FND 100 Lecture Notes - Lecture 2: Beta Sheet, Alpha Helix, Hydrogen Bond

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Structure of PRO (describing structure of PRO
A primary structure:
Simple level of organization
What is the AA sequence of the PRO?
20 AA, sequence will affect
o Influence - is protein acidic or basic, hydrophobic or hydrophilic, how does it fold
Chemistry and stability of the PRO (AA sequence influences the)
Chem: acidic, basic, hydrophobic
o What are the chemical descriptors ?
o Influences how PRO behaves in a solution
Certain proteins = hydrophobic or philic in nature
Hydrophobic AA (don’t interact with aqueous environment) = More likely to be folded towards
interior of peptide chain
Hydrophilic = Likely to be on exterior of folded protein
Secondary structure
Start to talk about the 3 dimensional characteristics
Secondary and primary structure stabilized through H bonding
Alpha helix
Beta pleated sheet
o H bonds
Random coil - Hydrogen bonding involved
Beta bend
Kink or bend in a polypeptide chain and stabilized by neighbouring bonds in the AA chains
AA residue
Arrows - beta pleated sheet
C - 3rd Structure
Intramolecular Bonding (within a particular polypeptide chain)
Disulfide bonds + bridges - bonding of 2 S on an adjacent portion of the chain
Alpha Helix:
Right handed helix, helix is made up of the polypeptide chain backbone; can see where the H
bond to stabilize that structure is
R groups: is the unique side chain of AA that is pointed to the exterior
Polypeptide bond is coming into play
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Document Summary

Simple level of organization: what is the aa sequence of the pro, 20 aa, sequence will affect. Certain proteins = hydrophobic or philic in nature. Hydrophobic aa (don"t interact with aqueous environment) = more likely to be folded towards interior of peptide chain. Hydrophilic = likely to be on exterior of folded protein. Start to talk about the 3 dimensional characteristics. Secondary and primary structure stabilized through h bonding: alpha helix, beta pleated sheet, h bonds. Kink or bend in a polypeptide chain and stabilized by neighbouring bonds in the aa chains. Disulfide bonds + bridges - bonding of 2 s on an adjacent portion of the chain. Right handed helix, helix is made up of the polypeptide chain backbone; can see where the h bond to stabilize that structure is. R groups: is the unique side chain of aa that is pointed to the exterior. A chain and the b chain are regarded as being parallel.

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