ORGANIC MOLECULES
& FUNCTIONAL
GROUPS
VITALISM
•Anything that was alive possessed a vital spark, while things that weren't
alive...didn’t.
•So what is a vital spark?
•Well, you can't see it, taste it, feel it, hear it, or smell it.
•You can't capture it in a bottle or any other vessel; you can't transfer it from
one object to another. You can't measure it or detect it. The only way to
determine if an object had one was to determine if it was alive or not.
MECHANISM
•Biologists don't believe that there are any substances or materials which are
exclusive to living things.
•What makes something alive is not what it's made of; it's how it's put
together and what activities (i.e, chemistry) go on within its structures.
adaptation
Response to
the environment
order
reproduction
Energy processing
regulation
Growth and development
Miller Urey Experiment
Demonstrated that organic compounds can be created by fairly simple physical
processes from inorganic substances. The experiment used conditions then thought
to provide an approximate representation of those present on the primordial Earth.
WHAT’S THE DIFFERENCE BETWEEN ORGANIC
COMPOUNDS & INORGANIC COMPOUNDS?
ORGANIC
INORGANIC
WHY IS CARBON SO SPECIAL?
The versatility of
carbon: Makes
possible the
great diversity of
organic
molecules
Where does the source of carbon for
all organic molecules come from?
Carbon Chains
Form the
Skeletons of
Most Organic
Molecules
What do you notice
about these molecules?
Name and
Comments
(a) Methane
CH4
(b) Ethane
C2H
Have suffix –ane if single
bonded.
6
(c) Ethene
Figure 4.3 A-C (ethylene)
Found in fossil fuels
Ball-andStick
Model
Molecular Structural
Formula Formula
C2H
4
H
H C H
H
SpaceFilling
Model
H H
H C C H
H H
H
H
C C
H
H
Hydrogen
Oxygen
Nitrogen
Carbon
(valence = 1)
(valence = 2)
(valence = 3)
(valence = 4)
H
O
N
C
Figure 4.4
Carbon atoms can form diverse molecules by bonding
to four other atoms
MOLECULAR SHAPE & FUNCTION
• Shapes are determined by the positions of the
atoms’ orbital.
• Molecular shape is very important in living
cells.
– It determines how the molecules recognize &
respond to each other.
• If they are complimentary; they will bond
ISOMERS
COMPOUNDS THAT HAVE THE SAME
NUMBERS OF ATOMS OF THE SAME
ELEMENTS BUT DIFFERENT STRUCTURES.
(THESE MOLECULES THEREFORE HAVE
DIFFERENT PROPERTIES)
Both of the molecules below are C5H12
Why are there different forms of the same chemical formula?
Because carbon can bond to either hydrogen or another carbon
What would it take to make these molecules identical?
Breaking and reforming a covalent bond
What type of isomer are molecules that
have more than 1 structural form?
Structural Isomer
LIGHTER
FLUID
REFRIGERANT
Both of the molecules below are C2H4Cl2
cis
trans
Why are there different forms of the same chemical formula?
Because the H and Cl can bond in any order around the central carbon atoms
What would it take to make these molecules identical?
Rotation around the carbon-carbon double bond
What type of isomer are molecules that
have double bonds & more than 1
geometric arrangement?
Cis-trans isomers/
geometric isomers
EX: A VISUAL PIGMENT IN OUR EYES
CALLED RHODOPSIN
• It changes shape when it absorbs light from
the cis isomer to the trans isomer.
– Process known as
“bleaching”
• When you move from a
very bright environment
to a very dark.
– There is too little light to stimulate your cones, &
it takes a few min. for your bleached rods to
become fully responsive again.
Both of the molecules below are CHIBrCl
dextro
levo
L isomer
D isomer
In what way are these molecules different from each other?
They are mirror images of each other
What would it take to make these molecules identical?
Breaking and reforming a covalent bond
What do we call these types of isomers?
Enantiomers
Functional groups
Are the chemically reactive
groups of atoms within an
organic molecule
THE COMPONENTS OF ORGANIC MOLECULES THAT ARE
MOST COMMONLY INVOLVED IN CHEMICAL REACTIONS
NOTICE THE
MOLECULES ON
THE RIGHT.
