BIOLOGY II
Aside
from water, most biologically important molecules are carbon-based (organic).
The
structural and functional diversity of organic molecules emerges from the ability of carbon to form large, complex
and diverse molecules by bonding to itself and to other elements such as H,
O, N, S and P.
Organic chemistry = The branch of chemistry that specializes
in the study of carbon compounds.
Organic molecules = Molecules containing carbon.
Vitalism = Belief in a life force outside the jurisdiction of
chemical/physical laws (Life is a supernatural
phenomenon that is governed by physical and chemical
laws.)
·
Early
19th century organic chemistry was built on a foundation of vitalism
because organic chemists could not artificially synthesize organic
compounds. It was believed that only
living organisms could produce organic compounds.
Mechanism = Belief that all natural phenomena are governed by
physical and chemical laws.
·
Pioneers
of organic chemistry began to synthesize organic compounds from inorganic
molecules. This helped shift mainstream biological thought from
vitalism to mechanism.
·
For
example, Friedrich Wohler synthesized urea in 1828; Herman Kolbe
synthesized acetic acid.
·
Stanley Miller (1953) demonstrated the possibility that organic
compounds could have been produced under the chemical conditions of primordial
Earth.
The carbon atom:
·
Has
an atomic number 6; therefore, it has 4 valence electrons.
·
Completes
its outer energy shell by sharing
valence electrons in four covalent bonds. (Not likely to form ionic bonds.)
Emergent properties, such as
the kinds and number of bonds carbon
will form, are determined by its tetravalent electron configuration.
·
It
makes large complex molecules possible.
The carbon atom is a central point from which the molecule branched off
into four directions.
·
It
gives carbon covalent compatibility with many different: elements. The
four major atomic components of organic molecules are:
·
It
determines an organic molecule’s 3-dimensional
shape,
which may affect molecular function. For example, when carbon forms four single
covalent bonds, the four valence orbitals hybridize into teardrop-shaped
orbitals that angle from the carbon atom towards the corners of an imaginary
tetrahedron.
Covalent bonds link carbon atoms together in long
chains that form the skeletal framework for organic molecules. These carbon skeletons may vary in:
·
Length.
·
Shape
(straight chain, branched, ring).
·
Number
and location of double bonds.
·
Other
elements covalently bonded to available sites.
This variation in carbon skeletons contributes to
the complexity and diversity of organic molecules.
Hydrocarbons = Molecules containing only carbon and hydrogen
·
Are
major components of fossil fuels produced from the organic remains of organisms
living millions of years ago, though they are not prevalent in living
organisms.
·
Have
a diversity of carbon skeletons, which produce molecules of various lengths and
shapes.
·
As
in hydrocarbons, a carbon skeleton is the framework for the large diverse
organic molecules found in living organisms.
Also, some biologically important molecules may have regions consisting
of hydrocarbon chains (e.g. fats).
·
Hydrocarbon chains are hydrophobic because the C-C and C-H bonds are
nonpolar.
A.
Isomers
Isomers = Compounds with the same
molecular formula but with
different structures and
hence different properties. Isomers
are
a source of variation among
organic molecules.
There are
three types of isomers:
1.
Structural isomers = Isomers that differ in the covalent arrangement of their atoms.
·
Number
of possible isomer increases as the carbon skeleton size increases.
·
May
also differ in the location of double bonds.
2.
Geometric isomers = Isomers which share the same covalent partnerships, but differ in
their spatial arrangements. (Functional groups differ in attachment sites)
·
Result
from the fact that double bonds will not allow the atoms they join to rotate
freely about the axis of the bonds.
·
Subtle
differences between isomers affects their biological activity.
3.
Enantiomers = Isomers that are mirror images of
each other.
·
Can
occur when four different atoms or groups of atoms are bonded to the same
carbon (asymmetric carbon).
·
There
are two different spatial arrangements of the four groups around the asymmetric
carbon. These arrangements are mirror
images.
·
Usually
one form is biologically active and its mirror image is not.
(i.e. drugs:
antibiotic-one good drug; heroine
arsenic-one bad drug)
IV. Functional groups also contribute to the molecular diversity of life
Small characteristic groups
of atoms (functional groups) are
frequently bonded to the carbon skeleton of organic
molecules. These
functional groups:
·
Have
specific chemical and physical properties.
·
Are
the regions of organic molecules, which are commonly chemically reactive.
·
Behave consistently from one organic molecule
to another.
·
Depending
upon their number and arrangement, determine unique chemical properties of
organic molecules in which they occur.
As with hydrocarbons, diverse organic molecules
found in living organisms have carbon skeletons. In fact, these molecules can be viewed as hydrocarbon derivatives
with functional groups in place if H bonded to carbon at various sites along
the molecule.
SIX
MAIN FUNCTIONAL GROUPS
A. The Hydroxyl Group
Hydroxyl group = A functional group that
consists of a hydrogen atom bonded to an oxygen atom, which in turn is bonded
to carbon (-OH).
·
Is
a polar group; the bond between the oxygen and hydrogen is a polar covalent
bond.
·
Makes
the molecule to which it is attached water soluble.
Polar water molecules are attracted to the polar hydroxyl group, which
can form hydrogen bonds.
·
Organic
compounds with hydroxyl groups are called alcohols.
B. The Carbonyl
Carbonyl group =Functional group that
consists of a carbon atom double-bonded to oxygen (-CO).
·
Is
a polar group. The oxygen can be
involved in hydrogen bonding, and molecules with his functional group are water
soluble.
·
Is
a functional group found in sugars.
·
If
the carbonyl is at the end off the carbon skeleton, the compound is an aldehyde.
·
If
the carbonyl is at the middle of the carbon skeleton, the compound is a ketone.
C. The Carboxyl Group
Carboxyl group =Functional group that
consists of a carbon atom which is both double-bonded to an oxygen and
single-bonded of a hydroxyl group (-COOH).
·
Is
a polar group and water soluble. The
covalent bond between oxygen and hydrogen is so polar, that the hydrogen
reversibly dissociates as H+. This
polarity results from the combined effect of the two electronegative oxygen
atoms bonded to the same carbon.
·
Since
it donates protons, this group has acidic properties. Compounds with this functional group are called carboxylic acids.
D. The Amino Group
Amino group =Functional group that consists of a
nitrogen atom bonded to two hydrogens and to the carbon skeleton (-NH2).
·
Is
a polar group and soluble in water.
·
Acts
as a weak base. The unshared pair of
electrons on the nitrogen can accept a proton, giving the amino group a +1
charge.
·
Organic
compounds with this function group are called amines.
E. The Sulfhydryl Group
Sulfhydryl group = Functional group which
consists of an atom of sulfur bonded to an atom of hydrogen (-SH).
· Help stabilize the structure
of proteins.
· Organic compounds with this
functional group are called thiols.
F. The Phosphate Group
Phosphate group = Functional group which is
the dissociated form of phosphoric acid (H3PO4).
·
Loss
of two protons by dissociation leaves the phosphate group with a negative
charge.
·
Has
acid properties since it loses protons.
·
Polar
group and soluble in water.
·
Organic
phosphates are important in cellular energy storage and transfer.