Chapter 2
Basic Chemistry
Matter and Energy
 Matter—anything that occupies space and
has mass
 Matter may exist as one of three states
o Solid: definite shape and volume
o Liquid: definite volume; shape of
container
o Gaseous: neither a definite shape nor
volume
 Matter may be changed
o Physically
 Changes do not alter the basic nature of a
substance
 Examples include changes in the state of
matter (solid, liquid, or gas)
o Chemically
 Changes alter the chemical composition of
a substance
 Energy—the ability to do work
o Has no mass and does not take up
space
o Kinetic energy: energy is doing work
o Potential energy: energy is inactive or
stored
 Forms of energy
o Chemical energy is stored in chemical
bonds of substances
o Electrical energy results from movement
of charged particles
o Mechanical energy is energy directly
involved in moving matter
o Radiant energy travels in waves; energy
of the electromagnetic spectrum
 Energy form conversions
o ATP (adenosine triphosphate) traps the
chemical energy of food in its bonds
Composition of Matter
 Elements—fundamental units of matter
o 96 percent of the body is made from
four elements:
1. Oxygen (O)—most common;
65% of the body’s mass
2. Carbon (C)
3. Hydrogen (H)
4. Nitrogen (N)
 Periodic table contains a complete listing of
elements
 Atoms
o Building blocks of elements
o Atoms of elements differ from one
another
o Atomic symbol is chemical shorthand for
each element
The Basic Atomic Subparticles
 Protons (p+) are positively charged
 Neutrons (n0) are uncharged or neutral
 Electrons (e–) are negatively charged
 All atoms are electrically neutral
o Number of protons equals numbers of
electrons in an atom
o Positive and negative charges cancel
each other out
 Ions are atoms that have lost or gained
electrons
Planetary and Orbital Models of an Atom
 Planetary model
o Portrays the atom as a miniature solar
system
o Protons and neutrons are in the atomic
nucleus
o Electrons are in orbitals around the
nucleus
 Orbital model
o Electrons are depicted by an electron
cloud, a haze of negative charge,
outside the nucleus
 Electrons determine an atom’s chemical
behavior and bonding properties
 Although outdated, the planetary model is
simple and easy to understand and use
Identifying Elements
 To identify an element, we need to know
the:
o Atomic number
o Atomic mass number
o Atomic weight
 Atomic number—equal to the number of
protons that the atom contains
o Unique to atoms of a particular element
o Indirectly tells the number of electrons in
an atom
 Atomic mass number—sum of the protons
and neutrons contained in an atom’s nucleus
 Atomic weight—approximately equal to the
mass number of the element’s most abundant
isotope (to be discussed in a moment)
Atomic Weight and Isotopes
 Isotopes
o Atoms that have the same number of
protons and electrons but vary in the
number of neutrons
o Isotopes have the same atomic number
but different atomic masses
 Radioisotope
o Heavy isotope of certain atoms
o Tends to be unstable
o Decomposes to more stable isotope
 Radioactivity—process of spontaneous
atomic decay
o Used to tag and trace biological
molecules through the body
Molecules and Compounds
 Molecule—two or more atoms of the same
elements combined chemically
 Example of a chemical reaction, shown as a
chemical equation, resulting in a molecule:
H (atom) + H (atom) → H2 (molecule)
o The reactants are the atoms on the left
o The product is the molecule on the right,
represented by a molecular formula
 Compound—two or more atoms of different
elements combined chemically to form a molecule
of a compound
 Example of a chemical reaction resulting in
a compound:
4H + C → CH4 (methane)
Chemical Bonds and Chemical Reactions
 Chemical reactions occur when atoms
combine with or dissociate from other atoms
 Chemical bonds are energy relationships
involving interactions among the electrons of
reacting atoms
Role of Electrons
 Electrons occupy energy levels called
electron shells (or energy levels)
 Electrons closest to the nucleus are most
strongly attracted to its positive charge
 Distant electrons further from the nucleus
