Organic chemistry with biological applications

Structures of Common Coenzymes
The reactive parts of the molecules are darkened, while nonreactive parts are ghosted.
Adenosine triphosphate—ATP (phosphorylation)
NH2
N
O

O
–O

P
O–

O

P

N

O
O

P

O–

OCH2

N

O

O–

N

OH

OH
Coenzyme A (acyl transfer)

NH2
N
O

O

CH3

N

O O

HSCH2CH2NHCCH2CH2NHCCHCCH2OPOPOCH2

O

O– O–

HO CH3

2–O PO
3

N

N

OH

Nicotinamide adenine dinucleotide—NAD+ (oxidation/reduction)
(NADP+)
NH2
CONH2

N

N

O O
+

CH2OPOPOCH2

N

O– O–

OH HO
O

N

O

OH

N

OH (OPO32–)

Flavin adenine dinucleotide—FAD (oxidation/reduction)
NH2
N
HO OH
HO

CHCHCHCH2OPOPOCH2
O– O–

CH2
H3C

N

H3C

N

N

O O

N

O
N

O

OH

N

N

OH

H

O

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Tetrahydrofolate (transfer of C1 units)
H
H 2N

H

N

N
N

N
O

H

H
N

CO2–

H

O

NHCHCH2CH2C

O–
1–5

O
S-Adenosylmethionine (methyl transfer)
NH2
N

N

CH3

O
–OCCHCH CH
2
2
+NH

S
+

CH2

N

O

N

3

OH

OH
Pyridoxal phosphate
(amino acid metabolism)

Lipoic acid (acyl transfer)
S

CH2OPO32–

S

CHO

CH2CH2CH2CH2CO2–
+
H

N

OH
CH3

Thiamin diphosphate
(decarboxylation)

Biotin (carboxylation)

H
S

O

NH2
+

N

H

N

O O
–OPOPOCH CH
2
2
O– O–

CH3

N

CH3

N

N

H

H
H
H

S

CH2CH2CH2CH2CO2–

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in our courses,
Dear Colleague:
of the students
t
os
m
at
th
ow
kn
er than in pure
fe sciences rath
ganic chemistry
li
or
e
h
th
ac
in
te
y
il

ho
ar
w
prim
d doctors
All of us
biochemists, an
s, are interested
,
or
ts
aj
is
m
og
y
ol
tr
bi
is
re
em
we
tu
even the ch
hing so many fu
questioning why
e
ac
te

ar
e
us
ar
e
of
w
e
or
se
m
ng the details of
ves, more and
chemistry. Becau
h time discussi
rsions of oursel
uc
ve
r
m
ge
so
un
d
yo
en
sp
an
ogy? Why
e

rather th
nnection to biol
e do. Why do w
co
w
le
ay
tt
li
w
e
ve
th
ha
h
t
ac
bu
sms?
continue to te
search chemists
of living organi
re
y
to
tr
is
st
re
em

te
ch
in
c
of
ni
e
sing the orga
reactions that ar
ore time discus
m
d
en
sp
ional way, but it
d
ea
st
try in the tradit
don’t we in
is
em
ch
c
ni
ga
s who want
or
id for teaching
those instructor

r
sa
fo
be
e
iv
to
at
h
rn
uc
te
m
al
l
logical
al
There is stil
mistry with Bio
e has been no re
he
er
C
th
ic
w
an
no
rg
l

ti
O
te
un
more
is also true that
that is why I wro
, I suspect that
nd
ce
A
en
y.
in
tl
en
om
er
pr
ff
di
in
hat
inues to gain
to teach somew
ical biology cont
em
ch
s
A

