BMS1021 Biochemistry

The Chemical Composition of Cells

Water Proteins Carbohydrates Lipids Nucleic Acids

Dr. Jérôme Le Nours

Group Leader
Jerome.lenours@monash.edu

Comparative Immunology Laboratory

Department of Biochemistry and Molecular Biology
Biomedicine Discovery Institute
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What are we?

• 75% of the earth’s surface is under water

• 0.02% of Earth’s mass 2

 Lecture 2
An introduction to water

Cohesion, high heat

capacity, boiling
point, density
Physical
properties

Intra- and Biological

Structure importance
intermolecular
of water bonding

Chemical
properties
Solvent properties,
ionisation,
relationship to pH
Lecture 1 Learning Objectives
Water is a simple but vital molecule, so it is important you
should be able to
• Describe water structure, geometry, polarity and dynamics
• Describe the role of hydrogen bonding in water with respect
to:
1. Cohesion
2. high heat capacity
3. boiling point/heat of vaporisation
4. relative density of water and ice
5. water as a solvent

• Describe the ionisation of water, pH and its effect on biological

molecules

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 Resources
Textbooks:
• Biology – Campbell
11th edn. (2017) Chapter 3 Pages 44-55 or
10th edn. (2015) Chapter 3 Pages 44-55

• Principles of Biochemistry – Lehninger 7th edn. (2017) Chapter 2

Pages 47-74

Moodle

• Biochemistry – A Metabolic Challenge – “Role of Water in Biology”

(http://mnhs-teaching1b.med.monash.edu.au/Dev/MetabolicChallenge/Water/)

• BMS1011 lectures on Water, pH and Buffers

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 Water is a polar molecule
+ +
O δ H H δ
H2O O
H H
-
Molecular Structural 2δ
formula formula Electron
shell
1cm
10mm
10,000μm
10,000,000nm

So in a 1cm length you ‘could’ fit 40 million

water molecules side-by-side – but water won’t ~106°
behave this way – we will find out why later!
~0.28nm
Ball and Space Electron
stick fill density
Intramolecular
forces
6
 Water is a polar molecule

H2O

Water is also diamagnetic https://terpconnect.umd.edu/~wbreslyn/magnets/do-magnets-work-under-water.html) 7

Water forms hydrogen bonds
• Hydrogen bonds represent relatively strong
attractive forces between water molecules
Hydrogen bond
o ~1/20th the strength of a covalent bond (0.177nm/1.77Å)
Polar covalent bonds
Bond type Strength (kJ/mol) (0.0965nm/0.965Å)
Covalent (O-H) ≈459
Hydrogen 12-30

o Forms up to four hydrogen bonds with

individual water molecules

This is why water does not ‘want’ be

INTERMOLECULAR FORCES arranged side-by-side without any spaces.

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Noncovalent interactions in biomolecules
Bond type Strength (kJ/mol)
Covalent >210
Ionic 4-80
Hydrogen 12-30
van der Waals 0.3-9
Hydrophobic 3-12

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 Some biologically important hydrogen bonds

H-bonds can occur not only between H and O in

water, but also between other atoms which form
dipoles e.g. between H and electronegative
atoms such as O and N in proteins and DNA
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 The structure of water remains a ‘mystery’
• 1950 - The ‘flickering cluster’ model of water
suggests that 85% of water molecules exist
in short lived (~10-12 s) hydrogen-bonded
clusters

• 1980…. Computer simulations yield many 2015 - Massimo Delle Piane, PBE-D2/TZV-P model
other models to help explain and simulate Slowed down 10 billion times
the properties of water. (20 seconds = 2.5 pico seconds)
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The properties of water
The hydrogen bonds that form between water molecules account
for many of the unique biologically important properties of water.

1. Cohesion
2. high heat capacity
3. boiling point/heat of vaporisation
4. relative density of water and ice
5. water as a solvent

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Cohesion
Water molecules remain close to one another as a result of
hydrogen bonds

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Water droplets on glass Walking on water

Decreasing capillary diameter

Capillary action in glass tubes

The properties of water
The hydrogen bonds between water molecules account for some
of the essential and unique properties of water.

