Protein lecture 2

Question 1

Dihedral angles

Answer 1

Phi, psi and omega are angles on angles of bond orientation on an amino acid molecule that determine how the amino acid is oriented in space. These angles along with the type of amino acids that make up majority of the protein determine the orientation of the protein chain and it’s side groups.

Question 2

Ramachandran plot

Answer 2

A plot that indicates where psi, phi and omega chains are located with respect to degree angle. The degree angle is directly correlated with the amount of energy required for each orientation and most structures such as right handed alpha helix and beta sheet are found in the areas with the loest energy.

Question 3

Regular geometry of secondary structures

Answer 3

2.3 resiudes per turn and 3.0 angstroms…

Question 4

Higher secondary structures

Answer 4

Triple helix: This is when three alpha helices connect with one another to form a triple helix. Every third residue must be a glycine molecule while everything else is proline and hydroxyproline.

Alpha coil coiled helix: This is when a right handed alpha helix coils around anotherhelix producing a left handed coiled helix. a, b, c, and d molecules connect with one another at the a and d ends of each molecule creating a hydrophobic complex after every 7.2 units.