Lecture 2

Life’s chemical basis

LIF101

Dr. R. Sankar, LIF 101 - 2015-2016 I

 You already know
Atoms, atomic number

Shell model – how the electrons populate

atoms

Electronegativity

Ionic bond

Covalent bond

Dr. R. Sankar, LIF 101 - 2015-2016 I

 http://sciencenotes.org/printable-periodic-table/

Dmitri Mendeleev (1834-1907)

Periodic Table was created in 1869
Dr. R. Sankar, LIF 101 - 2015-2016 I
 Elements present in humans and their
percentage of total body weight

http://en.wikipedia.org/wiki/Composition_of_the_human_body
Dr. R. Sankar, LIF 101 - 2015-2016 I
http://askabiologist.asu.edu/content/atoms-life Dr. R. Sankar, LIF 101 - 2015-2016 I
 Arsenic Poisoning and Mercury Poisoning

http://users.physics.harvard.edu/~wilson/arsenic/pictures/arsenic_project_pictures2.html
http://microdoshomoeopathi.blogspot.in/2013/05/mercury-poisoning.html
Dr. R. Sankar, LIF 101 - 2015-2016 I
 Hydrogen bond
A weak attraction between a covalently-bonded hydrogen atom
and another atom taking part in a separate polar covalent bond.

D-H…….A

Hydrogen bonds form

and break much more
easily than covalent or
ionic bonds
Dr. R. Sankar, LIF 101 - 2015-2016 I
Water is essential for
life because of its
unique properties

Dr. R. Sankar, LIF 101 - 2015-2016 I

 Water molecule is polar

Extensive hydrogen bonding

between water molecules imparts
unique properties to liquid water

Water is a solvent that dissolves other polar substances (solutes)

Salt, sugar and other compounds that dissolve in water are polar;
form so many hydrogen bonds with water molecules
A salt is a compound that dissolves easily in water and releases
ions other than H+ and OH-
Dr. R. Sankar, LIF 101 - 2015-2016 I
Water dissolves polar substances

Hydrogen bonds form

between water and
polar molecules of
hydrophilic substances

These bonds dissolve

solutes by pulling their
molecules away from
one another and
keeping them apart

Dr. R. Sankar, LIF 101 - 2015-2016 I

Water ‘s interactions with hydrophobic substances

Hydrophobic
substances repel
water

They do not form

hydrogen bonds
with water

The organization of membranes and – of life – depends on the

way water interacts with hydrophobic substances
Dr. R. Sankar, LIF 101 - 2015-2016 I
Cohesion is a life-sustaining property of water
Water molecules resist separating from one another

Hydrogen bonds collectively exert a continuous pull on individual

water molecules

Cohesion makes it possible for columns of

liquid water to rise from the roots to leaves
inside narrow pipeline of vascular tissue
Dr. R. Sankar, LIF 101 - 2015-2016 I
 Water stabilizes temperature
•Temperature is a way to measure of molecular motion

•Because of hydrogen bonding, it takes more heat to raise the

temperature of water compared with other liquids

•Temperature stability is important for homeostasis; most

molecules of life function within a certain temperature range

Sheets of ice near the surface of can insulate the water under them
from subfreezing air temperatures protecting aquatic organisms
Dr. R. Sankar, LIF 101 - 2015-2016 I
 Water and pH
In liquid water, water molecules spontaneously separate into
hydrogen ions (H+) and hydroxyl ions (OH-)

H2O (water) ↔ H+ (hydrogen ions) + OH– (hydroxide ions)

At neutral pH (7), the amounts of H+ and OH– ions are equal

Dr. R. Sankar, LIF 101 - 2015-2016 I

 Ionization of water and pH
Water dissociates into hydronium (H3O+) and hydroxyl
(OH-) ions. For simplicity, let’s refer to the hydronium
ion as a hydrogen ion (H+) and write the equilibrium as

The equilibrium constant Kc of this dissociation is given by

in which the terms in brackets denote molar concentrations.

Because the concentration of water (55.5 M) is changed little
by ionization, above expression can be simplified to give

Since water dissociates equal amounts of these two ions

Dr. R. Sankar, LIF 101 - 2015-2016 I

The pH of a solution is a measure of its concentration of H+.
The pH is defined as

The concentrations of H+ and OH- are reciprocally

related.

If the concentration of H+ is high, then the

concentration of OH- must be low, and vice versa.

For example, if [H+] = 10-2 M, then [OH-] = 10-12 M.

Dr. R. Sankar, LIF 101 - 2015-2016 I

pH scale ranges from 0 (most
acidic) to 14 (most basic)

One unit decrease on the

scale corresponds to a tenfold
increase in H+ ions

Soda (pH 9)
Distilled water (pH 7)
Lemon juice (pH 2)

Dr. R. Sankar, LIF 101 - 2015-2016 I

 ACIDS, BASES and BUFFERS
Most biological processes occur within a narrow range of pH,
typically around pH 7

pH : Measure of concentration of hydrogen ions (H+) in a fluid

Concentration : Amount of a particular solute that is dissolved

in a given volume of fluid

Acids release hydrogen ions in water; bases accept them

Acid : Substance that releases hydrogen ions in water ; lower

pH of fluids and make them acidic

Base :Substance that accepts hydrogen ions in water; raise

the pH of fluids and make them basic or alkaline
Dr. R. Sankar, LIF 101 - 2015-2016 I
Dr. R. Sankar, LIF 101 - 2015-2016 I
 Strong and weak acids
Strong acids give up more H+ ions than weak acids

Hydrochloric acid (HCl) is a strong acid that, when added to water,

easily separates into H+ and Cl–

HCl (hydrochloric acid) ↔H+ (hydrogen ions) + Cl– (chloride ions)

Inside stomach, HCl makes gastric fluid acidic

The acidity activates enzymes that digest proteins in the food

Dr. R. Sankar, LIF 101 - 2015-2016 I

 Buffers
A buffer keeps a solution within a consistent range of pH

Most cell and body fluids are buffered because most molecules
of life work only within a narrow range of pH

buffer : Set of chemicals that stabilize pH of a solution by

alternately donating and accepting ions that contribute to pH

An acid-base conjugate pair of a weak acid and its

corresponding base (such as acetic acid and acetate ion)
has an important property: it resists changes in the pH of
a solution. In other words, it acts as a buffer.

Dr. R. Sankar, LIF 101 - 2015-2016 I

 The Bicarbonate Buffer System
Carbon dioxide gas becomes a weak acid when it dissolves in
the fluid portion of human blood:

H2O + CO2 (carbon dioxide) → H2CO3 (carbonic acid)

Carbonic acid separates into hydrogen ions and bicarbonate

ions, which can recombine to form carbonic acid:

H2CO3 (carbonic acid) ↔ H+ + HCO3- (bicarbonate)

Exchange of ions between carbonic acid and bicarbonate keeps
blood pH between 7.3 and 7.5 – up to a point
Buffer failure can be catastrophic in a biological system
Example: Too much carbonic acid forms in blood when breathing is
impaired suddenly – the resulting decline in blood pH may cause
coma
Dr. R. Sankar, LIF 101 - 2015-2016 I
 Important points:
What are the basic kinds of interactions between atoms?

• Covalent Bond
• Non-covalent Bond
• Hydrogen Bond
• Hydrophobic interactions
• Polar covalent bond
What are properties of
water that make it suitable
for sustaining life?

What is pH? How is it calculated?

What is a buffer?

Why is pH important for living systems?

How is buffering done in living systems?

Dr. R. Sankar, LIF 101 - 2015-2016 I