.
3e
accordingly.
s
Application
ng their teaching
gi
an
ciple
ch
be
l
il
w
y
my guiding prin
ut
B
y.
tr
is
and more facult
em
ch
on organic
exclusively
to focus almost
is still a textbook
is
en

th
be
:
s
ke
ha
ta
t
is
ou
m
e
av
space saved
Make no
e and what to le
chemistry. The
ud
al
cl
ic
in
og
to
ol
t
bi
ha
in
w

t
action
ar
in deciding
direct counterp
r almost every re
a
fo
ve
e,
us
ha
at
od
th
go
s
to
s been put
e book is
on those reaction
gical reactions ha
ately 25% of th
lo
im
io
ox
nb
pr
no

ap
t
d
ou
an
g
e
ations. In
pl
by leavin
eir biotransform
biological exam
th
a
of
by
y
tr
ed
is
ow
em
ll
fo
ch
c
orter
discussed is
es and the organi
arly 200 pages sh

ul
ne
ec
is
ol
3e
om
s
bi
on
to
ti
a typical twogical Applica
devoted entirely
istry with Biolo
e entire book in
m
th
r
he
C
ve
ic
co
an
to
y
rg
lt
O

addition,
ssible for facu
xts, making it po
te
rd
da
an
st
an
th
xt; I believe
.
om any other te
fr
t
en
er
ff
semester course
di
is
pplications 3e
ith Biological A
w
y
tr
is
m
he
C

Organic
ts.
r today’s studen
fo
l
ea
id
is
it
at
th
Sincerely,
John McMurry

All royalties from Organic Chemistry with Biological Applications will be donated to the Cystic Fibrosis (CF) Foundation. This
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Organic Chemistry
w i t h B i o l o g i c a l a p p l i c at i o n s

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3rd Edition

Organic Chemistry
w i t h B i o l o g i c a l a p p l i c at i o n s

John McMurry
COrnEll UnivErsity

Australia • Brazil • Mexico • Singapore • United Kingdom • United States

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Organic Chemistry with Biological
Applications, 3e

John McMurry
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Library of Congress Control Number: 2013956751
ISBN-13: 978-1-285-84291-2
ISBN-10: 1-285-84291-X
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Brief Contents


1

structure and Bonding



2

polar covalent Bonds; acids and Bases

28

3

organic compounds: alkanes and their stereochemistry

59



4

organic compounds: cycloalkanes and their stereochemistry

87



5

stereochemistry at tetrahedral centers

113



6

an overview of organic Reactions

146

7

alkenes and alkynes

179



8

Reactions of alkenes and alkynes

212



9

aromatic compounds

265

10

1

structure Determination: Mass spectrometry, infrared spectroscopy, and Ultraviolet
spectroscopy

319

11

structure Determination: nuclear Magnetic Resonance spectroscopy

350

12

organohalides: nucleophilic substitutions and Eliminations

382

13

alcohols, phenols, and thiols; Ethers and sulfides

435

**

a preview of carbonyl chemistry

483

14

aldehydes and Ketones: nucleophilic addition Reactions

492

15

carboxylic acids and nitriles

530

16

carboxylic acid Derivatives: nucleophilic acyl substitution Reactions

555

17

carbonyl alpha-substitution and condensation Reactions

599

18

amines and heterocycles

644

19

Biomolecules: amino acids, peptides, and proteins

678

20

amino acid Metabolism

714

21

Biomolecules: carbohydrates

738

22

carbohydrate Metabolism

773

23

Biomolecules: lipids and their Metabolism

805

24

Biomolecules: nucleic acids and their Metabolism

852

To access the following online-only chapters, enter ISBN: 978-1-285-84291-2 at
www.cengagebrain.com and visit this book’s companion website.

e25

secondary Metabolites: an introduction to natural products chemistry

877

e26

orbitals and organic chemistry: pericyclic Reactions

905

e27

synthetic polymers

925
v

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D e ta i l e D C o n t e n t s