THEY DIFFER
ONLY IN THE
FUNCTIONAL
GROUP.
Produce differences in
males vs females.
Creating your
functional group
poster
Functional Groups being presented:
-hydroxyl
-carboxyl
-methyl
-carbonyl
-sulfhydryl
-amino
-phosphate
Create a large visual aid that conveys
the following information:
• Draw your functional group
• Describe the physical properties your functional
group adds to a molecule.
• Give the chemical naming suffix
• List examples
• Record any additional information associated with
your functional group.
YOU HAVE 15MINUTES TO COMPLETE YOUR POSTER FOR PRESENTING
A Few Discussion Questions
• Can a molecule have more than one functional group?
Yes, most do. EX: amino acids have both the amino group and the carboxyl
group.
• Which group(s) would change the pH of a solution? In
what way?
–Carboxylic acids & amines (bases)
• Which of the functional groups would hydrogen bond?
All of them
• Which groups are hydrophillic?
All of them…except methyl
Macromolecule Group Project
WHAT IS THE DIFFERENCE BETWEEN A MONOMER & A POLYMER?
SYNTHESIS AND BREAKDOWN
OF POLYMERS
 Enzymes help
Dehydration (Condensation) reaction
To connect monomers together
A water molecule is released
One molecule gives up a hydroxyl group
& the other a hydrogen
 Hydrolysis
Polymers are broken apart to monomers
A water molecule is added to split apart
the monomers
EX: Digestion
WHICH OF THESE IS A MONOMER OF CARBOHYDRATE?
HOW CAN YOU TELL?
Carbohydrate monomers generally have
molecular formulas that have some
multiple of the unit CnHxOn in ratios of
CH2O
WHAT DO WE CALL
THIS MONOMER?
Glucose
WHAT IS THE CHEMICAL SUFFIX
USED FOR CARBOHYDRATES?
-ose
VARIOUS MONOSACCHARIDES
What do all of these
sugars have in
common?
They are made of
one carbonyl group
and several hydroxyl
groups.
What’s the difference
between the top row
of sugars compared
to the bottom row?
The top sugars have their
carbonyl group at the end
of the carbon skeleton &
the bottom ones have their
carbonyl group in the
middle
Identify the difference between glucose & galactose.
What are the monomers used to
form?
Disaccharides and polysaccharides
Where does the polysaccharide bond occur and how?
At an oxygen off the 1’ carbon using a dehydration
reaction called glycosidic linkage.
WHAT IS GLYCOSIDIC LINKAGE?
Covalent bond between 2 monosaccharides through a dehydration reaction.
A water molecule is released
One molecule gives up a hydroxyl group & the other a hydrogen
2 Different Structures of Glucose
Linear
Ring
Write down how the linear structure becomes a
ringed structure. Be as specific as possible.
Why does this happen?
The ketone or aldehyde react with the
hydroxyl group in aqueous solution
Carbohydrates
• Also referred to as sugars
• Provide building materials and energy storage
• Are molecules that contain carbon, hydrogen and
oxygen in a 1:2:1 ratio
• Are of two main types
– Simple carbohydrates
– Complex carbohydrates
Simple Carbohydrates
Monosaccharide
Disaccharide
Consist of one subunit
Consist of two subunits
EX: glucose, fructose, galactose
EX: sucrose, maltose, lactose
Helps secrete
lactose
Chemical fuel
for the body
Glucose
Chemical formula:
C6H12O6
Formed by a
dehydration
reaction
Type of carbohydrate
transported from leaves
to roots
Makes fruit
sweet
Sucrose
Glycosidic
linkage
Complex Carbohydrates
Consist of long polymers of sugar subunits
Few hundred to a few thousand
Also termed polysaccharides
Serve as energy storage and/or building
material for structure and/or protection
Animals store
energy in the form of
glycogen, glucose
polymer, in their liver
and muscles.
Plants store energy
in the form of starch
which are made
from many glucose
molecules
Starch granules
Plants Use Cellulose in their Cell Walls to
give them structure & protection
Primary component of
plant cell walls. Most
animals cannot digest
this. Cows can.
