Transcript organic chemistry - Spokane Public Schools

Mr. Dill
AP Biology
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Organic molecules are any molecules that contain atoms from three
elements: carbon, hydrogen, and oxygen.
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For example, glucose is organic, since its molecular formula is C6H12O6
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Carbon dioxide (CO2) is inorganic since it does not contain hydrogen.
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Covalent bonds link carbon atoms together in long chains that form
the skeletal framework for organic molecules. These carbon skeletons
may vary in:
• Length
• Shape (straight chain, branched, ring)
• Number and location of double bonds
• Other elements covalently bonded to available sites
All organic molecules have two parts:
The carbon backbone & the functional group
Tetravalence of carbon allows for complex arrangement of
carbon compounds
Carbon atoms can form single, double, or triple covalent
bonds
Name and
Comments
(a) Methane
Molecular Structural
Formula
Formula
Ball-andStick Model
SpaceFilling
Model
H
CH4
H C H
H
(b) Ethane
C2H
H H
H C C H
6
(c) Ethene
(ethylene)
C2H4
H H
H
H
C C
H
H
Hydrocarbons
–Are molecules consisting of only carbon and hydrogen
–Hydrocarbon chains are hydrophobic because the C—C
and C—H bonds are nonpolar
Found in fossil fuels and makes up the “tails” of lipids
Fat droplets (stained red)
Figure 4.6 A, B
(a) A fat molecule
100 µm
(b) Mammalian adipose cells
groups of atoms acting as a unit, that give organic molecules their physical
properties,their chemical reactivity, & solubility in aqueous solutions.
most possess electronegative atoms (N, P, O, S... EASILY ATTRACT PROTONS)
key bonds are : ester (C-O-C) & amide (O=C-N-)
are ionizable at physiological pH
-NH2 AMINE=
amino acid
-C=Ox CARBONYL=
-COOHx CARBOXYL=
-OHx HYDROXYL =
-PO4 PHOSPHORYL=
-SH SULFHYDRYL=
-CH3 METHYL=
aldehyde/ketone
acid
alcohol
organic phosphate
disulfide
hydrocarbon
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Polar group; the bond between the oxygen
and hydrogen is a polar covalent bond.
Makes the molecule to which it is attached
water soluble. Polar water molecules are
attracted to the polar hydroxyl group which
can form hydrogen bonds.
Organic compounds with hydroxyl groups are
called alcohols.
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Functional group that consists of a carbon atom double-bonded
to oxygen (-C=O)
Is a polar group. The oxygen can be involved in hydrogen
bonding, and molecules with his functional group are water
soluble.
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Is a functional group found in sugars.
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Aldehyde = carbonyl group on end carbon of chain
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Ketone =- carbonyl group attached to internal carbon
Carboxyl Group
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Functional group that consists of a carbon atom which is both doublebonded to an oxygen and single-bonded to the oxygen of a hydroxyl
group (-COOH).
Is a polar group and water soluble. The covalent bond between
oxygen and hydrogen is so polar, that the hydrogen reversibly
dissociates as H+. This polarity results from the combined effect of
the two electronegative oxygen atoms bonded to the same carbon.
Since it donates protons, this group has acidic properties. Compounds
with this functional group are called carboxylic acids.
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Functional group that consists of a nitrogen atom bonded
to two hydrogen atoms & to the carbon skeleton (—NH2).
Is a polar group and soluble in water.
Acts as a weak base. The unshared pair of electrons on
the nitrogen can accept a proton, giving the amino group
a +1 charge.
Organic compounds with this
function group are called amines.
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Functional group which consists of an atom of sulfur
bonded to an atom of hydrogen (—SH).
Stabilize the structure of proteins. (Disulfide bridges of
proteins)
Organic compounds with this functional group are called
thiols.
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Functional group which is the dissociated form of phosphoric
acid (H3PO4).
Loss of two protons by dissociation leaves the phosphate group
with a negative charge.
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Has acid properties since it loses protons.
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Polar group and soluble in water.