1

structure and Bonding |
1-1
1-2
1-3
1-4
1-5
1-6
1-7
1-8
1-9
1-10
1-11
1-12

atomic structure: the nucleus
atomic structure: orbitals
atomic structure: Electron configurations
Development of chemical Bonding theory
Describing chemical Bonds: Valence Bond theory
sp3 hybrid orbitals and the structure of Methane
sp3 hybrid orbitals and the structure of Ethane
sp2 hybrid orbitals and the structure of Ethylene
sp hybrid orbitals and the structure of acetylene
hybridization of nitrogen, oxygen, phosphorus, and sulfur
Describing chemical Bonds: Molecular orbital theory
Drawing chemical structures
soMetHinG eXtra

2

1

polar covalent Bonds: Electronegativity
polar covalent Bonds: Dipole Moments
Formal charges
Resonance
Rules for Resonance Forms
Drawing Resonance Forms
acids and Bases: the Brønsted–lowry Definition
acid and Base strength
predicting acid–Base Reactions from pKa Values
organic acids and organic Bases
acids and Bases: the lewis Definition
noncovalent interactions between Molecules
soMetHinG eXtra

4
6
7
10
12
13
14
16
18
20
21

organic Foods: Risk versus Benefit

Polar Covalent Bonds; acids and Bases |
2-1
2-2
2-3
2-4
2-5
2-6
2-7
2-8
2-9
2-10
2-11
2-12

3

alkaloids: From cocaine
to Dental anesthetics

24

28
28
31
33
36
37

39
42
44
46
47
50
54
56

vi
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Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.


DetaileD Contents

3

organic Compounds:
alkanes and their stereochemistry |
3-1
3-2
3-3
3-4
3-5
3-6
3-7

Functional groups
alkanes and alkane isomers

alkyl groups
naming alkanes
properties of alkanes
conformations of Ethane
conformations of other alkanes
soMetHinG eXtra

4

66
69
72
78
79
81
85

87

naming cycloalkanes
cis–trans isomerism in cycloalkanes
stability of cycloalkanes: Ring strain
conformations of cycloalkanes
conformations of cyclohexane
axial and Equatorial Bonds in cyclohexane
conformations of Monosubstituted cyclohexanes
conformations of Disubstituted cyclohexanes
conformations of polycyclic Molecules
soMetHinG eXtra

88
91
93
95
97
99
102
105
108

Molecular Mechanics

stereochemistry at tetrahedral Centers |
5-1
5-2
5-3
5-4
5-5

59

gasoline

organic Compounds:
Cycloalkanes and their stereochemistry |
4-1
4-2
4-3
4-4
4-5

4-6
4-7
4-8
4-9

5

59

Enantiomers and the tetrahedral carbon
the Reason for handedness in Molecules: chirality
optical activity
pasteur’s Discovery of Enantiomers
sequence Rules for specifying configuration

111

113
114
115
119
121
122

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Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

vii

viii

DetaileD Contents

5-6
5-7
5-8
5-9
5-10
5-11
5-12

Diastereomers
Meso compounds
Racemic Mixtures and the Resolution of Enantiomers
a Review of isomerism
chirality at nitrogen, phosphorus, and sulfur
prochirality
chirality in nature and chiral Environments
soMetHinG eXtra

6

7-7
7-8
7-9

135
137
138

141
143

146

where Do Drugs come From?

alkenes and alkynes |
7-1
7-2
7-3
7-4
7-5
7-6

132

Kinds of organic Reactions
how organic Reactions occur: Mechanisms
Radical Reactions
polar Reactions
an Example of a polar Reaction: addition of h2o to Ethylene
Using curved arrows in polar Reaction Mechanisms
Describing a Reaction: Equilibria, Rates, and Energy changes
Describing a Reaction: Bond Dissociation Energies
Describing a Reaction: Energy Diagrams and transition states
Describing a Reaction: intermediates
a comparison between Biological Reactions and laboratory Reactions
soMetHinG eXtra

7

130

chiral Drugs

an overview of organic reactions |
6-1
6-2
6-3
6-4
6-5
6-6
6-7
6-8
6-9
6-10
6-11

127

146
148
149
152
156
159
162
166
168

170
173
176

179

calculating the Degree of Unsaturation
naming alkenes and alkynes
cis–trans isomerism in alkenes
alkene stereochemistry and the E,Z Designation
stability of alkenes
Electrophilic addition Reactions of alkenes

180

writing organic Reactions

196

orientation of Electrophilic addition: Markovnikov’s Rule
carbocation structure and stability
the hammond postulate

197

183
186
188
191
195

201
203

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Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.


