AP Biology
Biochemistry: Carbon
Carbon
What is the valence number ?
Organic Chemistry
• Branch of science dealing with the element
carbon and its many properties.
– It is usually associated with all living organisms.
• About 30% of an organism’s dry weight (called
Biomass) is Carbon in organic molecules.
– Helps to make the organic molecules: Carbohydrates, Lipids,
Proteins, and Nucleic Acids.
– The original source for Carbon in all life forms is Carbon
Dioxide. (CO2)(Photosynthesis)
» Also supported by the Stanley Miller experiment, as
discussed below.
• Stanley Miller Experiment (Took place in
1953.)
– He took inorganic substances found in Earth’s
early atmosphere, such as H2O vapor, H2, NH3, CH4,
and created organic amino acids and oils. (CO2
and CH4 are not considered organic compounds,
even though contain Carbon.)
• There are 20 amino acids that are used to make
proteins in living organisms.
• Early Earth? (He analyzed volcanic gases to determine
what the air must have been like.)
• Energy source to power the chemical reactions?
(Electricity replaces lightning.)
Stanley Miller
LE 26-2
CH4
Water vapor
Electrode
Condenser
Cold
water
H2 O
Cooled water
containing
organic
molecules
Sample for
chemical analysis
Early Earth
• Carbon’s e- configuration
– Carbon has versatility in four directions because of
its Tetravalence. (Tetra means “four”)
– The tetravalence allows carbon to act like an
intersection in the building of an organic molecule.
• This allows cells to build an almost infinite number of
different molecules.
– Covalent bonding capabilities of Carbon
• Single Bond between Carbon atoms.(shown as: C-C)
• Double Bond between Carbon atoms. (shown as: C=C)
• Triple Bond between Carbon atoms. (shown as: C=C)
.
Carbon
(valence = 4)
SINGLE BONDS
DOUBLE BONDS
TRIPLE BONDS
Carbon in a Tetrahedron!
• Has equidistant bond angles of 109.5°.
Carbon Bonding
Molecular
Formula
Methane
Ethane
Ethene (ethylene)
Structural
Formula
Ball-and-Stick
Model
Space-Filling
Model
• Hydrocarbons
– Molecules containing mostly Carbon and
Hydrogen.
– Most hydrocarbons are energy sources. (Some
examples are: Fossil fuels, Oils, And Fats)
• The more Hydrogen atoms in a molecule; the more
energy there is in the molecule.
– Hydrocarbons are important parts of cell
membranes. (The tails of phospholipids)
– All hydrocarbons are extremely hydrophobic
because they are nonpolar molecules. (“Afraid of”
water’s polarity.)
Hydrocarbon tails
Hydrocarbon Tails of a
Phospholipid
Choline
Phosphate
Glycerol
Fatty acids
Hydrophilic
head
Hydrophobic
tails
Structural formula
Space-filling model
Phospholipid symbol
Cell Membranes
• Functional Groups Associated with Organic
Molecules
– These are the sites of most organic molecules
chemical reactions or properties. (They have a
function to do.)
Functional groups serve important
purposes in molecules
Estradiol
Female lion
Testosterone
Male lion
7 functional groups are important in
the chemistry of life (Pg. 64)
–Hydroxyl
–Carbonyl
–Carboxyl
–Amino
–Sulfhydryl
–Phosphate
–Methyl
– Hydroxyls (-OH)
• This group allows molecules to act as an alcohol or
polar molecule.
• Name usually ends with “ol”.
LE 4-10aa
STRUCTURE
(may be written HO—)
Ethanol, the alcohol present in
alcoholic beverages
NAME OF COMPOUNDS
Alcohols (their specific names
usually end in -ol)
FUNCTIONAL PROPERTIES
Is polar as a result of the
electronegative oxygen atom
drawing electrons toward itself.
Attracts water molecules, helping
dissolve organic compounds such
as sugars (see Figure 5.3).
– Carbonyls (Only has one double bonded oxygen.)
(It takes one stroke to make a lower case “n”.)
• Aldehydes (A is at one end of the alphabet.)(Carbonyl is
located on the end of the molecule.)
• Ketones (K is in the middle of the alphabet.)(Carbonyl is
located in the middle of the molecule.)
LE 4-10ab
Acetone, the simplest ketone
STRUCTURE
EXAMPLE
Acetone, the simplest ketone
NAME OF COMPOUNDS
Propanal, an aldehyde
Ketones if the carbonyl group is
within a carbon skeleton
FUNCTIONAL PROPERTIES
Aldehydes if the carbonyl group is
at the end of the carbon skeleton
A ketone and an aldehyde may
be structural isomers with
different properties, as is the case
for acetone and propanal.
– Carboxyl (Has two oxygens…one double bonded
and one singled.)(It takes two strokes to make an
“x”)
• These molecules can act as an acid by losing a
Hydrogen atom and can also possibly polar too.
LE 4-10ac
STRUCTURE
EXAMPLE
Acetic acid, which gives vinegar
its sour taste
NAME OF COMPOUNDS
Carboxylic acids, or organic acids
FUNCTIONAL PROPERTIES
Has acidic properties because it is
a source of hydrogen ions.
The covalent bond between
oxygen and hydrogen is so polar
that hydrogen ions (H+) tend to
dissociate reversibly; for example,
Acetic acid
Acetate ion
In cells, found in the ionic form,
which is called a carboxylate group.
– Amine (Contains Nitrogen)
• Can act as bases by picking up free H+.
LE 4-10ba
STRUCTURE
EXAMPLE
Glycine
Because it also has a carboxyl
group, glycine is both an amine and
a carboxylic acid; compounds with
both groups are called amino acids.
NAME OF COMPOUNDS
Amine
FUNCTIONAL PROPERTIES
Acts as a base; can pick up a
proton from the surrounding
solution:
(nonionized)
(ionized)
Ionized, with a charge of 1+,
under cellular conditions
– Sulfhydrls (Contains Sulfur)
• Sulfur can make Di-Sulfide bridges for “pockets” in
protein formation .
LE 4-10bb
STRUCTURE
EXAMPLE
(may be written HS—)
Ethanethiol
NAME OF COMPOUNDS
Thiols
FUNCTIONAL PROPERTIES
Two sulfhydryl groups can
interact to help stabilize protein
structure (see Figure 5.20).
– Phosphate ( Contains Phosphorus)
• These molecules are usually involved in E Transfers,
such as associated with ATP. It can also act like an
Anion, a negative ion.
LE 4-10bc
STRUCTURE
EXAMPLE
Glycerol phosphate
NAME OF COMPOUNDS
Organic phosphates
FUNCTIONAL PROPERTIES
Makes the molecule of which it
is a part an anion (negatively
charged ion).
Can transfer energy between
organic molecules.
• Methyl