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Organic phosphates are important in cellular energy storage
and transfer
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methyl group (—CH3)
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Non-polar hydrophobic functional group
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Organic compounds are formed by
polymerization
Large carbon compounds are built up from
smaller simpler molecules called MONOMERS
Monomers can bind to one another to form
complex molecules known as POLYMERS
Macromolecules are very large polymers
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Monomers link to form polymers through a chemical
reaction called a CONDENSATION REACTION or
Dehydration Synthesis
Water is released during the formation of polymers
The BREAKDOWN of some complex molecules, such as
polymers, occurs through a process known as
HYDROLYSIS
Hydrolysis is the reversal of a condensation reaction
Dehydration Synthesis
Hydrolysis
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Carbohydrates (C-H-O 1:2:1 ratio)
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Lipids (C-H-O)
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Proteins (C-H-O-N)…sometimes S
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Nucleic Acids (C-H-O-N-P)
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MONOSACCHARIDES are simple sugars in a 1:2:1
ratio
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GLUCOSE
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GALACTOSE = sugar found in milk
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FRUCTOSE = fruit sugar
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Chemical composition (C6 H12 O6)
Glucose
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DISACCHARIDES consist of two single
sugars(monosaccharides) linked together by
glycosidic linkage (Dehydration synthesis)
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Lactose = Milk sugar
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Sucrose = Table sugar
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POLYSACCHARIDE is a carbohydrate made of long chains of
sugars (3 or more monosaccharides)
Starch - Plants convert excess sugars into starches for longterm storage (Alpha linkage)
Glycogen -Animals store glucose in the form of polysaccharide
glycogen in the liver and muscles to be used as quick energy
Cellulose -a structural polysaccharide contained in the cell walls
of plants (ß linkage)
Chitin – a polysaccharide found in the cell walls of fungi and the
exoskeletons of insects and arthropods
Glucose
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Lipids are large, NONPOLAR organic molecules
that DO NOT dissolve in water
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Oils, fats, waxes, and steroids are lipid based
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Lipid molecules use less OXYGEN than
carbohydrates to store energy efficiently
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Used in biological membranes and as chemical
messengers
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Monomers – Fatty acids & Glycerol
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UNSATURATED FATS are a liquid at room
temperature (OILS).
Double bonds
can have hydrogen added
SATURATED FATS are solid at room
temperature NO double bonds
Stearic acid
Oleic acid
Liquid at room temp
Solid at room temp
Hydrophilic = Water loving
Hydrophobic = Water fearing
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Chemical composition C-H-O-N-S
Proteins are made up of smaller monomers called AMINO ACIDS
Amino Acids differ ONLY in the type of R group they carry
Amino acids composed of 3 parts
1.
Amino Group
2.
Carboxylic group
3.
R-group (Makes 20 different amino acids)
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Each protein has a specific, and complex shape
Different shapes allow proteins to perform
different functions
Two Amino Acids bond to form a DIPEPTIDE during
a condensation reaction (2 Amino Acids form a
covalent bond, called a PEPTIDE BOND)
Amino Acids can bond to each other one at a time,
forming a long chain called a POLYPEPTIDE.
Proteins are composed of one or more polypeptides.
Primary Structure – sequence of amino acids
Secondary structure – Folding and coiling due
to H bond formation between carboxyl and
amino groups of non-adjacent amino acid. R
groups are NOT involved.
Tertiary structure – disulfide bridges, ionic
bonding, or h-bonding of R-groups
Quaternary structure – 2+ amino acid chains
R- group interactions, H bonds, ionic
interactions
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Amino acid structure: NH3 - C - COOH
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Amino acids differ due to the R group
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The structure of the R-group determines
the chemical properties of the amino acid
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The polar uncharged amino acids are hydrophilic &
can form h-bonds
Serine
Threonine
Glutamine
Asparagine
Tyrosine
Cysteine
The nonpolar amino acids are hydrophobic and are
usually found in the center of the protein. They also
found in proteins which are associated with cell
membranes.
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Glycine
Alanine
Valine
Leucine
Isoleucine
Methionine
Phenylalanine
Tryptophan
Proline)
The electrically charged amino acids have electrical
properties that can change depending on the pH.
Aspartic Acid
 Glutamic Acid
 Lysine
 Arginine
 Histidine
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The electrically charged amino acids (Aspartic
Acid, Glutamic Acid, Lysine, Arginine, and
Histidine) have electrical properties that can
change depending on the pH.
 Cysteine can form covalent disulfide bonds
 Proline had a unique structure and causes kinks in
the protein chain
When two amino acids are joined together, the bond
formed is called a peptide bond
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Transfer protein from aqueous solution to
an organic solvent (chloroform)
Any chemical that disrupts h-bonds, ionic
bonds, & disulfide bridges
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Excessive heat
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Changes in pH
Act as CATALYSTS that can speed up some reactions
by more than a billion times!
Enzymes work by a physical fit (Lock and Key)
between the enzyme molecule and its SUBSTRATE,
the reactant being catalyzed.
Enzymes reduces the activation energy for the
chemical reaction to occur.
After the reaction, the enzyme is released and is
unchanged, so it can be used many times
Enzyme names end in -ase
Enzyme & Substrate fit like
a lock & key (Shape specific)
pH or temperature can
change the active site
shape on any enzyme
Active site is where the
reactants bind to the enzyme
The energy require to start a reaction is called Activation Energy
•RNA and DNA made of nucleic acids
•C-H-O-N-P atoms
•Polymers of nucleotides
•Nucleotides consist of a 5-carbon sugar, a
phosphate group, and a nitrogenous base.
•Store and transmit genetic information
Nucleic Acids