Contents

7-10

Evidence for the Mechanism of Electrophilic additions:
carbocation Rearrangements
soMetHinG eXtra

8

terpenes: naturally occurring alkenes

reactions of alkenes and alkynes |
8-1
8-2
8-3
8-4
8-5
8-6
8-7
8-8
8-9

8-10
8-11
8-12
8-13
8-14
8-15

natural Rubber

learning Reactions

9

aromatic Compounds |
9-1
9-2
9-3
9-4
9-5
9-6
9-7
9-8

209

212

preparing alkenes: a preview of Elimination Reactions
halogenation of alkenes
halohydrins from alkenes

hydration of alkenes
Reduction of alkenes: hydrogenation
oxidation of alkenes: Epoxidation
oxidation of alkenes: hydroxylation
oxidation of alkenes: cleavage to carbonyl compounds
addition of carbenes to alkenes: cyclopropane synthesis
Radical additions to alkenes: chain-growth polymers
Biological additions of Radicals to alkenes
conjugated Dienes
Reactions of conjugated Dienes
the Diels–alder cycloaddition Reaction
Reactions of alkynes
soMetHinG eXtra

206

213
214
217
218
223
227
229
231
233
235
240
241
245
247

253
258
261

265

naming aromatic compounds
structure and stability of Benzene
aromaticity and the hückel 4n 1 2 Rule
aromatic ions and aromatic heterocycles
polycyclic aromatic compounds
Reactions of aromatic compounds: Electrophilic substitution
alkylation and acylation of aromatic Rings:
the Friedel–crafts Reaction
substituent Effects in Electrophilic substitutions

266
268
272
274
279
281
289
295

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Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

ix

x

DetaileD Contents

9-9
9-10
9-11

nucleophilic aromatic substitution
oxidation and Reduction of aromatic compounds
an introduction to organic synthesis: polysubstituted Benzenes
soMetHinG eXtra

10

306
308
314

structure Determination:
Mass spectrometry, infrared spectroscopy,
and Ultraviolet spectroscopy | 319
10-1
10-2
10-3
10-4
10-5
10-6
10-7

10-8
10-9
10-10
10-11

Mass spectrometry of small Molecules: Magnetic-sector instruments 320
interpreting Mass spectra
321
Mass spectrometry of some common Functional groups
326
Mass spectrometry in Biological chemistry: time-of-Flight (toF)
328
instruments
spectroscopy and the Electromagnetic spectrum
329
infrared spectroscopy
332
interpreting infrared spectra
334
infrared spectra of some common Functional groups
337
Ultraviolet spectroscopy
342
interpreting Ultraviolet spectra: the Effect of conjugation
345
conjugation, color, and the chemistry of Vision
346
soMetHinG eXtra

11

aspirin, nsaiDs, and coX-2 inhibitors

303

X-Ray crystallography

348

structure Determination: nuclear Magnetic
resonance spectroscopy | 350
11-1
11-2
11-3
11-4
11-5
11-6
11-7
11-8
11-9

nuclear Magnetic Resonance spectroscopy
the nature of nMR absorptions
chemical shifts
13c nMR spectroscopy: signal averaging and Ft-nMR
characteristics of 13c nMR spectroscopy
DEpt 13c nMR spectroscopy
Uses of 13c nMR spectroscopy
1h nMR spectroscopy and proton Equivalence
chemical shifts in 1h nMR spectroscopy

350
352
355
357
358
361
364
365
368

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Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.


