Chapter 2

Basic Chemistry

Lecture Presentation by
Patty Bostwick-Taylor
Florence-Darlington Technical College

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 Matter and Energy

▪ Matter—anything that occupies space and has

mass
▪Matter may exist as one of three states
▪ Solid: definite shape and volume
▪Liquid: definite volume; shape of container
▪Gaseous: neither a definite shape nor volume

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 Matter and Energy

▪Matter may be changed

▪Physically
▪ Changes do not alter the basic nature of a substance
▪ Examples include changes in the state of matter (solid,
liquid, or gas)
▪Chemically
▪ Changes alter the chemical composition of a substance

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 Matter and Energy

▪Energy—the ability to do work

▪Has no mass and does not take up space
▪Kinetic energy: energy is doing work
▪Potential energy: energy is inactive or stored

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 Matter and Energy

▪Forms of energy
▪Chemical energy is stored in chemical bonds of
substances
▪Electrical energy results from movement of charged
particles
▪Mechanical energy is energy directly involved in
moving matter
▪Radiant energy travels in waves; energy of the
electromagnetic spectrum

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 Matter and Energy

▪Energy form conversions

▪ATP (adenosine triphosphate) traps the chemical
energy of food in its bonds

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 Composition of Matter

▪Elements—fundamental units of matter

▪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

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Table 2.1 Common Elements Making Up the Human Body (1 of 3)

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Table 2.1 Common Elements Making Up the Human Body (2 of 3)

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Table 2.1 Common Elements Making Up the Human Body (3 of 3)

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 Composition of Matter

▪Atoms
▪Building blocks of elements
▪Atoms of elements differ from one another
▪Atomic symbol is chemical shorthand for each element

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 The Basic Atomic Subparticles

▪Protons (p+) are positively charged

▪Neutrons (n0) are uncharged or neutral
▪Electrons (e–) are negatively charged

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Table 2.2 Subatomic Particles

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 The Basic Atomic Subparticles

▪All atoms are electrically neutral

▪Number of protons equals numbers of electrons in an
atom
▪Positive and negative charges cancel each other out
▪Ions are atoms that have lost or gained electrons

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 Planetary and Orbital Models of an Atom

▪Planetary model
▪Portrays the atom as a miniature solar system
▪Protons and neutrons are in the atomic nucleus
▪Electrons are in orbitals around the nucleus

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Figure 2.1a The structure of an atom.

Nucleus

Helium atom

2 protons (p+)
2 neutrons (n0)
2 electrons (e−)

(a) Planetary model

KEY
: Proton Electron
Neutron
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 Planetary and Orbital Models of an Atom

▪Orbital model
▪Electrons are depicted by an electron cloud, a haze of
negative charge, outside the nucleus

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Figure 2.1b The structure of an atom.

Nucleus

Helium atom

2 protons (p+)
2 neutrons (n0)
2 electrons (e−)

(b) Orbital model

KEY:
Proton
Neutron Electron cloud
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 Planetary and Orbital Models of an Atom

▪Electrons determine an atom’s chemical behavior

and bonding properties
▪Although outdated, the planetary model is simple
and easy to understand and use

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 Identifying Elements

▪To identify an element, we need to know the:

▪Atomic number
▪Atomic mass number
▪Atomic weight

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 Identifying Elements

▪Atomic number—equal to the number of protons

that the atom contains
▪Unique to atoms of a particular element
▪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)

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Figure 2.2 Atomic structure of the three smallest atoms.

KEY
: Proton
Neutron
Electron

(a) Hydrogen (H) (b) Helium (He) (c) Lithium (Li)

(1p+; 0n0; 1e−) (2p+; 2n0; 2e−) (3p+; 4n0; 3e−)

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 Atomic Weight and Isotopes

▪Isotopes
▪Atoms that have the same number of protons and
electrons but vary in the number of neutrons
▪Isotopes have the same atomic number but different
atomic masses

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Figure 2.3 Isotopes of hydrogen.

