What are the advantages for proteins to form three-dimensional structures using non-covalent (weak) interactions? Solution PROTEIN FOLDING MODELS: 1. Frame work model: In this the protein local elements which are stretches of amino acids liked by one another by covalently with peptide bonds. The region of the primary amino acids sequence in peptide bonds makes different domains. In these domains some of regions are making with Alfa helix and some are beta sheet domains. These primary elements form secondary structure independently of tertiary structure (kim and baldwin).these elements can diffuse un till they collided, successfully adhering and coalescing to give the tertiary structure (diffuse-collision model),(karplus and weaven). 2. The classic nucleation model: It postulates that some neighboring residues in the sequence would form native secondary structure that would act as a nucleus form which the native structure would propagate in a step wise manner. Thus the tertiary structure would form as necessary consequence of the secondary structure (wetlaufer). 3. Hydrophobic collapse model: It is hypothesized that a protein would collapse rapidly around its hydrophobic side chain and then arrange from restricted conformational space occupied by the intermediate. Here the secondary structure would be directed by native like tertiary structure (ptitsyn & kwajima). Leviathan’s paradox: It is formulated by Cyrus Leviathan. There are vast too many different possible conformations for a protein to fold by a random search. Structural organization of protein: 1. Primary Structure: It refers the sequence of amino acids along with the disulphide bonds. 2. SECONDARY STRUCTURE: Alfa- Helices and Beta-Pleated sheets are most frequently occurring in secondary structure in polypeptides. Both of these can case local folding of protein. the Alfa - Helices in polypeptide made up of L Alfa amino acids are right handed, the - Helices is stabilized by hydrogen bonds formed between oxygen and amide hydrogen’s of peptide bonds that are a part of linear sequence. Beta-Pleated sheets: 2 types A. Parallel: in this the adjacent hydrogen bonding segments are connected by cross over connection [Right handed]. B. Anti-Parallel: In this the adjacent hydrogen bonding segments are connected by HAIRPIN turns or reverse turn [Left Handed]. 3. Tertiary structure: It is arisen because of the folding of poly peptides upon itself. 4. Quaternary structure: Some proteins are made up of 2 or more polypeptides chains, the interaction between different poly peptide are subunits gives rise to the quaternary structure. Non-covalent (weak) interactions advantages in proteins: In proteins mainly 4 types of non-covalent interactions are present. 1. Hydrophobic region R-CH3 ------- H 3 C-R 2. H-bonding between R-group G-OH ------ N=R 3. Salt bridge R-COO------ NH 3 -R 4. Van der Waals force The non-covalent bonds, which are present between the peptides, can forms interactions between indivi.

1. What are the advantages for proteins to form three-dimensional structures using non-covalent
(weak) interactions?
Solution
PROTEIN FOLDING MODELS:
1. Frame work model:
In this the protein local elements which are stretches of amino acids liked by one another by
covalently with peptide bonds. The region of the primary amino acids sequence in peptide bonds
makes different domains. In these domains some of regions are making with Alfa helix and some
are beta sheet domains. These primary elements form secondary structure independently of
tertiary structure (kim and baldwin).these elements can diffuse un till they collided, successfully
adhering and coalescing to give the tertiary structure (diffuse-collision model),(karplus and
weaven).
2. The classic nucleation model:
It postulates that some neighboring residues in the sequence would form native secondary
structure that would act as a nucleus form which the native structure would propagate in a step
wise manner. Thus the tertiary structure would form as necessary consequence of the secondary
structure (wetlaufer).
3. Hydrophobic collapse model:
It is hypothesized that a protein would collapse rapidly around its hydrophobic side chain and
then arrange from restricted conformational space occupied by the intermediate. Here the
secondary structure would be directed by native like tertiary structure (ptitsyn & kwajima).
Leviathan’s paradox:
It is formulated by Cyrus Leviathan. There are vast too many different possible conformations
for a protein to fold by a random search.
Structural organization of protein:
1. Primary Structure: It refers the sequence of amino acids along with the disulphide bonds.
2. SECONDARY STRUCTURE:
Alfa- Helices and Beta-Pleated sheets are most frequently occurring in secondary structure in
polypeptides. Both of these can case local folding of protein.
the Alfa - Helices in polypeptide made up of L Alfa amino acids are right handed, the - Helices is
stabilized by hydrogen bonds formed between oxygen and amide hydrogen’s of peptide bonds
that are a part of linear sequence.
Beta-Pleated sheets: 2 types

2. A. Parallel: in this the adjacent hydrogen bonding segments are connected by cross over
connection [Right handed].
B. Anti-Parallel: In this the adjacent hydrogen bonding segments are connected by HAIRPIN
turns or reverse turn [Left Handed].
3. Tertiary structure:
It is arisen because of the folding of poly peptides upon itself.
4. Quaternary structure:
Some proteins are made up of 2 or more polypeptides chains, the interaction between different
poly peptide are subunits gives rise to the quaternary structure.
Non-covalent (weak) interactions advantages in proteins:
In proteins mainly 4 types of non-covalent interactions are present.
1. Hydrophobic region R-CH3 ------- H 3 C-R
2. H-bonding between R-group G-OH ------ N=R
3. Salt bridge R-COO------ NH 3 -R
4. Van der Waals force
The non-covalent bonds, which are present between the peptides, can forms interactions between
individual polypeptide chains.
In the binding site of non-covalent bonds, the protein molecules interact with one another.
The sub units of the proteins are held together by non-covalent bonds.
Some prosthetic groups (Metals or vitamins) attaches to proteins by non-covalent bonds.