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COURSE BIOMOLECULES Lesson Various levels of protein structure Dr. Praveen Kumar Agrawal
Structure of proteins Proteins exhibit four types of structures or conformations- primary, secondary, tertiary and quaternary proteins. 1. Primary structure This represents the simple linear arrangement and sequence of amindo acids. It is the order, in which amino acids are held together. It also includes the location of any disulphide bonds (Note Di-sulphide bonds provide extra stability to the proteins molecules). The primary structure or simple linear arrangement of amino acids does not make protein functional. To be functional, a primary structure must attain a specific shape.
2. Secondary structure When a primary structure acquires a specific conformation it becomes the secondary structure. This specific conformation is obtained by characteristic folding, twisting or coiling of primary structure through hydrogen bonds. (Primary structure determines, where the chain will be folded or bend). Usually secondary structure occurs in two forms- (a) Alpha helix . When the chain is arranged like a coil, it is called or helical structure ( -helix), eg, keratin of hair. The a helix is stabilised by H-bonding. The bends in helix are produced by proline (an amino acid). Some amino acids such as alanine, glutamine, leucine and methionine are more common in helical structure. A helix may also be amphipathic in nature (containing both hydrophobic and hydrophilic ends). A helix has fixed dimensions, which are as follows - o Residues per turn (pitch) 3.6 Distance travelled per turn 0.54
Polypeptide chain H-bond Alpha helix
(b) Beta pleated sheet When two or more chains of amino acids (polypeptides), are joined together by intramolecular hydrogen bonding, then the structure is called or pleated sheet ( -pleated sheet), e.g., protein, silk fibroin in silk ibres. Two or more chains in a B pleated sheet may be parallel or antiparallel There is more hydrogen bonding in antiparallel structure. Alpha helix Beta pleated sheet It is a coiled structure These are compact molecules It involves usually single polypeptide chain These are parallel or antiparallel sheets These are extended molecules It involves two or more polypeptide chains
3. Tertiary structure Some complex proteins are not functional, even in secondary structure. These proteins undergo further folding and coiling to attain a functional 3- D conformation. Such a highly folded or coiled structure is called tertiary structure, e.g., Myoglobin. The folding and coiling occurs in such a way, as to hide the non-polar amino acid side chains inside and exposing polar side chains outwardly. . As a result of this, amino acid side chains come closer to each other and confer the functional activity to the protein. It also forms the active sites of enzymes. The extensive coiling and folding in a tertiary structure is due to many kinds of bonds, such as H-bonds, co va lent bonds, disulphide bonds and van der Waals' forces.
The three dimensional structure gives protein a functional ability. . The functional 3 - D form of a protein is called native state. The 3 - D or tertiary con formation of the proteins can be easily altered by change in pH, temperature and chemical sub stances. . Such a protein is said to be denatured and it loses its functional activity. In some cases the original structure of a denatured proteirn can be reobtained by a process called renaturation. However in most of the cases, it is not possible.
4. Quaternary structure . When two or more polypeptide chains are held together by non covalent forces (mainly H-bonds and ionic bonds), then such a structure is called quaternary structures. Such proteins are called oligomers. The individual polypeptide chains are called monomers or promoters, e.g., Haemoglo bin (respiratory pigment) molecule represents quaternary . structure. It contains two a and two b- chains . (Note - Haemoglobin is a quaternary structure while myoglobin represents only tertiary structure)
Primarystr ucture Lineararran gement ofamincac ids Secondarystructure Ariseswhen primarystru cture isfoldedon it selfandst abilised byH-bonds Alpha helix sheet Tertiarystru cture furthefolded asgest abilised vanderw aalsforcesetc. byH-bonds, disulphidebon ds covalentbo nds Quaternarystructure Ariseswhen twoomore polypeptdes are involvedand form 3-Dconform ation
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