KEY
: Proton
Neutron
Electron

Hydrogen (1H) Deuterium (2H) Tritium (3H)

(1p+; 0n0; 1e−) (1p+; 1n0; 1e−) (1p+; 2n0; 1e−)

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Table 2.3 Atomic Structures of the Most Abundant Elements in the Body

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 Atomic Weights and Isotopes

▪Radioisotope
▪Heavy isotope of certain atoms
▪Tends to be unstable
▪Decomposes to more stable isotope
▪Radioactivity—process of spontaneous atomic
decay
▪Used to tag and trace biological molecules through the
body

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 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)
▪The reactants are the atoms on the left
▪The product is the molecule on the right, represented
by a molecular formula

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 Molecules and Compounds

▪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)

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Figure 2.4 Properties of a compound differ from those of its atoms.

Sodium (silvery metal) Chlorine (poisonous gas) Sodium chloride (table salt)

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 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

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 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

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 Role of Electrons

▪Each electron shell has distinct properties

▪How to fill the atom’s electrons shells
▪Shell 1 can hold a maximum of 2 electrons
▪Shell 2 can hold a maximum of 8 electrons
▪Shell 3 can hold a maximum of 18 electrons
▪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

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Figure 2.5a Chemically inert and reactive elements.

(a) Chemically inert elements

Outermost energy level (valence shell) complete

8e
2e 2e
He Ne

Helium (He) Neon (Ne)

(2p+; 2n0; 2e−) (10p+; 10n0; 10e−)

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 Role of Electrons

▪Rule of eights
▪The key to chemical reactivity
▪Atoms are considered stable when their outermost
(valence) shell has 8 electrons
▪Atoms with 8 electrons in the valence shell are
considered stable and chemically inactive (inert)
▪The exception to this rule of eights is shell 1, which
can hold only 2 electrons

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 Role of Electrons

▪Reactive elements
▪Atoms will gain, lose, or share electrons to complete
their outermost orbitals when fewer than 8 electrons
are in the valence shell
▪Chemical bonding helps atoms achieve a stable
valence shell

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Figure 2.5b Chemically inert and reactive elements.

(b) Chemically reactive elements

Outermost energy level
(valence shell) incomplete

4e
1e 2e
H C

Hydrogen (H) Carbon (C)

(1p+; 0n0; 1e−) (6p+; 6n0; 6e−)

1e
6e 8e
2e 2e
O Na

Oxygen (O)
(8p+; 8n0; 8e−) Sodium (Na)
(11p+; 12n0; 11e−)
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 Types of Chemical Bonds

▪Ionic bonds
▪Form when electrons are completely transferred from
one atom to another
▪Allow atoms to achieve stability through the transfer of
electrons

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 Types of Chemical Bonds

▪Ions
▪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)
▪Tend to stay close together because opposite charges
attract

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Figure 2.6 Formation of an ionic bond.

+ −

Na Cl Na Cl

Sodium atom (Na) Chlorine atom (Cl) Sodium ion (Na+) Chloride ion (Cl−)
(11p+; 12n0; 11e−) (17p+; 18n0; 17e−)
Sodium chloride (NaCl)

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 Types of Chemical Bonds

▪Covalent bonds
▪Atoms become stable through shared electrons
▪Electrons are shared in pairs
▪Single covalent bonds share one pair of electrons
▪Double covalent bonds share two pairs of electrons

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Figure 2.7a Formation of covalent bonds.

Reacting atoms Resulting molecules

H H H H or

Hydrogen Hydrogen Molecule of

atom atom hydrogen gas (H2)
(a) Formation of a single covalent bond

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Figure 2.7b Formation of covalent bonds.

Reacting atoms Resulting molecules

O O O O or

Oxygen atom Oxygen atom Molecule of oxygen gas (O2)

(b) Formation of a double covalent bond

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Figure 2.7c Formation of covalent bonds.

Reacting atoms Resulting molecules

H
H

C H C H or

H
H

Hydrogen atoms Carbon atom Molecule of methane gas (CH4)

(c) Formation of four single covalent bonds

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 Types of Chemical Bonds

▪Covalent bonds can be described as either

nonpolar or polar
▪Nonpolar covalent bonds
▪ Electrons are shared equally between the atoms of the
molecule
▪ Electrically neutral as a molecule
▪ Example: carbon dioxide

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Figure 2.8a Molecular models illustrating the three-dimensional structure of carbon dioxide and water molecules.

