CHAPTER 2:

The Chemical Basis of Life I:

Atoms, Molecules, and Water

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.
Biology
Based on the principles of chemistry and
physics
All living organisms are a collection of atoms
and molecules (atoms bonded together)
Interact for function and structure
All life forms composed of matter
Anything that contains mass and occupies
space
Gas, liquid, solid

2
Atoms
Matter is composed of atoms
Smallest functional units of matter that form
all chemical substances
Cannot be further broken down into other
substances by ordinary chemical or physical
means
Each specific type of atom is a chemical
element
Pure substance with only one type of atom

3
Atoms
Can be split into three subatomic particles
Protons- positive, found in nucleus, same
number as electrons
Neutrons- neutral, found in nucleus, number
can vary
Electrons- negative, found in orbitals, same
number as protons
Entire atom has no net electric charge

4
5
Electrons occupy orbitals
Scientists initially visualized an atom as a
mini solar system
This is an oversimplified but convenient image
Electrons travel within regions surrounding
the nucleus (orbitals) in which the probability
is high of finding that electron (due to high
speed of electron)
Can be depicted as a cloud

6
7
Orbitals
s orbitals are spherical
p orbitals are propeller or dumbbell shaped
Each orbital can hold only 2 electrons
An atom with more than 2 electrons has more
than 1 orbital

8
Orbitals
Atoms with progressively more electrons
have orbitals within electron shells that are at
greater and greater distances from the center
of the nucleus

1st shell –
 1 spherical orbital (1s)
 holds 2 electrons

2nd shell –
 1 spherical orbital (2s) and
 3 propeller/dumbbell-shaped orbitals (2p)
 can hold 4 pairs of electrons

9
10
Nitrogen example
A nitrogen atom has seven protons and seven
electrons
2 electrons fill 1st shell (1s)
5 electrons in 2nd shell
2 fill 2s orbital
1 each in the 3p orbitals
Outer 2nd shell is not full
Electrons in the outer shell that are available
to combine with other atoms are called the
valence electrons

11
Valence
electrons
(outer shell)

12
13
Protons
Number of protons distinguishes one element
from another
Called Atomic Number
Also equal to the number of electrons in the
atom so that the net charge is zero

14
Periodic table
Organizes elements by atomic number
Rows (periods) correspond to number of
electron shells
Columns (groups), from left to right, indicate
the numbers of electrons in the outer shell
Similarities of elements within a column
occur because they have the same number of
electrons in their outer shells, and therefore
they have similar chemical bonding
properties
15
 # electrons in
outer shell
(valence)
# electron
shells

16
Atomic mass
H 0.0000000000000000000000167
grams
Protons and neutrons are nearly equal in
mass, and both are more than 1,800 times
the mass of an electron so have most of
mass

Atomic mass based on # protons and #

neutrons

= (#protons + # neutorns)

17
Mass or weight?
Weight is derived from the gravitational pull
on a given mass
A man weighs 154 pounds on Earth
On the moon he weighs about 25 pounds
On a neutron star’s surface he would weigh 21
trillion pounds
His mass is the same in all locations
Made up of same amount of matter

18
Units
Dalton (D)
Unit of measurement for atomic mass
Also known as atomic mass unit (amu)
Most abundant form of carbon has an atomic
mass of 12 Daltons
Mole
1 mole of any element contains the same
number of atoms—6.022 x 1023
Avogadro’s number

19
Isotopes
Multiple forms of an element that differ in the
number of neutrons
12C contains 6 protons and 6 neutrons
14C contains 6 protons and 8 neutrons
Atomic masses are averages of the weights of
different isotopes of an element

20
Hydrogen, oxygen, carbon, and nitrogen
Typically make up about 95% of the atoms in
living organisms
Hydrogen and oxygen occur primarily in water
Nitrogen is found in proteins
Carbon is the building block of all living matter
Mineral elements - less than 1%
Trace elements - less than 0.01%
Essential for normal growth and function

