Farha Jaffer/BIOLS 102/ Chapter 3

Chapter 3
The Chemistry of Organic Molecules

Organic
1.1 Organic
Molecules
Molecules

The Carbon Atom

Carbon is small, with only 6 electrons: 2 ē in the 1st ē shell and 4 on the
outer most shell.
Carbon atom almost shares ē with other elements, especially of
CHNOPS  made almost mass of bodies.
Carbon tends to bond with another carbon: C—C is quite stable. This can
give chains and rings.

hexane (a hydrocarbon), the

backbone of the organic molecules.

Branching of C atom is possible, also a hydrocarbon can turn back on

itself to form a ring when placed in water:

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Carbon atom can form a double bond with itself or other atoms:
I
—C=C— OR
I

can form a triple bond: acetylene

The Carbon Skeleton and Functional Groups

 Carbon chain of an organic molecules is called the “skeleton or backbone”
 reflects the shape.

 Reactivity of an organic molecule depends on the attached functional

groups.

 A functional group = a cluster of atoms attached to the carbon skeleton

and react always in same way regardless of carbon skeleton.

Functional Groups:

1. addition of —OH (hydroxyl group), the compound will be alcohol:

ethane; a 2 carbon molecule. It is hydrophobic (non polar,

not soluble in water).

BUT, when we add —OH group  ethanol (alcohol).

It turns the molecule to be hydrophilic (polar,

soluble in water).

—OH (hydroxyl group) is a polar functional

group.

Cells are 70–90% water; the degree organic molecules interact with water
affects their function.

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2. Organic molecules containing —COOH (carboxyl group) (acidic) are

polar. They tend to ionize in water and release H+:
H2O
—COOH  —COO- + H+

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Functional groups determine:  polarity of an organic

molecule &  the type of reaction they will undergo.

Examples:
1. Alcohol when react with carboxyl group  formation of fats.
2. Carboxyl when react with amino group  formation of protein.

Isomers: Organic compounds having same molecular formula BUT

differ in arrangement of atoms, e.g., glucose and fructose
and galactose; all are C6H12O6.
e.g., glyceraldehyde and dihydroxyacetone; both are
C3H6O3.

The Macromolecules of Cells

Cells contain 4 classes of macromolecules (carbohydrates, lipids,
proteins, and nucleic acids) and they provide great diversity.

The largest macromolecules are polymers made up of repeated same

type of small subunits called monomers that are linked together (e.g.,
monosaccharides  monomers of carbohydrates, glycerol and fatty
acids  are monomers of lipids, amino acids  are monomers of
proteins, and nucleotides  are monomers of nucleic acids).

Polymers are the large macromolecules composed of three to millions

of monomer subunits.

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Synthesis of a macromolecule is achieved by the

condensation of monomers through a reaction called condensation
reaction or dehydration synthesis.

During dehydration synthesis, a water is removed and a

bond is made (synthesis).
a. When two monomers join, a hydroxyl (— OH) group is
removed from one monomer and a hydrogen (— H) is removed
from the other.

b. This produces water.

Degradation of a macromolecule is achieved by opposite

type of reaction called hydrolysis.

Hydrolysis reactions break down polymers in reverse of

dehydration; a hydroxyl (— OH) group from water attaches to one
monomer and hydrogen (— H) attaches to the other.

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Cellular enzymes carry out condensation synthesis and hydrolysis of

polymers.

 Carbohydrates
In general, carbohydrates:
Immediate energy source in cells.
Play a role in cell structure.
Majority of carbohydrates have a C:H:O ratio of 1:2:1.
Range from a single sugar to chains of sugars (polymers).

1. Monosaccharides: Ready Energy

Monosaccharides are simple sugars with a carbon backbone of 3 to 7

carbon atoms.
Molecular formula is CH2O or multiple (CH2O)n.
Sugars have many (— OH) groups, making sugars polar.
Best known sugars have 6 carbons (hexoses) 
C6H12O6.


Example of these hexoses:
 Glucose  Fructose  Galactose
All are isomers.
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glucose

Glucose is commonly found in blood of animals; is immediate energy

source to cells.
Another family of monosaccharides that have 5
carbons is called pentoses: Ribose and deoxyribose
contribute to the backbones of RNA and DNA, respectively.

2. Disaccharides: Varied Uses

Disaccharides contain 2 monosaccharides joined together by

dehydration synthesis.

Maltose is a two glucose molecules; forms in digestive tract of

humans during starch digestion in mouth by amylase enzyme.

