An AP biology Mantra
Organisms are made of
organic compounds
whose…
• Shapes
• Charges
• Concentrations
• Interactions
and
• Reaction rates
rule the world.
And the most important
of these is shape.
Students will understand…
the reason that only C H N O P S can form the
millions of organic molecules found in
organisms.
Ch 3 Characteristics of an organic compound
• Covalently bonded
• Contains at least C and H
simplest organic compounds are
hydrocarbons made only with C & H
• Usually is built upon a chain of covalently
bonded C’s known as a backbone
• Has atoms or groups of atoms bonded to the C
backbone, and these are known as substituents
• Must have nonmetal atoms covalently bonded
so that each meets its need for a valence octet.
Carbon can link to other C’s in a “carbon backbone”, as well
as to side group—here in these hydrocarbons, the only side
chain is H. The longest continuous chain of C’s is termed
the backbone. Other chains of C attached as substituents
are termed functional or alkyl groups.
C backbones are variable in
• Length
• Shape (branched,
linear, cyclic)
• #, locations of double
and triple bonds
(no C=C: saturated—as many H as
it can hold; 1 or more C=C,
unsaturated—could bond more
H’s if the double bonds were
single bonds instead)
• Side groups (H or
functional groups)
Whatever the shape of the backbone & whatever the
nature of its side chains, these rules will help you
assess whether a structural formula is drawn
correctly.
# covalent bonds allowed—in this priority
H
1
never violated
C
4
never violated
O
2
hardly ever violated
P, N 3
unless part of a charged functional
group (the normally unbonded pair
can form a coordinate covalent bond)
S
2
unless part of a charged functional group
Stop—take 10 minutes to examine the ball and stick
models of atoms,
on your white boards identify them by color and H, P,
S, O, N, and C or halogens.
Build an organic compound that contains at least one of each atom in CHNOPS.
The model must meet the octet rule for each atom. Draw the full structural formula
and write a molecular formula for the organic compound that you made.
Short sticks are used to represent single covalent bonds (2 shared valence
electrons) between C and H or H and H, but long sticks are used elsewhere in single
bonds. For multiple bonds, springs are used (2 springs = 1 double bond; 3 springs = 1
triple bond).
Which balls represent which
elements?
Black
Red
Yellow
Green
Blue
C
4 holes
needs to share 4 veS, O 2 holes
needs to share 2 veH
1 hole (lots of them)
1 ve- shared
halogens
1 hole (few of them) 1 ve- shared
P, N 3 or 4 holes
shares 3 ve- but can also use coordinate
covalent bonds in charged ions (it
donates BOTH of its normally lone pair
to the bond in such a case)
Students will understand …
the methods used to convey the 3D structures
of molecules, and they will be able to build
physical models of small organic compounds
given either shorthand, condensed or full
structural formula representations.
Organic compounds can be
represented in several ways
Full structures—show every atom and every covalent
bond
Condensed structures—use the organization of the
atoms in a word-like format to convey structure
Organic shorthand—the C backbone and H side chains
are not shown, but functional groups (side chains
that are not H but one of several groups of atoms)
are shown
Ball and stick models
Space filling models
Ethanol
Full structure condensed organic shorthand
aka geometric structure
CH3CH2OH
butyric acid
Full structure condensed organic shorthand
CH3(CH2)2COOH
Summary: different shapes, lengths, #s, and
arrangements of CHONPS allows tremendous
molecular diversity
Another way that C compounds are
able to generate millions of organic compounds
is isomerism.
Isomers are organic compounds having the
same molecular formula, but a different
structure. Since their shape differs, then so
do their physiological functions!
Stop --move to your base groups—
take 10 minutes or less
Build 2 very different models that have the
formula C4H10O (stable if all holes are filled)—
keep them for us to examine together—then
draw the full, condensed, and organic
structures for both. Draw these in your
notebooks and also put a copy on the white
board– show work to me and be prepared to
present to the class if called on.
