Chapter 2

The Chemical
Basis of Life

Collagen and Elastic Fibers

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 Matter

• The “stuff” of the universe

• Anything that has mass and takes up
space
• States of matter
– Solid: has definite shape and volume
– Liquid: has definite volume, changeable
shape
– Gas: has changeable shape and volume
 Composition of Matter

• Elements: unique substances that cannot

be broken down by ordinary chemical
means
• Atoms: more-or-less identical building
blocks for each element
• Atomic symbol: one- or two-letter
chemical shorthand for each element
 Properties of Elements

• Each element has unique physical and

chemical properties
– Physical properties: those detected with our
senses
– Chemical properties: pertain to the way
atoms interact with one another
 Major Elements of the Human Body
• About 96% of body weight results from the
following elements:
Oxygen (O) Hydrogen (H)
Carbon (C) Nitrogen (N)

• Lesser elements make up 3.9% of the body:

Phosphorus (P) Potassium (K) Calcium (Ca)
Sulfur (S) Sodium (Na) Chlorine (Cl)
Magnesium (Mg) Iodine (I) Iron (Fe)

• Trace elements make up < 0.01% of the body:

– Required in minute amounts
– Found as part of enzymes
 Atomic Structure
• The nucleus consists of
neutrons and protons
– Neutrons:
• No charge
• Mass= one atomic mass unit (amu)
– Protons:
• Positive charge
• Mass of 1 amu
• Electrons are found orbiting
the nucleus
– Electrons:
• Negative charge
• Mass of 1/2000 amu
Fig. 2.1
 Atomic Structure
• Atoms are electrically neutral because the
number of protons in atoms equals the number
of electrons

Fig. 2.2
 Identification of Elements
• Atomic number: equal to the number of
protons
• Mass number: equal to the mass of the
protons and neutrons
• Atomic weight: average of the mass
numbers of all isotopes
• Isotope: atoms with same number of
protons but a different number of neutrons
 Chemical Bonds

• Electron shells (energy levels) surround the

nucleus of an atom
– Bonds are formed using the electrons in the
outermost electron shell
• Valence shell: outermost energy level
containing chemically active electrons
• Octet rule: except for the first shell, which
is full with two electrons, atoms interact in a
manner to have eight electrons in their
valence shell
 Types of Chemical Bonds

• Ionic bond: formed when one atom loses

an electron and another accepts that
electron
• Covalent bond: the sharing of electrons
• Hydrogen bond: hydrogen atoms (bound
covalently to either N or O atoms) have a
small positive charge that is weakly
attracted to the small negative charge of
other atoms
 Ionic Bonds

• Ionic bonds form between atoms by the transfer

of one or more electrons
• Ions: charged atoms resulting from the gain or
loss of electrons
– Anions: negatively charged ions due to gaining one or
more electrons
– Cations: positively charged ions due to losing one or
more electrons
• Ionic compounds form crystals instead of
individual molecules
Example: NaCl (sodium chloride)
Fig. 2.3
 Covalent Bonds
• Covalent bonds are
formed by the sharing
of two or more
electrons
• Electron sharing
produces molecules
– single covalent bond:
sharing of a pair of
electrons (H — H)
– double covalent bond:
sharing of two pairs of
electrons (O ═ C ═ O)

Fig. 2.4
 Polar and Nonpolar Molecules

• Electrons shared
equally between
atoms produce
nonpolar molecules
• Unequal sharing of
electrons produces
polar molecules

Fig. 2.5
 Hydrogen Bonds

• Too weak to bind atoms together

• Common in dipoles such as water
• Responsible for surface tension in water
• Important as intramolecular bonds, giving
the molecule a three-dimensional shape
Hydrogen Bonds

Figure 2.10a
 Molecules and Compounds

• Molecule: two or more atoms held

together by chemical bonds to form a
structure that behaves as an independent
unit
• Compound: two or more different kinds of
atoms chemically combined
– covalent compound: a molecule
– ionic compound: organized array of ions
 Dissociation

• Separation of ions in an ionic compound

by polar water molecules
– Dissociated ions are called electrolytes
because they can conduct electricity
– Molecules that do not dissociate in water are
called nonelectrolytes
Fig. 2.7
 Chemical Reactions
• Occur when chemical bonds are formed,
rearranged, or broken
– Reactants: substances that enter a chemical
reaction
– Products: substances that result from the
chemical reaction
• Written in symbolic form using chemical
equations
– Chemical equations contain:
• Number and type of reacting substances
• Products produced
• Relative amounts of reactants and products
 Synthesis Reaction
• Combination of reactants to form a new larger
product
– Dehydration reaction: a synthesis reaction in which
water is a product

Fig. 2.8
 Decomposition Reaction
• Breakdown of larger reactants into smaller
products
– Hydrolysis reaction: a decomposition reaction that
uses water