Contents

11-10
11-11
11-12
11-13

integration of 1h nMR absorptions: proton counting
spin–spin splitting in 1h nMR spectra
More complex spin–spin splitting patterns
Uses of 1h nMR spectroscopy
soMetHinG eXtra

12

organohalides: nucleophilic
substitutions and eliminations |
12-1
12-2
12-3
12-4
12-5
12-6
12-7
12-8
12-9
12-10
12-11
12-12
12-13
12-14
12-15
12-16

371
376
379
380

382

names and structures of alkyl halides
preparing alkyl halides from alkenes: allylic Bromination
preparing alkyl halides from alcohols
Reactions of alkyl halides: grignard Reagents

organometallic coupling Reactions
Discovery of the nucleophilic substitution Reaction
the sn2 Reaction
characteristics of the sn2 Reaction
the sn1 Reaction
characteristics of the sn1 Reaction
Biological substitution Reactions
Elimination Reactions: Zaitsev’s Rule
the E2 Reaction and the Deuterium isotope Effect
the E1 and E1cB Reactions
Biological Elimination Reactions
a summary of Reactivity: sn1, sn2, E1, E1cB, and E2
soMetHinG eXtra

13

Magnetic Resonance imaging (MRi)

370

naturally occurring organohalides

383
385
390
391
393
395
398
401

408
412
418
420
422
427
428
429
430

alcohols, Phenols, and thiols;
ethers and sulfides | 435
13-1
13-2
13-3
13-4
13-5

naming alcohols, phenols, and thiols
properties of alcohols, phenols, and thiols
preparing alcohols from carbonyl compounds
Reactions of alcohols
oxidation of alcohols and phenols

437
439
443
452
456

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Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

xi


xii

DetaileD Contents

13-6
13-7
13-8
13-9
13-10
13-11
13-12
13-13

protection of alcohols
preparation and Reactions of thiols
Ethers and sulfides
preparing Ethers
Reactions of Ethers
crown Ethers and ionophores
preparation and Reactions of sulfides
spectroscopy of alcohols, phenols, and Ethers
soMetHinG eXtra

460

463
464
466
467
472
474
475

Ethanol: chemical, Drug, poison

a Preview of Carbonyl Chemistry |
i
ii
iii
iV

14

14-1
14-2
14-3
14-4
14-5
14-6
14-7
14-8
14-9
14-10
14-11
14-12

483

Kinds of carbonyl compounds
nature of the carbonyl group
general Reactions of carbonyl compounds
summary

aldehydes and Ketones:
nucleophilic addition reactions |

483
485
485
491

492

naming aldehydes and Ketones
preparing aldehydes and Ketones
oxidation of aldehydes
nucleophilic addition Reactions of aldehydes and Ketones
nucleophilic addition of h2o: hydration
nucleophilic addition of hydride and grignard Reagents: alcohol
Formation
nucleophilic addition of amines: imine and Enamine Formation
nucleophilic addition of alcohols: acetal Formation
nucleophilic addition of phosphorus Ylides: the wittig Reaction
Biological Reductions
conjugate nucleophilic addition to a,b-Unsaturated aldehydes and

Ketones
spectroscopy of aldehydes and Ketones
soMetHinG eXtra

478

Enantioselective synthesis

493
495
497
497
501
503
505
509
513
516
518
522
526

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Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.


Contents

15

Carboxylic acids and nitriles |
15-1
15-2
15-3
15-4
15-5
15-6
15-7
15-8

naming carboxylic acids and nitriles
structure and properties of carboxylic acids
Biological acids and the henderson–hasselbalch Equation
substituent Effects on acidity
preparing carboxylic acids
Reactions of carboxylic acids: an overview
chemistry of nitriles
spectroscopy of carboxylic acids and nitriles
soMetHinG eXtra

