Transcript Organic and Biological Molecules

Organic and Biological
Molecules
Unique Nature of Carbon
Carbon has two properties that enable it to
form such an extensive range of compounds:
1. Catenation – the ability to form chains of
atoms.
2. The ability to form multiple bonds.
Catenation
Carbon readily forms long chains of bonds
with itself. This property is called catenation, and
is fairly unique. It results for several reasons:
1. Carbon can make up to 4 bonds.
2. The carbon-carbon bond is generally as
strong as bonds between carbon and other
elements.
3. The catenated compounds are inert.
Catenation in Phosphorus
white
black
phosphorus phosphorus
red
phosphorus
Elemental Phosphorus
Catenation in Sulfur
Catenation of Silicon
Silicon can also make long chains within its
compounds, but, since the silicon oxygen bond
is much stronger than that between two silicon
atoms, the chains typically contain –O-Si-O-Sitype links, rather than -Si-Si- bonds.
Silicon also has empty low-lying d orbitals
which make its compounds more reactive.
Typical Bond Energies
C−O
358
Catenation
Since carbon can undergo extensive
catenation and make as many as four bonds, the
array of compounds is limitless.
The simplest compounds, those with carbon
and hydrogen, are used as the basic structure of
all molecules.
Optical Isomerism
Optical Isomerism
When a carbon atom is bonded to four
different atoms or groups, optical isomers result.
The isomers have differing spatial arrangements,
with the two molecules being mirror images of
each other.
The mirror images are nonsuperimposable,
like a left hand and a right hand.
Optical Isomerism
Optical Isomerism
A molecule that exhibits optical isomerism is
called chiral. Most biological molecules are
chiral, often with one isomer performing
important biological functions while the other
may be biologically inactive.
Although inorganic molecules can also be
chiral, the chirality of organic molecules is of
major biochemical importance.
Optical Isomerism
Optical isomers are also called enantiomers. A
pair of enantiomers are identical in many
respects. They have the same melting point,
density, polarity and solubility.
The two differences are that they bend plane
polarized light in opposite directions, and they
behave differently in a chiral environment.
Chiral Environments
Many biologically active sites are chiral.
Examples might be the site of enzyme activity.
Only one configuration of the chiral molecule
fits properly into the reaction site, so only one
enantiomer will be biologically active.
Chiral Environments
Hydrocarbons
Hydrocarbons are compounds composed of
carbon and hydrogen. If all of the carboncarbon bonds are single bonds, the compound is
saturated. Hydrocarbons containing double or
triple bonds between carbon atoms are called
unsaturated.
Saturated Hydrocarbons
Saturated
hydrocarbons are
alkanes. Alkanes have
the general formula
CnH2n+2.
Saturated Hydrocarbons
Isomers
Butane, C4H10,
has two structural
isomers. That is, they
contain the same
atoms, but a different
arrangement of
bonds.
Structural Isomers
The two isomers of butane will have
different properties. The n-butane, with four
carbon atoms in a single chain, has a boiling
point of -.5oC. Isobutane, with the branched
chain, has a boiling point of -12oC.
Naming Organic Compounds
Many compounds are known by their
“common” names, such as acetic acid for
CH3COOH. A system of organic nomenclature
has been developed for naming compounds.
Nomenclature
The butyl groups have
three different structures.
Tert-butyl contains a
tertiary carbon atom- one
that is bonded to three
carbons. Sec-butyl
contains a secondary
carbon atom – one that is
bonded to two carbons.
Reactions of Alkanes
At room temperature, alkanes are relatively
inert, especially when compared to unsaturated
hydrocarbons.
At elevated temperatures, alkanes undergo
combustion (burn) with oxygen.
2 C4H10(g) + 13 O2(g)  8 CO2(g) + 10 H2O(g)
Reactions of Alkanes
Alkanes burn cleanly to form carbon dioxide
and water vapor. The reactions are
exothermic, so alkanes make excellent fuels.
Reactions of Alkanes
Alkanes undergo substitution reactions with the
halogens in the presence of light. One or
more hydrogen atom can be replaced with a
halogen atom. The other product is gaseous
HX.
hν
CH4 + Cl2  CH3Cl + HCl
Cyclic Alkanes
The carbon atoms in hydrocarbons can form
rings instead of chains. Cyclic alkanes have the
general formula CnH2n.
The smallest member of the series,
cyclopropane, has a three-membered ring, and
bond angles of 60o. However, each carbon
atom is sp3 hybridized, with orbitals at 109.5o.
Cyclic Alkanes
Three-membered rings
are quite strained, and
cyclopropane is very
reactive.
Cyclobutane is also
quite strained, with four
carbon atoms in a ring.
The bond angles are 88o,
and the molecule is fairly
unstable.
Cyclic Alkanes
Cyclopentane and cyclohexane both
have bond angles very close to tetrahedral
angles, and are quite stable as a result.
