The Backbone of Biological Molecules

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, lipids, DNA, carbohydrates and other

molecules that distinguish living matter are all
composed of carbon compounds

Organic chemistry is the study of carbon

compounds
Organic compounds range from simple
molecules to colossal ones
Most organic compounds contain hydrogen atoms
in addition to carbon atoms

Vitalism, the idea that organic compounds arise

only in organisms, was disproved when chemists
synthesized the compounds in the lab

EXPERIMENT
Atmosphere
Water vapor

CH4
Electrode

Condenser

Cooled water
containing
organic
molecules

H2O
sea

Sample for
chemical analysis

Cold
water

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

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

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

Hydrogen
(valence = 1)

Oxygen
(valence = 2)

Nitrogen
(valence = 3)

Carbon
(valence = 4)

Molecular Diversity Arising from Carbon Skeleton

Variation
Carbon chains form the skeletons of most organic
molecules
Carbon chains vary in length and shape

Ethane

Propane

Butane

2-methylpropane
(commonly called isobutane)

Length

Branching

1-Butene
Double bonds

Cyclohexane
Rings

2-Butene

Benzene

 Carbon atoms can partner with atoms other

than hydrogen; for example:
Carbon dioxide: CO2
O=C=O

Urea: CO(NH2)2

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

Fat droplets (stained red)

100 m
A fat molecule

Mammalian adipose cells

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

Pentane
(a) Structural isomers

2-methyl butane

cis isomer: The two Xs are

on the same side.
(b) Geometric isomers

trans isomer: The two Xs are

on opposite sides.

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

L-Dopa

D-Dopa

(effective against
Parkinsons disease)

(biologically
Inactive)

Drug

Condition

Ibuprofen

Pain;
inflammation

Albuterol

Effective
Enantiomer

Ineffective
Enantiomer

S-Ibuprofen

R-Ibuprofen

R-Albuterol

S-Albuterol

Asthma

Functional groups are the parts of molecules

involved in chemical reactions
Distinctive properties of organic molecules depend
not only on the carbon skeleton but also on the
molecular components attached to it
Certain groups of atoms are often attached to
skeletons of organic molecules

The Functional Groups Most Important in the

Chemistry 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

Estradiol

Female lion

Testosterone

Male lion

 The six 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

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).

Acetone, the simplest ketone

STRUCTURE

EXAMPLE

Acetone, the simplest ketone

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.

STRUCTURE

EXAMPLE

Acetic acid, which gives vinegar

its sour taste

NAME OF COMPOUNDS
Carboxylic acids, or organic acids

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.

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

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).

Methyl group (

CH3)

Methylated compound

5-Methyl cytosine, a
component of DNA that has
been modified by addition of
a methyl group

Figure 3.21d

Hydrogen
bond

Hydrophobic
interactions and
van der Waals
interactions

Disulfide
bridge

Ionic bond

Polypeptide
backbone

STRUCTURE

EXAMPLE

Glycerol phosphate

NAME OF COMPOUNDS
Organic phosphates

FUNCTIONAL PROPERTIES
Makes the molecule of which it
is a part an anion (negatively
charged ion).

Can transfer energy between

organic molecules.

Adenine

Phosphate groups
Ribose

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

Reacts
with H2O
P

P Adenosine

ATP

Pi

Inorganic
phosphate

Adenosine

ADP

Energy

Animations and Videos

Bozeman - Molecules of Life

Bozeman - Biological Molecules

Building Biomolecules
Properties of Biomolecules

Biochemical Pathway
A Biochemical Pathway

Functional Groups 1
Functional Groups - 2

Animations and Videos

Chapter Quiz Questions 1

Chapter Quiz Questions 2

What was the first organic molecule to be

synthesized in the laboratory?

ammonium cyanate

hydrogen cyanide

urea

acetic acid

methane

What was the first organic molecule to be

synthesized in the laboratory?

ammonium cyanate

hydrogen cyanide

urea

acetic acid

methane

Carbon is an unusual atom in that it can form

multiple bonds. Which statement is NOT true?

a) A carbon-to-carbon cis double bond is the type found in nature

and is associated with cardiovascular health.
b) A carbon-to-carbon trans double bond is made artificially in
food processing and is associated with poor cardiovascular
health.

c) Multiple carbon-to-carbon double bonds located near each

other can absorb light, so they are found in molecules in the
eye or in chloroplasts.
d) Multiple carbon-to-carbon bonds are stronger than single
bonds.
e) Saturated fats are those that have a carbon-to-carbon
double bond and are associated with good health.

