ORGANIC MOLECULES

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ORGANIC MOLECULES FUNCTIONAL GROUPS
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VITALISM

• Anything that was alive possessed a vital spark,
  while things that weren't
• alive...didnt.
• 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.

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Characteristics of life
Response to the environment
adaptation
order
reproduction
Energy processing
regulation
Growth and development
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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.
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WHATS THE DIFFERENCE BETWEEN ORGANIC COMPOUNDS
INORGANIC COMPOUNDS?
ORGANIC
INORGANIC
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WHY IS CARBON SO SPECIAL?
The versatility of carbon Makes possible the
great diversity of organic molecules
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Where does the source of carbon for all organic
molecules come from?
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Carbon Chains Form the Skeletons of Most Organic
Molecules
What do you notice about these molecules?
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Hydrocarbons
Have suffix ane if single bonded. Found in
fossil fuels
Number of Bonds
Carbon atoms can form diverse molecules by
bonding to four other atoms
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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

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example
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ISOMERS

• COMPOUNDS THAT HAVE THE SAME NUMBERS OF ATOMS OF
  THE SAME ELEMENTS BUT DIFFERENT STRUCTURES.
  (THESE MOLECULES THEREFORE HAVE DIFFERENT
  PROPERTIES)

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• 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
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LIGHTER FLUID
REFRIGERANT
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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
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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.

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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
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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
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NOTICE THE MOLECULES ON THE RIGHT. THEY DIFFER
ONLY IN THE FUNCTIONAL GROUP.
Produce differences in males vs females.
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Creating your functional group poster

• Functional Groups being presented
• -hydroxyl -carbonyl -amino
• -carboxyl -sulfhydryl -phosphate
• -methyl

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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
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A Few Discussion Questions

• Can a molecule have more than one functional
  group?
• Which group(s) would change the pH of a solution?
  In what way?
• Which of the functional groups would hydrogen
  bond?
• Which groups are hydrophillic?

Yes, most do. EX amino acids have both the
amino group and the carboxyl group.

• Carboxylic acids amines (bases)

All of them
All of themexcept methyl
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Macromolecule Group Project
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Carbohydrates (2 groups)

• Monomer
• Polymer
• Chemical structural differences
• Examples of each why they are important
• One group will present simple carbohydrates
• One group will present complex carbohydrates
• Glycosidic linkage

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Lipids

• 3 major types
• What is different about each of them
• Chemical structure differences
• Saturated vs unsaturated
• Examples of why/how they are important

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Nucleic acids

• Monomer
• Polymer
• 2 types
• Chemical structure
• Differences between them
• Similarities between them
• Examples of why/how they are important

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Proteins

• Monomer
• Polymer
• Basic chemical structure of a monomer
• What is different about the different about each
  type of monomer?
• Examples and why/how they are important

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WHAT IS THE DIFFERENCE BETWEEN A MONOMER A
POLYMER?
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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
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VARIOUS MONOSACCHARIDES
What do all of these sugars have in common?
They are made of one carbonyl group and several
hydroxyl groups.
Whats 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.
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What are the monomers used to form?

• Disaccharides and polysaccharides

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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

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2 Different Structures of Glucose
Linear
Ring
Write down how the linear structure becomes a
ringed structure. Be as specific as possible.
The ketone or aldehyde react with the hydroxyl
group in aqueous solution
Why does this happen?
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Carbohydrates

• Also referred to as sugars
• Provide building materials and energy storage
• Are molecules that contain carbon, hydrogen and
  oxygen in a 121 ratio
• Are of two main types
• Simple carbohydrates
• Complex carbohydrates

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WHICH OF THESE IS A MONOMER OF CARBOHYDRATE?
WHAT DO WE CALL THIS MONOMER?
HOW CAN YOU TELL?
Glucose
Carbohydrate monomers generally have molecular
formulas that have some multiple of the unit
CnHxOn in ratios of CH2O
WHAT IS THE CHEMICAL SUFFIX USED FOR
CARBOHYDRATES?
-ose
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Simple Carbohydrates

• Monosaccharide
• Consist of one subunit
• EX glucose, fructose, galactose

• Disaccharide
• Consist of two subunits
• EX sucrose, maltose, lactose

Helps secrete lactose
Chemical fuel for the body
Formed by a dehydration reaction
Makes fruit sweet
Type of carbohydrate transported from leaves to
roots
Chemical formula C6H12O6
Glycosidic linkage
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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

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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
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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.
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We (humans) can eat digest starch but we cannot
digest cellulose. WHY???
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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

Its all about the linkage alpha vs beta
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• 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

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• 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.

