BIOSCI 106

The chemical basis of life

Associate Professor Christopher Squire

c.squire@auckland.ac.nz

An image from the video “Powering the Cell: Mitochondria.” Credit Robert A. Lue
 LECTURE 3

“Well buffer me!”

(chemistry in an aqueous environment)
Homework
Explain this hair…

…and why I’m having

a bad hair day
 Learning Objectives
• Identify the properties of water that make it unique
• Compare and contrast how ionic compounds, polar molecules, and
hydrophobic molecules interact with water in an aqueous environment.
• Correlate the dual properties of amphipathic molecules with biological
compartmentalisation
• Classify functional groups as ionisable, their acid/base chemistry, describe
whether they are “weak” or “strong”, and correlate their acid/base chemistry
with the concept of pKa
• Apply the concept of chemical equilibrium to describe acid/base systems and
how they respond to perturbation by the addition of acid or base
• Evaluate whether an ionisable group is protonated or deprotonated at a
specific environmental pH
• Recall the pH range of human blood and describe the mechanisms that
maintain this pH
• Describe the interplay between chemical, respiratory, and renal systems in
maintain blood pH when the system is perturbed
• Apply any concepts learned to evaluate novel systems not described
in lectures
 pH and the body
saliva pH 6.0-7.4

blood cells in
lungs pH ~7.4

blood cells in
active tissues pH ~7.2

urine pH 4.5-8.0
 Blood pH and imbalance
• Blood pH maintained between 7.35 and
7.45
• Why do we need to maintain this balance?

• Three mechanisms to maintain pH

buffer
renal system respiratory system acid/base equilibrium
 Something to ponder
• If I were to run up and down the aisle a
couple of times, what would happen?
All about equilibrium
Laboratory 1 – next week
 Water, water everywhere
Water:
• Was the medium for our primordial
beginnings on earth and still covers
the planet
• Makes up ~90% of our body mass
• Mediates all of our biological
processes

What properties of water make it the universal

solvent and so important in biology?
 Unique water
Small molecule
Polar
Four hydrogen bonds
Compound Boiling Point (°C) Heat of Vapourisation
(kJ/mol)
CH4 -164 8.2
NH3 -33 23.3
H2O +100 40.7
H2S -61 18.7
 Ice vs water

Consider the differences in structure between

ice and liquid water – we’ll come back to this at
the end of the lecture for your homework.
 Water as solvent
Ionic compounds in aqueous solution
 Water as solvent
Hydrophilic molecules in aqueous solution
 Water as solvent
Hydrophobic molecules in aqueous solution

Ice:
 Water as solvent
Amphipathic molecules in aqueous solution
Compartmentalisation in
biology
Homework
Explain this hair…

…and why I’m having

a bad hair day
 -keratin (hair, wool etc.)

• a long -helix with a globular head

http://www.nanowerk.com/nanotech
nology-news/newsid=40919.php
 -keratin (hair, wool etc.)

• Higher assembly
to give wool
fibres or hair

Filaments held together by

hydrogen bonds, vdW,
charge-charge
interactions, disulfide
bonds
Bad hair day!
• When you wet hair, water
breaks hydrogen bonds
and other weak bonds and
the alpha-keratin filaments
can slide back and forth
and set in place when dry.

Filaments held together by

hydrogen bonds, vdW, charge-
charge interactions, disulfide bonds

Why my hair so bad?

What makes this lady’s hair so
AWESOME?
• It turns out that disulfide
bonds (between cysteines)
make hair strong and the more
you have the curlier your hair
• Average person 14% cysteine
• Burnt hair smells sulphurous –
and why perms work:
And this dudes hair so 80s hideous?

• It turns out that disulfide

PERM bonds (between cysteines)

make hair strong and the more
you have the curlier your hair
• Average person 14% cysteine

ABUSE • Burnt hair smells sulphurous –

and why perms work:
 Acid-base equilibria
• Many biomolecules contain functional
groups that when dissolved in water are
ionisable:

carboxylic acid carboxylate

ACID CONJUGATE
BASE
More weak acids/bases
(which one below is actually a strong acid?)

carboxylic acid

amine

hydrochloric acid

DNA phosphate
 HCl is a strong acid

hydrochloric acid – a strong acid, fully dissociates and so we

don’t show an equilibrium arrow.
 pKa
Describes the propensity of a weak acid to lose a proton at a
given pH (or conversely to hang on to a proton)

carboxylic acid ~4

amine ~10

DNA phosphate ~2
 Predicting protonation at
given pH

aspartic or Ka
glutamic acid pKa = 4.1

At pH < pKa: At pH = pKa side chain: At pH > pKa:

acid form (protonated) 50:50 mixture base form (de-protonated)

Below pH 4.1 Above pH 4.1

 Buffering
• An acid-base conjugate pair that resists
changes in pH in a solution

add strong acid add strong base

H+ H+ OH- OH-
OH- OH -
-
H+ H+ H+
OH

protons combined with strong base (OH-) take proton

conjugate base to produce from weak acid to produce
more weak acid weak conjugate base and water
 Something to ponder
• If I were to run up and down the aisle a
couple of times, what would happen?
Blood buffers to maintain
blood pH
• Bicarbonate buffer
• Phosphate buffer
• Protein buffer

carbonic acid bicarbonate hydrogen ion

a weak acid its conjugate base

actually hydronium ion
Bicarbonate in the blood

carbonic
anhydrase
Interplay between buffer, respiratory,
and renal systems

removal addition of
of H+ of H+

CO2 + H2O H2CO3 H+ + HCO3-

decrease increase
respiratory respiratory
rate rate

Renal
other regulation
buffer
systems

Respiratory
regulation
Interplay between buffer, respiratory,
and renal systems
 Homework
• Do the Post Lecture Quiz

• Consider why the density of ice

saves us from a “frozen planet”
scenario