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 and Energy

 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

Matter and Energy

 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

Matter and Energy

 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

Matter and Energy

 Energy form conversions
o ATP (adenosine triphosphate) traps the chemical energy of food in its bonds

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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

Composition of Matter
 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

The Basic Atomic Subparticles

 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

Planetary and Orbital Models of an Atom

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

Planetary and Orbital Models of an Atom

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 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

Identifying Elements
 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

Atomic Weights and Isotopes

 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

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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)

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

Role of Electrons
 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

Role of Electrons
 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

Role of 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

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 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

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Types of Chemical Bonds
 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

Types of Chemical Bonds

 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

Types of Chemical Bonds

 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

Types of Chemical Bonds

 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

Types of Chemical Bonds

 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

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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

Patterns of Chemical Reactions

 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

Patterns of Chemical Reactions

 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

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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

Inorganic Compounds
 High heat capacity
o Water absorbs and releases a large amount of heat before it changes
temperature
o Prevents sudden changes in body temperature

Inorganic Compounds
 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

Inorganic Compounds
 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

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

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Inorganic Compounds
 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

Inorganic Compounds
 Salts (continued)
o All salts are electrolytes
o Electrolytes are ions that conduct electrical currents

Inorganic Compounds
 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

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

Inorganic Compounds
 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

Inorganic Compounds
 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

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 o Each successive change of 1 pH unit represents a tenfold change in H +
concentration

Inorganic Compounds
 pH (continued)
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

Organic Compounds
 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)

Organic Compounds
 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

Organic Compounds
 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

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 Polysaccharides—long-branching chains of linked simple sugars

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Organic Compounds
 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

Organic Compounds
 Disaccharides—two simple sugars joined by dehydration synthesis
o Examples include sucrose, lactose, and maltose
o Too large to pass through cell membranes

Organic Compounds
 Polysaccharides: long, branching chains of linked simple sugars
o Large, insoluble molecules
o Function as storage products
o Examples include starch and glycogen

Organic Compounds
 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

Organic Compounds
 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

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Organic Compounds
 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”

Organic Compounds
 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

Organic Compounds
 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

Organic Compounds
 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

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Organic Compounds
 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

Organic Compounds
 Amino acid structure
o Contain an amine group (NH2)
o Contain an acid group (COOH)
o Vary only by R-groups

Organic Compounds
 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

Organic Compounds
 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

Organic Compounds
 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

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 o Examples include collagen and keratin

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Organic Compounds
 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

Organic Compounds
 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

Organic Compounds
 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

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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Organic Compounds
 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

Organic Compounds
 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

Organic Compounds
 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

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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