Chapter 2

Life’s Chemical Basis

BIO 121
Instructor: Dr. Marisa Khoo
 Chapter Overview

2. Why 3. From 4. Hydrogen

1. Building 5. Acids and
Electrons atoms to bonding and
blocks of Bases
Matter molecule water
Matter
BUILDING BLOCKS OF
MATTER
What Are the Basic Building Blocks
of All Matter?
• Living organisms are composed of matter, which
is anything that occupies space and has mass
(weight).
• Matter is composed of chemical elements
– Element—a substance that cannot be broken down to
other substances
– There are 92 elements in nature—only a few exist in a
pure state
• The behaviour of elements, which made up all
living things, starts with the structure of
individual atoms
Elements of the human body as percentage of body weight.

•Make up of about 99% of the

body.
Oxygen (O): 65% •The first four (O, C, H, N) are main
ingredients of the biological
molecule proteins, carbohydrates
and lipids.
•Calcium and phosphorus are the
Carbon (C): 18.5% major components of bone bones
Hydrogen (H): 9.5% and teeth.
Nitrogen (N): 3.3%
•The remaining 1 % are involved in
Calcium (Ca): 1.5%
functions such as nerve signalling
Phosphorus (P): 1.0%
and chemical reactions.
Potassium (K): 0.4%
Sulfur (S): 0.3%
•Trace elements- although required
Sodium (Na): 0.2%
Chlorine (Cl): 0.2% in very small quantities, but even
Magnesium (Mg): 0.1% those small requirements are
Trace elements: < 0.01% difficult to fulfil.
What Are the Basic Building Blocks
of All Matter?
• Atoms consist of subatomic particles:
– Positively charged protons (p+) and uncharged
neutrons are found in an atom’s nucleus (core)
– Negatively charged electrons (e–) move around
the nucleus
• Charge: electrical property; opposite charges attract,
and like charges repel
 − −
Nucleus −

+ +

+ +

−
Electron
cloud

2 + Protons
Nucleus
2 Neutrons
2 − Electrons

Figure: Two models of a helium atom

What Are the Basic Building Blocks
of All Matter?
• An atom’s mass number is the sum of the
number of protons and neutrons in the nucleus
• A typical atom has about the same number of
electrons and protons
• Atomic number: number of protons in the atomic
nucleus
• Element: pure substance that consists only of
atoms with the same number of protons
• Periodic table: tabular arrangement of all known
elements by their atomic number
What Are the Basic Building Blocks
of All Matter?
atomic number
element symbol

mass number
elemental substance

element name
carbon
 Isotopes and radioisotopes
• Although all atoms of an element have the same
number of protons, they can differ in the number
of other subatomic particles
• Isotopes: forms of an element that differ in the
number of neutrons their atoms carry
• Mass number: total number of protons and
neutrons in the atomic nucleus
 Isotopes and radioisotopes
• Radioisotope: isotope with an unstable
nucleus
• Radioactive decay: process by which atoms of
a radioisotope emit energy and/or subatomic
particles when their nucleus spontaneously
breaks up
 Isotopes and radioisotopes
• Living cells cannot distinguish between
isotopes of the same element
• Therefore, when radioactive compounds are used
in metabolic processes, they act as tracers
• Tracer: any substance with a detectable
component
• Radioactivity can be detected by instruments
• With instruments, the fate of radioactive
tracers can be monitored in living organisms
WHY ELECTRONS
MATTER
 Why do atoms interact?
• Electrons occupy different orbitals: volumes of
space around an atom’s nucleus
• Orbitals are filled from lower to higher energy
• The farther an electron is from the nucleus, the
greater its energy
• An electron can move to a higher energy orbital if
an input gives it a boost
– Electron then immediately emits the extra energy and
moves back down to the lower energy orbital
• A shell model helps us visualize how electrons
populate atoms
 Why do atoms interact?

1 one proton 2
one electron A The first shell
first shell hydrogen (H) helium (He)

6 8 10
B The second shell
carbon (C) oxygen (O) neon (Ne)

11 17 18 C The third shell

third shell sodium (Na) chlorine (Cl) argon (Ar)

 About vacancies
• No vacancies: an atom’s outermost shell is
filled with electrons
– Most stable state
• Vacancy: an atom’s outermost shell has room
for another electron
– Chemically active; atoms interact with one
another
– Example: sodium atom has one electron in its
outer (third) shell, which can hold eight
 About vacancies

11 17 18 C The third shell

sodium (Na) chlorine (Cl) argon (Ar)

The third shell corresponds to the third energy level, and it can hold up to 8
electrons. A sodium atom has 11 electrons, so its first two shells are full; the third
shell has one electron. Thus, sodium has seven vacancies. Chlorine has 17 electrons
and one vacancy. Argon has 18 electrons and no vacancies.
 About vacancies
• Solitary atoms that have unpaired electrons
are called free radicals
– Typically very unstable
• Atoms with an unequal number of protons
and electrons are called ions
– Carry a net (overall) charge
 About vacancies
electron loss electron gain

