Water

Water: Life is a water-based phenomenon.

see Biology, 5th edition, by Campbell, Reece and Mitchell, Chapters 2 and 3

97% by weight of most organism accounted for by 6 elements.
These elements are?

O, C, H, N, P, S.

The high % by weight of O in most organisms is accounted for by which component?

Water is the major component of most cells.

C is much more abundant in cells than the environment. Life often called a C-based phenomenon.
But why is it equally correct to call it a water-based phenomenon?

life probably started in water
all living cells depend on water as a solvent
in most cells water is the most abundant molecule (but not seeds or cysts)
the properties of water dictate the shape of some molecules
some molecules hate water and associate with each other
most biochemical reactions occur in aqueous environment -- enzymes

What are the unique properties of water compared to similar alcohols or hydroxides?

high melting point
high heat of fusion
high boiling point
high heat of vaporization
solid water less dense than liquid water

What gives water its unique properties?

Water is Polar
Water forms H-bonds

What is the molecular structure of water?

angle between the two O-H is 104.5 degrees, slightly less than that found for a regular tetrahedron (109 degrees)
two molecular orbitals form the two O-H bonds
two molecular orbitals with unshared pairs of electrons.
these 4 orbitals directed towards the corners of a tetrahedron
O more electronegative (electron attracting) than H
uneven distribution of charge
the bonds have polarity, the molecule has polarity
water is a permanent dipole

What are other examples of permanent dipoles?

ammonia, net dipole momment
CO2, no net dipole, O=C=O, the two dipoles along the >C=O cancel each other out
water, CO2 and ammonia are uncharged but polar

What is a H-bond?

attraction between H and O in different molecules, d+H......d-O, produces H-bond
water is both a H-bond donor and a H-bond acceptor
water can form a maximum of 4 H-bonds
two as H-bond donar, two as H-bond acceptor
water not the only molecule forming H-bonds.
occur between any electronegative atom and H covalently attached to another electronegative atom

In biological systems O and N are the principle electronegative atoms involved as H-bond donar/acceptors
The energy of a H-bond is approx1/20 that of covalent bond with a range of 10-30 kJoules/mole
examples:

between water molecules, HOH.....OH2
between water and ammonia, HOH.....NH3
between water and a carbonyl group in proteins, HOH.....O=C<
between water and an amine group in proteins, HOH.....NH2-
between a carbonyl and an amine in proteins, >C=O....NH2-

F is a small atom and very electronegative.
It is often used in drugs where these properties may be exploited.
For example, Fluorouracil is an analog of uracil.
The DNA base thymine is made from uracil by the enzyme thymidylate synthase.
Fluorouracil binds to the enzyme and inhibits it, stopping the synthesis of thymine and inhibiting DNA synthesis.
The growth of rapidly growing cells is prevented.

Why does your hair fall out when you undergo chemotherapy?

The strategy for chemotherapy is to kill the rapidly growing cancer cells before you kill the host. Rapidly growing cells of the host, hair follicles, blood progenitor (stem) cells, are killed as well. You become bald and anemic.

What are the properties of water?

Unlike other simple alcohols or hydroxides, energy has to be put in to break the H-bonds.
Therefore water has a high melting point and high boiling point as a function of its H-bonds.

Heat of fusion is high, heat of vaporisation is high, specific heat is high (raise 1gm 1¡C).
Comparativeley speaking, a lot of heat energy has to be put in to water to raise the temperature and break the H-bonds.
Therefore another consequence of life in an aqueous environment is that the effects of temperature fluctuations are minimized.

Heat of vaporisation: the water used in perspiration, evaporation absorbs a lot of heat cooling your body

Density of most substances increases on freezing (solidifying) but water gets less dense.
Why is solid water less dense than liquid water?
What are the consequences?

This is because water molecules form rigid H-bonds in ice. It has a more open structure than liquid water in which the water molecules move and can pack more closely than the H-bond distance at times, thereby increasing the density.
As a result, ice floats on top of water and the bulk water stays liquid. If water froze from the bottom up most of it, except for the surface, would be solid.

Why is water a good solvent for polar and charged molecules?
Why do polar and charged compounds dissolve in water?

The polar nature of water means that it is a good solvent for polar and charged molecules.
Hydrophilic = water loving
The water dipole forms solvation or hydration shells around charged molecules such as NaCl and around polar molecules such containing -OH (glucose, sucrose) or -NH2 (amino acids).

Why is water a poor solvent for non-polar compounds?

Hydrophobic = water fearing componds that cannot interact with the water dipole or H-bond.

How do Amphipathic compounds interact with water?

amphipathic = both polar or charged and non-polar
Hydrophobic effect

Soaps (sodium palmitate), cooking oils (mixtures of fatty acids), olive oil (rich in oleic acid, which has one C=C, a monounsaturated fatty acid) are amphipathic lipids that cluster together to form micelles, or monolayers, or bilayers (analogs for membranes) in aqueous solution.
This is because the polar/charged moieties or functional groups interact with water and the non-polar moieties interact with each other to exclude water molecules.
This process is driven by the entropy of the solvent.

So, what are the non-covalent bonds important in biochemical systems?

charge interactions
H-bonds
dipole interactions
van der Waals interactions (weakest), the weak attraction all molecules have for each other

Ionization of Water: pH scale

Water has a very slight tendency to ionize
H20 + H2O <--> H3O+ + OH-
H30+ is a hydrated proton. It too may become hydrated = H5O2+, etc
Therefore we simplify the ionization to H20 <--> H+ + OH-

for which we can write an equilibrium constant
Keq = ([H+][OH])/[H2O]
note: square parentheses refer to concentration, moles/liter

Because water has a very slight tendency to ionize,
[H2O] in water is approx constant = 55.5M {(1000g/liter)/(18 g.mol)}

Therefore:
Keq.[H2O] = [H+][OH] = 1x10E-14M^2, which is the ionic product of water, or Kw

At neutrality:
[H+] = [OH-] = 1x10E-7

pH is a log scale, in which pH = -log[H+]
log 1x10E-7 = -7, and the negative log, -log 1x10E-7 = 7

The pH of some common solutions and liquid mixtures:

1M HCl = pH0
gastric juice = pH2
fruit juices = pH4-5
milk = pH6.5
blood pH7.2 - 7.4
pancreatic juice = pH 8.5
1M ammonia = pH 11.5
1M NaOH = pH14

Buffers

Strong acids such as HCl completely dissociate.
Weak acids, like those important in biochemistry, only partially dissociate.

Therefore just as in the case of water we can write an Acid Dissociation Constant, Ka, for a weak acid such as acetate (vinegar)
CH3COOH <--> CH3COO- + H+
Ka = ([CH3COO-][H+])/[CH3COOH]

Then equating the [H+] to the acid dissociation constant, Ka, we have
Ka = [H+] x ([CH3COO-]/[CH3COOH])

And if we put it on a log scale to equate pH and pKa, where pKa = -logKa, we have
pH = pKa + log {[CH3COO-]/[CH3COOH]}

Titration curves for weak acids have a plateau where there is a resistance to a change in pH.
This is the buffer region where the weak acid in solution resists or buffers against a change in pH.
If you examine the titration curve you will see that this occurs at the midpoint of the curve, where Ka = [H+], or pH = pKa, because [CH3COO-] = [CH3COOH]

Buffers resist a change in pH

The physiologically important buffers are:

phosphate, inside cells and to some extent in blood plasma
bicarbonate/CO2, the most important buffer in blood plasma
and proteins, especially hemoglobin.

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Bich 107 lecture notes on Water last updated 09/13/06

Comments to Martyn Gunn