Chapter 3
The Molecules of Cells
Organic Chemistry: Carbon Based Compounds
A. Inorganic Compounds: Compounds without
carbon.
B. Organic Compounds: Compounds synthesized
by cells and containing carbon (except for CO
and CO2).
 Diverse
group: Several million organic compounds are
known and more are identified every day.
 Common:
After water, organic compounds are the
most common substances in cells.

Over 98% of the dry weight of living cells is made up of
organic compounds.

Less than 2% of the dry weight of living cells is made up of
inorganic compounds.
Carbon: unique element for basic building block of
molecules of life

Carbon has 4 valence electrons: Can form four
covalent bonds




Can form single , double, triple bonds.
Can form large, complex, branching molecules and
rings.
Carbon atoms easily bond to C, N, O, H, P, S.
Huge variety of molecules can be formed based
on simple bonding rules of basic chemistry
Organic Compounds are Carbon Based
Carbon Can Form 4 Covalent Bonds
Different Carbon Skeletons of Organic Compounds
Diversity of Organic Compounds

Hydrocarbons:
 Organic
molecules that contain C and H only.
 Good fuels, but not biologically important.
 Undergo combustion (burn in presence of oxygen).
 In general they are chemically stable.
 Nonpolar: Do not dissolve in water (Hydrophobic).
Examples:
 (1C) Methane:
CH4 (Natural gas).
 (2C) Ethane:
CH3CH3
 (3C) Propane:
CH3CH2CH3 (Gas grills).
 (4C) Butane:
CH3CH2CH2CH3 (Lighters).
 (5C) Pentane:
CH3CH2CH2CH2CH3
 (6C) Hexane:
CH3CH2CH2CH2CH2CH3
 (7C) Heptane:
CH3CH2CH2CH2CH2CH2CH3
 (8C) Octane:
CH3CH2CH2CH2CH2CH2CH2CH3
Hydrocarbons have C and H only
Isomers: Compounds with same chemical formula
but different structure (arrangement of atoms)
 Isomers
have different physical and chemical
properties
 Structural
Isomers: Differ in bonding arrangements
Butane (C4H10)
CH3--CH2--CH2--CH3
 Number
Isobutane (C4H10)
CH3
|
CH3---CH---CH3
of possible isomers increases with increasing
number of carbon atoms.
Functional groups play pivotal role in chemical &
physical properties of organic molecules
Compounds that are made up solely of carbon
and hydrogen are not very reactive.
Functional groups:
 One or more H atoms of the carbon skeleton may be
replaced by a functional group.
 Groups of atoms that have unique chemical and
physical properties.

Usually a part of molecule that is chemically active.

Similar activity from one molecule to another.

Together with size and shape, determine unique bonding and
chemical activity of organic molecules.
Functional Groups Determine Chemical &
Physical Properties of Organic Molecules
Four Important Functional Groups:
 Hydroxyl
(-OH)
 Carbonyl
(=C=O)
 Carboxyl
(-COOH)
 Amino
 Notice
polar.
(-NH2)
that all four functional groups are
A. Hydroxyl Group (-OH)
 Is
a polar group: Polar covalent bond between O and H.
 Can
form hydrogen bonds with other polar groups.
 Generally
makes molecule water soluble.
Example:
 Alcohols:
Organic molecules with a simple hydroxyl
group:

Methanol (wood alcohol, toxic)

Ethanol (drinking alcohol)

Propanol (rubbing alcohol)
B. Carbonyl Group (=CO)
 Is
a polar group: O can be involved in H-bonding.
 Generally makes molecule water soluble.
Examples:
 Aldehydes: Carbonyl is located at end of molecule
 Ketone: Carbonyl is located in middle of molecule
Examples:



Sugars (Aldehydes or ketones)
Formaldehyde (Aldehyde)
Acetone (Ketone)
Sugars Have Both -OH and =CO Functional Groups
C. Carboxyl Group (-COOH)
 Is
a polar group
 Generally
 Acidic
makes molecule water soluble
because it can donate H+ in solution
Example:
 Carboxylic
acids: Organic acids, can increase acidity
of a solution:

Acetic acid: Sour taste of vinegar.

Ascorbic acid (Vitamin C): Found in fruits and vegetables.

