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Chapter 02
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2.1 Basic Chemistry
2
A. Introduction
1.
Matter – anything that takes up space and
has mass
2. States of matter
a. Solid
b. Liquid
c. Gas
3
B. Elements and Atoms
1.
Elements – basic substances that make up
matter; 92 naturally occurring elements
a. Four elements that make up >90% of
the human body
1) Carbon (C)
2) Nitrogen (N)
3) Oxygen (O)
4) Hydrogen (H)
b. Represented by a symbol containing one
or two letters
4
Common Elements in Living Things
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2. Atoms
a.
Smallest unit of an element that has
chemical and physical properties of that
element
b. Smallest unit to enter into chemical
reactions
c. Structure
1) Central nucleus containing protons and
neutrons
2) Outer shells (energy levels) containing
electrons
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d. Subatomic particles
1) In the nucleus
a) Protons – positive charge
b) Neutrons – no charge
2) In shells
a) Electrons – negative charge
b) Innermost shell (1st energy level) can
have 2 electrons
c) Outer shells can have up to 8 electrons
d) Number of electrons in the outer-most
shell determines the chemical properties
of an atom
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Elements and Atoms
8
Atoms, cont
e.
Atomic number
1) Number of protons in the nucleus
2) Determines the identity of the element
3) Whole, consecutive numbers on the
Periodic Table
f.
Mass number
1) Number of protons plus the number of
neutrons
2) This number is NOT found on the
Periodic Table
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g. Mole
1)
2)
3)
Measurement for the number of atoms or
molecules of a compound
Avogadro’s number 6.02 x 10 23
Based on the number of atoms in exactly
12 grams of carbon-12 atoms
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C. Isotopes
1.
Isotopes are variations of one type of atom that
differ in the number of neutrons; the number of
protons does not change
2.
Radioactive isotopes
a. Unstable isotopes that break down over time
b. Releases detectable energy
c. Low levels of radiation can be used as tracers,
X-rays, mammograms
d. High levels of radiation can be harmful to cells,
but can also be useful, such as for cancer
treatment and sterilizing medical and dental
equipment
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D. Molecules and compounds
1.
2.
Molecules – form when atoms bond to
each other by covalent bonds
Compounds – form when atoms of
different elements bond
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3. Ionic bonds
a.
Ions form when an atom gains or loses electrons in
its outer energy level to become stable
1) Positive ion—has lost electrons; indicated by
superscript positive sign, as in Na+ or Ca2+
2) Negative ion—has gained electrons; indicated by
superscript negative sign, as in Cl– or O2b.
An ionic bond is formed when positive and negative
ions attract each other; the number of ions used is
what is needed to maintain electrical neutrality
c.
Ionic compounds can dissociate (separate into
ions) when dissolved in water and are then referred
to as electrolytes.
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Ionic Reaction
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4. Covalent bonds
a.
b.
Created when atoms share electrons
Atoms can share one or more pairs of
electrons
1) Single bonds – atoms share one pair of
electrons; ex – H2, H-H
2) Double bonds – atoms share two pairs of
electrons; ex – O2, O=O
3) Triple bonds – atoms share three pairs
of electrons between them; N2, N≡N
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c. Polar and nonpolar covalent bonds
1) Polar covalent bonds result when there is
an unequal sharing of electrons between
atoms
a) Electrons spend more time closer to
one atom than the other
b) Get areas of partial positive and partial
negative charges
c) Molecules act like little magnets
2) Nonpolar covalent bonds result from
equal attraction for shared electrons
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Covalent Reactions
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2.2 Water, Acids, and Bases
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A. Water
1.
Introduction
a. Most abundant molecule in living organisms;
60-70% of body weight
b. An inorganic molecule (does not contain carbon
atoms)
c. A polar molecule
1) Oxygen has a slight negative charge (δ-)
2) Hydrogen atoms have a slight positive charge
(δ+)
3) Attraction between slightly positive hydrogen
atoms and slightly positive oxygen atom
results in hydrogen bonds
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Polar water molecule
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Hydrogen bonding between water molecules
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2. Properties of water
a. Water is a solvent (liquid into which
particles are dissolved)
1) Facilitates chemical reactions
2) Molecules that dissolve in water are said
to be hydrophilic (water-loving)
3) Molecules that do not dissolve easily in
water are said to be hydrophobic (water
fearing)
4) Ionic compounds and polar molecules
tend to dissolve in water
5) Nonpolar molecules do not dissolve in
water
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Properties of water, cont
b. Water molecules are cohesive and adhesive
1) Cohesion - water molecules cling together
because of hydrogen bonding
2) Adhesion - water molecules cling to other
substances due to hydrogen bonds
3) Water flows freely, allowing it to
distribute evenly
4) Allows for transport
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Properties of water, cont
c. Water has a high specific heat capacity and
a high heat of vaporization
1) Specific heat capacity is the amount of
energy needed to change an object’s
temperature by 1C
2) Water can absorb large amounts of heat
without changing its temperature
3) Heat of vaporization is the amount of
energy needed to turn water into steam
which allows for release of heat
4) Both processes are necessary for
thermoregulation of body temperature
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B. Acids and Bases
1.
