Download Biol 1020 Ch. 4: organic molecules

Chapter 4: Life is based on molecules
with carbon (organic molecules)

organic compounds

isomers

functional groups
.
Much of the chemistry of life is
based on organic compounds
organic compounds have at least one
carbon atom covalently bound to either:
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another carbon atom
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or to hydrogen
the chemistry of organic molecules is
organized around the carbon atom
.
•
Discuss the chemistry of carbon. How
does it typically bond? What does it
typically bond to? What sort of shapes,
angles, freedoms, etc. are associated
with the bonds that it makes?
•
Draw a tetrahedron.
.
Organic Compounds
carbon atoms have six electrons –

2 in level 1
4 in their valence (outer) shell (level 2)
carbon is not a strongly electron seeking element,
and it does not readily give up its electrons;
therefore:
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carbon does not readily from ionic bonds
it almost always forms covalent bonds
carbon can form up to 4 covalent bonds (and
typically does form all four)
.
Organic Compounds
wide diversity in organic compounds

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over 5 million identified
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variety partially because carbon tends to
bond to carbon, hydrogen, oxygen,
nitrogen, sulfur, and phosphorus
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hydrocarbons – contain only hydrogen and
carbon

single carbon-carbon bonds allow rotation
around them and lend flexibility to molecules
.
Organic Compounds
building of organic macromolecules also leads to
diversity
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carbon works well as a molecular “backbone” for forming
long chain molecules
stronger carbon-carbon bonds can be made with double and
triple covalent bonds
carbon chains can branch
.
Organic Compounds
the shape of a molecule is important in
determining its chemical and biological
properties

When 4 separate bonds are formed
by carbon…
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formed at 109.5 degree angles
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form a pyramid with a triangular
base called a tetrahedron
When double bonds are formed…
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angles are 120 or 180 degrees apart,
and they all lie in the same plane
.
Organic Compounds

bond angles for carbon
play a critical role in
determining the shape of
molecules

generally there is freedom
to rotate around carbon to
carbon single bonds but
not double (or triple) bonds
.
•
Discuss the chemistry of carbon. How
does it typically bond? What does it
typically bond to? What sort of shapes,
angles, freedoms, etc. are associated
with the bonds that it makes?
•
Draw a tetrahedron.
.
Chapter 4: Life is based on molecules
with carbon (organic molecules)

organic compounds

isomers

functional groups
.
•
Discuss isomers. What are they? What
is the difference between structural
isomers and stereoisomers? Between
cis-trans isomers and enantiomers?
•
Draw an example of each of these:
structural isomers
cis-trans isomers
enantiomers
.
•
What type of isomer situation is this?
How do you know?
.
•
What type of isomer situation is this?
How do you know?
.
•
What type of isomer situation is this?
How do you know?
.
•
What type of isomer situation is this?
How do you know?
.
•
What type of isomer situation is this?
How do you know?
.
•
What type of isomer situation is this?
How do you know?
.
Isomers

have the same molecular formula

have different structures

there are two kinds of isomers
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structural isomers

stereoisomers
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Isomers

structural isomers - substances with the
same molecular formula that differ in the
covalent arrangement of their atoms

example: ethanol and dimethyl ether (C2H6O)
.
Isomers
stereoisomers - substances with the same
arrangement of covalent bonds, but the order
in which the atoms are arranged in space is
different
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two types: enantiomers and diastereomers
.
Isomers
cis-trans isomers – diastereomers associated with
compounds that have carbon-carbon double bonds
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since there is no rotation around the double bond the other
atoms attached to the carbons are stuck in place in
relationship to each other
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larger items together = cis; larger items opposite = trans
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examples: trans-2-butene and cis-2-butene
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Isomers
enantiomers – substances that are mirror
images of each other and that cannot be
superimposed on each other
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sometimes called optical isomers (kind of a loose
term, though)
.
Isomers
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typically, only one form of an enatiomer pair is found in and/or
used by organisms
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the enantiomers are given designations such as
[(+)- vs. (−)-] or [D- vs. L-] or [(R)- vs. (S)-]
biologically important enantiomers include
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amino acids (found in proteins) – most are L-amino acids
(e.g. L-leucine, L-alanine, etc)
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sugars – most are D-sugars
(e.g. D-glucose, D-fructose, etc.)
.
•
Discuss isomers. What are they? What
is the difference between structural
isomers and stereoisomers? Between
cis-trans isomers and enantiomers?
•
Draw an example of each of these:
structural isomers
cis-trans isomers
enantiomers
.
Chapter 4: Life is based on molecules
with carbon (organic molecules)

organic compounds

isomers

functional groups
.
•
What is a functional group, and why is it
useful to know them? Quiz each other
on the names and chemistry of the
functional groups in the notes.
.
Functional Groups
functional groups determine most of the
reactive properties (functions) of organic
molecules
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functional groups are groups of atoms
covalently bonded to a carbon backbone that
give properties different from a C-H bond

the properties of the major classes of organic
compounds (carbohydrates, lipids, proteins,
and nucleic acids) are determined mostly by
their functional groups
learn the seven functional groups on the
following slides
.
Functional Groups
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Functional Groups

hydroxyl group: polar; found in alcohols
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carbonyl group: polar; found in aldehydes
and ketones
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carboxyl group: weakly acidic; found in
organic acids (such as amino acids)
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Functional Groups
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amino group: weakly basic; found in such things as
amino acids
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sulfhydryl group: essentially nonpolar; found in
some amino acids
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phosphate group: weakly acidic; found in such
things as phospholipids and nucleic acids
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P
methyl group: nonpolar (thus hydrophobic); found in
such things as lipids, other membrane components
.