Chapter 2
Life’s Chemical
Basis
Albia Dugger • Miami Dade College
2.1 Mercury Rising
• Mercury is released into the atmosphere by volcanic activity,
and by human activities such as burning coal
• Once airborne, mercury can drift long distances before
settling to Earth’s surface, where microbes convert it to a
toxic substance called methylmercury
• Once mercury enters the body, it damages the nervous
system, brain, kidneys, and other organs
• All human bodies now have detectable amounts of mercury
Atmospheric Fallout from
Coal-Fired Power Plant Emissions
2.2 Start With Atoms
• The behavior of elements, which make up all living things,
starts with the structure of individual atoms
• The number of protons in the atomic nucleus defines the
element, and the number of neutrons defines the isotope
Structure of Atoms
• Atoms are the building blocks of all substances
• Made up of electrons, protons and neutrons
• Charge is an electrical property
• Attracts or repels other subatomic particles
Characteristics of Atoms
• Electrons (e-) have a negative charge
• Move around the nucleus
• The nucleus contains protons and neutrons
• Protons (p+) have a positive charge
• Neutrons (n) have no charge
Characteristics of Atoms
• Atoms differ in number of subatomic particles
• Atomic number (number of protons) determines the
element
• Elements consist only of atoms with the same atomic
number
• Mass number
• Total protons and neutrons in a nucleus
• Used to identify isotopes
Atoms
proton
neutron
electron
The Periodic Table
• Periodic table of the elements
• An arrangement of the elements based on their atomic
number and chemical properties
• Created by Dmitry Mendeleev
Periodic Table of the Elements
ANIMATED FIGURE: Atomic number, mass
number
To play movie you must be in Slide Show Mode
PC Users: Please wait for content to load, then click to play
Mac Users: CLICK HERE
Isotopes and Radioisotopes
• Isotopes
• Different forms of the same element, with different
numbers of neutrons
• Some radioactive isotopes – radioisotopes – are used in
research and medical applications
Radioisotopes
• Henri Becquerel discovered radioisotopes of uranium in the
late 1800s
• Radioactive decay
• Radioisotopes emit subatomic particles of energy when
their nucleus breaks down, transforming one element into
another at a constant rate
Radioactive Decay
• Example: 14C → 14N
nucleus of 14C, with
6 protons, 8 neutrons
nucleus of 14N, with
7 protons, 7 neutrons
Tracers
• Tracer
• Any molecule with a detectable substance attached
• Examples:
• CO2 tagged with 14C used to track carbon through
photosynthesis
• Radioactive tracers used in medical PET scans
brain
lungs
heart
liver
kidneys
Non-smoker
Smoker
Figure 2-4 p25
ANIMATED FIGURE: PET scan
To play movie you must be in Slide Show Mode
PC Users: Please wait for content to load, then click to play
Mac Users: CLICK HERE
Take Home Message:
The basic building blocks of all matter
• All matter consists of atoms, tiny particles that in turn consist
of electrons moving around a nucleus of protons and neutrons
• An element is a pure substance that consists only of atoms
with the same number of protons. Isotopes are forms of an
element that have different numbers of neutrons
• Unstable nuclei of radioisotopes disintegrate spontaneously
(decay) at a predictable rate to form predictable products
ANIMATION: Subatomic particles
To play movie you must be in Slide Show Mode
PC Users: Please wait for content to load, then click to play
Mac Users: CLICK HERE
ANIMATION: Isotopes of hydrogen
2.3 Why Electrons Matter
• Atoms acquire, share, and donate electrons
• Whether an atom will interact with other atoms depends on
how many electrons it has
About Vacancies
• Electrons move around nuclei in orbitals
• Each orbital holds two electrons
• Each orbital corresponds to an energy level
• An electron can move in only if there is a vacancy
• free radical
• Atom with an unpaired electron
Vacancy/ No Vacancy
Why Atoms Interact
• The shell model of electron orbitals diagrams electron
vacancies; filled from inside out
• First shell: one orbital (2 electrons)
• Second shell: four orbitals (8 electrons)
• Third shell: four orbitals (8 electrons)
• Atoms with vacancies in their outer shell tend to give up,
acquire, or share electrons
A The first shell corresponds to the first
energy level, and it can hold up to 2
electrons. Hydrogen has one proton, so
it has 1 electron and 1 vacancy. A
helium atom has 2 protons, 2 electrons,
and no vacancies. The number of
protons in each model is shown.
B The second shell corresponds to
the second energy level, and it can
hold up to 8 electrons. Carbon has 6
protons, so its first shell is full. Its
second shell has 4 electrons, and
four vacancies. Oxygen has 8
protons and two vacancies. Neon has
10 protons and no vacancies.
first shell
second shell
C The third shell, which corresponds
to the third energy level, can hold up to
8 electrons. A sodium atom has 11
protons, so its first two shells are full;
third shell
the third shell has one electron. Thus,
sodium has seven vacancies. Chlorine
has 17 pro tons and one vacancy.