(a) Carbon dioxide (CO2)

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 Types of Chemical Bonds

▪Covalent bonds can be described as either

nonpolar or polar (continued)
▪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

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Figure 2.8b Molecular models illustrating the three-dimensional structure of carbon dioxide and water molecules.

δ−

δ+ δ+
(b) Water (H2O)

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 Types of Chemical Bonds

▪Hydrogen bonds
▪Extremely weak chemical bonds
▪Formed when a hydrogen atom is attracted to the
negative portion, such as an oxygen or nitrogen atom,
of a polar molecule
▪Responsible for the surface tension of water
▪Important for forming intramolecular bonds, as in
protein structure

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Figure 2.9 Hydrogen bonding between polar water molecules.

δ+
H H
O
δ−

Hydrogen bonds

δ+

δ+
δ− δ− δ−
H H
O O
δ+
δ+
H H
H
δ+
O
H
δ−
(a) (b)

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 Patterns of Chemical Reactions

▪Synthesis reaction (A + B → AB)

▪Atoms or molecules combine to form a larger, more
complex molecule
▪Energy is absorbed for bond formation
▪Underlies all anabolic (building) activities in the body
▪Decomposition reaction (AB → A + B)
▪Molecule is broken down into smaller molecules
▪Chemical energy is released
▪Underlies all catabolic (destructive) activities in the
body

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Figure 2.10a Patterns of chemical reactions.

(a) Synthesis reactions

Smaller particles are

bonded together to form
larger, more complex
molecules.

Example
Amino acids are joined
together to form a protein
molecule.

Amino acid
molecules

Protein
molecule

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Figure 2.10b Patterns of chemical reactions.

(b) Decomposition reactions

Bonds are broken in larger

molecules, resulting in
smaller, less complex
molecules.

Example
Glycogen is broken down to
release glucose units.

Glycogen

Glucose
molecules
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 Patterns of Chemical Reactions

▪Exchange reaction
AB + C → AC + B
and
AB + CD → AD + CB
▪Involves simultaneous synthesis and decomposition
reactions as bonds are both made and broken
▪Switch is made between molecule parts, and different
molecules are made

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Figure 2.10c Patterns of chemical reactions.

(c) Exchange reactions

Bonds are both made and broken.

Example
ATP transfers its terminal phosphate
group to glucose to form glucose-
phosphate.

P P P

Glucose Adenosine triphosphate

(ATP)

P P

Glucose- Adenosine diphosphate

phosphate (ADP)

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 Patterns of Chemical Reactions

▪Most chemical reactions are reversible

▪Reversibility is indicated by a double arrow
▪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

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Table 2.4 Factors Increasing the Rate of Chemical Reactions

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 Biochemistry: The Chemical Composition of
Living Matter
▪Inorganic compounds
▪Lack carbon
▪Tend to be small, simple molecules
▪Include water, salts, and many (not all) acids and
bases
▪Organic compounds
▪Contain carbon
▪All are large, covalent molecules
▪Include carbohydrates, lipids, proteins, and nucleic
acids

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 Inorganic Compounds

▪Water
▪Most abundant inorganic compound in the body
▪Accounts for two-thirds of the body’s weight
▪Vital properties include:
▪ High heat capacity
▪ Polarity/solvent properties
▪ Chemical reactivity
▪ Cushioning

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 Inorganic Compounds

▪High heat capacity

▪Water absorbs and releases a large amount of heat
before it changes temperature
▪Prevents sudden changes in body temperature

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 Inorganic Compounds

▪Polarity/solvent properties
▪Water is often called the “universal solvent”
▪Solvents are liquids or gases that dissolve smaller
amounts of solutes
▪Solutes are solids, liquids, or gases that are dissolved
or suspended by solvents
▪Solution forms when solutes are very tiny
▪Colloid forms when solutes of intermediate size form a
translucent mixture

