4
Carbon Chapter and the Molecular
Diversity of Life
BIOL 1361 Introduction to Biological Sciences
Dr. Monique Ogletree
Dr.
Overview: Carbon: The Backbone of Life
Although cells are 7095% water, the rest
consists mostly of carbon-based compounds
Carbon is unparalleled in its ability to form
large, complex, and diverse molecules
Proteins, DNA, carbohydrates, and other
molecules that distinguish living matter are all
composed of carbon compounds
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Chapter 4 : Concept Outline
4.1 Organic chemistry is the study of carbon
compounds
4.2 Carbon atoms can form diverse molecules by
bonding to four other atoms
4.3 A small number of chemical groups are key to the
functioning of biological molecules
Copyright 2008 Pearson Education, Inc., publishing as Benjamin
Cummings
Concept 4.1: Organic chemistry is the study of
carbon compounds
Organic chemistry is the study of compounds
that contain carbon
Organic compounds range from simple
molecules to colossal ones
Most organic compounds contain hydrogen
atoms in addition to carbon atoms
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Vitalism, the idea that organic compounds arise
only in organisms, was disproved when
chemists synthesized these compounds
Organic : those thought to arise only in living organisms
Inorganic : found in the nonliving world
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Concept 4.2: Carbon atoms can form diverse
molecules by bonding to four other atoms
Electron configuration is the key to an atoms
characteristics
Electron configuration determines the kinds
and number of bonds an atom will form with
other atoms
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
The Formation of Bonds with Carbon
With four valence electrons, carbon can form
four covalent bonds with a variety of atoms
This tetravalence makes large, complex
molecules possible
In molecules with multiple carbons, each
carbon bonded to four other atoms has a
tetrahedral shape
However, when two carbon atoms are joined
by a double bond, the molecule has a flat
shape
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 4-3
Name
(a) Methane
(b) Ethane
(c) Ethene
(ethylene)
Molecular
Formula
Structural
Formula
Ball-and-Stick
Model
Space-Filling
Model
The electron configuration of carbon gives it
covalent compatibility with many different
elements
The valences of carbon and its most frequent
partners (hydrogen, oxygen, and nitrogen) are
the building code that governs the
architecture of living molecules
Fig. 4-4
Four major atomic components of organic molecules
Hydrogen
(valence = 1)
Oxygen
(valence = 2)
Nitrogen
(valence = 3)
Carbon
(valence = 4)
H
O
N
C
Carbon atoms can partner with atoms other
than hydrogen; for example:
Carbon dioxide: CO2
O=C=O
Urea: CO(NH2)2
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 4-UN1
Urea
CO(NH2)2
Molecular Diversity Arising from Carbon Skeleton
Variation
Carbon chains form the skeletons of most
organic molecules
Carbon chains vary in length and shape
(hydrocarbons)
Animation: Carbon Skeletons
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 4-5a
Differences ..
short vs. long
Ethane
Propane
Fig. 4-5b
Differences
straight vs. branching
Butane
2-Methylpropane
(commonly called isobutane)
Fig. 4-5c
Differences
single vs. double bonds
1-Butene
2-Butene
Fig. 4-5d
Differences
rings and bonds within rings
Cyclohexane
Benzene
Hydrocarbons
Hydrocarbons are organic molecules
consisting of only carbon and hydrogen
Many organic molecules, such as fats, have
hydrocarbon components
Hydrocarbons can undergo reactions that
release a large amount of energy
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 4-6
Fat droplets (stained red)
100 m
(a) Mammalian adipose cells
(b) A fat molecule
Isomers
Isomers are compounds with the same molecular
formula but different structures and properties:
Structural isomers have different covalent
arrangements of their atoms
Geometric isomers have the same covalent
arrangements but differ in spatial
arrangements
Enantiomers are isomers that are mirror
images of each other
Animation: Isomers
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 4-7
Pentane
2-methyl butane
(a) Structural isomers
cis isomer: The two Xs are
on the same side.
trans isomer: The two Xs are
on opposite sides.
(b) Geometric isomers
L isomer
(c) Enantiomers
D isomer
Fig. 4-7a
Structural
Pentane
(a) Structural isomers
2-methyl butane
Fig. 4-7b
Geometric
cis isomer: The two Xs are
on the same side.
(b) Geometric isomers
trans isomer: The two Xs are
on opposite sides.
Fig. 4-7c
Enantiomers
L isomer
(c) Enantiomers
D isomer
Enantiomers are important in the
pharmaceutical industry
Two enantiomers of a drug may have different
effects
Differing effects of enantiomers demonstrate
that organisms are sensitive to even subtle
variations in molecules
Go back
Animation: L-Dopa
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 4-8
Condition
Ibuprofen
Effective
Enantiomer
Ineffective
Enantiomer
S-Ibuprofen
Drug
R-Ibuprofen
R-Albuterol
S-Albuterol
Pain;
inflammation
Albuterol
Asthma
Concept 4.3: A small number of chemical groups
are key to the functioning of biological molecules
Distinctive properties of organic molecules
depend not only on the carbon skeleton but
also on the molecular components attached
to it
A number of characteristic groups are often
attached to skeletons of organic molecules
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
The Chemical Groups Most Important in the
Processes of Life
Functional groups are the components of
organic molecules that are most commonly
involved in chemical reactions
The number and arrangement of functional
groups give each its molecule unique
properties
Consider testosterone vs. estradiol
both organic, steriods with a common carbon
skeleton ring structure
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 4-9
Estradiol
Testosterone
The seven functional groups that are most
important in the chemistry of life:
Hydroxyl group
Carbonyl group
Carboxyl group
Amino group
Sulfhydryl group
Phosphate group
Methyl group
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 4-10a
CHEMICAL
GROUP
Hydroxyl
Carbonyl
Carboxyl
STRUCTURE
(may be written HO)
In a hydroxyl group (OH), a
hydrogen atom is bonded to an
oxygen atom, which in turn is
bonded to the carbon skeleton of
the organic molecule. (Do not
confuse this functional group
with the hydroxide ion, OH.)
