Peptides and proteins
Always start from amino group to carboxyl group (amino terminal and carboxyl terminal regions).
The amino terminal AA is number 1.
Nomenclature Ala-Lys (Alanil lysine).
Peptides below 40-50 amino acids..
Most of the proteins have 200-1000 AA (600-3000 base pair on DNA).
Hierarchical organization of protein structure.
There are 4 levels of protein structural organization:
- primary structure (AA sequence);
- secondary structure (the local folding of AAs into defined structures);
- tertiary structure (the way secondary structures interacts each other in space);
- quaternary structure (only for some proteins where with the association of more polypeptides occurs).
α-helix secondary structure
It is the main secondary structure of proteins. It is stabilized by H bonds between C=O and NH in position n+3 (every 4 AA).
Lateral chains are located on the external side of the helix.
Prolin interrupts the α helix (explain why!).
Stabilized by H bonds between H and C=O also of AA very far on the peptide sequence.
Don’t confusione these with beta sheet!
Allow peptide backbone to turn back on its(particularly in the globular proteins.
Different types of beta turns.
One of the more common has the sequence XPGX type. Pro starts to bend the backbone and Gly stays at the top of the turn. The two “X” interacts to stabilize the structure.
Hierarchical organization of the protein
The only covalent interaction to stabilize protein tertiary structures.
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