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 Inorganic Compounds

▪Chemical reactivity
▪Water is an important reactant in some chemical
reactions
▪Reactions that require water are known as hydrolysis
reactions
▪Example: water helps digest food or break down
biological molecules

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 Inorganic Compounds

▪Cushioning
▪Water serves a protective function
▪Examples: cerebrospinal fluid protects the brain from
physical trauma, and amniotic fluid protects a
developing fetus

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 Inorganic Compounds

▪Salts
▪Ionic compound
▪Contain cations other than H+ and anions other than OH–
▪Easily dissociate (break apart) into ions in the presence
of water
▪Vital to many body functions
▪ Example: sodium and potassium ions are essential for
nerve impulses

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Figure 2.11 Dissociation of salt in water.

δ+
H
δ− O
H
δ+
Water molecule

Na+

Na+

Cl− Cl−

Salt Ions in
crystal solution
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 Inorganic Compounds

▪Salts (continued)
▪All salts are electrolytes
▪Electrolytes are ions that conduct electrical currents

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 Inorganic Compounds

▪Acids
▪Electrolytes that dissociate (ionize) in water and
release hydrogen ions (H+)
▪Proton (H+) donors
▪Example: HCl → H+ + Cl–
▪Strong acids ionize completely and liberate all their
protons
▪Weak acids ionize incompletely

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 Inorganic Compounds

▪Bases
▪Electrolytes that dissociate (ionize) in water and
release hydroxyl ions (OH–)
▪Proton (H+) acceptors
▪Example: NaOH → Na+ + OH–

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 Inorganic Compounds

▪Neutralization reaction
▪Type of exchange reaction in which acids and bases
react to form water and a salt
▪Example: NaOH + HCl → H2O + NaCl

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 Inorganic Compounds

▪pH
▪pH measures relative concentration of hydrogen (and
hydroxide) ions in body fluids
▪pH scale is based on the number of protons in a
solution
▪pH scale runs from 0 to 14
▪Each successive change of 1 pH unit represents a
tenfold change in H+ concentration

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 Inorganic Compounds

▪pH (continued)
▪Neutral
▪ 7 is neutral
▪ Neutral means that the number of hydrogen ions exactly
equals the number of hydroxyl ions
▪Acidic solutions have a pH below 7
▪ More H+ than OH–
▪Basic solutions have a pH above 7
▪ Fewer H+ than OH–
▪Buffers—chemicals that can regulate pH change

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Figure 2.12 The pH scale and pH values of representative substances.
pH Examples

Sodium
14
hydroxide
(pH 14)
13 Oven cleaner,
lye

Increasingly basic
(pH 13.5)
12

OH− Household
OH−
OH− H+
OH− H+
11 ammonia
OH− OH− (pH 10.5−11.5)

10
Basic
Household
solution bleach
9 (pH 9.5)

Egg white
8
H+ (pH 8)

Neutral
[H ]=[OH ]
OH−

–
OH− H+
H H+
+
Blood
OH− OH− 7 (pH 7.4)

+
Neutral Milk
solution 6 (pH 6.3−6.6)

5 Black coffee
Increasingly acidic

(pH 5)
H+ OH−
H+ H+
H+ H+ 4
OH− H+

Wine
Acidic 3 (pH 2.5−3.5)
solution
Lemon juice;
2 gastric juice
(pH 2)
1

Hydrochloric
0 acid (pH 0)
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 Organic Compounds

▪Polymer: chainlike molecules made of many

similar or repeating units (monomers)
▪Many biological molecules are polymers, such as
carbohydrates and proteins

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 Organic Compounds

▪Dehydration synthesis—monomers are joined to

form polymers through the removal of water
molecules
▪A hydrogen ion is removed from one monomer while a
hydroxyl group is removed from the monomer it is to
be joined with
▪Water is removed at the site where monomers join
(dehydration)

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Figure 2.13a Dehydration synthesis and hydrolysis of biological molecules.

