JW - Structural Biology Flashcards
How can the atomic structure of a whole cell be examined?
Electron microscopy
What are three facts about the peptide bond?
A) Condensation reaction
B) Partial double bond character
C) Planarity (w=180)
Why is the trans configuration preferred for all amino acids?
Energetically much lower
What is the special property of Proline regarding its cis/trans isomerization?
Unfolded peptides are 2/3 trans & 1/3 cis, while in folded proteins, cis configuration is observed in some cases
What determines the backbone conformation of a protein?
Three dihedral angles determine the backbone conformation of a protein
- w (peptide bond) close to 180
- ϕ (pronounce phi) rotation around the NC bond
- ψ (pronounce psi) rotation around the CC’ bond
What does Ramachandran plot tell you?
The Ramachandran plot shows the statistical distribution of the combinations of the backbone dihedral angles ϕ and ψ.
What can be inferred from the Ramachandran plot of protein backbone conformation?
Regular secondary structure and the presence of extended backbone conformations like b-strands
How do multiple b-strands associate?
Via backbone H-bonds
How can various b-sheet configurations be made?
Mixing of parallel and antiparallel b-strands
How can the direction of the polypeptide chain be reversed in a protein?
Via turns and loops
What characterizes tight turns in proteins?
Various types with defined structure, typically less than 5 amino acids
What distinguishes loops from turns in protein structure?
Loops have more than 5 amino acids and are less regular structural elements
Provide an example of a mainly b-sheet protein
Fatty acid binding protein
What are the variations in a-helices based on f, y angles, turns per amino acid, and pitch?
- Regular a-helix
- 3-10 helix
- p helix
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