16

16-9
16-10

b-lactam antibiotics

Carbonyl alpha-substitution
and Condensation reactions |
17-1

17-2
17-3
17-4

533
537
538
540
543
543
548
550

naming carboxylic acid Derivatives
nucleophilic acyl substitution Reactions
Reactions of carboxylic acids
Reactions of acid halides
Reactions of acid anhydrides
Reactions of Esters
Reactions of amides
Reactions of thioesters and acyl phosphates:
Biological carboxylic acid Derivatives
polyamides and polyesters: step-growth polymers
spectroscopy of carboxylic acid Derivatives
soMetHinG eXtra

531

Vitamin c

Carboxylic acid Derivatives:
nucleophilic acyl substitution reactions |
16-1
16-2
16-3
16-4
16-5
16-6
16-7
16-8

17

530

555
556
559
564
570
576
578
584
587
589
592
594

599

Keto–Enol tautomerism
Reactivity of Enols: a-substitution Reactions
alpha Bromination of carboxylic acids
acidity of a hydrogen atoms: Enolate ion Formation

600
603
606
607

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Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

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DetaileD Contents

17-5
17-6
17-7
17-8
17-9
17-10
17-11
17-12
17-13

alkylation of Enolate ions
carbonyl condensations: the aldol Reaction
Dehydration of aldol products
intramolecular aldol Reactions
the claisen condensation Reaction
intramolecular claisen condensations: the Dieckmann cyclization
conjugate carbonyl additions: the Michael Reaction
carbonyl condensations with Enamines: the stork Reaction
Biological carbonyl condensation Reactions
soMetHinG eXtra

18

amines and Heterocycles |
18-1
18-2
18-3
18-4
18-5
18-6
18-7
18-8
18-9
18-10

620
623
626
627
629

632
634
637
639

644

naming amines
properties of amines
Basicity of amines
Basicity of arylamines
Biological amines and the henderson–hasselbalch Equation
synthesis of amines
Reactions of amines
heterocyclic amines
Fused-Ring heterocycles
spectroscopy of amines
soMetHinG eXtra

19

Barbiturates

610

green chemistry

645
647
649

652
653
654
659
665
669
672
674

Biomolecules: amino acids,
Peptides, and Proteins | 678
19-1
19-2
19-3
19-4
19-5
19-6
19-7

structures of amino acids
amino acids and the henderson–hasselbalch Equation:
isoelectric points
synthesis of amino acids
peptides and proteins
amino acid analysis of peptides
peptide sequencing: the Edman Degradation
peptide synthesis

679
684

687
689
691
693
696

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Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.


Contents

19-8
19-9
19-10

protein structure
Enzymes and coenzymes
how Do Enzymes work? citrate synthase
soMetHinG eXtra

20

22

Visualizing Enzyme structures

sweetness

Carbohydrate Metabolism |

22-1
22-2
22-3

hydrolysis of complex carbohydrates
catabolism of glucose: glycolysis
conversion of pyruvate to acetyl coa

715
719
723
728
731
735

738

classifying carbohydrates
Representing carbohydrate stereochemistry: Fischer projections
d,l sugars
configurations of the aldoses
cyclic structures of Monosaccharides: anomers
Reactions of Monosaccharides
the Eight Essential Monosaccharides
Disaccharides
polysaccharides and their synthesis
some other important carbohydrates
soMetHinG eXtra

710

714

Biomolecules: Carbohydrates |
21-1
21-2
21-3
21-4
21-5
21-6
21-7
21-8
21-9
21-10

707

an overview of Metabolism and Biochemical Energy
catabolism of amino acids: Deamination
the Urea cycle
catabolism of amino acids: the carbon chains
Biosynthesis of amino acids
soMetHinG eXtra

21

703

the protein Data Bank

amino acid Metabolism |
20-1
20-2
20-3
20-4
20-5

700

739
740
745
746
750
753
761
762
765
768
770

773
774
776
783

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Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

xv

xvi

DetaileD Contents

22-4
22-5

the citric acid cycle
Biosynthesis of glucose: gluconeogenesis
soMetHinG eXtra

23

Biomolecules: lipids and their Metabolism |
23-1
23-2
23-3
23-4
23-5
23-6
23-7
23-8
23-9
23-10
23-11

waxes, Fats, and oils
soap

phospholipids
catabolism of triacylglycerols: the Fate of glycerol
catabolism of triacylglycerols: b-oxidation
Biosynthesis of Fatty acids
prostaglandins and other Eicosanoids
terpenoids
steroids
Biosynthesis of steroids
some Final comments on Metabolism
soMetHinG eXtra

