| Between which atoms in a peptide bonds rotate to form φ and ψ angles, or form peptide bond? | -ϕ (phi): angle around the a-carbon—amide nitrogen bond (1.46A)
-ѱ (psi): angle around the a-carbon—carbonyl carbon bond (1.53A)
In a fully extended polypeptide, both ѱ and ϕ are 180° |
| why peptide bonds can't rotate? | Theoretically ϕ and ѱ angles could take any value, yet some angles of rotation around the Cα are not sterically possible. they all reside in a single plane,Because of the partial double bond between the α carbon and the amine nitrogen, no rotation is possible around that bond. |
| what contracts effect the stability of a a-helix? | -Not all polypeptide sequences adopt a-helical structures
-Small hydrophobic residues such as Ala and Leu are strong helix formers
-Pro acts as a helix breaker because the rotation around the N-Ca bond is impossible
-Gly acts as a helix breaker because the tiny R-group supports other conformations
-Attractive or repulsive interactions between side chains 3–4 amino acids apart will affect formation. |
| What are the Amino acids that form β-turns? | Proline in position 2 or glycine in position 3 are common in B-turns. |
| What's the structure of β-turns? | Most peptide bonds not involving proline are in the trans configuration (>99.95%).For peptide bonds involving proline, about 6% are in the cis configuration they include proline. |
| What are the forces that stabilize α-helix and β-sheets? | - a-helix are stabilized by hydrogen bonds between nearby residues.
- B-sheets are stabilized by hydrogen bonds between adjacent segments that may not be nearby. |
| what are the forces that stabilize tertiary and quaternary structures? | Tertiary structure is stabilized by Stabilized by numerous weak interactions between amino acid.
-Largely hydrophobic and polar interactions, also hydrogen bonds and
Van der Waals forces.
- Can be stabilized by disulfide bonds
-Quaternary structure is held together by noncovalent bonds between complementary surface hydrophobic and hydrophilic regions of polypeptide. |
| What are the major classes of proteins based on their tertiary structure? | -Fibrous proteins provide support, shape, and external protection (Insoluble ,hydrophobic amino acids ) Ex: a-Keratin,Silk,Collagen.
-Globular proteins enzymes and regulatory proteins (Water- soluble) Ex: plasma proteins and the immunoglobulin, Enzymes. |
| what's the definition of “motif”? | Motif (fold) is a recognizable pattern that involves two or more elements of secondary structure and connections between them. |
| what's the definition of “domain”? | Domain is a part of protein that independently stable or can move as a single entity with respect to the rest of the protein. |
| why some proteins (or parts of proteins) are intrinsically disordered? | They Contain protein segments that Disordered regions less-defined structure. (Lys, Arg, Glu, and Pro).
-they can conform to many different proteins, facilitating interaction with numerous different partner proteins.
-They lack a hydrophobic core, and instead are characterized by high densities of charged amino acid residues,
-Structural disorder and high charge density can facilitate the function of some proteins. |