Amino acids: Building blocks of proteins.
D. Amino Group (-NH2)
 Is
a polar group
 Generally
 Weak
makes molecule water soluble
base because N can accept a H+
 Amine
-general term given to compound with (-NH2)
Example:
 Amino
acids: Building blocks of proteins.
Amino acid Structure:
 Central
carbon with:
H atom
 Carboxyl group
 Amino group
 Variable R-group

Amino Acid Structure:
H
|
(Amino Group) NH2---C---COOH (Carboxyl group)
|
R
(Varies for each amino acid)
Amino Acids Have Both -NH2 and -COOH Groups
The Macromolecules of Life:
Carbohydrates, Proteins, Lipids, and Nucleic Acids
I. Most Biological Macromolecules are Polymers
 Polymer:
Large molecule consisting of many
identical or similar “subunits” linked through
covalent bonds.
 Monomer: “Subunit” or building block of a
polymer.
 Macromolecule:
Large organic polymer. Most
macromolecules are constructed from about 70
simple monomers.

Only about 70 monomers are used by all living things
on earth to construct a huge variety of molecules

Structural variation of macromolecules is the basis for
the enormous diversity of life on earth.
Relatively few monomers are used by cells to
make a huge variety of macromolecules
Macromolecule
Monomers or Subunits
1. Carbohydrates
20-30 monosaccharides
or simple sugars
2. Proteins
20 amino acids
3. Nucleic acids (DNA/RNA) 4 nucleotides (A,G,C,T/U)
4. Lipids (fats and oils)
~ 20 different fatty acids
and glycerol.
Making and Breaking Polymers
 There
are two main chemical mechanisms in
the production and break down of
macromolecules.
Condensation or Dehydration Synthesis
 Hydrolysis

 In
the cell these mechanisms are regulated by
enzymes.
Making Polymers
A. Condensation or Dehydration Synthesis reactions:
 Synthetic process in which a monomer is covalently
linked to another monomer.
 The equivalent of a water molecule is removed.
General Reaction:
X - OH + HO - Y -------->
Monomer 1 Monomer 2
(Unlinked)
 Anabolic
(or Polymer)
X - O - Y + H2 O
Dimer
Water
(or Polymer)
Reactions: Used by cells to make large
molecules from smaller ones.
 Require energy (endergonic)
 Require catalysis by enzymes
Condensation Synthesis: Monomers are
Linked and Water is Removed
Breaking Polymers
B. Hydrolysis Reactions: “Break with water”.
 Degradation of polymers into component monomers.
 Involves breaking covalent bonds between subunits.
 Covalent bonds are broken by adding water.
General Reaction:
X - O - Y + H2O ----------> X - OH + HO - Y
Polymer
Water
Monomer 1 Monomer 2
(or Dimer)
 Catabolic
Reactions: Used by cells to break large
molecules into smaller ones.
 Release energy (exergonic)

Reactions catalyzed by enzymes
Hydrolysis: Polymers are Broken Down as
Water is Added
Hydrolysis
Making and Breaking Polymers
Examples:
Dehydration Synthesis (Condensation):
Enzyme
Glucose + Fructose ---------> Sucrose
(Monomer) (Monomer)
(Dimer)
+
H2O
Water
Hydrolysis:
Sucrose
(Dimer)
+
Enzyme
H2O ---------> Glucose + Fructose
Water
(Monomer) (Monomer)
Synthesis and Hydrolysis of Sucrose
III. Carbohydrates: Molecules that store energy
and are used as building materials
 General
 Simple
Formula: (CH2O)n
sugars and their polymers.
 Diverse
group includes sugars, starches, cellulose.
 Biological
Functions:
• Fuels, energy storage
• Structural component (cell walls)
• DNA/RNA component
 Three types of carbohydrates:
A. Monosaccharides
B. Disaccharides
C. Polysaccharides
A. Monosaccharides: “Mono” single & “sacchar” sugar
 Preferred
source of chemical energy for cells (glucose)
 Can be synthesized by plants from light, H2O and CO2.
 Store energy in chemical bonds.
 Carbon skeletons used to synthesize other molecules.
Characteristics:
1. May have 3-8 carbons. -OH on each carbon; one with C=0
2. Names end in -ose. Based on number of carbons:


5 carbon sugar: pentose
6 carbon sugar: hexose.
3. Can exist in linear or ring forms
4. Isomers: Many molecules with the same molecular
formula, but different atomic arrangement.

