Chapter 2

Chemistry of Life
 Lesson 2.1: Atoms, Ions,
Chemical Bonds, and Chemical
Reactions
1. Define and describe matter, element,
atom, and ion.
2. Define and describe the atomic nucleus
and define atomic weight, neutron,
proton, electron, valence, and isotope.
3. Name, describe, and rank the different
types of chemical bonds.
4. Describe the different types of
chemical reactions.
5. Define the rules of chemical notation.
 Elements (1 of 2)
 Matter
 Anything that occupies space and has mass
 Matter can be in liquid, gaseous, or solid
form and is composed of elements, the
smallest particles of which are atoms.
 Elements
 Cannot be broken down further by natural
forces
 Oxygen, carbon, hydrogen, nitrogen,
phosphorus, and sulfur are some of the
elements most commonly found in living
cells.
 Elements (2 of 2)
 Atoms
 Smallest particles of an element
 Chemical compound
 Elements in combination
 Although chemical elements usually do not
exist in free form, they do occur in
combinations called chemical compounds.
 Chemical formula
 Shorthand expression for a chemical
compound
• NaCl or H2O
 Atomic Model (1 of 2)

 Atomic nucleus
 Contains protons and neutrons
 Protons
 Positively charged particles
 Neutrons
 Particles without charge
 Electrons
 Negatively charged particles
 Atomic Model (2 of 2)

 Atomic weight
 Equals the number of protons and neutrons
 Atomic number
 Equals the number of protons
 Orbitals/shells
 Volume of space that contains electrons
 Electron Shells/Orbitals (1 of 2)

 Are energy levels around nucleus

 Contain electrons
 Number of shells depends on atomic

number
 First shell can hold only two electrons
 Second shell can hold up to eight

electrons
 Electron Shells/Orbitals (2 of 2)

 Electrons in more distant shells have

higher energy
 Shells always fill sequentially from the

inside out
 Two electrons in the first shell
 Eight electrons in the next
 When the outermost shell is filled, the
atom is stable
 Valence Electrons

 Electrons in the outermost shell

 Can participate in chemical reactions
 Determine what kind of chemical bond,

if any, the atom can form

 If the outermost shell is filled, the atom

is stable (inert) and cannot react with

another atom
 Isotopes

 Atoms with the same number of protons

but a different number of neutrons
 Atomic number of isotopes is

unchanged
 Atomic weight is different
 Ions

 Electrically charged atoms, molecules,

particles
 + or – due to electron loss or gain
 Cations (+)
 Anions (–)
 Electrolytes: Free ions present in solvent

(e.g., water)
 Common Ions in Living
Organisms
Cations Anions

Sodium (NA+) Chloride (Cl-)

Potassium (K+) Bicarbonate (HCO3-)

Calcium (Ca2+) Phosphate (PO4-3)

Magnesium (Mg2+) Sulfate (SO42-)

 Chemical Bonds and Molecules

 Molecules form by chemical bonding

between valence electrons of atoms
 Number of bonds possible between atoms is
determined by the number of electrons
needed to complete the outermost shell
 Compounds are made from atoms of
different elements
 Covalent Bonds (1 of 2)

 Result from a sharing of electrons

 Nonpolar covalent bond
 Equal sharing of electrons
 Polar covalent bond
 Unequal sharing of electrons
• Electrons are pulled toward the larger atom
• Result: One end of the molecule is more negative,
the other more positive
 Covalent Bonds (2 of 2)

 Single covalent bond

 H–H
 Double covalent bond
 O=O
 Triple covalent bond
 N≡N
 Ionic Bonds

 Transfer of valence electrons from one

atom to another
 Forms charged atoms called ions
 Loss of electron(s): Positive charge
 Gain of electron(s): Negative charge
 Hydrogen Bonds

 Weak chemical bonds

 Attraction between charged atoms

within a large molecule (e.g., DNA) or

between adjacent molecules (e.g., H2O)
 Always involve a hydrogen atom (+)

attracted to an oxygen (–) or nitrogen

(–) atom
 van der Waals Forces

 Weakest of intermolecular forces

 Dependent on interatomic distance
 Determine final molecular arrangement
 “Lock and key” concept
 Example: Antibody and antigen complex
 Chemical Reactions (1 of 2)

 Synthesis (dehydration synthesis)

 Formation of a larger molecule from smaller
ones
 Removal of H2O
 Hydrolysis
 Breakdown of large molecules
 Requires H2O
 Chemical Reactions (2 of 2)

 Endergonic: Requires energy

 Synthesis
 Exergonic: Gives off energy
 Hydrolysis
 Redox (reduction-oxidation)
 Reduction: Gain of electrons
 Oxidation: Loss of electrons
 Simultaneous electron transfer
 Chemical Notations
 Also referred to as chemical shorthand
 Shows chemical compounds and reactions
 Rules
 The abbreviation of an element represents
one atom of that element and is its chemical
symbol
 The number before the chemical symbol is
the number of atoms; the number before the
chemical formula is the number of molecules
 The subscript after the chemical symbol of
an element shows the number of that atom in
the molecule
 A superscript of plus or minus after the atomic symbol
indicates an ion
 Chemical reactions do not form or destroy atoms; they
 Lesson 2.2: Inorganic
Compounds
and Organic Molecules
6. Discuss acid-base balance and the pH scale
7. Discuss the properties of water and define solvent,
solute, solution, hypertonic, hypotonic, isotonic,
hydrophilic, and hydrophobic
8. Describe the common properties of all organic
molecules
9. Name the monomers of carbohydrates and describe
the structure and function of disaccharides and
polysaccharides
10. Describe the structures and functions of amino acids,
peptides, and proteins
11. Name and describe the structures and functions of the
different lipids
12. Describe the structures of nucleic acids and
nucleotides; name and discuss the function of the
 Inorganic Compounds

