C12 Lecture 4
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Protein's amino acid sequence
Local spatial arrangement of a polypeptide's backbone atoms
Does secondary structure consider side chains of a polypeptide?
3D structure of the entire chain
Spatial arrangement of different polypeptides in a protein
Do all proteins have quaternary structure?
Some proteins are functional alone in their tertiary form.
How many amino acids in human Hgb α and β strands?
How is this relevant to Hgb separation by SDS-Page?
α: 142 a.a.
β: 147 a.a.
The chains are difficult to separate by weight (SDS-Page)
3D Hgb structure (1-4o)
- 1o: KAHGKKVLGA (62-71)
- 2o: alpha helix
- 3o: One complete protein chain (beta chain of Hgb)
- 4o: Four separate chains of Hgb assembled into an oligomeric protein
Space filling model
- Sphere = atom
- Shows the surface exposed to solvent and ligands
Ball and stick model
Excellent for bonding arrangement
Shows general course of polypeptide chains
Cartoon ribbon diagram
- Most common
- Easy to visualize 3D shape
- Can see interior
- Can see folds and patterns
- Can add ball and stick portions
How are proteins represented in a ribbon diagram
alpha helices: coils/thick tubes
beta strand: arrows
lines or thin tubes: random coils
What would you like to do?
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