NAME OF
COMPOUND
The carbonyl group ( CO)
consists of a carbon atom
joined to an oxygen atom by a
double bond.
When an oxygen atom is
double-bonded to a carbon
atom that is also bonded to
an OH group, the entire
assembly of atoms is called
a carboxyl group (COOH).
Alcohols (their specific names
usually end in -ol)
Ketones if the carbonyl group is
within a carbon skeleton
Carboxylic acids, or organic
acids
Aldehydes if the carbonyl group
is at the end of the carbon
skeleton
EXAMPLE
Ethanol, the alcohol present in
alcoholic beverages
Acetone, the simplest ketone
Acetic acid, which gives vinegar
its sour taste
Propanal, an aldehyde
FUNCTIONAL
PROPERTIES
Is polar as a result of the
electrons spending more time
near the electronegative
oxygen atom.
A ketone and an aldehyde may
be structural isomers with
different properties, as is the
case for acetone and propanal.
Can form hydrogen bonds with
water molecules, helping
dissolve organic compounds
such as sugars.
These two groups are also
found in sugars, giving rise to
two major groups of sugars:
aldoses (containing an
aldehyde) and ketoses
(containing a ketone).
Has acidic properties
because the covalent bond
between oxygen and hydrogen
is so polar; for example,
Acetic acid
Acetate ion
Found in cells in the ionized
form with a charge of 1 and
called a carboxylate ion (here,
specifically, the acetate ion).
Fig. 4-10b
CHEMICAL
GROUP
Amino
Sulfhydryl
Methyl
In a phosphate group, a
phosphorus atom is bonded to
four oxygen atoms; one oxygen
is bonded to the carbon skeleton;
two oxygens carry negative
charges. The phosphate group
(OPO32, abbreviated P) is an
ionized form of a phosphoric acid
group (OPO3H2; note the two
hydrogens).
A methyl group consists of a
carbon bonded to three
hydrogen atoms. The methyl
group may be attached to a
carbon or to a different atom.
(may be
written HS)
STRUCTURE
The amino group
(NH2) consists of a
nitrogen atom bonded
to two hydrogen atoms
and to the carbon
skeleton.
NAME OF
COMPOUND
Phosphate
The sulfhydryl group
consists of a sulfur atom
bonded to an atom of
hydrogen; resembles a
hydroxyl group in shape.
Amines
Thiols
Organic phosphates
Methylated compounds
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.
FUNCTIONAL
PROPERTIES
Acts as a base; can
pick up an H+ from
the surrounding
solution (water, in
living organisms).
(nonionized) (ionized)
Ionized, with a
charge of 1+, under
cellular conditions.
Glycerol phosphate
Cysteine
Cysteine is an important
sulfur-containing amino
acid.
In addition to taking part in
many important chemical
reactions in cells, glycerol
phosphate provides the
backbone for phospholipids,
the most prevalent molecules in
cell membranes.
Two sulfhydryl groups
can react, forming a
covalent bond. This
cross-linking helps
stabilize protein
structure.
Contributes negative charge
to the molecule of which it is
a part (2 when at the end of
a molecule; 1 when located
internally in a chain of
phosphates).
Cross-linking of
cysteines in hair
proteins maintains the
curliness or straightness
of hair. Straight hair can
be permanently curled
by shaping it around
curlers, then breaking
and re-forming the
cross-linking bonds.
Has the potential to react
with water, releasing energy.
5-Methyl cytidine
5-Methyl cytidine is a
component of DNA that has
been modified by addition of
the methyl group.
Addition of a methyl group
to DNA, or to molecules
bound to DNA, affects
expression of genes.
Arrangement of methyl
groups in male and female
sex hormones affects
their shape and function.
ATP: An Important Source of Energy for Cellular
Processes
One phosphate molecule, adenosine
triphosphate (ATP), is the primary energytransferring molecule in the cell
ATP consists of an organic molecule called
adenosine attached to a string of three
phosphate groups
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 4-UN3
Adenosine Triphosphate (ATP)
Adenosine
Fig. 4-UN4
Reacts
with H2O
P
P
P Adenosine
ATP
Pi
P
Inorganic
phosphate
P
Adenosine
ADP
Energy
The Chemical Elements of Life: A Review
The versatility of carbon makes possible the
great diversity of organic molecules
Variation at the molecular level lies at the
foundation of all biological diversity
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
You should now be able to:
1. Explain how carbons electron configuration
explains its ability to form large, complex,
diverse organic molecules
2. Describe how carbon skeletons may vary and
explain how this variation contributes to the
diversity and complexity of organic molecules
3. Distinguish among the three types of isomers:
structural, geometric, and enantiomer
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
1. Name the major functional groups found in
organic molecules; describe the basic
structure of each functional group and outline
the chemical properties of the organic
molecules in which they occur
2. Explain how ATP functions as the primary
energy transfer molecule in living cells
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 4-UN7
a
b
c
d
e
Fig. 4-UN8