Life’s Chemical Basis
Chapter 2
2.1 Start With Atoms
 Atoms
• Fundamental building blocks of matter
 Nucleus
• Positively charged protons
• Uncharged neutrons (except for hydrogen)
 Electrons move around the nucleus
• Negatively charged
Atoms
nucleus
electron
Fig. 2.3, p. 22
Fig. 2.3, p. 22
Fig. 2.3, p. 22
Elements
 Element
• A pure substance consisting of atoms with the
same number of protons (atomic number)
 Isotopes
• Atoms of the same element that differ in number
of neutrons (atomic weight)
Periodic Table of Elements
Abundance of Elements
Human
Hydrogen
62.0%
Oxygen
24.0
Carbon
12.0
Nitrogen
1.2
Phosphorus 0.2
Calcium
0.2
Sodium
0.1
Potassium 0.1
Chlorine
0.1
Earth
Hydrogen
Oxygen
Carbon
Nitrogen
Phosphorus
Calcium
Sodium
Potassium
Chlorine
3.1%
60.0
0.3
0.1
0.1
2.6
0.1
0.8
0.1
Seawater
Hydrogen
Oxygen
Carbon
Nitrogen
Phosphorus
Calcium
Sodium
Potassium
Chlorine
66.0%
33.0
0.1
0.1
0.1
0.1
0.3
0.1
0.3
Fig. 2.2, p. 21
Animation: Shell models of common
elements
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Animation: Chemical bookkeeping
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2.2 Putting Radioisotopes to Use
 Radioisotopes are radioactive isotopes
 They are not stable
• Emit particles and energy as they decay
spontaneously into other elements
Radioactive Decay
 A radioisotope decays at a constant rate into the
same products
• Example: 14C → 14N
 Tracer
• Molecule with a detectable substance attached
• PET scans
A PET Scan
portion of the patient’s
body being scanned
Fig. 2.5, p. 23
portion of the patient’s
body being scanned
detector ring inside
the PET scanner
Fig. 2.5, p. 23
The ring
intercepts
emissions
from the
labeled
molecules
Fig. 2.5, p. 23
Fig. 2.5, p. 23
Animation: PET scan
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Key Concepts:
ATOMS AND ELEMENTS
 Atoms are fundamental units of all matter
 Protons, electrons, and neutrons are their
building blocks
 Elements are pure substances consisting of
atoms that have the same number of protons
 Isotopes are atoms of the same element that
have different numbers of neutrons
2.3 Why Electrons Matter
 Electrons occupy orbitals (volumes of space)
around the nucleus
 Up to two electrons occupy each orbital
 Shell model represents orbital energy levels as
successively larger circles, or shells
• Used to view an atom’s electron structure
Shell Models
Electron Interactions
vacancy
 Atoms with unpaired
electrons in their outermost
shell tend to interact with
other atoms
• They donate, accept, or
share electrons to
eliminate vacancies
no
vacancy
electron
sodium
11p+ , 11e-
chlorine
17p+ , 17e-
argon
18p+, 18e-
carbon
6p+ , 6e-
oxygen
8p+ , 8e-
neon
10p+, 10e-
hydrogen
1p+ , 1e-
helium
2p+ , 2e-
Fig. 2.6, p. 24
Electrical Charge
 An atom with equal numbers of protons and
electrons has no net charge
 Ions (positive or negative)
• Atoms that have gained or lost electrons
 Electronegativity
• Measure of how strongly an atom attracts
electrons from other atoms
Ion Formation
Sodium atom
11p+
11eno net
charge
Chlorine atom
17p+
17eno net
charge
electron
loss
Sodium ion
11p+
10enet positive
charge
electron
gain
Chlorine atom
17p+
18enet negative
charge
Fig. 2.7, p. 25
Sodium atom
11p+
11eno net
charge
Chlorine atom
17p+
17eno net
charge
electron
loss
Sodium ion
11p+
10enet positive
charge
electron
gain
Chlorine atom
17p+
18enet negative
charge
Stepped Art
Fig. 2-7, p. 25
Molecules and Mixtures
 Chemical bond
• Attractive force that unites atoms into a molecule
 Compounds
• Molecules consisting of two or more elements
 Mixture
• Substances intermingle but don’t bond
Representing Molecules
Key Concepts:
WHY ELECTRONS MATTER
 Whether one atom will bond with others
depends on the number and arrangement of its
electrons
Animation: Electron arrangements in
atoms
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Animation: The shell model of electron
distribution
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Animation: How atoms bond
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2.4 What Happens When Atoms Interact?
