Carbon and Molecular
Diversity
Based on Chapter 4
Major Elements of life
Compounds and Molecules
Structure and Function
• Carbon molecule and ring structure
– Polysaccharides
Importance of Carbon
• Most molecules from which living organisms are
derived are based on C.
• C has the ability to form large, complex and
diverse molecules.
– Cells and tissues are made up of these basic molecules:
carbohydrates, lipids, proteins and nucleic acids.
• The study that deals with C and and C-H
molecules (hydrocarbons) is called organic
chemistry.
• In order to get familiar with macromolecules, we
need to examine C, hydrocarbons and the
functional groups which bond to hydrocarbons.
Properties of Carbon
• Chemical characteristics and bonds formed by an
atom are determined by the atom’s electrons.
– Carbon has 6 electrons (2 first shell, 4 second shell)
– With 4 valence electrons, it has little tendency to gain or
loose electrons and form ionic bonds.
• It forms covalent bonds to become stable. Most commonly
with H, O and N
• These bonds are in 4 different directions and C is known as
having tetravalence because of this.
– Carbon will form double and triple bonds with other C
atoms. Even though you will see molecules written in
their structural formula as flat, they are 3d structures
and their molecular shape often determine their
function.
Hydrocarbons
• When C is not bonding to itself, it covalently
bonds to other atoms (H, O and N)
• The basic C compound is called a hydrocarbon,
formed from C and H.
Hydrocarbons
• Hydrocarbons vary in:
– The number of C on the chain
– Straight, branching, or ring structures
– Where and how many H atoms are attached to the
carbon chain.
• Most hydrocarbons have similar properties (the
C-H bond is energy rich) so hydrocarbons are
capable of storing vast amounts of energy (fats
and petroleum)
• Carbon variations that differ only in the
arrangements of atoms are called isomers.
Isomers
•
•
Compounds that have the same
molecular formula, but different
structures and thus different functions.
There are 3 types of isomers:
1. Structural
2. Geometric
3. Enantiomers
Structural Isomers
• Vary in their covalent bonding
arrangement.
• Also may vary in the placement of double
C bonds.
Geometric Isomers
• Have the same covalent partnerships but differ in their spatial
arrangements.
• Geometric isomers share common covalent bonding, but because
double bonds are inflexible (prevent rotation) compared to single
bonds which rotate freely around the bonds axis.
• The differing shape of geometric isomers can dramatically affect
their biological function (sometimes called the cis-trans
difference).
Enantiomers (stereoisomers)
• Molecules that are mirror images
of each other and have the same
molecular formula.
• Enantiomers are formed when 4
different molecular groups are
bonded to a central (asymmetric)
carbon so that they can be
arranged in 2 different ways.
• The different shapes of
enantiomers can dramatically
alter function.
• One example is Vitamin E which
has a L and D form. One is more
active and found naturally, the
other is frequent in vitamin pills
but lacks the same biologic
activity.
• L-dopa example
Functional Groups
• These are molecular fragments which, when
substituted for one or more H atoms in a
hydrocarbon, confer particular chemical
properties to the new compound.1
• The functional group determines the “behavior”
of the molecule and is consistent in different
organic molecules.
• There are 6 main functional groups we will
consider.
1Richardson,
Rosemary, 2003 http://www.scidiv.bcc.ctc.edu/rkr/
Hydroxyl Group
• The hydroxyl function group is formed by an oxygen bonded
to a hydrogen, with the second bond of the oxygen free to
attach to the carbon chain (-OH).
• Hydroxyl functional groups confer properties of an alcohol to
hydrocarbons.
• Hydroxyl functional groups are polar (the oxygen end's
electronegativity), and attract water. This helps dissolve in
water those macromolecules, such as sugars, which have
hydroxyl functional groups in their structure.
• The naming convention for alcohols is to have the alcohol
end in "ol" and the prefix be determined by the number of
carbons (based on the alkane or pure hydrocarbon naming
convention). For example, the two-carbon alcohol is
ethanol.1
1Richardson,
Rosemary, 2003 http://www.scidiv.bcc.ctc.edu/rkr/
Carbonyl Group
• The carbonyl functional group is a double bonded oxygen (=O).
• Carbonyl functional groups confer properties of aldehydes or ketones to
hydrocarbons.
• Because double bonds restrict flexibility and rotation on the carbon
skeleton, the location of the carbonyl functional group affects structure,
and function.
• Carbonyl functional groups attached to an "end" carbon form aldehydes.
Carbonyl functional groups attached to a non-end carbon form ketones.
The naming convention for ketones uses the suffix “-one" and aldehydes
the suffix “-al". The prefix may be determined by the number of
carbons. It is not always so. For example, propanal is the 3-carbon
aldehyde, but the 3-carbon ketone, by convention, is called acetone.
Carboxyl Group
• The carboxyl function group combines the hydroxyl and
the carbonyl functional groups attached to a common
carbon atom. The carboxyl functional group will always
be at the end of a carbon chain.
• Carboxyl functional groups form organic (or carboxylic)
acids. The -OH portion of the functional group
dissociates in solution, donating a H+. This dissociation
is aided by the electronegativity of the =O of the
carbonyl portion of the functional group.
Amino Group
• The amino function group is - NH2 . The amino functional group
added to organic compounds forms amines. Most amines in living
organisms are found in molecules which also have carboxyl
function groups and form the important class of molecules called
amino acids.
• The amino functional group is a base. The nitrogen region of the
amino functional group can attract a proton (generally attached to
a hydrogen, thereby removing hydrogen ions from solution)
resulting in a positive charge (+1).
Sulfhydryl Group
• Sulfur, like oxygen, forms two covalent bonds. The
sulfhydryl functional group (-SH) is similar to the
hydroxyl functional group.
• Sulfhydryl functional groups are important in the
structure of proteins, where the sulfur bonds help
stabilize the protein's functional structure.
• Compounds containing sulfhydryl groups are called
-thiols.
Phosphate Group
• Phosphate is a negative ion composed of
phosphate bonded to 4 oxygen atoms. (PO4),
formed by the dissociation of phosphoric acid.
• The loss of two hydrogen ions from the acid results
in the negative charge. One of the oxygen
molecules of the phosphate functional group bonds
to the carbon chain.
• Phosphate functional groups are important in
energy transfer.