protein structure and forces Flashcards
name 4 levels of protein structure
primary, secondary, tertiary, quaternary
describe primary structure of proteins
chain of amino acids held by peptide bonds, free amino (N terminus) group and free carbonyl (C terminus) group at each end
describe secondary structure of proteins
alpha helix=all NH groups point up and all CO groups point down, hydrogen bonding between NH and CO responsible for formation, some hydrophobic interactions between helix promoting side chains help stabilise helix, CO forming backbone of protein is not from R group
beta sheet=anti/parallel, twisted, not flat, loops and turns and folds on itself to form hydrogen bonds between itself to make it more compact, beta turns, look at notes for parallel and antiparallel sheets
what are beta turns
loops with only 4 or 5 amino acid residues when they have internal hydrogen bonds
describe tertiary structure of proteins
-3D structure, individual amino acids from distant parts of the primary sequence can interact with interactive forces (hydrophobic interactions, hydrogen bonds, dipole dipole, salt bridge, disulfide bonds)
-these interactions (caused by side chains) changes the shape of the folding/protein
describe quaternary structure of proteins
-linking two or more polypeptide chains together, called oligomers (dimers/trimers/tetramers) depending on the number of subunits
-identitcal subunits use the prefix homo (homodimer) and different subunits use hetero
-subunits held together by noncovalent forces (and disulfide bonds)
name the physical forces responsible for different levels of structures
covalent bond, van der waal forces, hydrogen bonds, salt bridge/electrostatic interactions
what is covalent bond and what is it responsible for
-shared electrons, electrons form new obital arpund multiple nuclei
-lots of energy required to break
-responsible for tertiary structures
what is van der waal forces, what are the two types and what is it responsible for
-physical forces responsible for protein structure
-very weak
-includes:
london dispersion forces
-exist in non polar molecules, temporary dipole induced due to electron movement (bc of uneven distribution of electrons), weakest attraction force
dipole dipole interactions
-between polar molecules, permanent dipoles as more electronegative atoms pull the shared electron closer to themself,
what is hydrogen bond and what is it responsible for
-type of dipole dipole, strongest intermolecular attractions but weaker than covalent bond
-greater electronegativity of H bond acceptor=increased bond strength
-responsible for holding DNA together, proteins and macromolecules
what is salt bridge/electrostatic interactions and what is it responsible for
-positive and negative charge attracting
-coulombs law
what is coulombs law equation
what is electronegativity
measure of tendency of atom to attract shared electrons
name measurement methods used to characterise protein structures
primary- edman degradation
secondary- FTIR or circular dichroism
tertiary- xray crystallography
explain the measurement method used to characterise primary protein structure
edman degradation
-phenylisothiocyanate (amino terminal residue) cleaves one amino acid at a time from amino acid chain
-first N terminus amino acid incoporated into phenylthiohydantoin derivative of amino acid residue, first amino acid can be then identified
-can only accurately sequence up to 50 amino acids, so large peptides have to be cleaved into smaller peptides
