Life’s Chemical Basis
Chapter 2
Hsueh-Fen Juan
(阮雪芬)
Sep. 18, 2012
Video: What are you worth?
Impacts, Issues:
What Are You Worth?
• Fifty-eight elements make
up the human body
1.1 Start With Atoms
• The behavior of elements, which make up all
living things, starts with the structure of
individual atoms
Characteristics of Atoms
• Atoms are the building blocks of all substances
• Made up of electrons, protons and neutrons
• Electrons (e-) have a negative charge
• Move around the nucleus
• Charge is an electrical property
• Attracts or repels other subatomic particles
Characteristics of Atoms
• The nucleus contains protons and neutrons
• Protons (p+) have a positive charge
• Neutrons have no charge
• 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
Characteristics of Atoms
• Isotopes
• Different forms of the same element, with
different numbers of neutrons
• Mass number
• Total protons and neutrons in a nucleus
• Used to identify isotopes
Atoms
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
2.2 Putting Radioisotopes to Use
• 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
• Example: 14C → 14N
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
PET Scanning
Animation: PET scan
2.1-2.2 Key Concepts:
Atoms and Elements
• Atoms are particles that are the building blocks
of all matter; they can differ in numbers of
protons, electrons, and neutrons
• Elements are pure substances, each consisting
entirely of atoms with the same number of
protons
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
Atoms and Energy Levels
• 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
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
Shell Models
Animation: The shell model of electron
distribution
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
Ion Formation
Animation: How atoms bond
From Atoms to Molecules
• 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
A Compound: Water
2.3 Key Concepts:
Why Electrons Matter
• Whether one atom will bond with others
depends on the element, and the number and
arrangement of its electrons
2.4 What Happens When Atoms Interact?
• 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
Different Ways to
Represent the Same Molecule
Ionic Bonding
• Ionic bond
• A strong mutual attraction between two oppositely
charges ions with a large difference in
electronegativity (an electron is not transferred)
• Example: NaCl (table salt)
Ionic Bonds
Animation: Ionic bonding
Covalent Bonding
• 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)
Covalent Bonds
Animation: Covalent bonds
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
Hydrogen Bonds
Animation: Examples of hydrogen bonds
2.4 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’s Life-Giving 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
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
Water: Essential for Life
Fig. 2-10a, p. 28
Water: Essential for Life
Fig. 2-10b, p. 28
Water: Essential for Life
Fig. 2-10c, p. 28
Animation: Structure of water
Water’s Solvent Properties
• 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’s Solvent Properties
• 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
Animation: Spheres of hydration
Water’s Temperature-Stabilizing Effects
• 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’s Temperature-Stabilizing Effects
• 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’s Cohesion
• Hydrogen bonds give water cohesion
• Provides surface tension
• Draws water up from roots of plants
• Cohesion (內聚力)
• Molecules resist separation from one another
Cohesion of Water
2.5 Key Concepts:
Water of 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
2.6 Acids and Bases
• Hydrogen ions have far-reaching effects
because they are chemically active, and
because there are so many of them
• Chemical reactions involving acids and bases
are important to homeostasis
Biological Reactions Occur In Water
• Molecules in water (H2O) can separate into
hydrogen ions (H+) and hydroxide ions (OH-)
H20 ↔ H+ + OH-
The pH Scale
• 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 life chemistry occurs around pH7
A pH Scale
Animation: The pH scale
How Do Acids and Bases Differ?
• 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-
Acid Rain
• Sulfur dioxide dissolves in water vapor to form
an acidic solution
Salts and Water
• 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 system
• 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)
2.6 Key Concepts:
The Power of Hydrogen
• Life is responsive to changes in the amounts of
hydrogen ions and other substances dissolved
in water
Summary:
Players in the Chemistry of Life
Animation: Buffer system
Animation: Shell models of common
elements
ABC video: The Wine of Life