1. Cohesion
2. high heat capacity
3. boiling point/heat of vapourisation
4. relative density of water and ice
5. water as a solvent

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 Water has a relatively high specific heat
capacity
• The relatively high heat capacity
(specific heat) of water is a result
of hydrogen bonding.

• A calorie is defined as the amount

of energy that causes 1g of water
to change its temperature by 1°C.

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 Water has a high specific heat capacity
• Large bodies of water act as energy sinks Substance Specific heat (J/g)
Water 4.2
• Oceans moderate climate by absorbing
Chloroform 1.0
heat during the day / releasing it at night
Ethanol 2.5
• Living cells are mostly water. Helps Iron 0.4
maintain a constant temperature Glass 0.8

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The properties of water

The hydrogen bonds that form between water molecules account

for some of the essential and unique properties of water.

1. Cohesion
2. high heat capacity
3. boiling point/heat of vaporisation (latent heat)
4. relative density of water and ice
5. water as a solvent

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 Heat of vaporisation (latent heat)

It takes a lot of energy to break the hydrogen bonds and allow water molecules to escape
from the surface of the liquid
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The properties of water

1. Cohesion
2. High heat capacity
3. Boiling point/heat of vaporisation
4. Relative density of water and ice
5. Water as a solvent

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 Stable H-bonds The low density of ice
The density of water
1.00 changes with temperature
.99
.98
Density (g/mL)

.97
.96 Transient H-bonds
.95
.94
.93
.92
.91
.90
-20 0 20 40 60 80 100
Temperature (°C)
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 The low density of ice

• The lattice of molecules in ice forces water molecules further apart than for liquid water.

• Ice forms at the SURFACE of ponds and lakes

• Surface ice acts as an insulator from low air temperature. Lakes and oceans do not freeze.
• Life can continue beneath (Oceans not < 2oC)
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Molecular simulation showing water freezing
as temperature is lowered

12 second = 7 nano seconds 22

The properties of water

1. Cohesion
2. High heat capacity
3. Boiling point/heat of vaporisation
4. Relative density of water and ice
5. Water as a solvent

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Water as a solvent
• Water is the principal SOLVENT in cells

• Water is the medium through which all solute molecules are transported

• Water forms about 70% of the human body mass, and is divided into two
main compartments.

o Intracellular water (47%)

o Extracellular water (23%)
• Blood plasma 6%
• Interstitial fluid 17%

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 Water as a solvent
• Water is polar and can form hydrogen
bonds and dipole-dipole interactions
with other molecules

• Any molecule which can form a

hydrogen bond (as a hydrogen donor or
acceptor) can form hydrogen bonds
with water.

• Such molecules are hydrophilic or

‘water loving’

• Water dissolves polar molecules

• Excellent solvent for ionic molecules NaCl dissolving in water

such as salts 25
Water as a solvent Solid NaCl
Ionic lattice

Water dissolves by interacting with ions to

from hydration shells

Sea water contains many different types of

salt

δ+
δ-

δ+

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 Water as a solvent
• Proteins,
carbohydrates,
nucleic acids and
other are charged or
polar in nature

• Water will dissolve

macromolecules,
providing they have
polar regions on
their surface.

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Non-polar molecules are hydrophobic
Alkanes and related molecules are termed
hydrophobic (‘water hating’).

They do not readily dissolve in water.

The C-H bond is only very weakly polar due to

the similarity in electro-negativity of C and H
Oil
No dipole interactions occur between the
molecule and the water.
Water

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 Amphipathic molecules
• The fatty acid stearic acid is an example of a hydrophobic alkane-based
molecule.
CH3 – (CH2)16 – CO2H

• When the carboxylic acid dissociates it forms a stearate ion with a polar
grouping at one end - a charged carboxylate ion.

CH3 – (CH2)16 – CO2-

• Such a molecule with both hydrophobic and hydrophilic regions is termed
amphipathic
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Amphipathic
molecules

• Tend to cluster in water

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The ionisation of water
• Although H2O is essentially a neutral molecule, it can dissociate or ionise to release a
proton
H2O H+ + OH–

• In water a ‘free’ proton has a fleeting existence

• It combines with a water to form a hydronium ion.