Isomers are compounds of the same molecular formula, but different
atomic organization. Isomers have different shapes, so they also have
different properties.
a) butane is linear, isobutane is branched—
butane boils at a lower temperature.
b) cis-isomers: larger side chains (X) attached
to C at ends of a C=C are on the same plane
(double C=C bonds are stiff, whereas atoms
rotate around single covalent bonds)
trans-isomers: different sized side chains
attached Cs at either end of C=C are on the
same plane of the double bond
Trans-fats are less healthy to eat.
c) d (right) & l (left) hand mirror images form
stereoisomers (enantiomers) around chiral
C (4 different side groups on the same C)
The broadest class of isomer is
structural isomers.
This is the general term to describe molecules
having the same molecular formula but
different arrangements of the atoms and
covalent bonds.
Geometric and stereoisomers are subgroups of
structural isomers.
Examples for C4H10O—structural isomers
Example of how subtle rearrangements of atoms
between isotopes affects shape and function:
C5H10O has more than 10 structural isomers—some toxins,
others pleasant tasting food additives.
You can use the Merck index to look up properties of common organic
compounds. Look under the index of chemical formulas.
Isoprenol is a flammable gas that causes severe eye
irritation—industrial solvent
But, Valeraldehyde is a food flavoring or perfume
scent
http://www.alibaba.com/promotion/promotio
n_c5h10o-promotion-list.html
More C5H10O isomers
• Pain reliever (analgesic)
• Industrial solvent
Examples for C4H10O isomers
Geometric isomers have different
properties because of their shapes.
Cis-fatty acids are healthier for eating than trans
fatty acids because they are less likely to clog
blood vessels
9/2/2010 Which of these are cis isomers? Which are
trans isomers? Which are not geometric isomers?
Build and draw (complete and shorthand structures)
cis and trans isomers of CHOHCHOH
A third class of isomers is
stereoisomers, also called
enantiomers.
They are termed d or l according to how they
rotate a plane of polarized light shown
through their crystals. d-isomers: right
handed rotation of polarized light. l-isomers:
left handed rotation of polarized light)
Even though visually, stereoisomers seem nearly
identical—just mirror images—cells are very
specific about which form use.
Cells use d-sugars but l-amino acids.
L-valine amino acid
For example, one stereoisomer of
carvone tastes like spearmint, the
other like caraway seeds.
Huge molecules can be stereoisomers at more
than one site. D and l configuration is described
for a particular, stated chiral C. In this small
molecule, only C b is chiral (attached to 4
different side groups)
Still another way to increase diversity of organic
compounds is to use functional groups
• http://www.chemistry-drills.com/functional-groups.php?q=simple
• A functional group is a covalently bonded group of atoms that tends to give
organic compounds characteristic types of chemical reactions
• Molecules in the same class (like amino acids, sugars, fats, nucleotides) have
similar cell functions because they have similar functional groups
•
•
•
•
•
•
•
•
You need to recognize these functional groups
Carboxyl
Carbonyl
Amino (also called amine)
Phosphate
Sulfahydryl
Ester
hydroxyl
R means
the rest
of the
molecule
other
than the
R group
of
interest
Most functional groups render an organic compound polar
covalent if they are asymmetric in their organization. This
is because they often contain both highly electronegative
O or N bonded to either C or H atoms that have lower
electronegativity. For example, when a hydroxyl group
replaces one H of nonpolar ethane (a hydrocarbon), polar
ethanol is formed. Ethane is poorly soluble in water—is
very hydrophobic—while ethanol is highly soluble in
water—is very hydrophilic.
Finally, polymerization or use of
conserved motifs (ch 5 topics)
increases diversity
Simpler subunits are joined into chains
(e.g., glucose chains form glycogen, starch, and
cellulose; amino acid subunits form chains
called proteins; nucleotide chains form nucleic
acids DNA & RNA)