Lecture 3

Carbon: The Backbone of Life

 Living organisms consist 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

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 Carbon compounds: some history
 Organic chemistry is the study of compounds
that contain carbon.
 When chemists learnt to make simpler
compounds from elements, artificial synthesis
of compounds extracted from living matter
seemed impossible.
 Berzelius: organic compounds – from living
matter; inorganic compounds – non-living
world

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 Carbon compounds: some history
 Vitalism is the idea that organic compounds
arise only in organisms.
 This was disproved when Wöhler synthesized
urea in the laboratory.
 Mechanism is the view that all natural
phenomena are governed by physical and
chemical laws

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 Carbon compounds: some history
Organic Molecules and the Origin of Life on
Earth
 Stanley Miller’s classic experiment
demonstrated the abiotic synthesis of organic
compounds
 Experiments support the idea that abiotic
synthesis of organic compounds, perhaps near
volcanoes, could have been a stage in the
origin of life

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 “Atmosphere”
CH4
Stanley Miller’s Water vapor
Electrode
classical
experiment
Condenser

Abiotic synthesis of
Cooled “rain”
organic compounds containing
Cold
water
in the context of organic
molecules
evolution

H2O
“sea”

Sample for chemical analysis

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 Why is carbon so special?
 With four valence electrons, carbon can form
four covalent bonds with a variety of atoms
 This ability makes large, complex molecules
possible

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 Why is carbon so special?
 Carbon can form long carbon-to-carbon chains

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 Why is carbon so special?
 Carbon atoms can bind to each other not only
in straight chains, but in complex branchings,
including head-to-tail joints to make rings of
carbon atoms

Cyclohexane
2-Methylpropane
(commonly called isobutane)

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 Why is carbon so special?
 Carbon atoms can form double and triple
bonds

Acetylene

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 Why is carbon so special?
 The same collection of atoms and bonds, but
in a different geometrical arrangement within
the molecule, makes a molecule with
different shape and hence different
properties. These different molecules are
called isomers

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 (a) Structural isomers

Isomers

(b) Cis-trans isomers

cis isomer: The two Xs trans isomer: The two Xs

are on the same side. are on opposite sides.

(c) Enantiomers

CO2H CO2H

H NH2 NH2 H
CH3 CH3
L isomer D isomer
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 Isomers
 Isomers are compounds with the same
molecular formula but different structures
and properties
 Structural isomers have different covalent
arrangements of their atoms
 Cis-trans isomers have the same covalent
bonds but differ in spatial arrangements
 Enantiomers are isomers that are mirror
images of each other

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 Isomers
 Enantiomers are important in the
pharmaceutical industry
 Two enantiomers of a drug may have different
effects
 Usually only one isomer is biologically active
 Differing effects of enantiomers demonstrate
that organisms are sensitive to even subtle
variations in molecules

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Figure 4.8

Effective Ineffective
Drug Condition
Enantiomer Enantiomer

Ibuprofen Pain;
inflammation
S-Ibuprofen R-Ibuprofen

Albuterol Asthma

R-Albuterol S-Albuterol

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 Why is carbon so special?
 All the electrons that are not being used to bond
carbon atoms together into chains and rings can be
used to form bonds with atoms of several other
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
Hydrogen Oxygen Nitrogen Carbon
(valence  1) (valence  2) (valence  3) (valence  4)

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 Concept 3.2: A few chemical groups are
key to the functioning of biological
molecules
 Distinctive properties of organic molecules
depend on the carbon skeleton and on the
molecular components attached to it.
 A number of characteristic groups can replace
the hydrogens attached to skeletons of
organic molecules

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 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 molecule its unique
properties

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Figure 4.UN02

Estradiol
Testosterone

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 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

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Figure 4.9-a
CHEMICAL
GROUP Hydroxyl Carbonyl Carboxyl

STRUCTURE

(may be written HO—)

NAME OF Alcohols (Their specific names Ketones if the carbonyl group is Carboxylic acids, or organic acids
COMPOUND usually end in -ol.) within a carbon skeleton

Aldehydes if the carbonyl group

is at the end of the carbon skeleton

EXAMPLE

Ethanol Acetone Acetic acid

Propanal

FUNCTIONAL • Is polar as a result of the
PROPERTIES electrons spending more time
near the electronegative oxygen
atom.
• Can form hydrogen bonds with
water molecules, helping dissolve
organic compounds such as
sugars.
• A ketone and an aldehyde may be • Acts as an acid; can donate an
structural isomers with different H+ because the covalent bond
properties, as is the case for between oxygen and hydrogen
acetone and propanal. is so polar:
• Ketone and aldehyde groups are
also found in sugars, giving rise
to two major groups of sugars:
ketoses (containing ketone
groups) and aldoses (containing
aldehyde groups). Nonionized Ionized

• Found in cells in the ionized form

with a charge of 1 and called a
carboxylate ion.

