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Lecture notes of 12 pages for the course Techniques For Biological And Chemical Sciences at QMUL
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Fundamentals of protein structureLearning 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
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