Sodium atom Sodium ion Chlorine atom Chlorine ion

11p+ 11p+ 17p+ 17p+
11e- 10e- 17e- 18e-
charge: 0 charge: +1 charge: 0 charge: –1
Formation of ion: A sodium atom (Na) becomes a positively charged sodium ion
(Na+) when it loses the single electron in its third shell. The atom’s full second
shell is now its outermost, so it has no vacancies.
A chlorine atom (Cl) becomes a negatively charged chloride ion (Cl–) when it gains
an electron and fills the vacancy in its third, outermost shell.
FROM ATOMS TO
MOLECULE
 How do ions interact in chemical
bond?
• An atom can get rid of vacancies by
participating in a chemical bond with another
atom
• All atoms trying to achieve a stable octet
– Chemical bond: attractive force that arises
between two atoms when their electrons interact
– Compound: molecule that has atoms of more
than one element
 How do ions interact in chemical
bond?

one oxygen atom

two hydrogen atoms

The water molecule. Each water molecule has two hydrogen

atoms bonded to the same oxygen atom.
 Ionic bonds
• An ion is an atom or molecule with an
electrical charge resulting from gain or loss of
electrons
• When an electron is lost, a positive charge results;
when one is gained, a negative charge results
• Two ions with opposite charges attract each
other
• When the attraction holds the ions together, it is
called an ionic bond
 Transfer of –
electron +

Na Cl Na+ Cl–
Sodium atom Chlorine atom Sodium ion Chloride ion
Sodium chloride (NaCl)

Figure: Formation of an ionic bond, producing sodium chloride.

 Ionic bonds

Na+ Cl–

Each crystal of table salt consists of many sodium and chloride ions locked
together in a cubic lattice by ionic bonds.
 Ionic bonds
• Ions retain their respective charges when
participating in an ionic bond
– Polarity: separation of charge into positive and
negative regions
– A NaCl molecule is polar because the chloride ion
keeps a very strong hold on its extra electron
– Electronegativity: measure of the ability of an
atom to pull electrons away from other atoms
 Ionic bonds

positive charge negative charge

Ions taking part in an ionic bond retain their charge, so the molecule itself is polar.
One side is positively charged (represented by a blue overlay); the other side is
negatively charged (red overlay).
 Covalent bonds
• A covalent bond results when atoms share outer-
shell electrons
• A molecule is formed when atoms are held together
by covalent bonds.
• Two electrons are shared in each covalent bond.
• When sharing is equal, the bond is nonpolar
• In a covalent bond between two atoms of the same
element, the electrons are shared equally because two
atoms have the same electronegativity.
• When one atom exerts a greater pull on the electrons,
the bond is polar.
 Covalent bonds
• In H2O the oxygen
atom has a slight (–) (–)
negative charge
and the hydrogens
O
have a slight
positive charge
• Molecules with this H
H
unequal (+)
(+)
distribution of
charges are called
polar molecules.
Figure: A water molecule.
 Covalent bonds
1 1 MOLECULAR HYDROGEN Two hydrogen atoms,
each with one proton, share two electrons in a
MOLECULAR HYDROGEN (H—H) nonpolar covalent bond.

8 8 MOLECULAR OXYGEN Two oxygen atoms, each

with eight protons, share four electrons in a
double covalent bond.
MOLECULAR OXYGEN (O=O)

WATER Two hydrogen atoms share electrons with

1 8 1 an oxygen atom in two covalent bonds. The
bonds are polar because the oxygen exerts a
greater pull on the shared electrons than the
WATER (H—O—H) hydrogens do.
 Covalent bonds

• Structural formulas: lines between atoms

represent the number of covalent bonds
– Example: H-H
• H2 has one covalent bond between the atoms
– Example: O=O
• A double bond links the two oxygen atoms
– Example: N=N
• A triple covalent bond links the two nitrogen atoms
Covalent bonds
HYDROGEN BONDING
AND WATER
What are the life sustaining properties
of water?
• Hydrogen bonding in water
– Water has unique properties that arise from the two
polar covalent bonds in each water molecule
– In water, the oxygen atom carries a slight negative
charge; the hydrogen atoms carry a slight positive
charge
– The polarity of individual water molecules attracts
them to one another
– This type of interaction is called a hydrogen bond
• Hydrogen bond: attraction between a covalently bonded
hydrogen atom and another atom taking part in a separate
polar covalent bond
What are the life sustaining properties
of water?
slight negative charge