21
22
Chemical bonds and molecules
Molecule
2 or more atoms bonded together
Chemical bonds (more to come!)
Molecular formula
Contains chemical symbols of elements found in a
molecule
Subscript indicates how many of each atom are
present
Compound
Molecule composed of 2 or more atoms/elements

H2O NaCl
23
3 types of bonds
1. Covalent
 Polar covalent
 Nonpolar covalent

2. Hydrogen
3. Ionic

24
1. Covalent bonds
Atoms share a pair of electrons
Occurs between atoms whose outer
electron shells are not full
Covalent bonds are strong chemical
bonds, because the shared electrons
behave as if they belong to each atom
Can share …
1 pair of electrons – single bond H-F
2 pairs of electrons – double bond O=O
3 pairs of electrons – triple bond

25
Octet rule
Atoms are stable when their outer shell is full
For many atoms, the outer shell fills with 8
electrons
One exception is hydrogen, which fills its
outer shell with 2 electrons

26
27
28
29
Polar covalent bonds
When two atoms with different
electronegativities (attract electrons) form a
covalent bond:
Electrons not equally shared
Shared electrons are more likely to be in the
outer shell of the atom of higher
electronegativity
Creates a polarity, or difference in electric
charge, across the molecule

30
Water
Classic example of polar covalent bonds
Electrons tend to be in the more
electronegative oxygen atom rather than
either of the less electronegative hydrogen
atoms
Molecule has a partial negative charge region
and a partial positive charge region

31
32
Nonpolar covalent bonds
Bonds between atoms with similar
electronegativities
Equal sharing of electrons
C-H bonds

33
2. Hydrogen bonds
Hydrogen atom from one polar molecule
attracted to electronegative part of another
molecule
Represented as dashed or dotted lines
Each H-bond is weak but collectively very
strong
Individually, weak bonds can form and break
easily

34
35
3. Ionic bonds
An ion is an atom or molecule that has gained or
lost one or more electrons
Now has a net electric charge
Cations- net positive charge
Anions- net negative charge

Why?

More stable since outer shell is full of electrons

Ionic bond occurs when a cation binds to an
anion

36
37
Chemical Reactions
Occurs when one or more substances are
changed into other substances
Reactants → products
Important for life
Share many properties
All require a source of energy
Reactions in living organisms often require a
catalyst (enzymes)
Tend to proceed in a particular direction but
will eventually reach equilibrium
Occur in liquid environment - water

38
Properties of water
Living things composed largely of water (60-
80%)
So, many substances are found in water
And…biological reactions take place in water
A solution is made up of the
Solvent- liquid
Solutes- substances dissolved in solvent
Aqueous solution- water is the solvent

39
What will dissolve in water
Hydrophillic substances - “water-loving”
Readily dissolve in water
Ions or molecules that contain ionic and/or polar
covalent bonds
Electrically attracted to polar water molecules
Hydrophobic substances - “water-fearing”
Do not readily dissolve in water
Nonpolar molecules like hydrocarbon (oils)
Amphipathic molecule – “both loves”
Have both polar/ionized and nonpolar regions
May form micelles in water

40
41
Amphipathic molecules
 Polar
(hydrophilic)
regions at the
surface of the
micelle
 Nonpolar
(hydrophobic)
ends are oriented
toward the
interior of the
micelle
42
Solutions
Concentration
Amount of a solute dissolved in a unit volume of
solution
1 gram of NaCl was dissolved in 1 liter of water =