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CHITIN
Builds exoskeletons used by arthropods. Fungi
use this instead of cellulose for their cell
walls.
GLUSOSE (beta) WITH A NITROGEN APPENDAGE
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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

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Triglycerides

• Used for long-term energy storage
• Composed of three fatty acid chains (hydrocarbon
  tails) linked to glycerol
• EX Fats oils

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Types of fatty acids

• Fatty acids can be saturated or unsaturated

Most plant fats
Most animal fats
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Saturated fats Trans Fats
Linked to coronary disease
Trans fats are worse than saturated fats. Trans
fats are produced artificially where saturated
fats are natural Denmark has banned trans fats
in restaurants.
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We need fat in our diet!! Why?

• Essential fatty acids  Dietary fats that are
  essential for growth development and cell
  functions, but cannot be made by our bodys
  processes
• Proper functioning of nerves and brain- fats are
  part of myelin- a fatty material which wraps
  around our nerve cells so that they can send
  electrical messages. Our brains contain large
  amounts of essential fats
• Maintaining healthy skin and other tissues.  All
  our body cells need to contain some fats  as
  essential parts of cell membranes, controlling
  what goes in and out of our cells
• Transporting fat-soluble vitamins A, D, E and
  K through the bloodstream to where they are
  needed
• Forming steroid hormones needed to regulate many
  bodily processes

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A GREAT SOURCE OF HEALTHY FAT TO EAT ARE THE
OMEGAS

• Prevent coronary heart disease
• Prevent stroke
• Prevent diabetes
• Promote healthy nerve activity
• Improve vitamin absorption
• Maintain a healthy immune system
• Promote cell development

MAIN FUNCTION OF FATS IS ENERGY STORAGE -lipids
store twice as much chemical energy as the
carbohydrate.
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Lipids are needed for thermal insulation
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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.
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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.
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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

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Nitrogenous bases
Pyrimidines one 6 membered ring of carbon
nitrogen Purines 6 membered ring fused to a 5
membered ring
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The sugar and the phosphates are covalently
bonded.
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How DNA differs from RNA
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Nucleic Acids

• Two varieties
• Deoxyribonucleic acid (DNA)
• Ribonucleic acid (RNA)

DNA RNA
Sugar Deoxyribose Sugar Ribose
Bases A, G, C, T Bases A, G, C, U
Double-stranded Single-stranded
Cant leave the nucleus Can travel outside the nucleus
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Look at the ends of the DNA molecule
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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)

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Nearly every dynamic function of a living being
depends on proteins. They are instrumental in
almost everything we do.
Proteins
R Group

• Made up of subunits called amino acids
• There are 20 common amino acids, and they fall
  into one of four general groups

Six amino acids
Six amino acids
hydrophobic
hydrophillic
Five amino acids
Three amino acids
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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.

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Proteins

• Amino acids are linked together by peptide bonds

Amino group
Carboxyl group

• Long chains of amino acids are called polypeptides

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Protein Function
Hemoglobin Contains iron that transports oxygen from the lungs to all parts of the body in vertebrates
Actin myosin Interact to bring about muscle movement
insulin Hormone secreted by the pancreas that aids in maintaining blood glucose level
immunoglobulins group of proteins that act as antibodies to fight bacteria viruses
amylase Digestive enzyme that catalyses the hydrolysis of starch
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Types of Protein
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Other Types of Protein
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Protein Structure

• Determined by the sequence of its amino acids
• There are four general levels
• Primary
• Secondary
• Tertiary
• Quaternary

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Building a Protein

• Go to the back and grab a blue toober and a bag
  of thumb tacks
• Make sure your bag of thumb tacks have the
  following
• 2 blue
• 2 red
• 2 green
• 3 white
• 6 yellow

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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.
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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.
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Continue to fold your protein making sure that
your polar side-chains (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
side-chains (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.
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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.
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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
  multi-component protein

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Protein Structure

• Changes in a proteins environment can cause a
  protein to denature
• It loses its three-dimensional structure
• And becomes inactive

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Chaperonins aka Chaperone Proteins

• Help newly-produced proteins to fold properly

• Chaperone protein deficiencies may play a role in
  certain diseases
• Cystic fibrosis and Alzheimers disease ,
  Parkinsons disease mad cow disease

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Protein Structure

• Proteins can be divided into two classes

• 1. Structural
• Long cables
• Provide shape/strength

• 2. Globular
• Grooves and depressions
• Enzymes

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ENZYMES
ORGANIC MOLECULES WHICH ACT AS CATALYSTS
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Enzymes

• Are proteins
• So they are made up of ?
• Somewhere in this protein is an area thats
  designed to match a specific molecule active
  site.
• The molecule that matches the active site is
  called the enzymes substrate.

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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

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WHAT FACTORS MIGHT AFFECT ENZYME CATALYST
REACTIONS?
ENZYME LAB TIME!!!