protein secondary structure

where are hydrogen bonds normally found on a protein?

the surface

what is the resonance stabilization energy of a peptide bond

88 kJ/mol

what amino acids are in trans conformation

all except proline

what is the psi rotation around

Ca to C bond

what is the phi rotation around

Ca to N bond

what type of angles are psi and phi bonds

dihedral/torsional angles

what angle does an eclipsed conformation have

0

what angle does a staggered conformation have

180

what amino acid has the greatest rotational freedom

glycine

what does n stand for

#of residues per helical turn

what does p stand for

distance helix rises per turn

what is the n number for alpha helix

3.6

what is the p number for alpha helix

5.4

what is the n number for B sheets

2

what is the p number for parallel B sheets

6.5

what is the p number for antiparallel B sheets

7

what direction are alpha helixes

right handed

what direction is a right handed helix

counterclockwise

what direction is a left handed helix

clockwise

what helix maximizes intrachain hydrogen bonds

alpha helix

what direction do side chains of an alpha helix project

downward and outward

how do you calculate length

(#of amino acids/3.6) * 5.4

what destabilizes alpha helix

1. successive charged residues

2. successive bulky nonpolar groups

3. residues with same charge three residues apart

what cannot participate in helix H-bonds

first 4 amide H and last 4 carbonyl oxygens

why do proteins helix cap

to provide H bond to the bare N-H and C=O groups

what interactions provide a large stabilization energy for alpha helix

dipole-dipole helix

how does the peptide bond dipole moments align in alpha helix

aligned along helical axis creating an additive dipole effect producing a positive charge on n-term and negative charge on c-term

what frequently binds to n-terminus of alpha helix

negatively charged ligands like phosphates

does anything bind to c-terminus of alpha helix

rarely. positive ligands wont bond

what are the 5 constraints on the stability of the alpha helix

1. successive charged amino acids destabilize

2. successive bulky amino acids destabilize

3. proline or glycine destabilize

4. interactions

what can be 3 residues apart to stabilize alpha helix

opposite charged side chains or two aromatic residues

what is the n number in a 3¹⁰ helix

3

what is the p number in a 3¹⁰ helix

6

why is 3¹⁰ helix called one

10 atoms including H involved in H bonding

how does the 3¹⁰ compare to an alpha helix

it is thinner and rises more sharply

where does hydrogen bonding occur in B pleating sheets

between neighboring polypeptide chains

what is the average number of strands and width of a B antiparallel sheet

6 strands

25 A

what residues are on antiparallel sheets

hydrophobic on one side

hydrophillic on the other side

what is made of antiparallel sheets

silk

how many sheets does a parallel sheet need to be stable

5

why are parallel sheets less stable than antiparallel sheets

the hydrogen bonds are slightly distorted

what residues are on parallel sheets

hydrophobic on both sides

what type of twist do B pleated sheets have

right handed

what are B turns composed of

successive strands of anti parallel B sheets

4 amino acids

what are the 2 types of B turns

type 1- distorted 3¹⁰ helix

type 2- the oxygen atom of residue 2 crowds the C_B atom of residue 3 (usually glycine)

what is residue 2 of both B turns and why

proline, because it prefers cis peptide bond which makes a sharp turn