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Sucrose is composed of glucose and fructose and is transported

within plants.

Lactose is composed of galactose and glucose and is found in

milk.

3. Polysaccharides as Energy Storage Molecules

 Polysaccharides are polymers of monosaccharides.

 Big molecules, not soluble in water.
 Can not pass through plasma membrane.
 Short-term energy storage.

 When an organism needs energy:

breaking down
Polysaccharides release of simple sugars
hydrolysis by enzymes

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 In plants, they store excess of glucose in form of starch.

 Starch is long chain of glucose molecules with few side branches.

 2 forms of starch: amylose  unbranched chain of glucose.

amylopectin  more complex branched starch.

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BOTH starches work as main energy reservoir for plant cells.

 Humans and animals store excess of glucose in form of

glycogen in liver and muscles until needed.

 Glycogen is a long chain, highly branched polymer of glucose with

many side branches.

 Storage of glucose:

Insulin hormone
Glucose glycogen

 Release of glucose into blood:

Glucagon hormone
Glycogen glucose free in blood.

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4. Polysaccharides as Structural Molecules

polysaccharide where we found? structure

Cellulose Plants Long unbranched chains of glucose
monomers.
Chitin Animals & fungi Long chains of glucose monomers
attached to amino group.
peptidoglycan Bacteria More complex; long chain of glucose
monomers and each monomer has an
amino acid chain.

A. Cellulose:

Cellulose is glucose bonded to form microfibrils; primary

constituent of plant cell walls.

Cotton is nearly pure cellulose.

Cellulose is not easily digested due to the strong linkage between
glucose molecules; our digestive system can not digest cellulose.

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Grazing animals can digest cellulose due to special stomachs and

bacteria, like rabbits and cows.
Protozoa in guts of termites can also digest cellulose (wood).

B. Chitin:

Chitin is the primary constituent of the exoskeleton of

arthropods like crabs and related animals such as lobsters and
insects.
Fungi cell wall composed of chitin (not cellulose).
Chitin can not be digested by animals
Seed's coat composed of chitin; protect seeds from soil fungi.
Chitin has antibacterial and antiviral properties; used as a wound
dressing and suture material.

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 Lipids

Mostly not soluble in water (hydrophobic/nonpolar)  hydrocarbon

chains with no polar functional groups.

Types of lipids (varied in their structure):

1. Fats & Oils (Triglycerides): Long-Term Energy Storage

≈ 98% of our daily food.

One molecule of fat or oil: 1 glycerol + 3 fatty acids.

Glycerol is a polar compound with 3 hydroxyl groups (—OH

group)  polar.

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Each fatty acid molecule is a long chain of hydrocarbon ends

with a carboxyl (acid) group (—COOH group)  polar.

The acid group of the 3 fatty acids molecules react with (—OH
groups) of glycerol during dehydration synthesis  one
molecule of fat or oil + 3 H2O molecules.

Fats and oils are called “triglycerides” because the 3 fatty acids
joined to each glycerol molecule.

Most fatty acids in cells contain 16 to 18 carbon atoms per

molecule; although smaller also found.

Fatty acids are either: saturated f.a

Unsaturated f.a.
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Saturated Fatty Acids Unsaturated Fatty Acids

Have no double bond between C – C; Have double bonds between C-C; so

hydrogen is full. hydrogen atoms are less by 2 H/C.
Triglycerides containing saturated f.a. melt Triglycerides containing unsaturated f.a. melt at
at a higher temp. a lower temp.
Animal sources. Plant sources.
Solid at room temp. Liquid at room temp. even if put in refrigerator*.
* Penguin’s feet contain unsaturated f.a.; protect
these exposed feet from freezing.

Animals use fat rather than glycogen for long-term energy

storage; gram/gram, fat stores more energy.
Fat store 6 times energy more than glycogen, WHY?

 C-H bonds in fatty acids are rich source of chemical energy. While
glycogen has many C-OH bonds and are low in chemical energy.

 Fat (nonpolar) do not contain water  less dense.

Small birds store a great amount of fat before they start long spring
migration.

About 0.15g of fat/g of body mass of the bird accumulates

each day. If same amount of energy stored as glycogen, the bird will be
heavy  can not fly.

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2. Phospholipids:

 A Phospholipid molecule composed of 2 fatty acids bonded to a

glycerol and a phosphate group or a group with both
phosphate and nitrogen (polar groups).

 Plasma membrane consists of 2 layers of phospholipids + proteins.

