Lecture 12 Flashcards
Protein secondary structure
Refers to the 3-dimensional shapes of local segments of a protein chain
-established hydrogen bonding patterns of the peptide backbone of a protein
alpha helix and beta sheet are most common
Protein tertiary structure
The 3-dimensional structure of the entire polypeptide chain
Regular way to fold a polypeptide chain
1) common bond lengths and angles would be distorted as little as possible upon chain folding
2) Atoms should be no closer to each other than is allowed by their Van Der Waals radii
3) 6 atoms that form a peptide group must remain coplanar
4) non-covalent bonding is required to stabilize the folding pattern of a polypeptide. Hydrogen bonding will be maximized without violating principles 1,2 and 3
Basic structure of the alpha helix
- Each turn of the alpha helix is 3.6 AA residues long
- Peptide C=O oxygen atom of the first residues forms a hydrogen bond with the NH group four residues down the chain
- R-groups are not involved with the helix and extend out and away from the helix
Beta Sheet Details
- Formed when 2+ linear protein strands align through hydrogen bonding
- The planar amide groups lie in the faces of the pleats and the tetrahedral alpha carbon atoms form the creases
- side chains on carbon atoms are perpendicular to the sheet
Side Chain Preferences
- Large aromatic residues (Phe, Tyr, Trp)and beta branched alkyl side chains (Val, Ile, Thr) are found on middle strands of beta sheets
- Edge strands favor sterically demanding groups (Pro) or charged residues (Lys, Arg)
beta turn details
- ~1/3 residues in a protein are tight turns that reverse direction of the polypeptide chain, most common is beta turn
- Carbonyl group of residue i forms a h-bond to N-H group 3 residues away (i+3)
Characteristics of crystals
1) Crystals parallel edges and faces
2) shards of crystal have the same shape as the larger crystal
3) crystals are highly symmetrical
