Question

List the stabilizing forces at tertiary level of protein structure. An enzyme containing the amino aspartic acid (pK_a of the side chain = 3.65) and histidine (pK_a of the side chain= 6) in the active (catalytic ) site has an optimal activity at a pH of 5.0. What is the major stabilizing force at the catalytic site? Using structures and 1-3 complete sentences, predict and explain what is expected to happen to the activity if the pH is increased to 8.

"please answer in details"

Answer 1

Hi,

The primary structure of peptides and proteins refers to the linear number and order of the amino acids present. The convention for the designation of the order of amino acids is that the N-terminal end (i.e. the end bearing the residue with the free ?-amino group) is to the left (and the number 1 amino acid) and the C-terminal end (i.e. the end with the residue containing a free ?-carboxyl group) is to the right.

In this peptide bonds are seen..

The ordered array of amino acids in a protein confer regular conformational forms upon that protein. These conformations constitute the secondary structures of a protein. In general proteins fold into two broad classes of structure termed, globular proteins or fibrous proteins. Globular proteins are compactly folded and coiled, whereas, fibrous proteins are more filamentous or elongated. It is the partial double-bond character of the peptide bond that defines the conformations a polypeptide chain .

The ?-helix is a common secondary structure encountered in proteins of the globular class. The formation of the ?-helix is spontaneous and is stabilized by H-bonding between amide nitrogens and carbonyl carbons of peptide bonds spaced four residues apart. This orientation of H-bonding produces a helical coiling of the peptide backbone such that the R-groups lie on the exterior of the helix and perpendicular to its axis.
?-sheets are composed of 2 or more different regions of stretches of at least 5-10 amino acids. The folding and alignment of stretches of the polypeptide backbone aside one another to form ?-sheets is stabilized by H-bonding between amide nitrogens and carbonyl carbons. However, the H-bonding residues are present in adjacently opposed stretches of the polypetide backbone as opposed to a linearly contiguous region of the backbone in the ?-helix.

Tertiary structure refers to the complete three-dimensional structure of the polypeptide units of a given protein. Included in this description is the spatial relationship of different secondary structures to one another within a polypeptide chain and how these secondary structures themselves fold into the three-dimensional form of the protein. Secondary structures of proteins often constitute distinct domains. Therefore, tertiary structure also describes the relationship of different domains to one another within a protein. The interactions of different domains is governed by several forces: These include hydrogen bonding, hydrophobic interactions, electrostatic interactions and van der Waals forces

Many proteins contain 2 or more different polypeptide chains that are held in association by the same non-covalent forces that stabilize the tertiary structures of proteins. Proteins with multiple polypetide chains are oligomeric proteins. The structure formed by monomer-monomer interaction in an oligomeric protein is known as quaternary structure.

Oligomeric proteins can be composed of multiple identical polypeptide chains or multiple distinct polypeptide chains. Proteins with identical subunits are termed homo-oligomers. Proteins containing several distinct polypeptide chains are termed hetero-oligomers.

Hemoglobin, the oxygen carrying protein of the blood, contains two ? and two ? subunits arranged with a quaternary structure in the form, ?2?2. Hemoglobin is, therefore, a hetero-oligomeric protein.