M5 Three Dimensional Structure of Proteins

What is the one-letter code for amino acids used for?

to shorten sequences

What feature makes the peptide bond mostly trans and planar?

double bond character

Which torsion angles allow rotation in the polypeptide chain?

Phi and psi

What are the four main elements of secondary structure?

Helices, sheets, turns, random coils

What stabilizes the α-helix structure?

hydrogen bonds

Which amino acid is a known helix breaker?

proline

How do R-groups orient in a β-sheet?

Alternate above and below sheet

What type of turns involve 4 residues and H-bonding between 1st and 4th?

β-turns

In β-sheets, which arrangement has stronger H-bonds?

Antiparallel

What is shown on a Ramachandran plot?

Allowed torsion angles

secondary structure

stable arrangement of AA residues

tertiary structure

3D fold of single polypeptide chain

Quaternary structure

3D spatial arrangement of 2 or more polypeptide subunits

The planarity of the peptide bond restricts w to ___ degrees in very nearly all of the main chain peptide bonds

180

alpha helix structure

simplest arrangement of a peptide chain

right-handed

3₁₀

3.0 residues

10 atoms

alpha

3.6 residues

13 atoms

pi

4.4 residues

16 atoms

beta sheet

polypeptide forms zig zags

beta turns involve ___ amino acid residues in a 180 degree turn

4

gamma turns involve ___ amino acid residues in a 180 degree turn

3

beta sheet twist is __ handed

left

alpha helix frequency of AA

Kristin Has Marvelous LACE Q-tips

beta sheet frequency of AA

IVY For The Win

reverse turn frequency of AA

SPDNG

φ

(N–Cα)

ψ

(Cα–C)

w (peptide bond)

carboxyl-amino