are likely to interact with other atoms
 Each electron shell has distinct properties
 How to fill the atom’s electrons shells
o Shell 1 can hold a maximum of 2
electrons
o Shell 2 can hold a maximum of 8
electrons
o Shell 3 can hold a maximum of 18
electrons
o Subsequent shells can hold more
electrons
 Bonding involves interactions only between
electrons in the outermost (valence) shell
 Atoms with full valence shells do not form
bonds
 Rule of eights
o The key to chemical reactivity
o Atoms are considered stable when their
outermost (valence) shell has 8
electrons
o Atoms with 8 electrons in the valence
shell are considered stable and
chemically inactive (inert)
o The exception to this rule of eights is
shell 1, which can hold only 2 electrons
 Reactive elements
o Atoms will gain, lose, or share electrons
to complete their outermost orbitals
when fewer than 8 electrons are in the
valence shell
o Chemical bonding helps atoms achieve
a stable valence shell
Types of Chemical Bonds
 Ionic bonds
o Form when electrons are completely
transferred from one atom to another
o Allow atoms to achieve stability through
the transfer of electrons
 Ions
o Result from the loss or gain of electrons
 Anions have negative charge due to gain of
electron(s)
 Cations have positive charge due to loss of
electron(s)
o Tend to stay close together because
opposite charges attract
 Covalent bonds
o Atoms become stable through shared
electrons
o Electrons are shared in pairs
o Single covalent bonds share one pair of
electrons
o Double covalent bonds share two pairs
of electrons
 Covalent bonds can be described as either
nonpolar or polar
o Nonpolar covalent bonds
 Electrons are shared equally between the
atoms of the molecule
 Electrically neutral as a molecule
 Example: carbon dioxide
 Covalent bonds can be described as either
nonpolar or polar (continued)
o Polar covalent bonds
 Electrons are not shared equally between
the atoms of the molecule
 Molecule has a positive and negative side,
or pole
 Example: water
 Hydrogen bonds
o Extremely weak chemical bonds
o Formed when a hydrogen atom is
attracted to the negative portion, such
as an oxygen or nitrogen atom, of a
polar molecule
o Responsible for the surface tension of
water
o Important for forming intramolecular
bonds, as in protein structure
Patterns of Chemical Reactions
 Synthesis reaction (A + B → AB)
o Atoms or molecules combine to form a
larger, more complex molecule
o Energy is absorbed for bond formation
o Underlies all anabolic (building)
activities in the body
 Decomposition reaction (AB → A + B)
o Molecule is broken down into smaller
molecules
o Chemical energy is released
o Underlies all catabolic (destructive)
activities in the body
 Exchange reaction
AB + C → AC + B
and
AB + CD → AD + CB
o Involves simultaneous synthesis and
decomposition reactions as bonds are
both made and broken
o Switch is made between molecule parts,
and different molecules are made
 Most chemical reactions are reversible
 Reversibility is indicated by a double arrow
o When arrows differ in length, the longer
arrow indicates the more rapid reaction
or major direction of progress
 Factors influencing the rate of chemical
reactions are shown in Table 2.4
Biochemistry: The Chemical Composition of
Living Matter
 Inorganic compounds
o Lack carbon
o Tend to be small, simple molecules
o Include water, salts, and many (not all)
acids and bases
 Organic compounds
o Contain carbon
o All are large, covalent molecules
o Include carbohydrates, lipids, proteins,
 and nucleic acids
Inorganic Compounds
 Water
o Most abundant inorganic compound in
the body
o Accounts for two-thirds of the body’s
weight
o Vital properties include:
 High heat capacity
 Polarity/solvent properties
 Chemical reactivity
 Cushioning
 High heat capacity
o Water absorbs and releases a large
amount of heat before it changes
temperature
o Prevents sudden changes in body
temperature
 Polarity/solvent properties
o Water is often called the “universal
solvent”
o Solvents are liquids or gases that
dissolve smaller amounts of solutes
o Solutes are solids, liquids, or gases that
are dissolved or suspended by solvents