Argon has 18 protons and no
vacancies.
1 proton
1
1 electron
hydrogen (H)
2
helium (He)
6
8
carbon (C)
oxygen (O)
11
17
sodium (Na)
chlorine (Cl)
10
neon (Ne)
18
argon (Ar)
Stepped Art
Figure 2-5 p26
ANIMATED FIGURE: The shell model of
electron distribution
To play movie you must be in Slide Show Mode
PC Users: Please wait for content to load, then click to play
Mac Users: CLICK HERE
Atoms and Ions
• Ion
• An atom with a positive or negative charge due to loss or
gain of electrons in its outer shell
• Examples: Na+, Cl• Electronegativity
• A measure of an atom’s ability to pull electrons from
another atom
electron loss
electron gain
Sodium
atom
Chlorine
atom
11p+
11e–
17p+
17e–
charge: 0
charge: 0
Sodium
ion
Chloride
ion
11p+
10e–
17p+
18e–
charge: +1
charge: –1
Figure 2-6 p27
ANIMATED FIGURE: Ionic bonding
To play movie you must be in Slide Show Mode
PC Users: Please wait for content to load, then click to play
Mac Users: CLICK HERE
Take-Home Message:
Why do atoms interact?
• An atom’s electrons are the basis of its chemical behavior
• Shells represent all electron orbitals at one energy level in an
atom; when the outermost shell is not full of electrons, the
atom has a vacancy
• Atoms with vacancies tend to interact with other atoms
2.4 Chemical Bonds:
From Atoms to Molecules
• Chemical bonds link atoms into molecules
• The characteristics of a chemical bond arise from the
properties of the atoms taking part in it
Chemical Bonds
• Chemical bond
• An attractive force existing between two atoms when their
electrons interact
• Molecule
• Two or more atoms joined in chemical bonds
Combining Substances
• Compounds
• Molecules consisting of two or more elements whose
proportions do not vary
• Example: Water (H2O)
• Mixture
• Two or more substances that intermingle but do not bond;
proportions of each can vary
The Water Molecule
one oxygen atom
two hydrogen atoms
Bonds and Electrons
• Whether one atom will bond with others depends on the
element, and the number and arrangement of its electrons
• electronegativity
• Measure of the ability of an atom to pull electrons away
from other atoms
Three Types of Bonds
• The characteristics of a bond arise from the properties of the
atoms that participate in it
• The three most common types of bonds in biological
molecules are ionic, covalent, and hydrogen bonds
Ionic Bonds
• Ionic bond
• A strong mutual attraction between two oppositely charges
ions with a large difference in electronegativity (no
electron transferred)
• Example: NaCl (table salt)
Ionic Bond: Sodium Chloride
ionic bond
11
Sodium ion
11p+, 10e–
17
Chloride ion
17p+, 18e–
Ionic Bond: Sodium Chloride
Cl– Na+
Ionic Bond: Sodium Chloride
positive
charge
negative
charge
ANIMATED FIGURE: How atoms bond
To play movie you must be in Slide Show Mode
PC Users: Please wait for content to load, then click to play
Mac Users: CLICK HERE
Covalent Bonds
• Covalent bond
• Two atoms with similar electronegativity and unpaired
electrons sharing a pair of electrons
• Can be stronger than ionic bonds
• Atoms can share one, two, or three pairs of electrons
(single, double, or triple covalent bonds)
Characteristics of Covalent Bonds
• Nonpolar covalent bond
• Atoms sharing electrons equally; formed between atoms
with identical electronegativity
• Polar covalent bond
• Atoms with different electronegativity do not share
electrons equally; one atom has a more negative charge,
the other is more positive
Polarity
• Polarity
• Separation of charge into distinct positive and negative
regions in a polar covalent molecule
• Example: Water (H2O)
molecular hydrogen (H2)
molecular oxygen (O2)
water (H2O)
Figure 2-9 p29
ANIMATED FIGURE: Covalent bonds
Table 2-1 p29
Take-Home Message:
How do atoms interact in chemical bonds?