 Common interactions in biological molecules:
• Ionic bond
• Covalent bond
• Hydrogen bond
Ionic Bonds
 Strong association between a positive ion and a
negative ion (attraction of opposite charges)
Sodium ion
Chloride ion
a
A crystal of table salt is
a cubic lattice of many sodium
ions and chloride ions.
b
The mutual attraction of
opposite charges holds the
two kinds of ions together
closely in the lattice.
Fig. 2.8, p. 23
Animation: Ionic bonding
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Covalent Bonds
 Two atoms share a pair of electrons
 Nonpolar covalent bond
• Atoms share electrons equally
 Polar covalent bond
• Electrons are shared unequally
• One end slightly negative, other slightly positive
• Polar molecule has a separation of charge
Covalent Bonds
Molecular hydrogen (H—H)
Two hydrogen atoms, each with
one proton, share two electrons in
a single nonpolar covalent bond.
Molecular oxygen (O—O)
Two oxygen atoms, each with eight
protons, share four electrons in a
nonpolar double covalent bond.0
Water molecule (H—O—H)
Two hydrogen atoms each share an
electron with an oxygen atom in two
polar covalent bonds. The oxygen
exerts a greater pull on the shared
electrons, so it has a slight negative
charge. Each hydrogen has a slight
positive charge.
Fig. 2.9, p. 27
Hydrogen Bonds
 Form between a hydrogen atom and an
electronegative atom
• Each with separate polar covalent bonds
 Are not chemical bonds
• Do not make atoms into molecules
• Individually weak
• Collectively stabilize structures of large molecules
Hydrogen Bonds
hydrogen bond
water molecule
ammonia molecule
a Two molecules interacting in one hydrogen (H) bond.
b Numerous H bonds ( white dots) hold the two coiled-up
strands of a DNA molecule together. Each H bond is weak,
but collectively these bonds stabilize DNA’s large structure.
Fig. 2.10, p. 27
Animation: Examples of hydrogen bonds
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Key Concepts:
ATOMS BOND
 Atoms of many elements interact by acquiring,
sharing, and giving up electrons
 Ionic, covalent, and hydrogen bonds are the
main interactions between atoms in biological
molecules
2.5 Water Molecules
 Water molecules are polar
• Form hydrogen bonds with other polar molecules
• Hydrophilic substances (water-loving)
• Hydrophobic substances (water-dreading)
slight negative charge on the
oxygen atom
-
O
H
The positive and
negative charges
balance each
other; overall, the
molecule carries
no charge.
H
+
+
slight positive charge on the
hydrogen atoms
Fig. 2.11, p. 28
Animation: Structure of water
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Liquid Water: Hydrogen Bonds
Water’s Life-Giving Properties
 Polarity gives liquid water unique properties that
make life possible:
• Resistance to temperature changes
• Internal cohesion
• Dissolves polar and ionic substances
Water Temperature:
From Ice to Evaporation
Water’s Solvent Properties
 Solvents dissolve solutes (spheres of hydration)
Water’s Cohesion
Key Concepts:
NO WATER, NO LIFE
 Life originated in water and is adapted to its
properties
 Water has temperature-stabilizing effects,
cohesion, and a capacity to act as a solvent for
many other substances
 These properties make life possible on Earth
Animation: Spheres of hydration
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2.6 Acids and Bases
 pH scale
• Indicates hydrogen ion (H+) concentration of a
solution
• Ranges from 0 (most acidic) to 14 (most basic or
alkaline)
 At pH 7 (neutral) H+ and OH– concentrations are
equal
A pH Scale
battery acid
gastric fluid
acid rain
lemon juice
cola
vinegar
orange juice
tomatoes, wine
bananas
beer
bread
black coffee
urine, tea, typical rain
corn
butter
milk
pure water
blood, tears
egg white
seawater
baking soda
phosphate detergents
Tums
toothpaste
hand soap
milk of
magnesia
household ammonia
hair remover
bleach
oven cleaner
drain cleaner
Fig. 2.14, p. 30
Animation: The pH scale
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Acids and Bases
 Acids donate H+ in water
• More H+ than OH-
 Bases accept H+ in water
• More OH- than H+
Salts
 Compounds that dissolve easily in water, and
release ions other than H+ and OH• Form when an acid interacts with a base
• Example: NaCl
HCl + NaOH ↔ NaCl + H2O
Buffer System
 A set of chemicals (a weak acid or base and its
salt) that keeps the pH of a solution stable
• One donates ions, the other accepts them
• Example: bicarbonate (HCO3-)
OH- + H2CO3 → HCO3- + H2O
HCO3- + H+ → H2CO3
Functions of Buffer Systems
 Buffers help maintain homeostasis
 Most biological processes proceed only within a
narrow pH range, usually near neutrality
• Acidosis
• Alkalosis
Key Concepts:
HYDROGEN IONS RULE
 Life is responsive to changes in the amounts of
hydrogen ions and other substances dissolved
in water
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