Structure of Proteins Flashcards
What weak (non covalent) bonds are there in proteins
-The hydrophobic effect
-Hydrogen bonds
-London dispersion
-Electrostatic interactions
Where are hydrogen bonds in protein structure?
Interactions of N-H and C=O of peptide bond leads to local regular structures such as alpha helicies and ß sheets
Where does London dispersion effect in proteins?
Medium-range weak attraction between all atoms contributes significantly to the stability in interior of protein
Can the C-N bond rotate?
No. Rotation around the C-N bond is restricted due to the double-bond character of the resonance hybrid form - acts as a double bond
What are the bonds that can rotate?
Rotation around bonds connected to the alpha carbon are permitted. Not around the peptide bond.
What are the angles of rotation around the alpha bonds?
o (phi) is angle around the alpha carbon - amide bond
Y (psi) is angle around the alpha carbon - carbonyl carbon bond
Why are some o and Y combinations unfavourable?
Because of steric crowding of backbone atoms with other atoms in the back bone or side chain
Why are some o and Y combinations more favourable?
Because of chance to form favorable H-bonding interactions along the backbone
What are the 2 regular arrangements in the secondary structure of proteins?
-alpha helix - stabilised by hydrogen bonds between nearby structures
-ß sheet- stabilised by hyfdrogen bonds between adjacent segments that may not be nearby
How are alpha helices held together?
By hydrogen bonds between the backbone amides of an n and n+4 amino acid
N-H group of 1 hydrogen bonds with O-C of 4
What kind of helix is the alpha helix and how many residues does it have per turn?
A right handed helix with 3.6 residues per turn
What are the orientations of the peptide bonds and side chains in alpha helix
-Peptide bonds aligned parallel with helical axis
-Side chains point out and roughly perpendicular w helix
What kind of amino acids are strong helix formers?
Small hydrophobic residues like Alanine and Leucine are strong helix formers
What amino acids act as helix breakers and why?
Proline acts as a helix breaker because the rotation around the N-C (alpha c) bond is impossible - proline found at bend of alpha helix
Glycine acts as helical breaker because the tiny R group supports other conformations
What will affect the formation of alpha helices?
Attractive or repulsive interactions between side chains 3 to 4 amino acids apart
What often occur near the positive end of helix dipole?
Negatively charged residues
What creates the pleated sheet like structure of ß sheets?
-The planarity of the peptide bond and tetrahedral geometry of the alpha carbon.
-Side chains protrude from the sheet, alternating in an up and down direction
How are ß sheets held together?
By hydrogen bonding of amide and carbonyl groups of the peptide bond from opposite strands
Parallel ß sheets VS Antiparallel ß sheets
-In parallel- hydrogen bonded strands are in same direction- h bonds between strands are bent=weaker
-In antiparallel- hydrogen bonded strands are in opposite directions- h bonds between strands are linear=stronger
When do ß turns occur? How many amino acids does it take for a 180 turn?
Occur whenever strands in ß sheets change direction
Accomplished over 4 amino acids
How is the turn stabilised?
By a hydrogen bond between a carbonyl oxygen and amide proton three residues down the sequence
What amino acid is common in i) position 2 and ii) position 3 in ßturns?
Proline in pos 2
Glycine in pos 3
What are the 2 major classes of tertiary structure protein?
fibrous and globular
What is tertairy protein structure?
Refers to overall 3D spatial arrangement of atoms in a protein
How is teriary structue stabilised?
By numerous weak interactions between AA side chains
-Largely hydrophobic and polar interactions
-can be stabilised by disulphide bonds
What is collagen a repeat sequence of and what kind of helix is it?
Gly-X-Pro or Gly-X-4-Hyp
Left handed helical structure w 3 residues per turn
3 collagen chains intertwine into a right-handed superhelical triple helix
How are collagen fibrils formed?
Crosslinks (covalent bonds between lysine or HyLys hydroxyl lysine or histidine) of triple-helices
How does permanent waving of hair work chemically?
Disrupt the disulphide bridges in hair strands with oxidation reduction reaction
What is the main protein in silk from moths and spiders? and how is it structured?
Fibroin
-Antiparallel ß sheet struture
-Small side chains of ala and gly allow close packing of sheets
What is Quaternary structure?
Formed by the assembly of individual polypeptides into a larger functional cluster
What is the role of chaperones?
Prevent misfolding and aggregation of misfolded proteins