Fig. 2.8
 Reversible Reactions

• All chemical reactions are theoretically

reversible
A + B  AB
AB  A + B
• If neither a forward nor reverse reaction is
dominant, chemical equilibrium is reached
 Energy
• The capacity to do work (put matter into
motion)
• Types of energy
– Potential: stored (inactive) energy that could
do work
– Kinetic: energy that does work by causing the
movement of an object
 Energy
• Can be neither created nor destroyed
• Easily converted from one form to another
– Mechanical: directly involved in moving
matter
– Chemical: stored in the bonds of chemical
substances
– Electrical: results from the movement of
charged particles
– Radiant or electromagnetic: travels in waves
(i.e., visible light, ultraviolet light, and
X-rays)
 Energy
• Exists in chemical bonds as potential energy
• Released when the products contain less
potential energy than the reactants
– Energy can be “lost” as heat, can be used to
synthesize molecules, or can do work.
• Absorbed in reactions when the products contain
more potential energy than the reactants
 Adenosine Triphosphate (ATP)
• ATP stores and provides energy
• Source of immediately usable energy for
the cell

Fig. 2.9
Fig. 2.10
Factors Influencing Rate of Chemical Reactions

• Concentration: higher reacting particle

concentrations produce faster reactions
• Temperature: chemical reactions proceed
quicker at higher temperatures
• Catalysts: increase the rate of a reaction
without being chemically changed
– Enzymes are biological catalysts
• Particle size: the smaller the particle the
faster the chemical reaction
 Acids and Bases

• Acids release hydrogen ions (H+) and are

therefore proton donors
HCl  H+ + Cl –
• Bases release hydroxide ions (OH–) and
are proton acceptors
NaOH  Na+ + OH–
• Acid-Base concentration is measured
using a pH scale
 pH Scale

• Ranges from 0 to 14
• Indicates the H+ concentration of a solution
– Neutral solutions have an equal number of H+
and OH– and a pH of 7.0
– Acidic solutions have more H+ than OH– and a
pH of less than 7.0
– Basic (alkaline) solutions have fewer H+ than
OH– and a pH greater than 7.0
 pH Scale

• Neutral: pH 7.00
• Acidic: pH 0–6.99
• Basic: pH 7.01–14.00

Fig. 2.11
 Acids and Bases
• Salts are formed by the reaction of an acid and a
base
HCl + NaOH → NaCl + H2O

(acid) (base) (salt) (water)

• Buffers are chemicals that resist changes in pH

when acids or bases are added
– Example: Carbonic acid-bicarbonate system
• Carbonic acid dissociates, reversibly releasing bicarbonate ions
and protons
• The chemical equilibrium between carbonic acid and bicarbonate
resists pH changes in the blood
 Buffers
a) Addition of an acid to a
nonbuffered solution
results in an increase
of H+ and a decrease
in pH

b) In a buffered solution
the added H+ is bound
by the buffer and the
pH change is much
smaller
Fig. 2.12
 Biochemistry
• Inorganic chemistry
– Mostly concerned with non-carbon-containing
substances but does include such carbon-
containing substances as CO (Carbon
monoxide), CO2 (Carbon Doixide), and HCO3-
(Bicarbonate)
• Organic chemistry
– Substances contain carbon, are covalently
bonded, and are often large
– Usually have carbon-carbon or carbon-hydrogen
bonding
 Inorganic Compounds

• Oxygen (O2) is involved with the extraction

of energy from food molecules to make
ATP
• Carbon Dioxide (CO2) is a by-product of
the breakdown of food molecules
• Water (H2O) has many important
properties for living organisms and is
essential for life
 Properties of Water
• Stabilizes body temperature
– The high heat capacity of water allows it to absorb and release
large amounts of heat before changing temperature
• Protection
– acts as a lubricant or cushion
• Chemical reactions
– Most of the chemical reactions necessary for life do not take
place unless the reacting molecules are dissolved in water
– Water also directly participates in many chemical reactions
• Transport
– Polar solvent properties: dissolves ionic substances, forms
hydration layers around large charged molecules, and serves as
the body’s major transport medium
 Organic Compounds

• Molecules unique to living systems

• They include:
– Carbohydrates
– Lipids
– Proteins
– Nucleic Acids
 Carbohydrates

• Contain carbon, hydrogen, and oxygen

– Ratio of 1:2:1 (C:H:O)
• Their major function is to supply a source
of cellular food
• Examples
– Monosaccharides – glucose and fructose
– Disaccharides – sucrose and lactose
– Polysaccharides – starch and glycogen