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Figure 4.9-b

Amino Sulfhydryl Phosphate Methyl

(may be
written HS—)

Amines Thiols Organic phosphates Methylated compounds

Glycine Cysteine Glycerol phosphate 5-Methyl cytidine

• Acts as a base; can • Two sulfhydryl groups can • Contributes negative charge to • Addition of a methyl group
pick up an H+ from the react, forming a covalent the molecule of which it is a part to DNA, or to molecules
surrounding solution bond. This “cross-linking” (2– when at the end of a molecule, bound to DNA, affects the
(water, in living helps stabilize protein as above; 1– when located expression of genes.
organisms): structure. internally in a chain of • Arrangement of methyl
phosphates). groups in male and female
• Cross-linking of cysteines • Molecules containing phosphate sex hormones affects their
in hair proteins maintains groups have the potential to react shape and function.
the curliness or straightness with water, releasing energy.
of hair. Straight hair can be
Nonionized Ionized “permanently” curled by
shaping it around curlers
and then breaking and
• Found in cells in the re-forming the cross-linking
ionized form with a bonds.
charge of 1+.

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Figure 4.9a

Hydroxyl

STRUCTURE Alcohols NAME OF

(Their specific COMPOUND
names usually
(may be written end in -ol.)
HO—)

EXAMPLE • Is polar as a result FUNCTIONAL

of the electrons PROPERTIES
spending more
time near the
electronegative
oxygen atom.
Ethanol • Can form hydrogen
bonds with water
molecules, helping
dissolve organic
compounds such
as sugars.

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Figure 4.9b

Carbonyl

STRUCTURE Ketones if the carbonyl NAME OF

group is within a COMPOUND
carbon skeleton
Aldehydes if the carbonyl
group is at the end of the
carbon skeleton

EXAMPLE • A ketone and an FUNCTIONAL

aldehyde may be PROPERTIES
structural isomers
with different properties,
as is the case for
acetone and propanal.
• Ketone and aldehyde
Acetone groups are also found
in sugars, giving rise
to two major groups
of sugars: ketoses
(containing ketone
groups) and aldoses
(containing aldehyde
Propanal groups).
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Figure 4.9c

Carboxyl

STRUCTURE Carboxylic acids, or organic NAME OF

acids COMPOUND

EXAMPLE • Acts as an acid; can FUNCTIONAL

donate an H+ because the PROPERTIES
covalent bond between
oxygen and hydrogen is so
polar:

Acetic acid

Nonionized Ionized

• Found in cells in the ionized

form with a charge of 1– and
called a carboxylate ion.
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Figure 4.9d

Amino

STRUCTURE Amines NAME OF

COMPOUND

EXAMPLE • Acts as a base; can FUNCTIONAL

pick up an H+ from the PROPERTIES
surrounding solution
(water, in living
organisms):

Glycine

Nonionized Ionized

• Found in cells in the

ionized form with a
charge of 1.
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Figure 4.9e

Sulfhydryl

STRUCTURE Thiols NAME OF

COMPOUND

(may be
written HS—)

EXAMPLE • Two sulfhydryl groups can FUNCTIONAL

react, forming a covalent PROPERTIES
bond. This “cross-linking”
helps stabilize protein
structure.

• Cross-linking of cysteines
in hair proteins maintains
the curliness or straightness
Cysteine
of hair. Straight hair can be
“permanently” curled by
shaping it around curlers
and then breaking and
re-forming the cross-linking
bonds.
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Figure 4.9f

Phosphate

STRUCTURE Organic phosphates NAME OF

COMPOUND

EXAMPLE • Contributes negative FUNCTIONAL

charge to the molecule PROPERTIES
of which it is a part
(2– when at the end of
a molecule, as at left;
1– when located
internally in a chain of
phosphates).
Glycerol phosphate • Molecules containing
phosphate groups have
the potential to react
with water, releasing
energy.

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Figure 4.9g

Methyl

STRUCTURE Methylated compounds NAME OF

COMPOUND

EXAMPLE • Addition of a methyl group FUNCTIONAL

to DNA, or to molecules PROPERTIES
bound to DNA, affects the
expression of genes.
• Arrangement of methyl
groups in male and female
sex hormones affects their
shape and function.
5-Methyl cytidine

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