3D Structure of Proteins Flashcards
4 Interactions in Proteins
- Hydrophobic Effect
- Hydrogen Bonds: lead to alpha helix and beta sheet structures
- London Dispersion: Weak interactions between atoms contributes to stability of interior of the protein
- Electrostatic Interactions: Strong interactions
What are the repeating atoms in the peptide backbone
N-C-C
Characteristics of the peptide bond
- Planar
- Polar
- Rigid
- Limited rotation around peptide bond
- Behaves like a double bond
what bond is the peptide bond (atom wise)
C-N bond
Why is rotation around the peptide bond not permitted
Due to the resonance structure
Rotations around what bonds are permitted
Rotations around bonds connected to the alpha carbon are permitted:
* The alpha carbon - carbon bond (carbonyl carbon bond)
* The alpha carbon - nitrogen bond (amide nitrogen bond)
What does secondary structure refer to
- Local spatial arrangement
- Interactions within the polypeptide backbone
What are both alpha helices and beta sheets stabilised by
hydrogen bonds
What is irregular arrangement of the polypeptide chain called
Random coil
Which AAs are strong helix formers
Alanine (Ala)
Leucine (Leu)
What AAs are helix breakers and why (2)
- Proline (Pro): the rotation around the alpha carbon - nitrogen bond is impossible
- Glycine (Gly): the tiny R group supports other conformations (R group = H)
What creates a pleated sheet like structure
- The planarity of the peptide bond
- The tetrahedral geometry of the alpha carbon
What are beta sheets held together by
The hydrogen bonding of amide and carbonyl groups of the peptide bond from opposite strands
Characteristic of the h. bonds in parallel beta sheets
The hydrogen bonds between strands are bent and therefore weaker
Characteristic of the h. bonds in antiparallel beta sheets
The h. bonds between sheets are linear (straight) and therefore stronger
What AAs are common in beta turns
Proline & Glycine
What does tertiary structure refer to
the overall 3D spatial arrangement of atoms in a protein
what is the tertiary structure stabilised by
Multiple weak interations between AA side chains:
* Mostly hydrophobic and polar interactions
* Can be stabilised by disulphide bonds
Structure of collagen (a fibrous protein)
- Triple alpha helix coming together into a collagen fibril
- Triple helices crosslinked to form collagen fibrils
- Triple helix gives rigidity
What is the structre of silk fibroin
Antiparallel beta sheet structure results in soft, flexible filaments
How is the quaternary structure formed
The assembly of individual polypeptides into a larger functional cluster
4 ways proteins can be denatured
- Heat/cold
- Extremes of pH
- Organic solvents
- Chaotropic agents: e.g: urea
Function of chaperones in protein folding
Aid in folding protein into its native conformation.
They prevent misfolding & aggregation of unfolded peptides.
(Disaggregation, remodeling, folding)
