Part I: Structure & Catalysis
-Edward Buchner in 1897 Germany, discovered yeast extracts can ferment sugar. Life can be
studied & explained outside a cellular context; he showed chemistry & not vital forces are
responsible for life processes giving rise to BIOCHEMISTRY.
Chapter 2 Water
-H2O is 70% of weight of cells. There are attractive forces b/w H2O molecules & b/w H2O &
solutes due to hydrogen bonding which results in the strength & specificity of recognition among
biomolecules (also influenced by H2O’s solvent properties). H2O has the tendency to ionize to
H+ & OH- which influence the structure, self-assembly& properties of all cellular components,
incl pro, NA & lipids. This tendency forms the pH scale & is involved in buffers (controls # of
protons in soln).
2.1 Weak Interactions in Aq systems
-There are many types of non-covalent interactions in H2O such as H bonds, ionic bonds,
hydrophobic bonds & van der waals forces; each are weak on their own but collectively have a
very sig influence on the 3D structures of pro, NA, polysaccharides & membrane lipids.
-H bonds hold H2O molecules together & is what keeps it liquid at room temp; polar molecules
can dissolve easily in H2O since they can easily replace H2O—H2O interactions with more
favourable H2O—solute ones vs. non-polar molecules don’t dissolve in H2O since they tend to
Hydrogen bonding gives water its unusual properties
-H2O has a higher mp, bp & heat of vaporization than most other common solvents (table 2-1)
due to hydrogen bonding b/w H2O molecules & a lot of energy is req to overcome these
-The O nucleus in a H2O molecule is more electronegative, ie. Attracts e-s more strongly than
does a H nucleus (proton) thus the shared e-s are closer to O than H & this unequal sharing leads
to 2 electric dipoles. There is an electrostatic attraction b/w O of one H2O molecule & H of
another in what is called a H bond.
-H bonds are rel weak & only lasts picoseconds (10^-12) in liquid water (Are usually referred to
as “flickering clusters”), req a bond dissociation energy of ~23kJ/mol. Each H2O molec can form
up to 4 H bonds but at liquid state room temp & atm pressure, only 3.4 H bonds; 10% covalent
due to overlaps in bonding orbitals & ~90% electrostatic. At solid state, ie. Ice, each H2O
molecule is fixed in space thus forming 4 H bonds yielding a crystal lattice structure & this is
what accounts for the high mp.
*Why isn’t the earth a ball of ice? H2O’s crystal lattice structure in solid state makes ice less
dense than liquid H2O & ice floats. The way the H2O expands when frozen makes it so.
-At room temp, thermal energy of aq soln (molecular motion) is of the same order as the bond
dissociation energy of hydrogen bonds; when water is heated, inc temp=faster motion of H2O.
-When ice melts (ΔH=+5.9kJ/mol) or water evaporates (ΔH=+44kJ/mol), heat is taken up by the
system. The entropy of the aq system inc as H2O molecules are more disorganized. At room temp
((--ΔG=(+ve)—(++ve)), both processes occur spontaneously due to H2O’s tendency to form H
bonds (outweighs the push for randomness); because ΔH is positive for melting & evaporation,
the inc in entroypy makes ΔG neg & drive theses changes.
Water forms H bonds w/ polar solutes
- C—H bonds don’t are weakly polar b/c they have only tiny diff in e.n. Uncharged but polar
biomolecules, eg. Sugars, dissolve readily in H2O b/c of the stabilizing effect of H bonds b/w
hydroxyl groups & carbonyl oxygen of sugar & polar H2O molecules. Alcohols, aldehydes,
ketones & compounds w/ N-H bonds all form H bonds w/ H2O & tend to be soluble in H2O.