slight positive charge

Hydrogen bond

Figure : Hydrogen bonds between water

molecules.
What are the life sustaining properties
of water?
• Hydrogen bonding in water
– Hydrogen bonds form and break much more easily
than covalent or ionic bonds
• Collectively they are quite strong
– Hydrogen bonds stabilize DNA and protein
structures
– Extensive hydrogen bonding among water
molecules gives liquid water several special
properties that make life possible
 Water’s special properties
• Water is an excellent solvent
– Substances that dissolve easily in water are
hydrophilic
– Ionic solids, such as sodium chloride (NaCl),
dissolve in water:
• The slight positive charge on each hydrogen atom in a
water molecule attracts negatively charged Cl–
• The slight negative charge on the oxygen atom attracts
positively charged Na+
 Water’s special properties
• Water is an excellent solvent
– Salt: releases ions other than H+ and OH– when it dissolves
in water (e.g., NaCl)
– Solute: a dissolved substance
– Solution: uniform mixture of solute completely dissolved in
solvent
• Chemical bonds do not form between molecules of solute and
solvent
– Substances that resist dissolving in water are hydrophobic
(e.g., oils)
– Oils consist of nonpolar molecules, and hydrogen bonds
do not form between nonpolar molecules and water
Ion in Salt
solution crystal
Figure: A crystal of salt (NaCl) dissolving in water.
 Water’s special properties
• Water has cohesion
– Cohesion: tendency of molecules to resist
separating from one another
– Water has cohesion because hydrogen bonds
collectively exert a continuous pull on its
individual molecules
– Cohesion takes energy
• Evaporation (transition of a liquid to a vapor) is resisted
by hydrogen bonding among water molecules
 Water’s special properties
• Cohesion is related to
surface tension—a
measure of how
difficult it is to break
the surface of a liquid
• Hydrogen bonds are
responsible for surface
tension
Figure: Surface tension allows a water strider
to walk on water.
 Lizards filmed 'walking on water'

https://www.youtube.com/watch?v=JF-UMgdkph4
• After it rains, spherical
water beads remain on
the waxy surfaces of
leaves. Can you explain
why water clusters into
spherical drops?

Cohesion between water molecules is

stronger than their adhesion to wax and
therefore water clusters into drops on the
surfaces of leaves. Surface tension
promotes minimal surface/volume ratio,
hence the spherical shape.
 Water’s special properties
• Water stabilizes temperature
– Temperature: measure of molecular motion
– Because of hydrogen bonding, it takes more heat
to raise the temperature of water compared with
other liquids
– Heat is absorbed when hydrogen bonds break and
released when hydrogen bonds form.
 Water’s special properties
• Below 0°C (32°F), water molecules become
locked in the bonding pattern of ice
• Sheets of ice that form on the surface of ponds, lakes, and
streams insulate the water
• Protects aquatic organisms during cold winters
• When water freezes, each molecule forms a
stable hydrogen bond with four neighbors
• A three-dimensional crystal results
• There is space between the water molecules
• The ice crystals has fewer water molecules than an equal volume of
liquid water.
• Ice is less dense than water, so it floats.
 Hydrogen bond

Ice Liquid water

Hydrogen bonds Hydrogen bonds
are stable constantly break and re-form

Figure: Hydrogen bonds between water molecules in ice and water.

ACIDS AND BASES
 Why are hydrogen ions important in
biological system?
• In liquid water, a small percentage of water
molecules break apart into hydrogen ions (H+)
and hydroxide ions (OH–)
• A substance that donates hydrogen ions to
solution is called and acid.
• A base is a substance that reduces the
hydrogen ion concentration of a solution.
 Why are hydrogen ions important in
biological system?
• pH scale is used to describe how acidic or basic a
solution is.
– Each pH unit represents a 10-fold change in the
concentration of H+ in a solution.
• pH: measure of the number of hydrogen ions in a
fluid
• Base: accepts hydrogen ions in water
– Above pH 7
• Acid: releases hydrogen ions in water
– Below pH 7
14 drain cleaner
oven cleaner
13
bleach
12 hair remover

household ammonia
11
milk of magnesia
10 hand soap
toothpaste
Tums
9 detergents
baking soda
8 seawater
egg white
blood, tears
7
pure water
6 milk
butter
corn
5 urine, tea, typical rain
black coffee
bread
4 beer
bananas
tomatoes, wine
3 orange juice
vinegar
2 cola
lemon juice
acid rain
1 gastric fluid

0 battery acid
 Why are hydrogen ions important in
biological system?
• Pure water and aqueous solutions that are neither
acidic or basic are said to be neutral (pH 7, H+ and OH-
ions are equal).
• Most biological molecules can function properly only
within a narrow range of pH
– Buffer failure can be catastrophic in a biological system
• pH of human blood- pH 7.4.
• Biological fluids contain buffer, a substances that
minimizes changes in pH.
– Buffer: set of chemicals that can keep the pH of a solution
stable by alternately donating and accepting ions that
contribute to pH