 Compounds that do not contain carbon

 Exceptions: CO (carbon dioxide) and
2
CO (carbon monoxide)
 Acids and Bases

 Substances that dissociate in water can

form acids, bases, or salts
 Acids
 Substances that release hydrogen ions
 Bases
 Substances that release hydroxyl ions
 The higher the hydrogen ion
concentration in the solution, the more
acidic the solution.
 A low hydrogen ion concentration of a

solution indicates a basic solution.

 pH Scale

 Measures the alkalinity or acidity of a

solution
 Based on the hydrogen ion

concentration
 pH scale runs from 0 to 14
 Pure H O is neutral: pH of 7
2
 Acids: pH <7
 Bases: pH >7
 Buffers

 Chemicals that can absorb hydrogen or

hydroxyl ions
 Can resist pH changes of a solution
 Buffers are essential for maintaining the

pH necessary for the survival of living

cells
 All biological fluids, both intracellular

and extracellular, are heavily buffered.

 Salts
 Substances that dissociate in water and
do not release hydrogen or hydroxyl
ions
 Formed by acid-base reaction or metal-

acid reaction
 Naming: Specific
 Starts with name of cation
 Followed by name of anion
 Different salts can stimulate sensations
of all five basic tastes: Salty (sodium
chloride), sweet (lead diacetate), sour
(potassium bitartrate), bitter
(magnesium sulfate), and umami
 Water (1 of 3)

 Necessary for all life forms on earth

 Exists in three different temperature-

dependent states
 Important solvent
 Held together by hydrogen bonds
 Consists of hydrogen and oxygen in a

ratio of two to one

 Polar molecule (polar covalent bond)
 Water (2 of 3)

 Solutions
 Isotonic
• Solute concentration equal on inside and
outside of cell
 Hypertonic
• Solute concentration in cell less than outside
of cell
 Hypotonic
• Solute concentration in cell higher than
outside of cell
 Water (3 of 3)

 Hydration spheres
 Ions attract polar water molecules
 Hydrophilic
 Water-soluble (water-loving) compounds
 Hydrophobic
 Insoluble in water (water-repelling)
 Organic Molecules

 Carbon (hydrocarbon) backbone

 Chain
 Ring
 Monomer
 Building block, unit molecule
 Polymer
 Consists of monomers
 Carbohydrates (1 of 3)

 Contain carbon, hydrogen, oxygen in a

ratio of 2:1:2
 Monomers: Monosaccharides
 Glucose
 Fructose
 Galactose
 Ribose
 Deoxyribose
 Carbohydrates (2 of 3)

 Disaccharides: Two monosaccharides

joined covalently
 Sucrose
• Glucose + fructose
 Lactose
• Glucose + galactose
 Maltose
• Glucose + glucose
 Carbohydrates (3 of 3)

 Polysaccharides: Many
monosaccharides linked together
 Starch
• Storage form of glucose in plants
 Glycogen
• Storage form of glucose in animals
 Cellulose
• Component of the cell walls of plants, fungi, and
most algae
 Proteins

 Monomers: Amino acids

 20 naturally occurring amino acids
 All consist of an amino group, carboxyl
group, and variable side chain (R group)
 Dipeptide: Two amino acids joined by a
peptide bond
 Polypeptide: 10 or more amino acids
 Proteins:
Structural Arrangements
 Primary structure
 Single chain of amino acids
 Secondary structure
 α Helix or β sheet
 Tertiary structure
 Globular shape: Three-dimensional
 Quaternary structure
 More than one tertiary protein
 Lipids (1 of 4)

 Triglycerides
 Fats and oils
• Saturated and unsaturated
 Consist of glycerol and fatty acid chains
(neutral fats)
 Insoluble in water
 Room temperature
• Fats: Solid
• Oils: Liquid
 Lipids (2 of 4)

 Phospholipids
 Glycerol, two fatty acid chains, phosphate
group on one end
 Polar heads, nonpolar tails
 Main component of the plasma (cell)
membrane
 Basis of biological barrier properties
 Lipids (3 of 4)

 Steroids
 Anabolic steroids
 Sex steroids
 Mineralocorticoids
 Glucocorticoids
• Metabolism and immune function
 Phytosterols
• Steroid alcohols: Naturally occur in plants such as
yeast and fungi
 Lipids (4 of 4)

 Cholesterol
 Precursor of steroids and vitamin D
 Prostaglandins
 Local hormones
 In a variety of tissues
 Involved in:
• Defense mechanisms: Blood clotting and
inflammation
 Nucleic Acids (1 of 2)

 Monomers: Nucleotides
 Functions
 DNA: Deoxyribonucleic acid
• Storage of genetic information
 RNA: Ribonucleic acid
• Directing protein synthesis
 ATP: Adenosine triphosphate
• Energy transfer
 Nucleic Acids (2 of 2)

 The bases in a nucleic acid polymer can

form hydrogen bonds with the
neighboring bases by a process called
complementary base pairing
 Nucleotides
 Pentose sugar
 Phosphate
 Nitrogen base
• Purines
 Adenine (A) and guanine (G)
• Pyrimidines
 Cytosine (C), thymine (T), and uracil (U)