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Carbon and the Molecular
Diversity of Life
chapter 4
Site: wikipedia.org
1
Carbon—The Backbone of
Biological Molecules
 Cells 70–95% water – remainder mostly carbon-based
compounds

Unparalleled ability to form large, complex, diverse
molecules
 Proteins, DNA, carbohydrates, and other molecules
that distinguish living matter are all composed of
carbon compounds
2
3
Organic chemistry -- the study of
carbon compounds
 Organic compounds -- simple molecules to
colossal ones
 simplest
-- hydrogen atoms in addition to carbon
atoms
4
Carbon atoms form diverse
molecules by bonding to up to four
other atoms
5
LE 2-8
Hydrogen
1H
2
Atomic number
He
Atomic mass
First
shell
4.00
Helium
2He
Element symbol
Electron-shell
diagram
Lithium
3Li
Beryllium
4Be
Boron
5B
Carbon
6C
Nitrogen
7N
Oxygen
8O
Fluorine
9F
Neon
10Ne
Sodium
11Na
Magnesium
12Mg
Aluminum
12Al
Silicon
14Si
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Second
shell
Third
shell
6
Carbon and partners (hydrogen, oxygen, and
nitrogen) -- building blocks of organic
molecules
Hydrogen
(valence = 1)
Oxygen
(valence = 2)
Nitrogen
(valence = 3)
Carbon
(valence = 4)
7
Components of Carbon Diversity
 Skeleton
Variation
 Isomerization
 Functional Groups
8

Each carbon bonded to four other atoms has
a tetrahedral shape
 Two
carbon atoms joined in a double bond, the
molecule is flat
9
LE 4-3
Molecular
Formula
Methane
Ethane
Ethene (ethylene)
Structural
Formula
Ball-and-Stick
Model
Space-Filling
Model
Molecular Diversity Arising from
Carbon Skeleton Variation
Carbon chains form the skeletons of most
organic molecules
 Carbon chains vary in length and shape

single, double, or triple
 straight or branched chains
 rings


Bond with many different elements
11
LE 4-5
Ethane
Propane
Butane
2-methylpropane
(commonly called isobutane)
Length
Branching
1-Butene
2-Butene
Double bonds
Cyclohexane
Rings
Benzene
Ethane
1-Butene
Isobutane
Propane
2-Butene
Isopentane
Cyclopentane
Benzene
Histidine (an amino acid)
13
Fig. 3-1, p. 46
Isomers

Isomers are compounds with the same molecular
formula but different structures and properties

Structural isomers -- different covalent arrangements
of their atoms
14
Isomers

Structural isomers

different covalent arrangements
Ethanol (C2H6O)
Dimethyl ether (C2H6O)
15
Isomers

Isomers are compounds with the same molecular
formula but different structures and properties
Structural isomers -- different covalent arrangements
of their atoms
 Geometric isomers -- covalent arrangements but differ
in spatial arrangements

16
Isomers

Geometric isomers (cis–trans isomers)

different spatial arrangements
trans-2-butene
cis-2-butene
17
Isomers

Isomers are compounds with the same molecular
formula but different structures and properties
Structural isomers -- different covalent arrangements
of their atoms
 Geometric isomers -- covalent arrangements but differ
in spatial arrangements
 Enantiomers -- mirror images of each other

18
Isomers

Enantiomers

mirror images
19
Enantiomers



Important in the pharmaceutical industry
Different enantiomers may have different effects
Organisms are sensitive to even subtle variations
20
LE 4-7
Structural isomers differ in covalent partners, as shown in this
example of two isomers of pentane.
cis isomer: The two Xs
are on the same side.
trans isomer: The two Xs
are on opposite sides.
Geometric isomers differ in arrangement about a double bond. In
these diagrams, X represents an atom or group of atoms
attached to a double-bonded carbon.
L
isomer
D
isomer
Enantiomers differ in spatial arrangement around an
asymmetric carbon, resulting in molecules that are mirror
images, like left and right hands. The two isomers are
designated the L and D isomers from the Latin for left and
right (levo and dextro). Enantiomers cannot be superimposed
on each other.
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Isomers

Isomers are compounds with the same molecular
formula but different structures and properties
Structural isomers -- different covalent arrangements
of their atoms
 Geometric isomers -- covalent arrangements but differ
in spatial arrangements
 Enantiomers -- mirror images of each other


SHAPE -- critical
22
Molecular Shape and Function



shape very important (can be critical) to
function
shape determined by the positions of its
atoms’ valence orbitals
In a covalent bond, the s and p orbitals may
hybridize, creating specific molecular
shapes
23
LE 2-16a
s orbital
z
Three p orbitals
Four hybrid orbitals
x
y
Tetrahedron
Hybridization of orbitals


Biological molecules (especially proteins)
recognize and interact with each other with
a specificity based on molecular shape
Molecules with similar shapes can have
similar biological effects
25
LE 2-17a
Carbon
Hydrogen
Natural
endorphin
Sulfur
Oxygen
Morphine
Structures of endorphin and morphine
Nitrogen
Functional groups -- involved in
chemical reactions

Distinctive properties
 depend
not only on the carbon skeleton
 depend on the molecular components
attached to it
27
LE 4-9
Estradiol
Female lion
Testosterone
Male lion
Functional Groups

Properties depend on functional groups:
Polar -- hydroxyl and carbonyl groups
 Non-polar -- alkyl
 Acidic and Basic

o
o
carboxyl and phosphate groups (acidic)
amino groups (basic)
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Most important Functional Groups

Hydrocarbons -- Alkyl most common



Hydroxyl group -- ROH
Carbonyl group -- RCOR′




Aldehyde group -- RCOH
Carboxyl group -- RCOOH


Alkenyl and Alkynyl
Ester group -- RCOOR′
Amino group
Phosphate group
Sulfhydryl group
30
Hydrocarbons

Organic compounds
nonpolar
 carbon and hydrogen only
 hydrophobic


Methyl group
31
Polar and Ionic
Functional Groups

Partial charges on atoms
at opposite ends of a bond
 interact with one another
 hydrophilic


Hydroxyl and carbonyl groups
32
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).
LE 4-10ab
Acetone, the simplest ketone
EXAMPLE
STRUCTURE
RCOR′
Acetone, the simplest ketone
RCOH
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.
Acidic and Basic Groups

Acidic
release hydrogen ions
 become negatively charged
 carboxyl and phosphate groups

35
LE 4-10ac
STRUCTURE
EXAMPLE
Acetic acid, which gives vinegar
its sour taste
NAME OF COMPOUNDS
Carboxylic acids, or organic acids
RCOOH -- /carboxyl group  makes acids
RCOOR′ -- Ester group
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.
LE 4-10bc
STRUCTURE
EXAMPLE
Glycerol phosphate
NAME OF COMPOUNDS
Organic phosphates
ATP – Adenosine TriPhosphate
FUNCTIONAL PROPERTIES
Makes the molecule of which it
is a part an anion (negatively
charged ion).
Can transfer energy between
organic molecules.
Acidic and Basic Groups

Acidic
release hydrogen ions
 become negatively charged
 carboxyl and phosphate groups


Basic
release hydroxide ions
 become positively charged
 amino group

38
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
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).
Also RCOOR′
41
Table 3-1a, p. 49
42
Table 3-1b, p. 49
ATP: An Important Source of
Energy for Cellular Processes


One phosphate molecule, adenosine triphosphate
(ATP), is the primary energy-transferring molecule in
the cell
ATP consists of an organic molecule called adenosine
attached to a string of three phosphate groups
43
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
44