1 g/L
Molarity (M)
Number of moles of a solute dissolved in 1 L of
water
1 mole of NaCl (6.022 x 1023) in 1 liter of water
= 1M NaCl solution
43
Molecular Mass and Moles
Molecular mass = Atomic mass of all atoms x
the number there are of each one
Sucrose = C12H22O11 = (12 x 12) + (22 x 1) + (11
x 16)
= 342 D (Daltons)
1 mole of a substance is the amount of the
substance in grams equal to its atomic or
molecular mass
1 mole of sucrose = 342 grams of sucrose
= 6.022 x 1023 molecules of
sucrose
Moles continued
Also, 1 mole of ANYTHING contains the same
number of molecules
1 mole of NaCl = 6.022 x 1023 molecules =
58 grams
 NaCl = 58 D
1 mole of Sucrose = 6.022 x 1023 molecules =
342 grams
DIFFERENT masses SAME # of Molecules
Molarity - another way to
specify concentration
Concentration amount Solute/Solvent
Moles/Liter = Molar solution = M
1 M NaCl = 58g NaCl/L = 1 mole NaCl/1L
water
1 M Sucrose = 342 g sucrose/L
H2O in 3 states of matter
Solid (ice), liquid (water), and gas (water
vapor)
Changes in state, such as changes between
the solid, liquid, and gas states of H 2O,
involve an input or release of energy
Heat of vaporization (energy supplied; boiling
water)
Heat of fusion (energy removed; freezing
water)
Water is extremely stable as a liquid
47
Colligative properties of water
Temperature at which a solution freezes or
vaporizes influenced by amounts of
dissolved solutes
Addition of solutes to water lowers its
freezing point below 0°C and raises its
boiling point above 100°C
Some animals produce antifreeze
molecules that dissolve in their body fluids,
thereby lowering the freezing point of the
fluids and preventing their blood and cells
from freezing in the extreme cold
Ethylene glycol
48
49
Not just a solvent
Water has many important functions in living
organisms:
 Participates in chemical reactions (hydrolysis
or condensation)
 Provides force or support
 Removes toxic waste components
 Evaporative cooling
 Cohesion and adhesion
 Surface tension
 Lubrication

50
 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

H2O

Hydrolysis
+ +

(a) Water participates in

chemical reactions.

Blood enters and

is purified by (b) Water provides support.
kidney cells. The plant on the right is wilting
due to lack of water.

Waste products
are carried away
in the watery urine.

(c) Water is used to eliminate

soluble wastes.

(d) Evaporation helps some

animals dissipate body heat.

(e) The cohesive force of water

molecules aids in the
movement of fluid through
vessels in plants.

(f) Water in saliva serves as a

lubricant during—or as
(g) The surface tension of water shown here, in anticipation
explains why this water strider of—feeding.
doesn’t sink.
51
b: © Aaron Haupt/Photo Researchers, Inc.; d: © Chris McGrath/Getty Images; e: © Dana Tezarr/Getty Images;
f: © Anthony Bannister/Gallo Images/Corbis; g: © Hermann Eisenbeiss/Photo Researchers, Inc.
Properties of Water due to
Hydrogen Bonding
Cohesion
Water Molecules stick together
 Water transport in plants
Adhesion
Water Molecules stick to surfaces
 Papertowel
Surface Tension
Attraction of molecules at surface
Acids and Bases
Pure water has the ability to ionize to a very
small extent into hydrogen ions (H+) and
hydroxide ions (OH-)

H2O H+ + OH-

In pure water

[H+][OH-] = [10-7 M][10-7 M] = 10-14

M
53
Acids and Bases
Other molecules can also release these ions
Acids are molecules that release hydrogen
ions in solution
A strong acid releases more H+ than a weak
acid
Bases lower the H+ concentration
Some release OH- (bind with H+’s to form H2O)
Others react with water to form OH-
NH3 + H2O NH4+ + OH-

54
pH – Measure of acidity
pH = -log10 [H+]
A measure of H+ concentration in a solution
Acidic solutions are below pH 7
pH 7 is neutral
Alkaline (basic; low acidity) solutions are
above pH 7

55
pH – Measure of acidity
Because each pH unit is a log scale, a drop or
increase of 1 pH unit means a 10 fold
difference in the Hydrogen ion concentration
pH 7 has 10 x more H+ than a solution at pH
8
 pH 7 has 1000 x more H+ than a solution at
pH 10!
57
pH
The pH of a solution can affect
The shapes and functions of molecules
The rates of many chemical reactions
The ability of two molecules to bind to each
other
The ability of ions or molecules to dissolve in
water

58
Buffers
Organisms usually tolerate only small
changes in pH
Buffers help to keep a constant pH range
An acid-base buffer system can shift to
generate or release H+ to adjust for changes
in pH

59