We (humans) can eat & digest starch
but we cannot digest cellulose.
WHY???
The hydroxyl group
attached to the number
1 carbon is positioned
either below or above
the plane of the ring.
GLYCOSYLIC LINKAGE
GIVE THESE
CARBOHYDRATES
DIFFERENT SHAPES:
•Starch = helical
•Cellulose= straight non branched
It’s all about the linkage
alpha vs beta
• Your body contains enzymes (amylase) that
break starch down into glucose to fuel your
body. But we humans don't have enzymes
that can break down cellulose.
• Some animals do:
• Cellulose is a lot stronger than starch.
cellulose is strong enough to make fibers
from, and make rope, clothing, etc.
• Cellulose doesn't dissolve in water the way
starch will, and doesn't break down as easily.
• This is a good thing… since our clothes are
made of cellulose, wooden park benches and
wooden houses would all dissolve after one
good rain.
CHITIN
Builds exoskeletons
used by arthropods.
Fungi use this
instead of cellulose
for their cell walls.
GLUSOSE (beta)
WITH A NITROGEN
APPENDAGE
Lipids
• Large nonpolar molecules that are insoluble in
water
• They are NOT polymers but they are large
molecules assembled from smaller molecules.
• Three major types
– Triglycerides
– Phospholipids
– Steroids
Triglycerides
• Used for long-term
energy storage
– Composed of three
fatty acid chains
(hydrocarbon tails)
linked to glycerol
– EX: Fats & oils
Types of fatty acids
• Fatty acids can be saturated or unsaturated
Most plant
fats
Most animal
fats
Saturated fats &
Trans Fats:
Linked to coronary
disease
Trans fats are even worse
than saturated fats.
Trans fats are produced
artificially where saturated fats
are natural
Denmark has banned trans
fats in restaurants.
•Some fat is needed in a regular healthy diet.
•Omega-3 fatty acids
•Normal growth in children
•Fights off heart disease in adults
MAIN FUNCTION OF FATS IS ENERGY STORAGE
-lipids store twice as much chemical energy as the
carbohydrate.
Lipids are needed
for thermal
insulation
Phospholipids
• A modified fat
– One of the three fatty acids is replaced by a
phosphate and a small polar functional group
Essential to cells:
they make up the cell
membrane.
Steroids
• Composed of four carbon rings
Examples:
Cholesterol
Found in most animal
cell membranes & in
vertebrates it is
synthesized in the liver
Male and female sex
hormones
Progesterone,
estrogen, &
testosterone
The attaching chemical
groups to the 4 carbon
rings is what gives variety.
Nucleic Acids
• Serve as information storage molecules
• Store, transmit and help express hereditary
information
• Long polymers of repeating subunits termed
nucleotides
• A nucleotide is composed of three parts
– Five-carbon sugar
– Nitrogen-containing base
– Phosphate
The structure of a nucleotide
Nitrogenous bases
Pyrimidines: one 6 membered ring of carbon & nitrogen
Purines: 6 membered ring fused to a 5 membered ring
The sugar and the
phosphates are
covalently bonded.
How DNA
differs from
RNA
Nucleic Acids
• Two varieties
– Deoxyribonucleic acid (DNA)
– Ribonucleic acid (RNA)
DNA
Sugar = Deoxyribose
Bases = A, G, C, T
Double-stranded
Can’t leave the nucleus
RNA
Sugar = Ribose
Bases = A, G, C, U
Single-stranded
Can travel outside the nucleus
Space-filling
model
Look at the ends of the
DNA molecule
AMONG THE DNA SEQUENCE ARE
GENES WHICH ARE CODES FOR
SPECIFIC PROTEINS.
5’ –ATTGCAATGGCTAGGGCCAATGC- 3’
3’ -TAACGTTACCGATCCCGGTTACG- 5’
In the above DNA sequence the code is different
•DNA is read in one direction (5’ to 3’)
Proteins
Nearly every dynamic function of a living being
depends on proteins.
They are instrumental in almost everything we do.