Acids and Bases
a. When water molecules break up, an
equal number of hydrogen ions (H+) and
hydroxide ions (OH-) are released
H+ + OH-  H20
b. Acids are substances that release
hydrogen ions (H+); also called protons
c. Bases are substances that release
hydroxide ions (OH-) or accept hydrogen
ions (protons)
d. Acids and bases can be strong or weak
depending on the number of H+ or OH25
Acids and Bases, cont
2.
Salts
a. A salt is an electrolyte (ionic compound)
formed when an acid and a base are
combined.
b. Water also forms.
c. HCl + NaOH → NaCl + H2O
sodium chloride is a salt
d. Electrolytes
1) Substances that release ions when put
into water and conduct a current
2) The balance of electrolytes in the blood
affects the functioning of vital organs
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Acids and Bases, cont
3. pH Scale
a. Used to indicate the acidity and basicity
(alkalinity) of a solution
b. pH 7 is neutral (an equal number of
hydrogen ions and hydroxide ions are
released)
c. pH above 7 is a base (more hydroxide
ions are released than hydrogen ions)
d. pH below 7 is an acid (more hydrogen
ions are released than hydroxide ions)
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pH Scale
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4. pH of body fluids
a.
b.
c.
d.
Normal pH of blood is 7.4
Acidosis – blood pH less than 7.35
Alkalosis – blood pH greater than 7.45
Blood pH needs to be maintained within a
narrow range
1) Respiratory and urinary systems work to
maintain pH balance
2) Buffers (chemicals that take up excess
hydrogen or hydroxide ions) to prevent
rapid, drastic pH changes
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e. Blood buffer
1)
2)
3)
Blood uses a bicarbonate/carbonic acid
buffer system
Excess H+ + HCO3-  H2CO3
Excess OH- + H2CO3  HCO3- + H2O
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2.3 Molecules of Life
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A.
Four categories of molecules are unique to
cells (called macromolecules or polymers)
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic acids
B. Synthesis of macromolecules involves a
dehydration reaction
C. Breakdown of macromolecules involves a
hydrolysis reaction
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Synthesis and Decomposition of
Macromolecules
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2.4 Carbohydrates
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A. Introduction
1.
2.
3.
4.
Carbohydrates contain carbon, hydrogen,
and oxygen
The ratio of hydrogen (H) atoms to oxygen
(O) atoms is approximately 2:1
This group is made up of sugars and
starches
Function for quick, short-term cellular
energy
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B. Simple Carbohydrates
1.
2.
Low number of carbon atoms (3-7)
Monosaccharides or simple sugars
a. Glucose – main carbohydrate building block
b. Fructose – found in fruits
c. Galactose – found in milk
3.
Disaccharides
a. Two monosaccharides joined together by
dehydration reaction
b. Sucrose (table sugar) – glucose + fructose
c. Lactose (milk sugar) – glucose + galactose
d. Maltose (grain sugar) – glucose + glucose
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Glucose and maltose
Glucose, C6H12O6
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C. Complex Carbohydrates (polysaccarides)
1.
Contain many glucose (monosaccharide)
units
2. Starch – storage form of glucose in plants
3. Glycogen – storage form of glucose in
animals
4. Cellulose
a. Found in plant cell walls
b. Humans are unable to digest (passes
through digestive tract as fiber)
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Starch Structure and Function
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Glycogen Structure and Function
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2.5 Lipids
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A. Introduction
1.
2.
3.
4.
Contain more energy per gram than other
biological molecules
Some function as long-term energy
storage in organisms
Do not dissolve in water
Consist mostly of carbon and hydrogen
atoms; contain few oxygen atoms
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B. Fats and Oils
1.
2.
Also called triglycerides or neutral fats
Formed when one glycerol molecule reacts
with three fatty acid molecules
3. Fats
a. Usually of animal origin
b. Solid at room temperature
c. Used for long-term energy storage,
insulation, and cushioning
4. Oils
a. Usually of plant origin
b. Liquid at room temperature
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Fats and Oils, cont
5. Emulsification
a. Emulsifiers are molecules with a polar
end and a nonpolar end that can
surround fats so they can mix with water
b. Examples – soaps, detergents, bile
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6. Saturated and Unsaturated Fatty Acids
a. Fatty acid (long carbon-hydrogen
chain ending with an acidic group –
COOH
b. Saturated fatty acids have only
single covalent bonds; lard and
butter are examples
c. Unsaturated fatty acids have double
bonds between carbon atoms
wherever fewer than two hydrogens
are bonded to a carbon atom;
vegetable oils
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Synthesis & degradation of a fat molecule
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C. Phospholipids
1.
