Chapter 3: Organic Molecules
Biology 100
Spring 2009
Carbon: The Central Atom

Organic Molecules contain Carbon, and
are usually complex.
◦ Carbon atoms can be arranged in rings or
chains
Carbon: The Central Atom
Carbon is the central atom in all organic
molecules.
 Can bond to one another, creating long
chains or rings.
 Carbon likes to have ______ covalent
bonds.
 When several carbon are present, they
form the backbone to which other
elements or molecules attach.

Carbon: The Central Atom
C-C and C-H bonds are rich in______. The
simplest hydrocarbon is methane (CH4),
which is dominant in natural gas.
 A major component of gasoline is the 8carbon molecule called octane.

Carbon: The Central Atom
In addition, carbon can also form double
and triple bonds.
 A double bond is indicated by two lines
between atoms.

◦ C=O or C=C

Triple bonds are denoted by three lines
between atoms.
Carbon: The Central Atom

Empirical Formula of a chemical formula is
a simple expression of the relative
number of atoms in it.
◦ C2H6O

Structural Formula is the graphic
arrangement and bonding of atoms.
Isomers

An isomer has the same empirical formula,
but different structural formulas.
◦ Example is the empirical formula C3H8O, but
can be structurally different.
Propan-1-ol
Propan-2-ol
Methoxyethane
Isomers

Structural isomers may also involve
differences in the carbon backbone itself.
Isomers


Geometric isomers have the same carbon backbone and even
the same elements or functional groups attached to the
same carbons.
But they differ from each other in ______________ these
elements or groups are located around a C=C bond.
Isomers
While we draw biological molecules as if they were
two-dimensional, they are actually three-dimensional.
 Enantiomers are ________ images of one another, like a
right hand and left hand.

Functional Groups

As mentioned earlier, carbon is the backbone of
organic molecules. However, attached to these
carbon atoms are combinations of other
elements, including carbon. These are known as
functional groups.
Macromolecules
Macromolecules are very large, organic
molecules.
 Macromolecules are organized into four
major classes because of similarities in
structure and form

Carbohydrates
Nucleic Acids
Proteins
Lipids
Macromolecules



Monomer is a small molecule
◦ Monomers may have their own specific functions and/or
can be linked by covalent bonds to form larger
molecules.
Polymers are composed of identical or similar monomers
linked together by covalent bonds.
Glucose is a monomer, but when many glucose molecules
chemically bond to one another, it can become the
polymer, starch.
Carbohydrates
Carbohydrates are also known as sugars and
their names often end in –ose (fructose, sucrose,
cellulose).
 Carbohydrates are composed of carbon,
hydrogen, and oxygen.

◦ They have a typical chemical formula: CnH2nOn, with
twice as many hydrogen atoms as carbon and equal
numbers of carbon and oxygen atoms.
•
Is it a carbohydrate?
• C6H1206
• C2H6O
Monosaccharide
Glucose, C6H12O6, is a very
common monosaccharide
 It has a terminal carbonyl
group
 And 5 hydroxyl groups


Glucose and many other
monosaccharides are an
important sources of fast
energy.
Monosaccharide



Important 5C
monosaccharides are ribose
(C5H10O5) and deoxyribose
(C5H10O4).
Glucose is the most
common 6C
monosaccharide, but its
structural isomer, fructose, is
common as well.
An enzyme, isomerase (ase
= enzymes), converts one
isomer to the other.
Disaccharide

A disaccharide is formed by a dehydration reaction
between two monosaccharides.

Disaccharides function in extracellular
transport of sugars (e.g., sucrose in plant
sap, lactose in mammalian milk).
The monosaccharides glucose and fructose combine to form
the disaccharide, sucrose (plant sugar).
Disaccharides function in extracellular transport of sugars
(e.g., sucrose in plant sap, lactose in mammalian milk).
Disaccharide
While most babies are able to digest lactose into glucose
and fructose, many people have a hard time digesting
lactose as they age.
◦ Unfortunately, intestinal bacteria will take advantage of
this food source, producing gas, and inducing diarrhea,
bloating, and nausea.
 One major reason for this problem is that levels of the key
enzyme for this hydrolysis, lactase, decline as we age,
starting as early as age 2.
 There are also geographic differences in lactose
intolerance.

web.lemoyne.edu/~hevern/psy340/graphics/lactose.intolerance.jpg
Polysaccharide


Polysaccharides are long chains with hundreds or
thousands of monosaccharides.
Polysaccharides have two functions:
◦ Energy Storage (e.g. glycogen, starch)
◦ Extracellular Structural Materials (cellulose)
Proteins
Proteins are polymers composed of amino acids.
 Amino acids have C, N, O, and H in their
structure. Made of four different parts.

