Chapater 4

1
Chapater 4 Protein Secondary Structure

• Levels of protein structure.
• Ways of viewing proteins.
• Methods for determining protein structure.
• The conformation of the peptide bond.
• The alpha helix
• The beta sheet

2
(No Transcript)
3
(No Transcript)
4
(No Transcript)
5

• Ways of viewing proteins
• Spacefilling
• Ribbon
• Combination active site
• Ribonuclease

6
(No Transcript)
7
(No Transcript)
8

• Methods for determining the structure of
  proteins.
• Conformation shape
• Polypeptide chain Group of amino acids held
  together by
• peptide bonds.
• X-ray crystallography
• NMR

9

• X-ray crystallography
• 1) First crystallize the protein.
• 2) Bombard the crystal with X-rays.
• 3) Obtain an X-ray diffraction pattern.
• 4) Determine the structure.

10
X-ray diffraction Pattern.
11
NMR Nuclear magnetic resonance. Can be done
for proteins in solution but But it is limited to
proteins ,35000 MW. Nuclei absorb
electromagnetic radiation (microwave
range) Apply a magnetic field different nuclei
will absorb at different fields depending on
their environment. These values can be used to
determine the structure.
12
NMR structure.
13

• The conformation of
• the peptide bond.

Resonance structures
14
The peptide bond is planar.
15
(No Transcript)
16
5. The alpha helix
17
(No Transcript)
18
6. The Beta- sheet
19
(No Transcript)
20
Backbone Namino-Ca-Ccarbonyl-
Namino-Ca-Ccarbonyl--Namino-Ca-Ccarbonyl- Side
chains R groups


Namino-Ca-Ccarbonyl- Namino-Ca-Ccarbonyl-
R1 R2
Primary structure backbone covalent
(peptide) bonds between Carboxyl C and the N of
the amino groups of the next amino acid.
21
Secondary structure Hydrogen bonds. Alpha
helix Between the CO of one amino acid the H of
the NH group four amino acids down the
chain. Beta sheet - Between the CO of one amino
acid and the NH of another amino acid on another
part of the chain.
22
Arrangements of secondary structure.
23
Alpha helical protein
24
Beta sheet protein