1
He is best known for accidently discovering how to
create urea. His experiment, now termed the Wohler
synthesis, consists of creating urea. He was trying to
make ammonium cyanate, by combining ammonium
ions and cyanate ions, but instead found out how to
make urea, which is ORGANIC. This occurred in 1828.
This experiment is considered the starting point of
organic chemistry.
The Wohler synthesis is of great historical significance
because for the first time an organic compound was
produced from inorganic reactants. This finding went
against the mainstream theory of that time, called
Vitalism, which stated that physical and chemical laws
do not apply to living things. For this reason, a sharp
boundary existed between organic and inorganic
compounds. Urea was discovered in 1799 and could
only be obtained from biological sources such as urine
until Wohler came up with a way to synthesize it.
2
Stanley Lloyd Miller was an American chemist
and biologist who is known for his studies into
the origin of life, particularly the Miller-Urey
experiment which demonstrated that organic
compounds can be created by fairly simple
physical processes from inorganic substances.
The Miller-Urey experiment was an experiment
that simulated hypothetical conditions present on
the early Earth and tested for the occurrence of
chemical evolution. Specifically, the experiment
tested that conditions on the primitive Earth
favored chemical reactions that synthesized
organic compounds from inorganic precursors.
Considered to be the classic experiment on the
origin of life, it was conducted in 1953 by Stanley L.
Miller and Harold C. Urey at the University of
Chicago.
It was later found that the mixture of gasses Miller used did not accurately reflect the
early atmosphere. However, since then the experiment has been repeated with the
3
more appropriate mixture of gasses and organic substances are still created.
The experiment used water (H2O),
methane (CH4), ammonia (NH3) and
hydrogen (H2). The chemicals were all
sealed inside a sterile array of glass
tubes and flasks connected together in
a loop, with one flask half-full of liquid
water and another flask containing a
pair of electrodes.
The liquid water was heated to induce evaporation, sparks were fired between the electrodes to
simulate lightning through the atmosphere and water vapor, and then the atmosphere was cooled
again so that the water could condense and trickle back into the first flask in a continuous cycle.
At the end of one week of continuous operation Miller and Urey observed that as much
as 10-15% of the carbon within the system was now in the form of organic compounds. Two
percent of the carbon had formed amino acids, including 2-3 of the 22 that are used to make
proteins in living cells, with glycine as the most abundant. Sugars, lipids, and some of the building
blocks for nucleic acids were also formed. This helped disprove the vitalism theory. Instead,
scientists embraced the idea of mechanism, the belief that the same physical and chemical laws
govern all natural phenomena, including the processes of life.
4
5
6
The ability of carbon to form four covalent bonds makes large, complex
molecules possible.
7
8
Isomers are compounds
that have the same
molecular formula but
different structures, and
therefore, different chemical
properties.
9


Same molecular
formula but differ in
covalent arrangement
of atoms
May also differ in the
location of the double
bond
10


Have the same covalent partnership but differ in the spatial
arrangement of atoms around a carbon=carbon DOUBLE
BOND!
These are formerly called GEOMETRIC ISOMERS!
Subtle changes in shape
can dramatically affect the
function of the molecule.
For example, the
biochemistry of vision
involves a light-induced
change of retinal, a
chemical compound in the
eye, from the cis isomer to
the trans isomer.
11
Molecules that are mirror images of each
other. They are referred to as “left-handed”
and “right-handed” versions. This is the
case when 4 DIFFERENT molecules or
groups of molecules are attached to an
asymmetric carbon. (asymmetric carbon
just means it is attached to 4 different
things).
Even subtle structural differences
in two enantiomers may have important
functional significance because of emergent
properties from specific arrangements of
atoms.
For example, methamphetamine
occurs in two enantiomers with very
different effects. One is a highly addictive
street drug called “crank”, while the other
is sold for treatment of nasal congestion.
12
The basic structure of testosterone (a male sex hormone) and estradiol (a female
sex hormone) is the same. Both are steroids with four fused carbon rings, but
the hormones differ in the chemical groups attached to the rings. As a result,
testosterone and estradiol have different shapes, causing them to interact
differently with many targets throughout the body.
13
Chemical groups known
as functional groups
affect molecular function
through their direct
involvement in chemical
reactions.
All of the functional
groups are
HYDROPHILIC and
INCREASE the
SOLUBILITY of organic
compounds in water.
There are seven that you
need to know…see charts
on the following slides…
14