Cyclohexane, C6H12, doesn’t lie flat, but
“puckers” to attain the proper bond angles.
Cyclic Alkanes
The cyclohexane
molecule exists in two
forms. The “chair”
form has 4 carbon
atoms in a plane, with
one end “flipped up”
and the other “flipped
down.”
Cyclic Alkanes
The “boat” form
has 4 carbon atoms
in a plane, with both
ends “flipped up.”
This arrangement is
less stable, with
repulsion between
hydrogen atoms.
Alkenes and Alkynes
Hydrocarbons containing at least one
carbon-carbon double bond are called alkenes.
Alkenes have the general formula CnH2n.
The simplest alkene is ethylene, H2C=CH2.
Ethylene
The double bond between the carbon atoms
prevents rotation of one side of the molecule
relative to the other.
Ethylene
As a result, cis and
trans isomers are
possible. The isomers
have different
polarities, melting
points and boiling
points.
cis
trans
Alkynes
Alkynes contain at least one carbon-carbon
triple bond. Acetylene, H−C≡C−H, is the
simplest alkyne.
Reactions of Alkenes and Alkynes


In addition to combustion and substitution
reactions, alkenes and alkynes can undergo
addition reactions, in which atoms are added across
the multiple bond.
Hydrogenation:
catalyst
H2C=CH2 + H2  H3C−CH3
Bromination:
H2C=CH2 + Br2  H2BrC−CH2Br
Aromatic Hydrocarbons
There is a separate class of cyclic unsaturated
hydrocarbons called aromatic hydrocarbons.
These compounds have a planar ring structure
and a delocalized π system. The extended pi
bonding provides exceptional stability to these
molecules. Unlike other hydrocarbons, they do
not burn well or cleanly. During reactions, the
extended pi system remains intact.
Aromatic Hydrocarbons
Benzene C6H6
Aromatic Hydrocarbons
Benzene C6H6
Aromatic Hydrocarbons
Benzene, C6H6, is the simplest aromatic
hydrocarbon. It undergoes substitution
reactions rather than addition reactions. The
aromatic ring behaves more like a saturated
hydrocarbon than an unsaturated one.
FeCl3
+ Cl2  HCl +
−Cl
Aromatic Hydrocarbons
In similar reactions, NO2 or a methyl
group (CH3) can be added to the benzene
ring. All of these reactions require the use
of catalysts.
AlCl3
+ CH3Cl  HCl +
−CH3
Functional Groups
Many organic molecules can be viewed as
hydrocarbons that have an additional atom or
group of atoms called a functional group.
For example, hydrocarbons with an –O-H
bonded to them are called alcohols. Alcohols
tend to undergo similar reactions and have
similar properties.
F
U
N
C
T
I
O
N
A
L
G
R
O
U
P
S
Alcohols
All alcohols contain the hydroxyl group, OH. This greatly changes the properties of the
hydrocarbon to which it is attached.
Hydrocarbons are non-polar, with low boiling
points and poor solubility in polar solvents. The
presence of an –OH group increases the polarity
of the molecule, and provides a site for
“hydrogen bonding” or protonic bridging.
Alcohols
Alcohols have higher boiling points than
expected (as does water) due to the presence of
protonic bridging between molecules.
Although hydrocarbons are insoluble in
water, the presence of the hydroxyl group
enables smaller alcohol molecules to fully
dissolve in water.
Alcohols
Methyl alcohol, or methanol, is also called
wood alcohol. Its formula is CH3OH.
Methanol is very toxic, and causes blindness and
death of it is consumed.
Methanol is used to make other compounds,
notably acetic acid. It is also used as a motor
fuel.
Alcohols
Ethanol, CH3CH2OH,
is consumed in beverages
such as beer, wine and
liquor. It is produced by
the fermentation of
sugars.
yeast
C6H12O6  2 CH3CH2OH
+ 2 CO2
Aldehydes and Ketones
Both aldehydes and ketones contain the
carbonyl group:
C=O
In aldehydes, the carbon atom is attached to
at least one hydrogen atom. In ketones, the
carbon atom is attached to two other carbon
atoms.
Aldehydes
The simplest aldehyde is formaldehyde, CH2O.
It has a pungent odor and is used as a
preservative and disinfectant. Aromatic
aldehydes have pleasant odors, and cause the
aromas of vanilla, cinnamon and almonds.
Ketones
The simplest ketone is acetone, (CH3)2CO.
Acetone is used in nail polish remover. Other
ketones are responsible for the smell of cloves,
raspberries and spearmint.
Carboxylic Acids & Esters
Carboxylic acids taste sour, and are found in
vinegar (acetic acid), insect stings and bites
(formic acid), and citrus fruits (citric acid).
Esters are known for their pleasant aromas,
such as the smell of apples, pineapples or
bananas.