Example: Glucose and fructose are both C6H12O6.
Fructose is sweeter than glucose.
Monosaccharides Can Have 3 to 8 Carbons
Linear and Ring Forms of Glucose
B. Disaccharides: “Di” double & “sacchar” sugar
 Covalent
bond formed by condensation reaction
between 2 monosaccharides.
Examples:
1. Maltose: Glucose + Glucose.
• Energy storage in seeds.
• Used to make beer.
2. Lactose: Glucose + Galactose.
• Found in milk.
• Lactose intolerance is common among adults.
• May cause gas, cramping, bloating, diarrhea, etc.
3. Sucrose: Glucose + Fructose.
• Most common disaccharide (table sugar).
• Found in plant sap.
Maltose and Sucrose are Disaccharides
C. Polysaccharides: “Poly” many (8 to 1000)
Functions: Storage of chemical energy and structure.
 Storage
polysaccharides: Cells can store simple sugars
in polysacharides and hydrolyze them when needed.
1. Starch: Glucose polymer (Helical)

Form of glucose storage in plants (amylose)

Stored in plant cell organelles called plastids
2. Glycogen: Glucose polymer (Branched)

Form of glucose storage in animals (muscle and liver
cells)
Three Different Polysaccharides of Glucose
 Structural
Polysaccharides: Used as structural
components of cells and tissues.
1. Cellulose: Glucose polymer.

The major component of plant cell walls.
CANNOT be digested by animal enzymes.
 Only microbes have enzymes to hydrolyze.

2. Chitin: Polymer of an amino sugar (with NH2 group)
Forms exoskeleton of arthropods (insects)
 Found in cell walls of some fungi

Cellulose: Polysaccharide Found in Plant
and Algae Cell Walls
Proteins: Large three-dimensional
macromolecules responsible for most cellular
functions
 Polypeptide
chains: Polymers of amino acids linked
by peptide bonds in a SPECIFIC linear sequence
 Protein:
Macromolecule composed of one or more
polypeptide chains folded into SPECIFIC 3-D
conformations
Proteins have important and varied functions:
1. Enzymes: Catalysis of cellular reactions
2. Structural Proteins: Maintain cell shape
3. Transport: Transport in cells/bodies (e.g. hemoglobin).
Channels and carriers across cell membrane.
4. Communication: Chemical messengers, hormones, and
receptors.
5. Defensive: Antibodies and other molecules that bind to
foreign molecules and help destroy them.
6. Contractile: Muscular movement.
7. Storage: Store amino acids for later use (e.g. egg white).
Protein function is dependent upon its 3-D shape.
Polypeptide: Polymer of amino acids connected in
a specific sequence
A. Amino acid: The monomer of polypeptides

Central carbon
• H atom
• Carboxyl group
• Amino group
• Variable R-group
Protein Function is dependent upon Protein
Structure (Conformation)
CONFORMATION: The 3-D shape of a protein is
determined by its amino acid sequence.
Four Levels of Protein Structure
1. Primary structure: Linear amino acid
sequence, determined by gene for that protein.
2. Secondary structure: Regular coiling/folding
of polypeptide.
Alpha helix or beta sheet.
 Caused by H-bonds between amino acids.

Primary Structure of Protein: Amino Acid
Sequence is Determined by Gene
Secondary Structure of Protein: Regular Folding
Patterns (Alpha Helix or Pleated Sheet)
3. Tertiary structure: Overall 3-D shape of a polypeptide
chain.
4. Quaternary structure: Only in proteins with 2 or more
polypeptides. Overall 3-D shape of all chains.

Example: Hemoglobin (2 alpha and 2 beta polypeptides)
Tertiary Structure: Overall 3-D Shape of Protein
Tertiary Structure of Lysozyme
Quaternary Structure: Overall 3-D Shape of
Protein with 2 or More Subunits
What determines a protein’s shape?
A. Primary structure: Exact location of each amino
acid along the chain determines the protein’s
folding pattern.
Example: Sickle Cell Hemoglobin protein

Mutation changes amino acid #6 on the alpha chain.

Defective hemoglobin causes red blood cells to assume
sickle shape, which damages tissue and capillaries.

Sickle cell anemia gene is carried in 10% of African
Americans.
B. Chemical & Physical Environment:
Presence of other compounds, pH,
temperature, salts.
Denaturation: Process which alters native
conformation and therefore biological
activity of a protein. Several factors can
denature proteins:

pH and salts: Disrupt hydrogen, ionic bonds.