(a) Dehydration synthesis

Monomers are joined by removal of OH from one monomer
and removal of H from the other at the site of bond formation.
H2O

Monomer 1 Monomer 2

Monomers linked by covalent bond

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 Organic Compounds

▪Hydrolysis—polymers are broken down into

monomers through the addition of water
molecules
▪As a water molecule is added to each bond, the bond
is broken, and the monomers are released

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Figure 2.13b Dehydration synthesis and hydrolysis of biological molecules.

(b) Hydrolysis
Monomers are released by the addition of a water molecule,
adding OH to one monomer and H to the other.
H2O
Monomer 1 Monomer 2

Monomers linked by covalent bond

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 Organic Compounds

▪Carbohydrates
▪Contain carbon, hydrogen, and oxygen
▪Include sugars and starches
▪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

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 Organic Compounds

▪Monosaccharides—simple sugars
▪Single-chain or single-ring structures
▪Contain three to seven carbon atoms
▪Examples: glucose (blood sugar), fructose, galactose,
ribose, deoxyribose

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Figure 2.14a Carbohydrates.

(a) Simple sugar (monosaccharide)

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 Organic Compounds

▪Disaccharides—two simple sugars joined by

dehydration synthesis
▪Examples include sucrose, lactose, and maltose
▪Too large to pass through cell membranes

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Figure 2.14b Carbohydrates.

(b) Double sugar (disaccharide)

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Figure 2.14c Carbohydrates.

Dehydration
synthesis
H2O
Hydrolysis

Glucose Fructose Sucrose Water

(c) Dehydration synthesis and hydrolysis of a molecule of sucrose

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 Organic Compounds

▪Polysaccharides: long, branching chains of linked

simple sugars
▪Large, insoluble molecules
▪Function as storage products
▪Examples include starch and glycogen

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Figure 2.14d Carbohydrates.

(d) Starch (polysaccharide)

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 Organic Compounds

▪Lipids
▪Most abundant are the triglycerides, phospholipids,
and steroids
▪Contain carbon, hydrogen, and oxygen
▪ Carbon and hydrogen outnumber oxygen
▪Insoluble in water, but soluble in other lipids

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Table 2.5 Representative Lipids Found in the Body (1 of 2)

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Table 2.5 Representative Lipids Found in the Body (2 of 2)

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 Organic Compounds

▪Triglycerides, or neutral fats

▪Found in fat deposits
▪Source of stored energy
▪Composed of two types of building blocks—fatty acids
and one glycerol molecule
▪ Saturated fatty acids
▪ Unsaturated fatty acids

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Figure 2.16a Examples of saturated and unsaturated fats and fatty acids.

Structural formula of a
saturated fat molecule

(a) Saturated fat. At room temperature, the

molecules of a saturated fat such as this butter
are packed closely together, forming a solid.

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 Organic Compounds

▪Fatty acid chains of triglycerides

▪Saturated fats
▪ Contain only single covalent bonds
▪ Chains are straight
▪ Exist as solids at room temperature since molecules
pack closely together
▪Unsaturated fats
▪ Contain one or more double covalent bonds, causing
chains to kink
▪ Exist as liquid oils at room temperature
▪ “Heart healthy”

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Figure 2.16a Examples of saturated and unsaturated fats and fatty acids.

Structural formula of a
saturated fat molecule

(a) Saturated fat. At room temperature, the

molecules of a saturated fat such as this butter
are packed closely together, forming a solid.

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Figure 2.16b Examples of saturated and unsaturated fats and fatty acids.

Structural formula of an
unsaturated fat molecule

(b) Unsaturated fat. At room temperature, the

molecules of an unsaturated fat such as this
olive oil cannot pack together closely enough
to solidify because of the kinks in some of
their fatty acid chains.
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 Organic Compounds

▪Trans fats
▪Oils that have been solidified by the addition of
hydrogen atoms at double bond sites
▪Increase risk of heart disease
▪Omega-3 fatty acids
▪Found in cold-water fish and plant sources, including
flax, pumpkin, and chia seeds; walnuts and soy foods
▪Appear to decrease risk of heart disease

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 Organic Compounds

▪Phospholipids
▪Contain two fatty acids chains rather than three; they
are hydrophobic (“water fearing”)
▪Phosphorus-containing polar “head” carries an
electrical charge and is hydrophilic (“water loving”)
▪Charged “head” region interacts with water and ions
while the fatty acid chains (“tails”) do not
▪Form cell membranes

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Figure 2.15b Lipids.