H
OH
C
_________
group
O
C
R
Hydrogen
H
N
H
“R” group or
variable side
chain
________ group
Amino Acids

There are 20
different R
groups and
these produce
the 20 amino
acids that are
used for
producing
proteins.
Amino Acids
Humans cannot synthesize 8
of the 20 amino acids.
 While a diet with animal
products provides all these
essential amino acids, a purely
______________ diet may
lead to problems because
some plants are deficient in
these 8.
 Since the body does not
store amino acids, a single
deficiency of an essential
amino acid, can lead to a
protein deficiency.

Polypeptides

Peptide bond is a bond formed by two molecules when a
carboxyl group of one molecule reacts with an amine
group in another molecule.

Polypeptides are polymers of amino acids linked by peptide
bonds.
Polypeptides
Proteins are polypeptides that fold into
complex 3-D shapes.
 There are four different structures of
proteins.

◦
◦
◦
◦
Primary
Secondary
Tertiary
Quartenary
Proteins

Primary structure of a protein, the order of the
amino acids will ultimately determine it’s shape.

Secondary structure of a protein are from amino
acids forming weak bonds with other amino acids.
Proteins

Tertiary structure of proteins is shaped due
interactions of side chains.

Quaternary structure is caused by interactions
among separate polypeptides, each with their
own tertiary structure.
 Hemoglobin has
2 alpha and 2 beta
globin proteins
Small Changes Add Up

The genetic disease, sickle-cell anemia, is due to a change
of a single amino acid in the oxygen-carrying protein
hemoglobin.

In individuals with sickle-cell anemia, valine (a non-polar
AA) replaces the sixth amino acid, glutamine (a polar AA)
of a normal globin.
Protein Shape


Protein shape depends on the primary structure of
polypeptides and also on the physical environment and the
presence of other proteins.
◦ Smaller proteins “self-assemble” into their functional
shape.
◦ Others require ________________ proteins to assist
in proper folding.
Changes in the environment or binding (or release) of
other molecules cause proteins to change shape.
Protein Shapes

Two proteins may have the same amino
acid sequence, but do not fold in the
same way. This can cause them to function
differently.

Prions are misfolded proteins, and when
they enter the body, they can cause
normal proteins to fold differently.
Prions


Mad cow disease (BSE or bovine spongiform
encephalopathy) and related illnesses (scrapie in sheep,
variant Creutzfeldt-Jakob disease in humans) are caused
by an abnormal protein which can alter the shape of
normal proteins.
In humans, the
disease leads to
neurological problems
and death within a
year of the onset of
symptoms.
Mad-Cow Disease
www.cnn.com/interactive/world/europe/0010/cjd/bse.gif
Functions of Proteins




Structural proteins (e.g., collagen) are intra- and
extracellular supports.
Storage proteins (e.g., ovalbumin) are a source of
amino acids to support the synthesis of new
proteins during development.
Transport proteins either carry materials around the
organism (e.g., hemoglobin) or carry molecules past
biological membranes (e.g., Na+-K+ pump).
Hormonal proteins (e.g., insulin) are intercellular
messengers.
Function of Proteins

Receptor proteins detect chemical signals (e.g.,
hormones) and alter the intracellular environment.

Contractile proteins (e.g., myosin) are responsible for
organismal and cell movement.

Defensive proteins (e.g., antibodies) attack foreign
molecules like viruses, bacteria, and other parasites.

Enzymatic proteins control specific chemical reactions.
Nucleotides

Nucleotides are molecules that comprise the
.
structural
units of DNA and RNA
A 5C sugar
Nitrogen
Base
Phosphate
Group
Fig. 3.15, pg. 57
Nucleotides

The 5-carbon sugar in nucleotides can be
either ribose or deoxyribose.
Ribose (C5H10O5) is found in ribonucleotides.
 Deoxyribose (C5H10O4) is found in
deoxyribonucleotides.

Nucleotides

There are five possible nitrogenous bases.

In DNA there is Adenine, Guanine,
Cytosine, and Thymine.
◦ In RNA Thymine is replaced with Uracil.
Classes of Nucleic Acids
Polynucleotides (ribonucleic acid: RNA and
deoxyribonucleic acid: DNA) carry the
information for and participate in protein
synthesis.
 ATP (adenosine triphosphate) and GTP (guanine
triphosphate) store and release energy to
support normal metabolic activities.
 Nucleotides coenzymes transport high energy
electrons from one site in the cell to another.