Temperature: Can disrupt weak interactions.
• Example: Function of an enzyme depends
on pH, temperature, and salt concentration.
Nucleic acids store and transmit hereditary
information for all living things
There are two types of nucleic acids in living things:
A. Deoxyribonucleic Acid (DNA)
Contains genetic information of all living organisms.
 Has segments called genes which provide information to
make each and every protein in a cell
 Double-stranded molecule which replicates each time a
cell divides.

B. Ribonucleic Acid (RNA)
Three main types called mRNA, tRNA, rRNA
 RNA molecules are copied from DNA and used to make
gene products (proteins).
 Usually exists in single-stranded form.

DNA and RNA are polymers of nucleotides that
determine the primary structure of proteins

Nucleotide: Subunits of DNA or RNA.
Nucleotides have three components:
1. Pentose sugar (ribose or deoxyribose)
2. Phosphate group to link nucleotides (-PO4)
3. Nitrogenous base (A,G,C,T or U)

Purines: Have 2 rings.
Adenine (A) and guanine (G)

Pyrimidines: Have one ring.
Cytosine (C), thymine (T) in DNA or uracil (U) in RNA.
James Watson and Francis Crick Determined the 3D Shape of DNA in 1953
 Double
helix: The DNA molecule is a double helix.
 Antiparallel: The two DNA strands run in opposite
directions.


Strand 1: 5’ to 3’ direction (------------>)
Strand 2: 3’ to 5’ direction (<------------)
 Complementary


Base Pairing: A & T (U) and G & C.
A on one strand hydrogen bonds to T (or U in RNA).
G on one strand hydrogen bonds to C.
 Replication: The
double-stranded DNA molecule can
easily replicate based on A=T and G=C
--- pairing.
 SEQUENCE
of nucleotides in a DNA molecule dictate
the amino acid SEQUENCE of polypeptides
DNA: Double Helix of Two Complementary
Strands Held Together by H-Bonds
A Gene is a specific segment of a DNA molecule with
information for cell to make one polypeptide
DNA
(transcribed into single stranded RNA “copy”)
!
!
mRNA
(single stranded “copy” of the gene)
!
!
Polypeptide (mRNA message translated into polypeptide)
Genetic Information Flow: DNA to RNA to Protein
Lipids: Fats, phospholipids, and steroids
Diverse groups of compounds.
Composition of Lipids:
 C, H, and small amounts of O.
Functions of Lipids:
 Biological
fuels
 Energy storage
 Insulation
 Structural components of cell membranes
 Hormones
Lipids: Fats, phospholipids, and steroids
1. Simple Lipids: Contain C, H, and O only.
A. Fats (Triglycerides).
Glycerol : Three carbon molecule with three hydroxyls.
 Fatty Acids: Carboxyl group and long hydrocarbon
chains.

 Characteristics
of fats:
Most abundant lipids in living organisms.
 Hydrophobic (insoluble in water) because nonpolar.
 Economical form of energy storage (provide 2X the
energy/weight than carbohydrates).
 Greasy or oily appearance.

Fats (Triglycerides): Glycerol + 3 Fatty Acids
Lipids: Fats, phospholipids, and steroids
Types of Fats
 Saturated
fats: Hydrocarbons saturated with H.
Lack -C=C- double bonds.

Solid at room temp (butter, animal fat, lard)
 Unsaturated

fats: Contain -C=C- double bonds.
Usually liquid at room temp (corn, peanut, olive oils)
Saturated Fats Contain Saturated Fatty Acids
2. Complex Lipids: In addition to C, H, and O,
also contain other elements, such as phosphorus,
nitrogen, and sulfur.
A. Phospholipids: Are composed of:
Glycerol
 2 fatty acid
 Phosphate group

 Amphipathic
Molecule
Hydrophobic fatty acid “tails”.
 Hydrophilic phosphate “head”.

Function: Primary component of the plasma
membrane of cells
Phospholipids: Amphipathic Molecules
In Water Phospholipids Spontaneously
Assemble into Organized Structures
B. Steroids: Lipids with four fused carbon rings
Includes cholesterol, bile salts, reproductive, and adrenal
hormones.

Cholesterol: The basic steroid found in animals
• Common component of animal cell membranes.
• Precursor to make sex hormones (estrogen,
testosterone)
• Generally only soluble in other fats (not in water)
• Too much increases chance of atherosclerosis.
C. Waxes: One fatty acid linked to an alcohol.
Very hydrophobic.
 Found in cell walls of certain bacteria, plant and insect
coats. Help prevent water loss.

Cholesterol: The Basic Steroid in Animals