The Three Dimensional Structure of Proteins Flashcards
what drives protein structure
the hydrophobic effect
what are the four levels of protein structure
primary, secondary, tertiary and quaternary structure
describe the favorable interactions in proteins and what they do for protein structure
- hydrophobic effect - release of water from solvation layer (area between solvent and solute) when the protein is folding increases the net entropy
- hydrogen bonds - interaction of N-H and C=O of peptide bonds leads to formation of a helices and B sheets
- london dispersion - weak attraction between all atoms, contributes to the stability of the interior of the protein
- electrostatic interactions - include long range strong interactions between permanently charged groups. salt bridges i.e in the hydrophobic environment strongly stabilize the proteins
what is the primary structure of protein
the peptide bond
what is the constant triple repeat (backbone) of the amino chain
N-C-C repeats through the amino chain
are peptide bonds polar or non polar
polar since the O2 and N atoms have partial pos and neg charges
why is there restriction around the C-N bond
due to the double bond in the resonance form - the molecule switches back and forth from the resonance structure and in turn it cannot rotate around the C-N bond as it exists somewhere between its two forms
explain where there is rotation in the peptide bond
there is rotation around the alpha carbons (phi and psi) where phi = the amide nitrogen and psi = the carbonyl carbon
when fully extended what degrees are psi and phi
180 degrees
what is the effect of steric crowding on psi and phi
means that certain psi and phi combinations are very unfavorable
what may occur with favourable psi and phi combinations
favorable H bonding interactions may form
what does secondary structure refer to
local spatial arrangement within the polypeptide backbone resulting in two regular arrangements - a helix and B sheets
what is a random coil
occurs when irregular arrangement of the polypeptide chain happens
describe the structure of the a helix
held together by hydrogen bonds at n and n+ 4 amino acids. is a right handed helix and has 3.6 residues per turn. peptide bonds are aligned roughly parallel and the side chains point out and are roughly perpendicular with the helicial axis
give examples of strong helix formers
Ala and Leu
which residues are typically found in the turn of the helix
Pro and Gly
where are negatively charged residues found on the helix dipole
near the positive end (amino terminus) of the helix dipole
what holds beta sheets together
hydrogen bondings between amide and carbonyl groups of the peptide bonds from opposite places on the strands
describe the structure of the H bonds in parallel B sheets
the sheets are in the same directions and the H bonds are BENT between each sheet (weak)
describe the H bonding between antiparallel sheets
strands run in opposite directions - H bonds are LINEAR between each sheet (strong)
when do B turns occur
when the strands in B sheets change directions- occurs over 4 amino acids
proline and glycine are commonly seen in turns in position 2 and 3 respectively in the antiparallel structure
what is tertiary structure
overall 3D spatial arrangements of atoms in a protein
what stabilises tertiary structure
stabilised by weak interactions between amino side chains: hydrophobic and polar interactions. can also be stabilised by disulphide bonds
what are the two major classes of tertiary structure
fibrous and globular
fibrous proteins
i.e collagen- made of three collagen chains intertwined into a right handed triple helix- many triple helices assemble into a collagen fibril
what type of bonds are crosslinks
covalent bonds- occur between Lys, or HyLys or His amino acid residues
function of chaperones?
assist in the correct folding of protein and can unfold incorrect foldings for it to refold.