 Each phospholipid molecule has a polar (hydrophilic) head:

glycerol + the phosphate group; both are polar groups.
and 2 nonpolar (hydrophobic) tails: the 2 fatty acid chains.

 Phospholipids arrange themselves in a double layer in water, so the

polar heads face outward toward water molecules and
nonpolar tails face toward each other away from water
molecules.
 This property enables them to form an interface or separation between
two solutions (e.g., the interior and exterior of a cell); the plasma
membrane is a phospholipid bilayer. Phospholipids can be
synthesized in liver.

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3. Steroids:

Structure: steroids have a backbone of 4 fused carbon rings

and attached functional groups.

 Steroid functions vary due to different attached functional groups.

 Cholesterol is a part of an animal cell’s membrane and a

precursor of all steroids, including aldosterone and sex
hormones.

 Testosterone is the male sex hormone; estrogen is the female

sex hormone.

 A diet high in saturated fats and cholesterol can lead to circulatory

disorders like high blood pressure.

4. Waxes:

Structure: Waxes are a long-chain fatty acid bonded to a

long-chain alcohol.

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Solid at room temperature, waxes have a high melting point and are
waterproof and resist degradation.

Waxes form a protective covering in plants (cuticle) that protect water

loss in leaves and fruits.
In animals, waxes maintain animal skin and fur, and forms honeycomb.

In human, the ears produce wax in the outer ear canals. This wax
contain cerumin (organic compound) that repels and kills insects,
and traps dust and dirt from reaching the eardrum.

Summary:
Type of Lipid Structure
Fats & oils 3 fatty acids + 1 glycerol
Phospholipids 2 fatty acids + 1 glycerol + a phosphate group
Steroids 4 fused carbon rings bonded to a functional
group (no fatty acids)
Waxes Long chain of fatty acid + long chain of alcohol

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 Proteins
Proteins are of primary importance to the structure and function of cells.

A. Protein Functions

1. Support proteins: include keratin, which makes up hair and nails, and
collagen fibers, which support many organs.

2. Enzymes are proteins that act as organic catalysts to speed chemical

reactions within cells. Each reaction has specific enzyme.

3. Transport functions include channel and carrier proteins in the

plasma membrane and hemoglobin that carries oxygen in red
blood cells.

4. Defense functions include antibodies that prevent infection. They

combine with foreign substances (antigens) and destroy them.

5. Hormones are regulatory proteins. All hormones are intracellular

messengers that secreted by a gland and transported by blood to a target
 affect metabolism of cells.
e.g., insulin hormone is a protein that regulates glucose content of
blood.
growth hormone affect the height of an individual.

6. Motion is provided by myosin and actin proteins (contractile

proteins) that make up the bulk of muscle and cause the muscles to
contract  allow parts of body to move.

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B. Amino Acids: Subunits of Proteins (the building blocks).

 The α carbon atom is bonded to H atom and 3 other groups:

 All amino acids contain an acidic group (— COOH) and an

amino group (—NH2); that’s why they are called amino acids.

 Each amino acid is bonded with R group (remainder of molecule).

 Amino acids differ in nature of R group, ranging in complexity

from single hydrogen to complicated ring compounds.

 Each R group has different chemical property; R could be polar or

nonpolar.

 R group of amino acid cysteine ends with a sulfhydryl (— SH) that

serves to connect one chain of amino acids to another by a disulfide
bond (— S— S—).

 There are 20 different amino acids commonly found in cells.

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C. Peptides:

 Peptide bond is a covalent bond between amino acids in a

peptide.
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 Atoms of a peptide bond share electrons unequally (oxygen is more

electronegative than nitrogen); so O shows δ - and H shows δ+.

 Polarity of the peptide bond permits hydrogen bonding between (—

CO-) of one amino acid and (—NH) of another amino acid in a
polypeptide.

 A peptide is two or more amino acids bonded together.

 Polypeptides are chains of many amino acids joined by peptide bonds.

 Protein may contain more than one polypeptide chain; it can have large
numbers of amino acids.

 Each polypeptide has its own normal sequence  influence the 3-D
shape.

 The 3-dimensional shape of the protein is critical; an abnormal

sequence will have the wrong shape and not function normally.

D. Shape of Proteins:

Protein shape determines the function of the protein in the organism;

proteins can have up to 4 levels of structure, but not all
proteins have the 4 levels.

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1. Primary structure is sequence of amino acids joined by

peptide bonds and give a simple polypeptide chain.

