Class notes
Biochemistry Module (part 1) - Biochemistry 1st year
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A summary of - The forces holding proteins together, The unusual nature of water, First law of thermodynamics and Carbohydrate metabolism.
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The forces holding proteins together (1)Covalent bonds are strong (several hundred kJ mol-1) and do not get broken during the protein’s lifetime
(except S-S bonds). Non-covalent forces are only a few kJ mol-1 each after one takes into account how
water weakens many of them.
The stability of proteins under physiological conditions is about 20-60 kJ mol -1, much less than the strength
of a single covalent bond: the stability of a protein is a delicate balance between large total energies.
Electrostatic and van der Waals forces and hydrogen bonds are enthalpically driven.
Rarely encounters a naked charge. Dipole moment of water acts to screen charges from each other and
makes significant than one might expect.
1. Electrostatic forces: inter-molecular forces are all charge-charge
interactions, most obviously the forces between permanently
charged ions. In water, charges are solvated by water or ions. Many
protein atoms have partial charges that also attract and repel.
The forces holding proteins together (2)
2. Hydrogen bond: Formed from two electronegative atoms with a hydrogen between them, bonded to
one of the atoms. Highly directional: for an amide NH and CO hydrogen bond, the optimal angles are 180°
(linear) for NH - - - O and between 120° and 180° for C=O - - - H.
3. Van der Waals forces
Interatomic forces due to transient redistribution of electron density
induced by neighboring atoms. Individually small, collectively can be
significant. Strongest forces arise from most polarisable atoms e.g. sulfur
stronger than oxygen.
H bonds are directional. Peptide-peptide and peptide-h2O.
H bonds have similar energy so if peptide groups hydrated hen net energy of
formation of h bond in h20 is small.
The forces holding proteins together (3)
4. Hydrophobic interaction: entropic in origin
A hydrophobic group cannot form H bonds and therefore hydrophobic groups in water reduce the number of H
bonds that neighboring waters can make, putting the waters in an energetically unfavourable state. Water molecules
respond by becoming more ordered around hydrophobic groups which allows them to H bond to each other better.
There is a small change in enthalpy but a substantial loss of entropy, overall energetically unfavourable.
To minimize energy loss, hydrophobic groups cluster and reduce hydrophobic area exposed to water, allowing water
molecules to become more mobile – fewer H bonds per molecule but entropy is increased, with entropy dominant at
normal biological temperatures.
, The unusual nature of water (1) Relatively high melting and
boiling points, expands when it freezes, high surface tension,
high heat capacity, dissolves many ionic materials – all due to
H bonding.
The unusual nature of water (2) H bonding leads towards ice-like structures in which every H atom
forms a H bond and every O atom forms two H bonds (four H bonds per H2O).
(a) Ice is a 3D lattice which is enthalpically favourable but entropically unfavourable, and hence ice is
favoured at low temperatures.
(b) There is some ice-like structure in water but fewer H bonds per H2O on average. H bonds are rapidly
broken and formed. Hydrophobic molecules in water induce ice-like structure around them.
Proteins are highly cooperative, partly because H bond networks are cooperative. (beta-hairpin structure,
with hydrogen bonds between strands) All hydrogen bonds are effected by the presence of each other –
remove one h bond makes the whole network weaker. Add a H bond, makes the whole structure stronger.
How proteins find partners faster
e.g. reduce search to two dimensions (exploit membrane as 2D surface) or one dimension (DNA-binding
proteins), smaller compartments, electrostatics
Short range interactions e.g. sticky arms – need to be hydrophobic but stiff and extended so they don’t coil up
in water. Stiffness helps as it reduces loss of entropy upon binding; this is important because sticky arms usually
cannot form many bonding interactions with the target, so the favorable DH is relatively small.
Poly-Pro sequences make good sticky arms
Pro has a hydrophobic side chain but also has a more electron-rich carbonyl than other amino acids, so is a
good H bond acceptor and is therefore also well hydrated and hydrophilic. Poly-Pro sequences are very
soluble in water, much more so than most poly-amino acids.
Pro has restricted backbone conformational range – small DS upon binding. Poly-Pro tends to form
extended polyproline II helices (120° rotation per amino acid and therefore a 3-residue repeat) in water
with no tendency to coil up and with a large available binding surface.
A sticky arm should not be totally rigid
Ideally, it should have rigid sections with flexible linkers, providing the optimum combination of rigidity
(and hence minimal entropy loss upon binding) and flexibility.
Proline-rich sticky arms are found in signalling proteins
SH3, WW and EVH1 domains recognise proline-rich sequences. Many WW domains, for example, recognise
one or more PPxY motifs in partner proteins.
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