Figure 2.14a
Fig. 2.13
 Lipids
• Dissolve in nonpolar solvents, such as alcohol or
acetone, but not in polar solvents, such as water
• Contain C, H, and O, but the proportion of
oxygen in lipids is less than in carbohydrates
• Examples:
– Fats or triglycerides: energy
– Phospholipids: structural components of cell
membranes
– Eicosanoids: regulate physiological processes
– Steroids: regulate physiological processes
 Examples of Lipids Found in the Body

• Fats: found in subcutaneous tissue and around

organs
• Phospholipids: chief component of cell
membranes
• Steroids: cholesterol, bile salts, vitamin D, sex
hormones, and adrenal cortical hormones
• Eicosanoids: prostaglandins, leukotrienes, and
thromboxanes
• Fat-soluble vitamins: vitamins A, D, E, and K
• Lipoproteins: transport fatty acids and
cholesterol in the bloodstream
 Fats (Triglycerides)
• Composed of three fatty acids bonded to a
glycerol molecule

Fig. 2.14
 Fatty Acids
• Saturated: only single covalent bonds between carbons
• Unsaturated: one or more double covalent bonds
between carbons

Fig. 2.15
 Other Lipids
• Phospholipids: modified triglycerides with two
fatty acid groups and a phosphorus group

Fig. 2.16
 Other Lipids
• Eicosanoids: 20-carbon fatty acids found in cell
membranes
• Steroids: flat molecules with four interlocking
hydrocarbon rings

Fig. 2.17
 Proteins
• Macromolecules
• Contain C, H, O, N, and some S
• Composed of 20 basic types of amino
acids bound together with peptide bonds
– Dipeptide: Two amino acids
– Tripeptide: Three amino acids
– Polypeptide: Many amino acids
• Proteins are polypeptides of hundreds of
amino acids
 Amino Acids (AA)
• Building blocks of
proteins
• Organic acids
containing
– amino group (-NH2)
– a carboxyl group (COOH)
– a hydrogen atom
– a side chain designated by
the symbol R attached to the
same carbon atom as the
hydrogen
 Structural Levels of Proteins
• Primary: determined by the number, kind, and
arrangement of amino acids
• Secondary: results from folding or bending of
the polypeptide chain caused by the hydrogen
bonds between amino acids (helices and pleated
sheets)
• Tertiary: results from the folding of the helices or
pleated sheets and the hydrogen bonds formed
with water
• Quaternary: spatial relationships between two
or more proteins that associate to form a
functional unit
 Fig.
2.19ab
 Fig.
2.19cd
 Proteins
• Functions
– regulate chemical reactions (enzymes)
– structural proteins provide the framework for many of the
body’s tissues
– responsible for muscle contraction
– Fibrous proteins
• Extended and strand-like proteins
• Examples: keratin, elastin, collagen, and certain contractile fibers
– Globular proteins
• Compact, spherical proteins with tertiary and quaternary structures
• Examples: antibodies, hormones, and enzymes
• Denaturation
– Disruption of hydrogen bonds, which changes the shape of
proteins and makes them nonfunctional
 Characteristics of Enzymes
• Speed up chemical reactions by lowering the
activation energy
• Most are globular proteins that act as biological
catalysts
• Are chemically specific
• Frequently named for the type of reaction they
catalyze
• Names usually end in -ase
• Chemical events of the body are regulated
primarily by mechanisms that control
– concentration of enzymes
– activity of enzymes
Fig. 2.20
 Enzymes
• Enzymes bind to
reactants according to the
lock-and-key model
– The shape of both the
enzyme and reactants are
critical to the function of the
enzyme
– By bringing the two reactants
close to each other it reduces
the activation energy for the
reaction
– Each enzyme catalyzes only
one type of chemical reaction
– After each reaction the
enzyme is released and can
be used again
Fig. 2.21
 Nucleic Acids
• Composed of C, O, H, N, and P
• The basic unit of nucleic acids is the
nucleotide, which is a monosaccharide with
an attached phosphate and organic base
• Five nitrogenous bases contribute to
nucleotide structure:
– adenine (A)
– guanine (G)
– cytosine (C)
– thymine (T)
– uracil (U)
• Two major classes: DNA and RNA
 Deoxyribonucleic Acid (DNA)
• Double-stranded helical molecule found in the
nucleus of the cell
• Genetic material of the cell
• Replicates itself before the cell divides, ensuring
genetic continuity
• Provides instructions for protein synthesis
• Contains the monosaccharide deoxyribose and
the organic bases
– adenine
– thymine
– guanine
– cytosine
Fig. 2.22
 Ribonucleic Acid (RNA)

• Single-stranded molecule found in both

the nucleus and the cytoplasm of a cell
• Composed of the monosaccharide ribose
and uses the organic base uracil instead
of thymine
• Three varieties of RNA:
– messenger RNA
– transfer RNA
– ribosomal RNA