 Just as English alphabet contains 26 letters, 20 amino acids can

join to form a huge variety of “words.”
 Each protein has a unique sequence of amino acids.
 Proteins in nature are not this simple to give active shape. So
primary proteins are not functional.
 The primary shape is the newly synthesized proteins and need to
be modified to be active and functional.

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2. Secondary structure results when a polypeptide of a

primary shape coils or folds in a particular way.

 2 patterns of secondary structures:

a. The  (alpha) helix was the first pattern discovered by
Linus Pauling and Robert Corey.

In peptide bonds, oxygen is partially negative, hydrogen is

partially positive.
Allows hydrogen bonding between the C=O of one amino acid and
the N—H of another.
Hydrogen bonding between every 4 amino acid makes the
chain to coil from the right, and holds the spiral shape of an
helix.
helices covalently bonded by disulfide (—S—S—) linkages
between two cysteine amino acids.
Best example of helix proteins is keratin.

b. The  pleated sheet was the second pattern

discovered.

Pleated sheet polypeptides turn back upon themselves.

Hydrogen bonding occurs between extended lengths.
Best examples of pleatedsheet are: silk and spider web.

Fibrous proteins are structural proteins with helices and/or

pleated sheets that hydrogen bond to each other.

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3. Tertiary structure results when proteins of secondary

structure are folded, due to various interactions between the R
groups of their constituent amino acids.

 Also called “Globular proteins” because they tend to ball up

into rounded shapes.

 Various types of bonding between R groups of the constituent

amino acids: strong disulfide linkages maintain the tertiary
shape; hydrogen, ionic, and covalent bonds also
contribute.

 Hydrophobic R groups also found in the tertiary structure, BUT

do not bond to the hydrophilic R groups; instead they
collect in a region not exposed to water.

 Most enzymes are globular proteins and have a tertiary structure;

changes in pH and temp. can change the polarity of R
groups and disrupt the enzyme action or denature the
protein  loses its normal 3-D shape  not functional.

 The primary structure of a protein determine if the denatured

proteins can renature or not.

4. Quaternary structure results when two or more

polypeptides combine.

 Hemoglobin is globular protein with a quaternary structure of 4

polypeptide chains. Each polypeptide in hemoglobin has 4 levels
of structures: primary, secondary, tertiary and quaternary.

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 Nucleic Acids

A. Nucleic Acid Functions

Nucleic acids are polymers of nucleotides with very specific

functions in cells.

DNA (deoxyribonucleic acid) is the nucleic acid whose nucleotide

sequence stores the genetic code for its own replication and
for the sequence of amino acids in proteins.

RNA (ribonucleic acid) is a single-stranded nucleic acid that

translates the genetic code of DNA into the amino
acid sequence of proteins.

Nucleotides have independent metabolic functions in cells.

a. Coenzymes are molecules which facilitate enzymatic
reactions.
b. ATP (adenosine triphosphate) is a nucleotide used to supply
energy.

B. Structure of DNA and RNA

Each nucleotide is a molecular complex of 3 types of molecules:

1. a phosphate group (derived from phosphoric acid)

2. a pentose sugar: deoxyribose (in DNA)

ribose (in RNA)

3. and a nitrogen-containing base: purines

double ring
(A, G)

Pyrimidines
Single ring
(T, C, U)

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DNA and RNA differ in the following ways:

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The nucleotides sequenced along making a strand.

The backbone of the strand is P-S-P-S- ………..

Nitrogen bases project from one side of the backbone.

Complementary base pairing occurs where two strands of DNA

are held together by hydrogen bonds between purine and pyrimidine
bases.

The number of purine bases always equals the number of pyrimidine

bases.
Two strands of DNA twist to form a double helix; RNA generally does
not form helices.

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C. ATP (Adenosine Triphosphate)

 ATP (adenosine triphosphate) is a nucleotide of adenosine composed of

ribose and adenine.

 Triphosphate derives its name from three phosphates attached to the five-
carbon portion of the molecule.

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 ATP is a high-energy molecule because the last two unstable

phosphate bonds are easily broken; however it is the entire molecule that
releases the energy.

 Usually in cells, the terminal phosphate bond is hydrolyzed,

leaving ADP (adenosine diphosphate).

 ATP is used in cells to supply energy for energy-requiring processes

(e.g., synthetic reactions, muscle contraction, nerve cells); whenever a
cell carries out an activity or builds molecules, it “spends” ATP.

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