• A chemical bond forms between atoms when their electrons
interact
• A chemical bond may be ionic or covalent depending on the
atoms taking part in it
• An ionic bond is a strong mutual attraction between two ions
of opposite charge
• Atoms share a pair of electrons in a covalent bond; when the
atoms share electrons unequally, the bond is polar
2.5 Hydrogen Bonds and Water
• The unique properties of liquid water arise because of the
water molecule's polarity
• Extensive hydrogen bonds form among water molecules
Polarity of the Water Molecule
• Overall, water (H2O) has no charge
• The water molecule is polar
• Oxygen atom is slightly negative
• Hydrogen atoms are slightly positive
• Hydrogen bonds form between water molecules
• Gives water unique properties
Polarity of the Water Molecule
negative charge
positive charge
Hydrogen Bonding
• Hydrogen bond
• A weak attraction between a highly electronegative atom
and a hydrogen atom taking part in a separate polar
covalent bond
• Hydrogen bonds do not form molecules and are not
chemical bonds
• Hydrogen bonds stabilize the structures of large biological
molecules
a hydrogen bond
Figure 2-11a p31
Figure 2-11b p31
Figure 2-11c p31
ANIMATED FIGURE: Structure of water
To play movie you must be in Slide Show Mode
PC Users: Please wait for content to load, then click to play
Mac Users: CLICK HERE
Water’s Special Properties
• Living organisms are mostly water; all the chemical reactions
of life are carried out in water
• Water is essential to life because of its unique properties
• The properties of water are a result of extensive hydrogen
bonding among water molecules
Water Has Cohesion
• Hydrogen bonds give water cohesion
• Provides surface tension
• Draws water up from roots of plants
• Cohesion
• Molecules resist separation from one another
Water Cohesion and Surface Tension
Water Stabilizes Temperature
• Compared with other molecules, water absorbs more heat
before it becomes measurably hotter
• Temperature
• A way to measure the energy of molecular motion
• Molecules move faster as they absorb heat
Water Stabilizes Temperature
• The surface temperature of water decreases during
evaporation
• Evaporation
• Conversion of a liquid to a gas by heat energy
• Ice is less dense than liquid water
• Hydrogen bonds form a lattice during freezing
Water is a Solvent
• Solvent
• A substance (usually liquid) that can dissolve other
substances (solutes)
• Water is a solvent
• The collective strength of many hydrogen bonds pulls ions
apart and keeps them dissolved
Water is a Solvent
• Water dissolves polar molecules
• Hydrogen bonds form between water molecules and other
polar molecules
• Polar molecules dissolved by water are hydrophilic
(water-loving)
• Nonpolar (hydrophobic) molecules are not dissolved by
water
Water Molecules
Surrounding an Ionic Solid
Take-Home Message:
What gives water the
special properties that make life possible?
• The polarity of a water molecule gives rise to extensive
hydrogen bonding among water molecules
• Hydrogen bonding among water molecules imparts cohesion
to liquid water, and the ability to stabilize temperature and
dissolve many substances
2.6 Acids and Bases
• pH is a measure of the number of hydrogen ions in a solution
• The more hydrogen ions, the lower the pH
• pH 7 is neutral (pure water)
• Most biological processes occur within a narrow range of
pH, typically around pH 7
• Concentration refers to the amount of a particular solute that
is dissolved in a given volume of fluid
—0
battery acid
—1
gastric fluid
—3
more acidic
—2
—4
acid rain
lemon juice
cola
vinegar
orange juice
tomatoes, wine
bananas
beer
bread
black coffee
urine, tea, typical rain
—5
corn
—6
butter
milk
pure water
—7
blood, tears
egg white
seawater
—8
— 10
toothpaste
hand soap
milk of magnesia
— 11
household ammonia
— 12
— 13
— 14
more basic
—9
baking soda
detergents
Tums
hair remover
bleach
oven cleaner
drain cleaner
Figure 2-12 p32
Biological Reactions Occur In Water
• Molecules in water (H2O) can separate into hydrogen ions
(H+) and hydroxide ions (OH-)
H20
↔H
+
+ OH-
Acids and Bases
• Acids donate hydrogen ions in a water solution
• pH below 7
• Bases accept hydrogen ions in a water solution
• pH above 7
Acids: Weak or Strong
• Acids and bases can be weak or strong
• Gastric fluid, pH 2-3
• Acid rain
• Example: Hydrochloric acid is a strong acid
HCl
↔H
+
+ Cl-
Salts
• Salt
• A compound that dissolves easily in water and releases
ions other than H+ and OH-
HCl (acid) + NaOH (base) → NaCl (salt) + H20
Buffers Against Shifts in pH
• Buffer
• A set of chemicals (a weak acid or base and its salt) that
can keep the pH of a solution stable
OH- + H2CO3 (carbonic acid) →
HCO3- (bicarbonate) + H20
H+ + HCO3- (bicarbonate) →
H2CO3 (carbonic acid)
Buffering Carbon Dioxide in Blood
• Carbon dioxide in blood forms carbonic acid, which separates
into H+ and bicarbonate
H2O + CO2 (carbon dioxide)
H2CO3 (carbonic acid)
→
H+ + HCO3- (bicarbonate)
→
Take Home Message: Why is hydrogen
important in biological systems?
• pH reflects the number of hydrogen ions in a fluid. Most
biological systems function properly only within a narrow
range of pH
• Acids release hydrogen ions in water; bases accept them
• Salts release ions other than H+ and OH–
• Buffers help keep pH stable. Inside organisms, they are part
of homeostasis
Table 2-1 p34