ATP is an important source
of energy for cellular
processes.
Adenosine triphosphate,
or ATP, is the primary
energy transfer molecule in
living cells.
ATP consists of an organic
molecule called adenosine
attached to a string of three
phosphate groups.
When one inorganic
phosphate ion is split off as
a result of a reaction with
water, ATP becomes
adenosine diphosphate, or
ADP.
In a sense, ATP “stores” the
potential to react with
water, releasing energy that
can be used by the cell.
15
16
17
18
Dehydration Reaction (Condensation
Reaction)  Taking water OUT;
FORMING a BOND; Builds Polymers
from Monomers; Ex. Making a protein
from amino acids
Hydrolysis  Putting water IN to
BREAK a BOND; breaks down to form
monomers from a larger polymer; Ex.
Digestion and breaking down food
We take in food as organic polymers that are too
large for our cells to absorb. In the digestive tract,
enzymes direct the hydrolysis of specific polymers.
The resulting monomers are absorbed by the cells
lining the gut and transported to the bloodstream
for distribution to body cells.
The cells of our body then use dehydration
reactions to assemble the monomers into new and
different polymers that carry out functions specific
to the particular cell type.
19
Carbohydrates
Main Function: Short term energy storage
Monomer: Monosaccharides
Bond Name: Glycosidic Linkage
20
- Monomer for Carbohydrates
- Examples are Glucose, Fructose,
Galactose
- Can form in a ring or linear
structure…usually a ring.
21
Two monosaccharides
together are called a
DISACCHARIDE. This
is formed by
Dehydration Synthesis
to make the bond and
therefore you create a
molecule of water.
Examples of
Disaccharides are
Maltose, Sucrose, and
Lactose
The type of bond
between two
monosaccharides is
called a glycosidic
linkage (covalent).
22



Hundreds to thousands of monosaccharides
linked together form polysaccharides
Formed by dehydration synthesis and use
glycosidic linkages
Four polysaccharides you need to know:




Plant Storage = STARCH
Animal Storage = GLYCOGEN
Plant Structure = CELLULOSE
Animal Structure = CHITIN
23
STARCH  PLANT
STORAGE!
Animals that feed on
plants, especially parts
rich in starch, have
digestive enzymes that
can hydrolyze starch to
glucose, making the
glucose available as a
nutrient for cells. Grains
and potato tubers are the
main sources of starch in
the human diet.
GLYCOGEN  ANIMAL
STORAGE!
24
CELLULOSE PLANT
STRUCTURE!
Plants produce almost 1014
kg (100 billion tons) of
cellulose per year. It is the
most abundant organic
compound on Earth.
CHITIN ANIMAL
STRUCTURE!
25
The linkages are different in
starch vs. cellulose because
glucose has two slightly different
ring structures. These two ring
forms differ in whether the
hydroxyl group attached to the
number 1 carbon is fixed above
(beta) or below (alpha) the plane
of the ring.
26
27
Lipids
Main Function: Long term energy storage,
protection, insulation, component of cell membranes
Monomer: No real monomer!!
28
- No technical monomer for fats
- Fats are constructed from two
smaller kinds of molecules:
glycerol and fatty acids
- Many NON-POLAR bonds in
fatty acid chains, so fats are
hydrophobic and do not
dissolve in water
- When 3 fatty acid chains bond
with one glycerol (via
dehydration synthesis) a
TRIGLYCERIDE is created
using 3 ESTER LINKAGES
29
Because plants are immobile, they
can function with bulky energy
storage in the form of starch. Plants
use oils when dispersal and
compact storage are important, as
in seeds. Animals must carry their
energy stores with them, so they
benefit from having a more
compact fuel reservoir of fat.
Saturated Fats  all single bonds; straight chain; animal fats; solid at room
temperature
**A diet rich in saturated fats may contribute to cardiovascular disease
(atherosclerosis) through plaque deposits. The process of hydrogenating vegetable
oils produces saturated fats and also unsaturated fats with trans double bonds.
These trans fat molecules contribute more than saturated fats to atherosclerosis.
Unsaturated Fats  at least one C =C double bond; kinks in chain; plant and fish
fats; liquid at room temperature
30
- Structure: Two fatty
acid chains attached to
a phosphate and
glycerol molecule
- Head: Phosphate and
hydrophilic
- Tail: FA chains and
hydrophobic
- Major component of
cell membrane;
arranged in bilayer so
heads can come into
contact with water and
tails are protected
from it in the interior
- Amphipathic is the
term used when
something has both
hydrophobic and
hydrophilic regions
31
32
Steroids are lipids with a carbon skeleton consisting of four fused rings.
Different steroids are created by varying the functional groups attached to the
rings. Cholesterol, an important steroid, is a component in animal cell
membranes. Cholesterol is the precursor from which all other steroids are
synthesized. Many of these other steroids are hormones, including the vertebrate
sex hormones.
33
Proteins
Main Function: Everything!
Monomer: Amino Acids
Bond Name: Peptide Bonds
34
Proteins are instrumental in almost everything an organism does (structural support,
storage, transport, cellular communication, movement, and defense). ENZYMES are
also proteins and function as catalysts in chemical reactions.
35
-Carboxyl Group (COOH)
- Amino Group (-NH2)
-Central Carbon
-Hydrogen
-“R” group
36
This is a
“charged” amino
acid, overall it is
neutral, but it
affects the bonds
it will make. You
need to be able to
recognize that
this is an amino
acid if you see it.
37
The “R” groups are
all different. There
are 4 different
categories that they
fall into:
-Nonpolar
-Polar Neutral
-Polar Acidic
-Polar Basic
20 Amino Acids
These make up
proteins – they are
the monomers…link
them together to
form a polymer  a
PROTEIN!
38
A PEPTIDE BOND is
formed between the H of
one amino acid (amino
group) and the OH of
another AA (carboxyl
group). A molecule of
water is produced. This
process is done by
dehydration synthesis.
39
PEPTIDE BONDS – bonds between one
amino acid and the next; these are created
by dehydration synthesis (condensation)
In almost every case, the function of a
protein depends on its ability to recognize
and bind to some other molecule.
For example, an antibody binds to a
particular foreign substance. Natural signal
molecules called endorphins bind to specific
receptor proteins on the surface of brain
cells in humans, producing euphoria and
relieving pain. Morphine, heroin, and other
opiate drugs mimic endorphins because they
are similar in shape and can bind to the
brain’s endorphin receptors.
40
The primary
structure of a protein
is the order of the
amino acids. This is
coded for by DNA in
the cell.
41
This disease is caused
by a substitution in
ONE amino acid. It
affects the primary
structure of the protein
hemoglobin causing
this disorder.
Even a slight change in the primary structure can affect a protein’s conformation and
ability to function. The substitution of one amino acid (valine) for the normal one
(glutamic acid) at a particular position in the primary structure of hemoglobin, the
protein that carries oxygen in red blood cells, can cause sickle-cell disease, an
inherited blood disorder. The abnormal hemoglobin molecules crystallize, deforming
some of the red blood cells into a sickle shape and clogging capillaries.
42
The secondary structure
of a protein is due to
HYDROGEN BONDS
within the polypeptide
chain.
It can form either an
Alpha Helix or Beta
Pleated Sheets
depending on whether it
folds or coils…different
parts of the protein can
do different things.
43
Tertiary Structure is
determined by interactions of
the “R” groups of the amino
acids.
Interactions include
clustering of hydrophobic
groups, hydrogen bonds, van
der waals interactions,
disulfide bridges, and ionic
bonds.
44
Hemoglobin is a
globular protein with
quaternary structure.
Hemoglobin consists
of four polypeptide
subunits: two  and
two  chains. Both
types of subunits
consist of primarily helical secondary
structure.
**Only occurs if there is more than one polypeptide chain!
Each subunit has a
nonpeptide heme
component with an
iron atom that binds
oxygen
45
Accumulation of incorrectly folded polypeptides is associated with many
diseases, including Alzheimer's, Parkinson’s, and mad cow disease.
46
Denaturation occurs when a protein comes unraveled and it loses its form, and
therefore its function. Some can renature, others cannot. Several factors cause
denaturation: pH, temperature, salt concentration
An example how denaturation can occur in humans is when you get a fever. The
extreme heat can denature the proteins in the blood and thus they become nonfunctional. This is why high fevers can be fatal.
47
These proteins help protect developing proteins while they are folding up and
forming. They act as chaperones. Chaperonins do not specify the final structure
of a polypeptide but rather work to segregate and protect the polypeptide while
it folds spontaneously.
48
Nucleic Acids
Main Function:
Storing genetic
information
Monomer:
Nucleotides
Bond Name:
Phosphodiester
Linkages and
Hydrogen Bonds
49