A Closer Look at Nucleotides
RNA (Ribonucleic Acid) is a
__________ strand.
 In single strands of RNA and
DNA, the sugar group of one
nucleotide bonds to the
phosphate of the next.
 RNA will only have Guanine,
Adenine, Uracil,and Cytosine
bases.

RNA

RNA molecules have multiple roles
◦ rRNA (ribosomal RNA) combines with proteins
to form ribosomes which synthesize new
proteins
◦ mRNA (messenger RNA) sets the order with
which amino acids should be bonded to
synthesize a polypeptide
◦ tRNA (transfer RNA) transfers or carries
specific amino acids to the ribosome
A Closer Look at Nucleotides



DNA molecules are
___________ stranded.
The two strands are
linked together by
hydrogen bonds between
nitrogen bases on the two
strands.
Specific bases on one
strand match up with
specific bases on the
other strand
◦ ______ with C and ______
with T

The order of a section of
nucleotides on DNA (a gene)
contains the information for
producing a
__________________.
Each of the 100,000 different
proteins synthesized by humans
begins with a section of DNA.
 This gene is transcribed from
DNA to _______________.
◦ The mRNA is complementary to
the nucleotides of DNA.
 At the ribosome, the order of
nucleotides on mRNA directs the
addition of amino acids to form a
protein during translation.

Fig. 3.19, pg. 59
Lipids

Lipids are large, nonpolar organic
molecules that don’t dissolve in polar
solvents well.
◦ They are not polymers, and do not have the
same ratio of C, H, O as carbohydrates do.
They usually have fewer oxygen in their
empirical formula.

Classes of Lipids:
◦ Fats
◦ Phospholipids
◦ Steroids
Fatty Acids
Fatty Acids are the monomers of fats.
 Fatty acids have lots of C & H atoms and
two O atoms.
 There is a long backbone of C & H with a
carboxyl (COOH) group at one end.

Fatty Acids

Saturated Fatty Acids lack the C=C in the
backbone.
Most saturated fats are solid at room
temperature. (animal fats)
 It has as many Hydrogens attached to it as
possible.

Fatty Acids

Unsaturated Fatty Acids have one
(monounsaturated) or more (polyunsaturated)
C=C bonds in the backbone.
Most unsaturated fatty acids are liquid at room
temperature (plant oils).
 Fatty acids are a major source of
________________ in cells.

Fatty Acids

While your body can synthesize most of the fatty
acids that it requires, it cannot synthesize two
essential fatty acids.

These fatty acids are used in the production of hormones
that control cell growth and specialization. A lack of them
can cause impaired growth, skin problems and neurological
problems.
Omega-3 fatty acids are also linked with reduced risk of
heart attack.

Fatty Acids
Normally, polyunsaturated and monounsaturated
fats, from plant oils have positive effects on health.
 However, in the many processed foods (cookies,
fried foods, candies, crackers), some natural fats
are converted to trans fats.
 Trans fats elevate levels of cholesterol and LDL
(low density lipoprotein) in the blood.
 This can lead to elevated risk of heart attacks.
Now manufacturers are required to list trans fat
content.

Triacylglycerides

Triacylglycerides are a fat that has one glycerol
molecule, attached to three fatty acids.

Account for 95% of fat stored in human tissue.
Triacylglycerides

One major function of
triacylglycerides is
space-efficient (no water),
high value, energy storage
(e.g., seeds, fatty deposits).
◦ Fats contain 9 calories per
gram, while carbohydrates or proteins have only 4 calories
per gram.
◦ Benefits
 Creates layers of adipose cells (filled with vacuoles of
fat) under skin to insulate from cold
 Pads of fat cells packed around joints or internal organs
protect these structures by absorbing sudden forces.
Phospholipids



Phospholipids have C, H,
O, P, and sometimes N.
In phospholipids, one
fatty acid in a
triacylglyceride is
replaced by a
phosphate group
(-RPO4).
The phosphate group
gives the phospholipid a
net charge.
Phospholipids
Phospholipids are a major component of cell
membranes. They separate the cell contents
from the exterior environment.
 In cell membranes, they form bilayers with the
hydrophilic heads on the outside and the
hydrophobic tails on the inside.

Hydrophilic Heads
Hydrophobic Tails
Steroids
All steroids consist of four rings of 6C, 6C, 6C, and
5 carbons.
 Cholesterol has a large hydrophobic functional
group off the 5 carbon ring. Cholesterol is an
important component of cell membranes and the
manufacturing of vitamin D.
 Cholesterol is
synthesized by the
body, as well as
acquired by food.

Steroids

Some steroids are
________________
messengers - hormones.

Modified steroids (bile
salts) are secreted by
the liver into the
intestine to aid lipid
_________________
and absorption.