24

influenza pandemics

statin Drugs

787
794
802

805
806
809
811
813
816
820
826
829

837
842
848
849

Biomolecules: nucleic acids
and their Metabolism | 852
24-1
24-2
24-3
24-4
24-5
24-6
24-7
24-8
24-9
24-10

nucleotides and nucleic acids
Base pairing in Dna: the watson–crick Model
Replication of Dna
transcription of Dna
translation of Rna: protein Biosynthesis
Dna sequencing
Dna synthesis
the polymerase chain Reaction
catabolism of nucleotides
Biosynthesis of nucleotides
soMetHinG eXtra

Dna Fingerprinting

852
855
858
859
861
864
866
869
871
873
875

Copyright 2015 Cengage Learning. All Rights Reserved. May not be copied, scanned, or duplicated, in whole or in part. Due to electronic rights, some third party content may be suppressed from the eBook and/or eChapter(s).
Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.


Contents

To access the following online-only chapters, enter ISBN: 978-1-285-84291-2 at
www.cengagebrain.com and visit this book’s companion website.

e25

secondary Metabolites: an introduction
to natural Products Chemistry | 877
25-1
25-2
25-3

25-4

classifying natural products
Biosynthesis of pyridoxal phosphate
Biosynthesis of Morphine
Biosynthesis of Erythromycin
soMetHinG eXtra

e26

879
884
894

Bioprospecting: hunting for natural products 903

orbitals and organic Chemistry:
Pericyclic reactions | 905
26-1
26-2
26-3
26-4
26-5
26-6
26-7
26-8
26-9

Molecular orbitals of conjugated pi systems
Electrocyclic Reactions

stereochemistry of thermal Electrocyclic Reactions
photochemical Electrocyclic Reactions
cycloaddition Reactions
stereochemistry of cycloadditions
sigmatropic Rearrangements
some Examples of sigmatropic Rearrangements
a summary of Rules for pericyclic Reactions
soMetHinG eXtra

e27

878

Vitamin D, the sunshine Vitamin

synthetic Polymers |
27-1
27-2
27-3
27-4

905
908
910
912
913
914
917
919
921

922

925

chain-growth polymers
stereochemistry of polymerization: Ziegler–natta catalysts
copolymers
step-growth polymers

926
928
930
932

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Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

xvii


xviii

Contents

27-5
27-6

olefin Metathesis polymerization
polymer structure and physical properties
soMetHinG eXtra

Biodegradable polymers

934
936
940

appendices
a
B
c
D

nomenclature of polyfunctional organic compounds
acidity constants for some organic compounds
glossary
answers to in-text problems

index |

a-1
a-7
a-9
a-31

i-1

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Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.