2.
3.
Contain a
phosphate group
Have a
hydrophilic head
and hydrophobic
tails
Form backbone of
cellular
membranes
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D. Steroids
1.
Structure consists of four fused carbon
rings with attached functional groups
2. Cholesterol
a. Structural component of animal cell
membrane
b. Precursor of several other steroids
including testosterone and estradiol
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Steroids
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2.6 Proteins
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A. Functions of proteins
1.
2.
3.
4.
5.
6.
Fibrous structural proteins – collagen and
keratin
Hormones – chemical messengers; growth
hormone, insulin
Muscle contraction – actin and myosin
Transport - hemoglobin
Protection – antibodies, clotting proteins
Enzymes – globular proteins
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B. Structure of proteins
1.
Made of amino acid subunits
a. Amino group
b. Acid group
c. R (Remainder) group – differentiates the
20 amino acids
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Structure of proteins, cont
2.
Amino acids can be joined together by
peptide bonds through the dehydration
reaction
a. Dipeptide – two amino acids joined
together
b. Polypeptide – three or more amino acids
joined together
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3. Levels of polypeptide structure
a. Primary structure – sequence of amino acids
b. Secondary structure – due to hydrogen
bonding that may occur in a polypeptide;
forms coils and folds
c. Tertiary structure results from bonding
between R groups; extensive folding and
twists
d. Quaternary structure – arrangement of
individual polypeptides in a protein
containing more than one polypeptide
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Levels of Protein Structure
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Levels of Protein Structure
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4. Denaturation
a.
b.
c.
The final three-dimensional shape of the
protein determines its function
If a protein loses its shape, it becomes
nonfunctional
Denaturation – irreversible change in the
normal shape of a protein due to
extremes in heat and pH
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C. Enzymatic reactions
1.
Metabolism - sum of all chemical reactions that
occur in a cell
2.
Enzymes - protein catalysts that enable metabolic
reactions at the body’s normal temperature
a. Named for their substrate or type of reaction
b. Lower the activation energy needed to start a
reaction
c. The shape of the active site and its chemical
composition determines specificity of enzyme
d. The reactant the enzyme catalyzes is the
substrate
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3. Enzyme catalyzed reactions
a.
b.
c.
d.
Enzyme and substrate(s) fit together like
pieces of a puzzle
Forms the enzyme-substrate complex
The active site catalyzes the reaction
The enzyme is released to be used again
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Enzymatic Action
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4. Cofactors and coenzymes
a.
b.
c.
Some enzymes require nonprotein
components to become an active enzyme
Cofactor – inorganic metal; ex – Cu, Zn,
Fe
Coenzyme – organic, nonproteins molecule
like the B-vitamins
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D. Types of reactions
1. Synthesis Reactions
a. Two or more reactants combine – bonds
form
b. Require energy
c. Dehydration is a synthesis reaction
2. Degradation (Decomposition) Reactions
a. Larger, more complex molecule breaks
down into smaller, simpler products
b. Hydrolysis is a degradation reaction
3. Replacement (Exchange) Reactions –
involve both degradation and synthesis
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2.7 Nucleic Acids
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A. Introduction
1.
Huge macromolecules composed of
nucleotides
2. Nucleotides composed of 3 subunit
molecules:
a. A phosphate
b. A pentose sugar
c. A nitrogen-containing base
3. Two classes of nucleic acids
a. DNA
b. RNA
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Nucleotide Structure
65
B. DNA
1.
Deoxyribonucleic acid
a. Contain pentose sugar deoxyribose
b. Nitrogen-containing bases
1) Adenine (A)
2) Thymine (T)
3) Guanine (G)
4) Cytosine (C)
2. Usually double stranded – double helix
3. Makes up the genes that contain
hereditary information that determines the
proteins a cell makes
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DNA, cont
4.
DNA is like a twisted ladder with
alternating sugar – phosphate on the sides
and complementary nitrogenous base pairs
as the rungs
a. Adenine – thymine
b. Cytosine – guanine
5. The sequence of groups of three bases
codes for an amino acid
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Overview of DNA structure
68
C. RNA
1.
Ribonucleic acid
a. Contain pentose sugar ribose
b. The nitrogen-containing base uracil (U)
replaces thymine
c. Usually single stranded
2. Carries the instructions from DNA for
making a protein
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Comparison of DNA and RNA
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D. ATP – adenosine triphosphate
1.
2.
3.
4.
5.
6.
7.
A modified nucleic acid
Primary energy currency of cells
Cells break down glucose and convert released
energy into ATP and heat
Used when cellular reactions require energy
Breakdown of ATP results in one molecule of ADP
(adenosine diphosphate) and one molecule of
inorganic phosphate
ATP is rebuilt by the addition of inorganic
phosphate to ADP
One glucose molecule can build 36 to 40 ATP
molecules
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Breakdown and formation of ATP
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Summary of macromolecules and monomer
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