-H bonds are directional & are the strongest when oriented in a straight line, ie. The acceptor
atom is in line w/ the covalent bond b/w the donor atom & H putting partial + charge of the H directly b/w the 2 partial neg. charges. This is to maximize electrostatic interactions. H bonds are
also intra-molecular & inter-molecular
*H donor=has a + charge to enter into the bond vs. H acceptor=has a – charge to enter into the
* Polar molecules dissolve far better even at low temp vs. non polar at high temps.
Water interacts electrostatically w/ charged solutes
-H2O is a polar solvent & readily dissolves in polar compounds which are hydrophilic (H2O-
loving). In contrast, non polar solvents, eg. Benzene & chloroform are poor solvents for polar
biomolecules but readily dissolve in non-polar (hydrophobic—avoids H2O) compounds (Table 2-
2, Table 2-3). Ampiphatic biomolecules have both polar end & non polar end (this end causes a
dec in entropy of ΔG which results in +ΔG, a unfavourable rxn, eg. Phenylalanine (no change,
will still want to get away from H2O)
-H2O is effective at screening the electrostatic interactions b/w dissolved ions b/c it has a high
dielectric constant (reflects the # of dipoles in a solvent): F=Q1Q2 ;
F is the force of ionic interactions, Q is the magnitude of charges, r is the dist b/w
charged groups & E is the dielectric constant of the solvent. Ie. Ionic interactions b/w dissolved
ions are much stronger in less polar environments; these interactions & repulsions only operate at
short distances depending on [electrolyte] when H2O is the solvent.
Entropy inc as crystalline substances dissolve
-formation of soln occurs w/ favourable free energy change, ΔH has a small + value, TΔS has a
large + value thus ΔG is –
Nonpolar gases are poorly soluble in H2O
-The biologically important gases, CO2, O2, & N2 are nonpolar. Movement of molecules from
disordered gas phase into aq soln constrains their motion & motion of H2O thus representing dec
in entropy which is what makes them very poorly soluble in H2O. Carrier pro, eg. Hemoglobin &
myoglobin facilitate transport of O2 & bicarbonate system: CO2 forms H2CO3 in soln &
transported as HCO3- (either free or bound to Hb)
*O2 & CO2 are non polar which is why we need hemoglobin & the bicarbonate system to deal w/
these substances in the body which is mostly composed of H2O.
Nonpolar compounds force energetically unfavourable changes in the structure of H2O
-When H2O is mixed w/ nonpolar substances, eg. Benzene/hexane, 2 phases form both
hydrophobic & insoluble. They’re unable to form favourable interactions w/ H2O& disrupt H
bonding. Breaking of H bonds requires input of energy as well as dissolving hydrophobic
substances in H2O cause dec in entropy.
-H2O molecules near nonpolar solutes are then constrained in their possible orientations as they
form highly ordered cagelike shell around each solute molecule (effect the same in clathrates—
crystalline compounds of nonpolar solutes & H2O in that ordered H2O molec reduce entropy but
these cagelike shells are not as highly oriented)
-# of ordered H2O molec is proportional to the SA of hydrophobic solute enclosed w/in cages of
H2O molecules. ΔH is +, ΔS is - & thus ΔG is +.
-Ampiphatic compounds contain polar regions so when mixed w/ H2O, hydrophilic region
interacts favourably w/ solvent & tends to dissolve & the hydrophobic end still avoids H2O.
Nonpolar ends cluster together to present the smallest hydrophobic area to the aq solvent & polar
ends are arranged to maximize interaction w/ solvent, these stable structures are called micelles.
Hydrophobic interactions hold these nonpolar regions together; its strength is due to the greatest
thermodynamic stability that is achieved by minimizing # of ordered H2O molec. Eg. Pro,
pigments, some vit, sterols & phospholipids of membranes
-H bonding b/w H2O & polar solutes causes ordering of H2O molec but energetic effect is less
sig than w/ nonpolar solutes. Part of the driving force for binding polar substrate to complementary polar surface of an enzyme is the entropy inc as enzyme displaces ordered H2O
molecules from the substrate & as the substrate displaces ordered water from enzyme surface.
