into filaments

Involves in muscle movement

(Hames and Hooper, 2006)


The three dimensional structure of this globular proteins was found out by John Kendrew and his colleagues in 1957 using x ray diffraction process. (Nelson and Cox, 2000)

Myoglobin is a oxygen binding protein of the muscle cell, consists of a single polypeptide chain of 153 amino acids. Myoglobin is an extremely compact molecule folded into 8 α helices. The interior of the helix is entirely of non polar residue such as leucine, valine, methionine and phenylalanine, which maintains stability.

(Berg et al, 2006)


Hemoglobin is the type of transport proteins i.e. Transport small molecules from one place to another. It is an oxygen binding protein found in vertebrates .Hemoglobin are tetrameric protein which consists of four polypeptide chain that is 2 α chains and 2 β chains (α2β 2).

Hemoglobin A which is found in adult is made up of 2 α chains each consists of 141 amino acids and 2 β chain each consists of 146 amino acids residues. Each hemoglobin chain has eight α helices and a heme prosthetic group. Therefore hemoglobin can bind with four molecules of oxygen and transport the oxygen in the bloodstream.

(Hames and Hooper, 2005)


Insulin is the types of signaling proteins secreted by the pancreas. They are dimers i.e. consist of two polypeptide chain. One chain is made of 21 amino acids and the other chain consists of 30 amino acids. It also has 3 sulphide bonds.

Function: helps to decrease the blood concentration.

(Weil, 2005)

Fibrous Proteins

Fibrous proteins have elongated 3 dimensional structures. These types of proteins are simple and insoluble in water. The main function of this protein is to provide mechanical support, external protections and provide shape to the cell and tissue. It includes structural protein like collagen, keratin, actin etc.


This extracellular protein is a rod shaped molecules found in mammels and constitutes the connective tissue such as tendon, cartilages, skin, bones and teeth. It consists of 3 polypeptide chain and is about 3000 Ao long and 15 Angstrom in diameter. Each polypeptide chain is nearly 1000 residue long and contains glycine at every third residue in the amino acid sequence. The sequence glycine-proline-hydroxyproline recurs frequently. In collagen there is no H bond within the strand but steric repulsion of the pyrolidine rings of proline and hydroxyproline residue stabilized the helix. The three strands wrap around each other to form a triple helix that is stabilized by the H bonds between strands.

(Berg et al, 2006)

Alpha keratin

Keratins are found in the mammals in the form of structures like hairs, nail, claws, hooves, horns, wool and outer layer of the skin. It consists of 2 right handed alpha helices wrapped about each other to form a type of left handed super helix called alpha coiled-coil. Keratin is rich in hydrophobic residues, weak interaction like vander waals forces, ionic interactions, disulfide bond which stabilize the helix. Thus the actin filaments are extremely stable. (,2006)

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