o Solution forms when solutes are very
tiny
o Colloid forms when solutes of
intermediate size form a translucent
mixture
 Chemical reactivity
o Water is an important reactant in some
chemical reactions
o Reactions that require water are known
as hydrolysis reactions
o Example: water helps digest food or
break down biological molecules
 Cushioning
o Water serves a protective function
o Examples: cerebrospinal fluid protects
the brain from physical trauma, and
amniotic fluid protects a developing
fetus
 Salts
o Ionic compound
o Contain cations other than H+ and
anions other than OH–
o Easily dissociate (break apart) into ions
in the presence of water
o Vital to many body functions
 Example: sodium and potassium ions are
essential for nerve impulses
o All salts are electrolytes
o Electrolytes are ions that conduct
electrical currents
 Acids
o Electrolytes that dissociate (ionize) in
water and release hydrogen ions (H+)
o Proton (H+) donors
o Example: HCl → H+ + Cl–
o Strong acids ionize completely and
liberate all their protons
o Weak acids ionize incompletely
 Bases
o Electrolytes that dissociate (ionize) in
water and release hydroxyl ions (OH–)
o Proton (H+) acceptors
o Example: NaOH → Na+ + OH–
 Neutralization reaction
o Type of exchange reaction in which
acids and bases react to form water and
a salt
o Example: NaOH + HCl → H2O + NaCl
 pH
o pH measures relative concentration of
hydrogen (and hydroxide) ions in body
fluids
o pH scale is based on the number of
protons in a solution
o pH scale runs from 0 to 14
o Each successive change of 1 pH unit
represents a tenfold change in H+
concentration
o Neutral
 7 is neutral
 Neutral means that the number of hydrogen
ions exactly equals the number of hydroxyl ions
o Acidic solutions have a pH below 7
 More H+ than OH–
o Basic solutions have a pH above 7
 Fewer H+ than OH–
o Buffers—chemicals that can regulate pH
change
Organic Compounds
 Polymer: chainlike molecules made of many
similar or repeating units (monomers)
 Many biological molecules are polymers,
such as carbohydrates and proteins
 Dehydration synthesis—monomers are
joined to form polymers through the removal of
water molecules
o A hydrogen ion is removed from one
monomer while a hydroxyl group is
removed from the monomer it is to be
joined with
o Water is removed at the site where
monomers join (dehydration)
 Hydrolysis—polymers are broken down into
monomers through the addition of water molecules
o As a water molecule is added to each
bond, the bond is broken, and the
monomers are released
 Carbohydrates
o Contain carbon, hydrogen, and oxygen
o Include sugars and starches
o Classified according to size and
solubility in water
 Monosaccharides—simple sugars and the
structural units of the carbohydrate group
 Disaccharides—two simple sugars joined by
dehydration synthesis
 Polysaccharides—long-branching chains of
linked simple sugars
 Monosaccharides—simple sugars
o Single-chain or single-ring structures
o Contain three to seven carbon atoms
o Examples: glucose (blood sugar),
fructose, galactose, ribose, deoxyribose
 Disaccharides—two simple sugars joined by
dehydration synthesis
o Examples include sucrose, lactose, and
maltose
o Too large to pass through cell
membranes
 Polysaccharides: long, branching chains of
linked simple sugars
o Large, insoluble molecules
 o Function as storage products
o Examples include starch and glycogen
 Lipids
o Most abundant are the triglycerides,
phospholipids, and steroids
o Contain carbon, hydrogen, and oxygen
 Carbon and hydrogen outnumber oxygen
o Insoluble in water, but soluble in other
lipids
 Triglycerides, or neutral fats
o Found in fat deposits
o Source of stored energy
o Composed of two types of building
blocks—fatty acids and one glycerol
molecule
 Saturated fatty acids
 Unsaturated fatty acids
 Fatty acid chains of triglycerides
o Saturated fats
 Contain only single covalent bonds
 Chains are straight
 Exist as solids at room temperature since
molecules pack closely together
o Unsaturated fats
 Contain one or more double covalent
bonds, causing chains to kink
 Exist as liquid oils at room temperature
 “Heart healthy”