PrefaCe

I’ve taught organic chemistry many times for many years. Like most faculty, I
began by trying to show 19-year-old students the logic and beauty of the subject, thinking that they would find it as fascinating as I did. It didn’t take long,
though, before I realized what a disconnect there was between my own interests and expectations and those of my students. Some students did develop a
real appreciation for the subject, but most seemed to worry primarily about
getting into medical school. And why not? If a student has a clear career goal,
why shouldn’t that person focus his or her efforts toward meeting that goal?
All of us who teach organic chemistry know that the large majority of our
students—90% or more, and including many chemistry majors—are interested primarily in medicine, biology, and other life sciences rather than in
pure chemistry. But if we are primarily teaching future physicians, biologists,
biochemists, and others in the life sciences (not to mention the occasional
lawyer, politician, or business person), why do we continue to teach the way
we do? Why do our textbooks and lectures spend so much time discussing
details of topics that interest professional chemists but have no connection to
biology? Wouldn’t the limited amount of time we have be better spent paying
more attention to the organic chemistry of living organisms and less to the
organic chemistry of the research laboratory? Wouldn’t it better serve our students if we helped them reach their goals rather than reach goals we set for
them? I believe so, and I have written this book, Organic Chemistry with Biological Applications, third edition, to encourage others who might also be
thinking that the time has come to do things a bit differently.
This is, first and foremost, a textbook on organic chemistry. Look through
it and you’ll find that almost all the standard topics are here, although the
treatment of some has been attenuated to save space. Nevertheless, my guiding principle in writing this text has been to put a greater emphasis on those
organic reactions and topics that are relevant to biological chemistry than on
those that are not.
Organic chemistry, which began historically as the chemistry of living
organisms, is now shifting back in that direction, judging from the increasing
amount of biologically oriented research done in many chemistry departments and from the renaming of many departments to include chemical biology. Shouldn’t our teaching reflect that shift?

c

organization of the text

Four distinct groups of chapters are apparent in this text. The first group
(Chapters 1–6 and 10–11) covers the traditional principles of organic chemistry and spectroscopy that are essential for building further understanding.
xix
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Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.


xx

PrefaCe

The second group (Chapters 7–9 and 12–18) covers the common organic
reactions found in all texts. As each laboratory reaction is discussed, however,
a biological example is also shown to make the material more interesting and
meaningful to students. For instance, trans fatty acids are described at the
same time that catalytic hydrogenation is discussed (Section 8-5); biological
methylations with S-adenosylmethionine are covered with SN2 reactions
(Section 12-11); and biological reductions with NADH are introduced along
with laboratory NaBH4 reductions (Section 13-3).
The third group of chapters (19–24) is unique to this text in its depth of
coverage. These chapters deal exclusively with the main classes of biomolecules—amino acids and proteins, carbohydrates, lipids, and nucleic acids—
and show how thoroughly organic chemistry permeates biological chemistry.
Following an introduction to each class, major metabolic pathways for that
class are discussed from the perspective of mechanistic organic chemistry.
And finally, for those faculty who want additional coverage of natural
products, polymers, and pericyclic reactions, the book ends with a fourth

group of chapters (25–27) devoted to those topics. This final group is available
in both electronic and hard-copy formats at the request of the adopter.

c

What’s new

Text content has been revised substantially for this 3rd edition as a result of
user feedback. Most noticeably, two new chapters have been made available
for those who want them: Chapter 26 on Pericyclic Reactions and Chapter
27 on Synthetic Polymers. Other changes include:
• Every chapter ends with a brief Something Extra essay that has been repositioned to follow immediately after the last text section where it is more
likely to be noticed and read.
• The problems at the ends of chapters are now organized by topic to make
it easier for students to find questions on specific subjects.
• New problems have been added in every chapter, 164 in all.
• Text references to all numbered fiGUres and taBles are called out in color
to help students move more easily between text and art.
• All figure captions have a boldfaced title, and the captions themselves
use colored text to make it easier to focus on specific features in the figure art.

new topics in this 3rd edition include:
• A new Something Extra, “Organic Foods: Risk versus Benefit,” in Chapter 1
• A new Something Extra, “Alkaloids: From Cocaine to Dental Anesthetics,” in Chapter 2
• New coverage of bridged bicyclic molecules in Section 4-9
• New coverage of mercury-catalyzed alkyne hydration in Section 8-15
• New coverage of aromatic fluorination and fluorinated drugs in Section 9-6
• New coverage of alcohol to alkyl fluoride conversions in Section 12-3
• A new Section 12-5, “Organometallic Coupling Reactions,” covering both
organocopper reactions and the palladium-catalyzed Suzuki–Miyaura

reaction
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Editorial review has deemed that any suppressed content does not materially affect the overall learning experience. Cengage Learning reserves the right to remove additional content at any time if subsequent rights restrictions require it.