helixes 9/26

Question 1

the most preferred secondary structures will…

Answer 1

maximize formation of hydrogen bonds between backbone amino and carboxyl groups, and fall within the range of phi and psi angles dictated by the ramachandran plot

Question 2

how is an alpha or helical structure described

Answer 2

by the number of amino acid residues per turn, the pitch (distance covered by turn) and the number of atoms in the hypothetical ring closed by the hydrogen-bond formation

Question 3

^2.27 helix

Answer 3

• never observed
• unfavorable ram. angles

Question 4

^3.010 helix

Answer 4

• tighter than alpha helix
• mildly forbidden Ram. angles but short stretches of it are sometimes observed (usually at end of alpha helix)
• pitch of 6.0 A

Question 5

^3.613 helix

Answer 5

• alpha helix
• most common
• right handed helix (L AA) with pitch of 5.4 A
• core tightly packed fo groups on opposite sides of helix are in van der waals contact (no empty space inside)
• side chains all project outward from helix
• dipole moment; amino end is positive relative to cabroxyl end
• stable
• H bonds all lock into place

Question 6

^4.416 helix

Answer 6

• looser than alpha helix
• pi helix
• rarly observed because it has mildly unfavorable Ram. angles and axial hole (empty space) inside
• pitch of 5.2 A

Question 7

polyproline or polyglycine

Answer 7

prolin or glycine form a left handed helix with 3.0 residues per turn and a pitch of 9.4 A; basis for structure of collagen

Question 8

beta sheets

Answer 8

• formed when backbone amino and carboxyl groups form extensive hydrogen bonds with neighbouring polypeptide chains
• can be parallel (face same direction) or antiparallel (face opposite direction)
• 7 A repeat for 2 residues (3.5 A per AA)
• parallel slightly less stable

Question 9

beta turns

Answer 9

• most common type of turns
• four residues with the carboxyl C of first hydrogen bonded with the amino N of fourth

Question 10

what charges are most stable for the amino and carboxyl ends

Answer 10

• amino = negative
• carboxyl = positive

Question 11

what are leucine zipper proteins

Answer 11

• bind to DNA and control transcription/expression of genes
• stick by hydrophobic strips (dimer)

Question 12

bovine rhodopsin

Answer 12

proteins (helix) go through membrane