H2O + H+ H3O+

• Water acts both as a proton donor and a proton acceptor.

• In pure water H+ (i.e. H3O+ ) and OH– are present in equal concentrations (1x10–7 M at
25°C)
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 The pH of water
• Consider the equilibrium:
H2O H+ + OH–

• The dissociation constant = [H+] [ OH–] = 1.8 x 10-16 at 25°C

[H2O]

• Since [H2O] = 55.6 moles/L

[H+] [ OH–] = 1 x 10-14 M

• The concentration of H+ and OH- in pure water are the same

•
So, [H+] = [OH–] = 1x 10-7M

• A short hand for [H+] is pH. Defined as – log10[H+].

•
The pH of pure water is – log10[10-7] = 7
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The pH scale
If an acidic or basic solute is
added to water that changes [H+] -
the pH will change

[H+] pH [OH-]

10-1 1 10-13

10-2 2 10-12

10-3 3 10-11

10-4 4 10-10

etc.

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Effect of pH on dissolved molecules
• Many biological molecules contain more than one dissociable proton.

• Amino acids contain at least two

• The charge on such molecules is dependent on pH in a complex manner

• The amino acid alanine has one amino group and one carboxylic acid group.

H H O

N C C

H CH O
H
Alanine
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 Charge = +1
Ionisation states of Alanine Charge = -1

H H O H H O
H H O
H N+ C C A B H N+ C C D N C C

H CH O H CH O-
H CH O-
H

Charge = 0

Isolectric point (pI) is the pH at

pKa value is also the pH where each form is present at 50% which the molecule has NO net 35
charge
 pH affect structure and activity of
enzymes
• Enzymes often have optimal pH for
activity
Enzyme 1
• Activity is determined by the ionization
Enzyme 2
state of charged groups of the different

Enzyme activity (%)

constituent amino acids
• Protein structure (general). Protein
structure is dependent on charges
• Active site (specific).
Enzyme 3
• Small changes in pH affect metabolism
greatly and can be life threatening
(remember pH is a log10 relationship…)
• Maintenance of pH inside cells achieved
by buffering systems

H bonds stabilising protein structure

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 Buffers in biological systems
Buffers are a mixture of a weak acid and it’s conjugate base that show
maximum buffering capacity when both species are present in equal
amounts. They resist change in pH caused by addition of H+ or OH-, due to
a balancing act between the two processes

HA ↔ H+ + A-
Adding H+ pushes this equation to left ‘soaking up added H+

H2O ↔ H+ + OH-

Adding OH- pushes this equation to left causing more HA to

dissociate to H+ + A-

Both scenarios help to reduce (ie buffer) any change in pH

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 Buffers in biological systems
• Phosphate (intracellular) and
Bicarbonate (extracellular) buffer
systems maintain optimal physiological
pH
• Internal pH of cells is close to 7
• Human blood pH is close to 7.4 (7-7.8)
• Level of Carbonic Acid (H2CO3) regulated
by respiratory rate

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Maintaining blood pH
Human blood is maintained at pH 7.4 (7-7.8)

This is vital for oxygen carrying capacity.

Oxygen binding of haemoglobin is pH dependent.

Disease states such as Acidosis arise from:

• Metabolic cause: release of acidic metabolites due to starvation, uncontrolled diabetes,

over-exertion by runners leading to lactic acidosis

• Respiratory cause: hypoventilation due to lung diseases such as emphysema, asthma,

pneumonia
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 Summary
• Water is a polar molecule that is able to form hydrogen bonds and to ionise.

• These features give rise to the strong cohesion of water that is manifest both at a macroscopic and a
cellular level.
• Presence of hydrogen bonds can explain water’s high specific heat and heat of vapourisation, as well as

the low density of ice.

• Non-polar molecules are subject to the “hydrophobic effect” and polar molecules and ions can be

dissolved in water.
• Ionisation of water and changes in pH of a solution result in changes to charges on dissolved biological
molecules.
• Buffering systems maintain pH of cells and tissues at optimal levels for metabolic functioning.

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