Polar “head”

Nonpolar “tail”
(schematic
phospholipid)

Phosphorus-containing Glycerol 2 fatty acid chains

group (polar head) backbone (nonpolar tail)
(b) Typical structure of a phospholipid molecule (phosphatidylcholine). Two fatty acid chains and
a phosphorous-containing group are attached to a glycerol backbone.

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 Organic Compounds

▪Steroids
▪Formed of four interlocking rings
▪Include cholesterol, bile salts, vitamin D, and some
hormones
▪Some cholesterol is ingested from animal products;
the liver also makes cholesterol
▪Cholesterol is the basis for all steroids made in the
body

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Figure 2.15c Lipids.

(c) Cholesterol. Simplified structure

of cholesterol, a steroid, formed
by four interlocking carbon rings.

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 Organic Compounds

▪Proteins
▪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
▪Contain carbon, oxygen, hydrogen, nitrogen, and
sometimes sulfur
▪Built from building blocks called amino acids

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 Organic Compounds

▪Amino acid structure

▪Contain an amine group (NH2)
▪Contain an acid group (COOH)
▪Vary only by R-groups

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Figure 2.17 Amino acid structures.

Amine
(basic Acid
) group
group

(a) Generalized (b) Glycine is the (c) Aspartic acid (d) Lysine (a basic (e) Cysteine (a
structure of simplest (an acidic amino amino acid) basic amino
all amino acids. amino acid. acid) has an acid has an amine acid) has a
group (—COOH) in group (—NH2) sulfhydryl (—SH)
the R group. in the R group. group in the
R group.

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 Organic Compounds

▪Protein structure
▪Polypeptides contain fewer than 50 amino acids
▪Proteins contain more than 50 amino acids
▪Large, complex proteins contain 50 to thousands of
amino acids
▪Sequence of amino acids produces a variety of
proteins

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 Organic Compounds

▪Structural levels of proteins

▪Primary structure—strand of amino acid “beads”
▪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
▪Tertiary structure—compact, ball-like (globular)
structure
▪Quaternary structure—result of a combination of two
or more polypeptide chains

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Figure 2.18a The four levels of protein structure.

Ala Ala
Glu Leu Ala
Cys Ala
Met Lys Arg Aps
His Gly Leu

Amino
acids
(a) Primary structure. A protein’s primary structure is the unique sequence
of amino acids in the polypeptide chain.

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Figure 2.18b The four levels of protein structure.

Hydrogen bonds

β-pleated sheet
Alpha-
helix
(b) Secondary structure. Two types of secondary structure are the
alpha-helix and beta-pleated sheet. Secondary structure is reinforced
by hydrogen bonds, represented by dashed lines in this figure.
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Figure 2.18c The four levels of protein structure.

Protein (if > 50

amino acids) or
polypeptide (if < 50
amino acids)

(c) Tertiary structure. The overall three-dimensional

shape of the polypeptide or protein is called tertiary
structure. It is reinforced by chemical bonds
between the R-groups of amino acids in different
regions of the protein chain.

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Figure 2.18d The four levels of protein structure.

Complex protein
with four polypeptide
subunits, each with
tertiary structure

(d) Quaternary structure. Some proteins consist of

two or more polypeptide chains. For example, four
polypeptides construct the protein hemoglobin, a
blood protein.

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 Organic Compounds

▪Fibrous (structural) proteins

▪Appear in body structures
▪Exhibit secondary, tertiary, or even quaternary
structure
▪Bind structures together and exist in body tissues
▪Stable proteins
▪Examples include collagen and keratin

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Figure 2.19a General structure of (a) a fibrous protein and (b) a globular protein.

(a) Triple helix of collagen

(a fibrous or structural protein).

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 Organic Compounds

▪Globular (functional) proteins

▪Function as antibodies, hormones, or enzymes
▪Exhibit at least tertiary structure
▪Hydrogen bonds are critical to the maintenance of
structure
▪Can be denatured and no longer perform physiological
roles
▪Active sites “fit” and interact chemically with other
molecules

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Figure 2.19b General structure of (a) a fibrous protein and (b) a globular protein.