 Trans fats
o Oils that have been solidified by the
addition of hydrogen atoms at double
bond sites
o Increase risk of heart disease
 Omega-3 fatty acids
o Found in cold-water fish and plant
sources, including flax, pumpkin, and
chia seeds; walnuts and soy foods
o Appear to decrease risk of heart disease
 Phospholipids
o Contain two fatty acids chains rather
than three; they are hydrophobic (“water
fearing”)
o Phosphorus-containing polar “head”
carries an electrical charge and is
hydrophilic (“water loving”)
o Charged “head” region interacts with
water and ions while the fatty acid
chains (“tails”) do not
o Form cell membranes
 Steroids
o Formed of four interlocking rings
o Include cholesterol, bile salts, vitamin D,
and some hormones
o Some cholesterol is ingested from
animal products; the liver also makes
cholesterol
o Cholesterol is the basis for all steroids
made in the body
 Proteins
o Account for over half of the body’s
organic matter
 Provide for construction materials for body
tissues
 Play a vital role in cell function
 Act as enzymes, hormones, and antibodies
o Contain carbon, oxygen, hydrogen,
nitrogen, and sometimes sulfur
o Built from building blocks called amino
acids
 Amino acid structure
o Contain an amine group (NH2)
o Contain an acid group (COOH)
o Vary only by R-groups
 Protein structure
o Polypeptides contain fewer than 50
amino acids
o Proteins contain more than 50 amino
acids
o Large, complex proteins contain 50 to
thousands of amino acids
o Sequence of amino acids produces a
variety of proteins
 Structural levels of proteins
o Primary structure—strand of amino acid
“beads”
o Secondary structure—chains of amino
acids twist or bend
 Alpha helix—resembles a metal spring
 Beta-pleated sheet—resembles pleats of a
skirt or sheet of paper folded into a fan
o Tertiary structure—compact, ball-like
(globular) structure
o Quaternary structure—result of a
combination of two or more polypeptide
chains
 Fibrous (structural) proteins
o Appear in body structures
o Exhibit secondary, tertiary, or even
quaternary structure
o Bind structures together and exist in
body tissues
o Stable proteins
o Examples include collagen and keratin
 Globular (functional) proteins
o Function as antibodies, hormones, or
enzymes
o Exhibit at least tertiary structure
o Hydrogen bonds are critical to the
maintenance of structure
o Can be denatured and no longer
perform physiological roles
o Active sites “fit” and interact chemically
with other molecules
 Enzymes
o Act as biological catalysts
o Increase the rate of chemical reactions
o Bind to substrates at an active site to
catalyze reactions
o Can be recognized by their –ase suffix
 Hydrolase
 Oxidase
 Nucleic acids
o Form genes
o Composed of carbon, oxygen,
hydrogen, nitrogen, and phosphorus
atoms
o Largest biological molecules in the body
o Two major kinds:
 DNA
 RNA
 Nucleic acids are built from building blocks
called nucleotides
 Nucleotides contain three parts
1. A nitrogenous base
 A = Adenine
 G = Guanine
 C = Cytosine
 T = Thymine
 U = Uracil
2. Pentose (five-carbon) sugar
3. A phosphate group
 Deoxyribonucleic acid (DNA)
o The genetic material found within the
cell’s nucleus
o Provides instructions for every protein in
the body
o Organized by complementary bases to
form a double-stranded helix
o Contains the sugar deoxyribose and the
bases adenine, thymine, cytosine, and
guanine
o Replicates before cell division
 Ribonucleic acid (RNA)
o Carries out DNA’s instructions for
protein synthesis
o Created from a template of DNA
o Organized by complementary bases to
form a single-stranded helix
o Contains the sugar ribose and the bases
adenine, uracil, cytosine, and guanine
o Three varieties are messenger, transfer,
and ribosomal RNA
 Adenosine triphosphate (ATP)
o Composed of a nucleotide built from
ribose sugar, adenine base, and three
phosphate groups
o Chemical energy used by all cells
o Energy is released by breaking high-
energy phosphate bond
 ADP (adenosine diphosphate) accumulates
as ATP is used for energy
 ATP is replenished by oxidation of food
fuels
 Three examples of how ATP drives cellular
work are shown next