Lecture 5 - Primary & Secondary structures

Question 1

what makes up backbone of peptide chain

Answer 1

N - C alpha - C unit

Question 2

what is native conformation

Answer 2

any polypep chain has a single stable shape that it should always fold into, determined by the AA chain

Question 3

what are the 2 factors that determine protein structure

Answer 3

allowable bond rotation (referring to the psi and phi rotation thing and how some rotations aren’t favourable)

weak non-covalent interactions between the backbone and the side chains

Question 4

which is more favourbale: cis or trans conformation

Answer 4

trans
cuz cis has steric interference of alpha carbons and their side chains

Question 5

which AA has restricted rotation around N-C alpha bond

Answer 5

proline
cuz of the fat ring blocking the turn,
so the phi rotation basically cant happen

Question 6

what does ramachandran plot demonstrate

Answer 6

all combos of psi and phi turns a protein can have, and it shows how some turns are more or less favoured

Question 7

in an alpha helix, where are the H bonds formed

Answer 7

between C=O (n) and the amide hydrogen of n+4

Question 8

how is the aplha helix a dipole

Answer 8

the C=O groups point toward C terminus
so N to C is +ve to -ve

Question 9

what is pitch

Answer 9

length of a whole turn in alpha helix

Question 10

what is rise

Answer 10

the length occupied by one residue

Question 11

what can be worked out using the pitch and rise

Answer 11

how many AAs per turn

Question 12

diff between parallel and antiparallel beta sheets

Answer 12

parallel - the strands are all N-C
antiparallel - stands are alternating N-C

Question 13

which type of beta sheet is more stable and why

Answer 13

antiparallel more stable
cuz the H bonds are more perpendicular

Question 14

how are parallel beta sheets connected

Answer 14

have to be connected via a big loop or alpha helix

Question 15

what characteristic forms the pleated conformation of a beta sheet

Answer 15

R groups will be on alternating surfaces

Question 16

how are alternating side chains important in beta sheet

Answer 16

each side chain may have diff properties, meaning each side of the sheet can interact with different things (e.g. one side being hydrophobic means it can interact w/ lipid membrane)

Question 17

what connects alpha helices and beta strands

Answer 17

loops and turns

Question 18

diff between loops and turns

Answer 18

loops are usually longer than 5 residues, and may contain hydrophillic residues

turns are short (5 residues or less)