Carbon is an unusual atom in that it can form

multiple bonds. Which statement is NOT true?

a) A carbon-to-carbon cis double bond is the type found in nature

and is associated with cardiovascular health.
b) A carbon-to-carbon trans double bond is made artificially in food
processing and is associated with poor cardiovascular health.
c) Multiple carbon-to-carbon double bonds located near each other
can absorb light, so they are found in molecules in the eye or in
chloroplasts.
d) Multiple carbon-to-carbon bonds are stronger than single bonds.
e) Saturated fats are those that have a carbon-to-carbon
double bond and are associated with good health.

What type of chemical bond joins a functional

group to the carbon skeleton of a large
molecule?

covalent bond

hydrogen bond

ionic bond

double bond

disulfide bond

What type of chemical bond joins a functional

group to the carbon skeleton of a large
molecule?

covalent bond

hydrogen bond

ionic bond

double bond

disulfide bond

Which of the following is NOT one of the seven

functional groups found in biological
molecules?

amino

hydroxyl

carboxyl

cyanate

phosphate

Which of the following is NOT one of the seven

functional groups found in biological
molecules?

amino

hydroxyl

carboxyl

cyanate

phosphate

Which functional group behaves as a weak

acid in organic molecules?

amino

carboxyl

carbonyl

sulfhydryl

hydroxyl

Which functional group behaves as a weak

acid in organic molecules?

amino

carboxyl

carbonyl

sulfhydryl

hydroxyl

Which functional group behaves as a weak

base in organic molecules?

amino

carboxyl

carbonyl

sulfhydryl

hydroxyl

Which functional group behaves as a weak

base in organic molecules?

amino

carboxyl

carbonyl

sulfhydryl

hydroxyl

Which type of molecule always contains

phosphate groups?

carbohydrates

lipids

proteins

nucleic acids

none of the above

Which type of molecule always contains

phosphate groups?

carbohydrates

lipids

proteins

nucleic acids

none of the above

What type of isomer is propanal compared to

acetone?

cis-trans isomer

structural isomer

enantiomer

none of the above; these are not isomers

What type of isomer is propanal compared to

acetone?

cis-trans isomer

structural isomer

enantiomer

none of the above; these are not isomers

Which type of molecule may contain sulfhydryl

groups?

carbohydrate

lipid

protein

nucleic acid

all of the above

Which type of molecule may contain sulfhydryl

groups?

carbohydrate

lipid

protein

nucleic acid

all of the above

Which functional group is best known for its

ability to change the shape of a molecule
without affecting its reactivity?

amino

carboxyl

sulfhydryl

phosphate

methyl

Which functional group is best known for its

ability to change the shape of a molecule
without affecting its reactivity?

amino

carboxyl

sulfhydryl

phosphate

methyl

Scientific Skills Questions

The table below gives the molar ratios of some

of the products from Stanley Millers abiotic
synthesis of organic molecules experiment.
What is the molar ratio of serine?

1 mole of serine per mole of glycine

3.0 x 102 moles of serine per mole of glycine

3.0 x 102 moles of glycine per mole of serine

1 mole of serine per 3.0 x 102 moles of glycine

The table below gives the molar ratios of some

of the products from Stanley Millers abiotic
synthesis of organic molecules experiment.
What is the molar ratio of serine?

1 mole of serine per mole of glycine

3.0 x 102 moles of serine per mole of glycine

3.0 x 102 moles of glycine per mole of serine

1 mole of serine per 3.0 x 102 moles of glycine

The table below gives the molar ratios of some

of the products from Stanley Millers abiotic
synthesis of organic molecules experiment.
Which amino acid is present in higher
amounts than glycine?

serine

methionine

alanine

serine and methionine

The table below gives the molar ratios of some

of the products from Stanley Millers abiotic
synthesis of organic molecules experiment.
Which amino acid is present in higher
amounts than glycine?

serine

methionine

alanine

serine and methionine

Based on these results, how many molecules

of methionine are present per mole of
glycine?

1.08 x 1070 molecules

1.8 x 103 molecules

1.08 x 1021 molecules

6.02 x 1023 molecules

Based on these results, how many molecules

of methionine are present per mole of
glycine?

1.08 x 1070 molecules

1.8 x 103 molecules

1.08 x 1021 molecules

6.02 x 1023 molecules

The synthetic atmosphere in this experiment

contained H2S instead of water vapor. Which
of these amino acids could not have been
produced in Millers original abiotic
synthesis experiment?

serine

methionine

alanine

glycine

The synthetic atmosphere in this experiment

contained H2S instead of water vapor. Which
of these amino acids could not have been
produced in Millers original abiotic
synthesis experiment?

serine

methionine

alanine

glycine