• Made up of subunits
called amino acids
Six amino
acids
• There are 20
common amino hydrophobic
acids, and they fall
into one of four
general groups
Six amino
acids
hydrophillic
Five amino
acids
Three amino acids
Polar and non-polar amino acids
• Amino acids with non-polar chains are found
in regions of proteins that are linked to the
hydrophobic area of the cell membrane.
• Amino acids with polar side chains are found
in regions of proteins that are exposed to
water.
• Membrane proteins: create a hydrophillic
channel in proteins through which polar
substances can move.
Proteins
• Amino acids are
linked together
by peptide
bonds
Long chains of
amino acids are
called
polypeptides
Amino
group
Carboxy
l group
Protein
Function
Hemoglobin
Contains iron that transports oxygen from
the lungs to all parts of the body in
vertebrates
Interact to bring about muscle movement
Actin & myosin
Hormone secreted by the pancreas that
aids in maintaining blood glucose level
immunoglobulins group of proteins that act as antibodies to
fight bacteria & viruses
insulin
amylase
Digestive enzyme that catalyses the
hydrolysis of starch
Types of Protein
Other Types of Protein
Protein Structure
• Determined by the sequence of its amino acids
• There are four general levels
– Primary
– Secondary
– Tertiary
– Quaternary
Building a Protein
• Take your 15 tacks and place them in any order
along the toober. Just make sure they are equal
distance from each other and they are on the
same side.
Fold your protein so that all of the hydrophobic
sidechains (yellow tacks) are buried on the
inside of your protein, where they will be hidden
from polar water molecules.
Fold your protein so the acidic and basic (charged)
sidechains are on the outside surface of the protein
and pair one negative sidechain (red tack) with
one positive sidechain (blue tack) so that they
come within one inch of each other and neutralize
each other. This positive-negative pairing
helps stabilize your protein.
Continue to fold your protein making sure that your
polar sidechains (white tacks) are also on the
outside surface
of your protein where they can hydrogen bond with
water.
Last, fold your protein so that the two cysteine
sidechains (green tacks) are positioned opposite
each other on
the inside of the protein where they can form a
covalent disulfide bond that helps stabilize
your protein.
Every toober had a different random
sequence of tacks & therefore each toober
folded into a different structure.
Some sequences were more easily
folded than others.
The 30,000 proteins encoded by the
human genome have been selected from
an enormous number of possible amino
acid sequences based on their ability to
spontaneously fold into a stable structure
that simultaneously satisfies these basic
laws of chemistry.
Protein Structure
• Primary structure
– The specific amino acid sequence of a protein
• Secondary structure
– The initial folding of the amino acid chain by hydrogen
bonding
• Tertiary structure
– The final three-dimensional shape of the protein
• Quaternary structure
– The spatial arrangement of polypeptides in a multicomponent protein
Protein Structure
• Changes in a
protein’s
environment can
cause a protein to
denature
– It loses its threedimensional
structure
– And becomes
inactive
Chaperonins aka Chaperone Proteins
• Help newly-produced proteins to fold properly
Chaperone protein deficiencies may play a role in
certain diseases
Cystic fibrosis and Alzheimer’s disease , Parkinson’s disease &
mad cow disease
Protein Structure
• Proteins can be divided into two classes
1. Structural
2. Globular
Long cables
Provide shape/strength
Fibrin
Silk
Keratin
Grooves and depressions
Enzymes
ORGANIC MOLECULES WHICH ACT AS CATALYSTS
Enzymes
• Are proteins
– So they are made up of ?
• Somewhere in this protein is an area that’s
designed to match a specific molecule = active
site.
• The molecule that matches the active site is
called the enzyme’s substrate.
Enzymes
• Influence the rate of reaction
• A set of reactants present with enzymes will
form products at a faster rate than without
enzymes.
• Enzymes cannot force reactions to occur that
would not normally occur
• The enzymes role is to lower the energy level
needed to start the reaction.
– Enzymes lower the activation energy of reactions
• Enzymes are not used up during the reaction
WHAT FACTORS MIGHT
AFFECT ENZYME
CATALYST REACTIONS?