Heme group

Globin
protein

(b) Hemoglobin molecule composed of the

protein globin and attached heme groups.
(Globin is a globular, or functional, protein.)

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Table 2.6 Representative Classes of Functional Proteins

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 Organic Compounds

▪Enzymes
▪Act as biological catalysts
▪Increase the rate of chemical reactions
▪Bind to substrates at an active site to catalyze
reactions
▪Can be recognized by their –ase suffix
▪ Hydrolase
▪ Oxidase

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Figure 2.20 A simplified view of enzyme action.

Energy is
absorbed; Product (P)
bond is e.g., disaccharide
Substrates (S)
formed by Water is
e.g., simple sugars
dehydration released.
synthesis. H2O

Active site

Enzyme-substrate
complex (E-S)
Enzyme (E) 1 Substrates bind at active 2 The E-S complex Enzyme (E)
site, temporarily forming an undergoes structural
3 The enzyme
enzyme-substrate complex. changes that form the
releases the product
product.
of the reaction.

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 Organic Compounds

▪Nucleic acids
▪Form genes
▪Composed of carbon, oxygen, hydrogen, nitrogen, and
phosphorus atoms
▪Largest biological molecules in the body
▪Two major kinds:
▪ DNA
▪ RNA

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 Organic Compounds

▪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

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Figure 2.21ab Structure of DNA.

Pentose Nitrogen-
Phosphate sugar: containing base:
group Deoxyribose Adenine (A)

(b) Adenine nucleotide

(Diagrammatic representation)

(a) Adenine nucleotide

(Chemical structure)

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 Organic Compounds

▪Deoxyribonucleic acid (DNA)

▪The genetic material found within the cell’s nucleus
▪Provides instructions for every protein in the body
▪Organized by complementary bases to form a double-
stranded helix
▪Contains the sugar deoxyribose and the bases
adenine, thymine, cytosine, and guanine
▪Replicates before cell division

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Figure 2.21c Structure of DNA.

(c) Computer-generated image of a DNA molecule

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Figure 2.21d Structure of DNA.

Hydrogen bonds

KEY
: Thymine (T)

Adenine (A)

Cytosine (C)
Deoxyribose
sugar Guanine (G)
Phosphate

Sugar-phosphate
backbone

(d) Diagram of a DNA molecule

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 Organic Compounds

▪Ribonucleic acid (RNA)

▪Carries out DNA’s instructions for protein synthesis
▪Created from a template of DNA
▪Organized by complementary bases to form a single-
stranded helix
▪Contains the sugar ribose and the bases adenine,
uracil, cytosine, and guanine
▪Three varieties are messenger, transfer, and ribosomal
RNA

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 Organic Compounds

▪Adenosine triphosphate (ATP)

▪Composed of a nucleotide built from ribose sugar,
adenine base, and three phosphate groups
▪Chemical energy used by all cells
▪Energy is released by breaking high-energy phosphate
bond

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Figure 2.22 ATP—structure and hydrolysis.

Adenine base
High-energy
phosphate
bonds

P P P
Ribose
Phosphate groups sugar

(a) Adenosine triphosphate (ATP)

H2O

P P P P P Pi Energy
Hydrolysis
Adenosine diphosphate
ATP
(ADP)

(b) Hydrolysis of ATP

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 Organic Compounds

▪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

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Figure 2.23 Three examples of how ATP drives cellular work.

P Pi
A
ADP
ATP +
B A B
Pi

(a) Chemical work. ATP provides the energy

needed to drive energy-absorbing chemical
reactions.

Solute

ADP
ATP +
Pi

Membrane P Pi
protein

(b) Transport work. ATP drives the transport of

certain solutes (amino acids, for example)
across cell membranes.
ADP
ATP +
Relaxed Contracted Pi
muscle cell muscle cell
(c) Mechanical work. ATP activates contractile
proteins in muscle cells so that the cells can
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shorten and perform mechanical work.