topic 1 - biochemistry Flashcards
equation for gibbs free energy
delta G = delta H - T delta S
orrrr
delta G = delta G naught + R x T x log ( [C][D]/[A][B])
how are biochemistry standard conditions different from normal ones
they occur in buffered aqueous solutions at pH 7, not 1 M
how can we make an ‘unfavourable’ reaction go
by adding reactants than they are consumed, removing products faster than they are produces, or be pairing an unfavourable reaction with a favourable one
what type of amino acid are proteins made of
L-amino acids
how do we name amino acid isomsers
if, looking down the H-C carbon bond, the substituents read ‘CORN’ in a clockwise direction, it is an L-amino acid, while anticlockwise in a D-aminoacid
what is the pKa
the pH at which a molecule will be in a 50-50 split between its protonated and deprotonated forms
what type of structure does histidine contain
imidazole ring
what group does arginine contain
guanodino (when deprotonated
what is phenolate
a deprotonated phenol ring
what type of amino acids have the ability to fluoresce visible light and absorb UV light
aromatic amino acids (there are 3)
what is an aliphatic amino acid
one that has a completely non-polar side chain
are peptide bonds planar? why?
yes,. Because the lone pair of electrons on the nitrogen can push onto the carbon, forming a double bond, and pushing the double bond between carbon and oxygen onto the oxygen molecule, giving it a partial negative charge.
what are omega, phi, psi and chi 1/2/3/ angles
omega is looking down the C-N bond (so the angle between c alphas, which will be 0 for cis isomers and 180 for trans), phi is looking down the N-C alpha and psi is looking down the C alpha-C. Chi 1 is the angle of rotation around the C alpha-C beta bond, Chi 2 is the angle of rotation around the C beta- C gamma bond et cetera
what amino acids are typically found in the folds/turns of a protein? Why?
glycine and proline. Because glycine has no side chain and is therefore more flexible because it has less hinderance than other amino acids, and because prolines side chain is fixed to the backbone, allowing for different geometries compared to other amino acids, including turns
can a protein be partially unfolded?
No. Once part of the protein begins denaturing, the rest will follow
do disulfide bonds direct protein folding
No, protein folding directs disulfide formation - shown by anfisens experiments with urea
what is the role of a chaperone
the binds to the exposed hydrophobic regions of an unfolded protein, preventing them form interacting with other molecules and therefore allowing them to fold correctly
what does a ramachandran plot show
the phi and psi angles of every residue in a protein
how many amino acid residues make a full rotation in an alpha helix
3.6
are alpha helicies left or right handed and why
right handed, as it allows the side chains of the residues to point out from the structure, rather than i
what are macrodipoles
because of the way that dipoles line up in an alpha helix, with all amino acids facing the same direction, the amino terminus with be positive and the carboxy terminus will be negative
how many residues in an alpha helix to complete nearly 2 full rotations
7 (basis of the ‘heptad repeat’)
2 strong helix formers and 2 strong helix breakers
alanine and luecine are strong formers as they are less likely to interfere with hydrogen bonds of the backbone and proline and glycine are strong breakers, as proline can’t form backbone hydrogen bonds and glycine’s side chain is too small to contribute to the stability of the helix
what causes a reverse turn in beta sheets
it occurs using just 4 amino acids, and a hydrogen bond between residues 1 and 4 of this. Proline is often seen as residue 2 and glycine is often seen as residue 3
