Lecture Notes

Fundamentals of protein structure
Learning objectives:
1. Draw AA and their functional groups
2. Describe nature of peptide bond
3. Draw dipeptide and indicate phi, psi and omega torsion angles
4. Draw Ramachandran plot
5. Describe key features of alpha helix and beta sheets
6. List how the fold of a protein is stabilised
7. Describe how the primary sequence can be used to predict the tertiary fold.


6 topics covered

1. Protein expression
2. Chromatography- purify biological molecules
3. Mass spectroscopy
4. Optical spectroscopy
5. NMR spectroscopy – study biological molecule at the atomical level
6. Crystallography

Protein function

 From most to least function carried out by proteins in a cell
1. Energy metabolism
2. Folding
3. Cytoskeleton
4. ATP-related
5. Transcription
6. Signalling
7. detoxification
8. Ca2+ signalling
9. Cell cycle
10. Neurotransmitter metabolism
11. Degradation
12. Other

Amino acids

 Proteins are polymers built from monomer units called AA
 AA consist of:
- Central C atom (Cα)
- Amino group (NH2)
- Carboxylic acid (COOH)
- H atom
- R group
 The central C atom is chiral (asymmetric)
- Only L isomers found in protein

CORN law

 Used to determine whether an AA is an L/D-isomer
 CORN is an acronym for
- COOH
- R
- NH2
 Read CORN clockwise = L isomer
 Read CORN anticlockwise = D isomer

, Protonation state of carboxylic acid and amino group depends on pH

 pH7 : neutral
- amino group protonated
- carboxylic acid group deprotonated Zwitterion
 PH9: basic
- Amino group deprotonated
- Carboxylic acid group still deprotonated
 PH 3: acidic
- Amino group protonated
- Carboxylic acid group protonated




20 common AA

 Side chains vary in
- Size
- Shape
- Charge
- Chemical reactivity
- H-bond capacity
- Hydrophobic character
 Functional groups in AA side chains
- Alkanes
- Alcohols
- Aromatics
- Basic groups
- Carboxamides
- Carboxyli
c acid
- Thiols
- Thioether
s