Organic Chemistry
Chemistry Basics
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All elements can react to form chemical bonds.
There are three classifications for true
chemical bonds
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Covalent: Share electrons equally, between two
atoms of the same type. Ex: O2
Polar Covalent : Share electrons (almost) equally,
between non-metals Ex: CO
Ionic: Electrons are transferred from one element
to another, between metals and non-metals;
uncommon in biology and organic chemistry
Intermolecular Forces
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These are interactions between molecules that
allow attractions like cohesion and adhesion
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Hydrogen Bonding: Not a true chemical bond but
is when hydrogen is attracted to Nitrogen, Oxygen
or Fluorine (and sometimes Sulfur)
Dipole-Dipole: attractions caused by polar bonds
and ionic bonds
London Dispersion: weak attractions between
covalent molecules
Chemistry Basics
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All elements will create chemical bonds until
their orbitals are full (8 total electrons) giving
them noble gas configurations
Elements can only make bonds to fill empty
orbital spaces
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So…Oxygen can make 2 bonds, Nitrogen can
make 3 bonds, Carbon can make 4 bonds
Organic Molecules
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Organic molecules are named using the longest
carbon chain – which is not always in a strait
line
Prefixes are used to identify how many
carbons are in the chain
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Meth, Eth, Prop, But, Pent, Hex, Hept, Oct, Non,
Deca
Alkanes, Alkenes and Alkynes
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Alkanes are hydro-carbons that are saturated,
meaning they have only single bonds.
Alkenes contain one or more double bonds that
are identified by the carbon number they start
on
Alkynes contain one or more triple bonds
identified by the carbon they start on
Functional Groups
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Most organic molecules contain at least one
functional group. These are groupings of
elements that change the properties of the
organic molecule.
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Functional groups will allow hydrogen bonding,
di-sulfide bridges and polar interactions.
Functional Groups
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Hydroxyl Group
H bonded to O; alcohols;
soluble in water because they are polar
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Carbonyl Group
C double bond to O;
some polarity
At end of chain:
aldehyde
Otherwise:
ketone
Functional Groups, II
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Carboxyl Group
O double bonded to C to hydroxyl;
carboxylic acids; bond between O and H; polar;
likely to dissociate an H ion creating an acidic environment and the
ability to easily bond with a positively charged functional group
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Amino Group
N to 2 H atoms; called amines;
the name amino acids is derived from this functional group
acts as a base (+1) and will attract the carboxyilic acid
Functional Groups
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Sulfhydral Group sulfur bonded to H;
called thiols; used in proteins to create di-sulfide bridges in
3-D structure
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Phosphate Group phosphate ion; covalently attached by 1 of
its O to the C skeleton; is used in ATP to store energy
within this bond or release energy by breaking it
Cyclic Molecules
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Sometimes organic molecules can form ring
structures.
These ring structures are not as reactive as
linear molecules but can still be involved in
chemical reactions.
The most common ring structure in Biology is
a benzene ring containing 6 Carbons, 6
Hydrogens and 3 double bonds
Bonding in Molecules
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Bonds are created in organic molecules using
functional groups.
These bonds most often produce water when
formed in a condensation reaction
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The most common involve amino groups and
carboxylic acids or carbonyl groups and carboxylic
acids
Isomers
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Isomers are molecules that contain the same
number of each element but have those
elements arranged in a differently.
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Structural Isomer: Differ in arrangement
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Geometric Isomers: Differ in spacial arrangement
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Butane v. Isobutane
Cis and Trans arrangements
Enatiomers: mirror images
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Right v. Left Hand