*Fig 2.8—H2O molecules are more disordered, S inc & ΔG – ; enzyme-substrate interaction
stabilized by H-bonding, ionic & hydrophobic interactions.
Van der Waals interactions are weak interatomic attractions
-aka London forces, are weak attractions in which 2 dipoles weakly attract one another bring 2
nuclei closer & as they get closer, e- clouds begin to repel each other; at the maximal pt of net
attraction, nuclei are in van der waals radium (measure of how close atom will allow another to
Weak interactions are crucial to macromolecular structure & function
-ionic interactions & H bonds vary in strength, depending on the polarity of solvent & alignment
of H bonded atoms but are still sig weaker than covalent bonds. Covalent bonds, eg. C-C, C-H
takes 350-410 kJ/mol to break vs. non-covalent ones are broken & reformed w/ req
energy=4kJ/mol. 3D structure of macromolecules results from N-C bonds.
-Stability measure by Keq of binding rxn varies exponentially w/ binding energy. Molecular
stability due to 5-20 weak interactions is much greater than expected from a simple summation of
small binding energies (b/c these interactions req simultaneous disruption)
-One consequence of large size of enzymes & receptors relative to their substrates & ligands, is
their high SA to provide many opportunities for weak interactions; at molec level,
complementarity b/w interacting biomolecules reflects complementarity & weak interactions b/w
polar, charged & hydrophobic groups on surfaces of molecules.
-H2O molecules can bind tightly to macromolecules that they’re part of the crystal structure, eg.
Hb 2 alpha & 2 beta subunits. Fig. 2-10: Water in chain cytochrome f (proton-hopping)=H2O is
bound in a proton channel of cytochrome f which is part of e- transport chain in chloroplasts. 5
H2O molecules are H bonded to each other & to func groups of the pro, so the peptide backbone
atoms of valine, proline, arginine & alanine residues & side chains of asparagine & 2 glutamine
residues. The pro has a bound heme, the Fe facilitates e- flow during photosynthesis & is couple
to the movement of pro across the membrane via this chain of bound H2O molec.
Solutes affect colligative (linked together) properties of aq solns
-various solutes alter H2O’s vapor pressure, bp, mp/freezing pt & osmotic pressure, these are
called colligative properties b/c the effect of solutes on all 4 properties has the same basis which
is the [ ] of H2O is lower in solns than in pure H2O. Effect of solute [ ] on colligative properties
of H2O is independent of chemical properties of the solute but dependent on the amt of solute
present in a given amt of H2O.
-H2O tends to move from region of high [ ] region of low [ ] in accordance w/ favor of inc
entropy. Osmotic pressure (II) is produced when 2 solns are separated by a selectively permeable
membrane that only allows passage of H2O molecules & not solutes; measured as the force
necessary to resist water movement, represented as Van’t Hoff equan:
ic=osmolarity; i—Van’t hoff factor (extent which solute dissociates into 2/more ionic
species) & c—molar [ ] of solute
*In dilute NaCl solns, NaCl dissociates completely thus i=2; all non-ionizing solutes, i=1
& for several solns, II is the sum of the contributions [II=RT (i1c1+i2c2…)
-Osmosis the H2O movement across a semi-permeable membrane from area of highlow [ ]
solutes (fig 2-11)
-initial state: tube contains aq soln & beaker is pure H2O; semi-permeable membrane
allows passage of H2O only & H2O flows from beaker into tube to equalize [ ] -final state: water moved into soln diluting it & raising vol column of H2O w/in tube. At
equilibrium, gravity operating on the tube balances tendency of H2O to move into the
tube where its [ ] lower.
-osmotic pressure: measured as the force that must be applied to return soln into the tube
to the level of that in the beaker, i.e force is proportional to height of column in ‘b’
-Cells in various solns:
-Isotonic=ic of soln is same as cytosol, ie.same amt of [solutes] in & out of