Two main types of nucleic acids






DNA
RNA
DNA controls gene expression, in which RNA has
a vital role in synthesizing proteins
Organisms inherit their DNA from their parents
Although DNA is the genetic code, it is not
involved in the day-to-day operations of the cell
(that is the role of the proteins)
DNA and RNA are made up of nucleotides
50
DNA carries the genetic code
RNA carries out protein
synthesis in the ribosomes.
This process includes mRNA,
rRNA, and tRNA. We will
learn more about these in
another unit.
51
Nucleotides:
- Pentose Sugar
- Nitrogen bases
-Phosphate Groups
52
Two Types of Bases:
-Purines – two rings
- Pyrimidines – one ring
DNA: A, T, C, G
RNA: A, U, C, G
53
A sugar and a
nitrogen base are
called a
nucleoside.
When you add
the phosphate
group, it
becomes a
nucleotide.
54
Strands in DNA run antiparallel!
Bonding in DNA 
Bonds in the sugar/phosphate backbone are
called phosphodiester linkages. These are
covalent bonds between the sugar of one
nucleotide and the phosphate of the next.
There are also hydrogen bonds in DNA between
the nitrogen bases. These hold the two strands
together.
55



Genomics is an approach of addressing
problems by analyzing large sets of genes or
comparing whole genomes of different species.
Similar to genomics, proteomic is the approach
that analyzes large sets of protein sequences.
We will learn much more about this, and these
specific processes, in the biotechnology unit.
56
Two species that appear to be closely
related based on fossil and molecular
evidence should also be more similar
in DNA and protein sequences than
are more distantly related species.
Scientists can compare the sequence
of 146 amino acids in the
polypeptide chain of human
hemoglobin to the sequences in five
other vertebrates. Humans and
gorillas differ in just 1 amino acid,
while humans and frogs differ in 67
amino acids. Despite these
differences, all the species have
functional hemoglobin.
57