Professional Documents
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1 Introduction: why biologists need chemistry
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2 Atoms: the foundations of life
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3 Compounds and chemical bonding: bringing atoms together
4 Molecular interactions: holding 1t all together
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5 Moles, concentrations, and dilutions: making sense of
chemical numbers 127
6 Organic compounds 1: hydrocarbons as the framework of life 166
7 Organic compounds 2: adding function to the framework of life 192
8 Molecular shape and structure: life in three dimensions 228
9 Isomerism: generating chemical variety 257
10 Biological macromolecules: providing life’s infrastructure 293
11 Metals in biology: life beyond carbon 346
12 Chemical reactions 1: bringing molecules to life 373
13 Chemical reactions 2: reaction mechanisms driving the
chemistry of life 414
14 Energy: what makes reactions go? 463
15 Equilibria: how far do reactions go? 514
16 Kinetics: what a仔ects the speed of a reaction? 559
17 Acids, ba.ses, and buffer solutions: life in an aqueous environment 606
18 Chemical analysis: characterizing chemical compounds 660
Bibliognαphy 717
A门swers to self-check questions 720
l门dex 728
This pαge intentionαlly left blαnk
ontents
22
11
2 Atoms: the foundations of life
2.1 The chemical elements 4
3
34
11
The periodic table
What does 'element' real ly mean?
15
2.2 Atomic composition
6789
1111222
Protons, electrons, and electrical charge
Identifying the composition of an atom: atomic number a门d mass number
The formation of ions: varying the number of electrons
Ionization energies: how easy is it to let go?
12
Isotopes: varying the number of neutrons
Relative abu 门dances and relative atom ic mass
5
How protons determine chemical identity
26
2.3 Atomic structure
26
Atomic orbitals
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2.5 Valence shells and valence electrons: an atom's outer limits
44
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Valence electrons a门d the underlying logic of the periodic table
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The variety of life: not so varied after al l?
92
4.2 Electrostatic forces: the foundations of molecular interactions
93
Polar bonds in non-polar molecu les
95
4.3 The van der Waals interaction
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。1 spersion forces
Permanent di polar interactions
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Steric repu lsion
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Balancing attraction and repu lsion: the van der Waals interaction
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4.4 Beyond van der Waals: other biologically essential interactions
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Hydrogen bonds
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Ionic fo「ces
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Hydrophobic forces
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Holding it together: non-covalent interactions in biological molecules
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4.5 The impact of molecular interactions on water solubility
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The role of solvation in aqueous systems
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4.6 Breaking molecular interactions: the three phases of ma忧er
222
123
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phases
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The transition between phases
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The impact of non-covalent interactions on phases
framework of life
6.1 Organic chemist叩
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Ca「bon in our world ’
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丁he key components of organic compou 门ds
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9 .1 What are isomers?
88
55
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Structural isomers
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Stereoisomers
59
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9.2 Structural isomers
5666
9002
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Distinguish ing structural isomers
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Generating st「uctural isomers: the shape of the carbon framework
Generating structural isomers: the positioni 门g of functio 门al groups
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Structural isomerism: un i fyi 门g chem ical famil ies
64
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9.3 Cis-trans isomers
67
40
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Cis-trans isomerism in molecules with a double bond
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Cis-trans isomerism in cyclic structures
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71
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9.4 Enantiomers and chirality
370
778
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Chirality
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How do we distinguish one e门antiomer from its mirror image?
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Chiral ity in biological systems
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81
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9.5 The chemistry of isomers
The biological chemistry of enantiomers 284
The impact of chiral ity on medicinal chem istrγ285
14.6 Gibbs free energy: the driving force of chemical reactions 501
The Gibbs free energy of spontaneous reactions 504
Gibbs f「ee energy and ce川 metabolism 507
15.2 Forward and back reactions: where is the balance struck? 522
The equ ilibrium co 门stant 523
The equ ilibrium co 门stant using partial pressures 525
The magnitude of equi librium constants 527
The dependence of equi l ib 「ium constants on temperature and concentration 530
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16.1 The rate of reaction
66
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What is the rate of a reaction 7
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The dependence of reaction rate o门 concentratio 门
Rd 69
16.2 The collision theory of reaction rates
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Increasing substrate co 门centration: the limitation of the enzyme兰 active site 588
Determining the values of KM and νmax 591
17.2 The strength of acids and bases: to what extent does the
dissociation reaction occur? 614
Juggling hydroge 门 ions: the tug- o乎war between conjugate acid- base pairs 616
The acid dissociation constant: to what e×tent does a门 acid dissociate? 617
The base dissociation co门stant 619
pKaand pKb 620
26
77
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Electrophoresis
Centrifugation
80
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18.3 Measuring mass: mass spectromet叩
03
88
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How does mass spectrometry work?
丁he mass spectrum: the outcome of mass spectrometry
80
89
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18.4 Coupling separation and identification
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18.5 Building up the picture: spectroscopic techniques
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Spectroscopy and electromagnetic radiation
What are we measuring during spectroscopy?
Using spectroscopy to characterize chem ical compounds
Bibliography 717
Answers to self-check questions 720
Index 728
cKnow1e e 门丁 e nts
We are grateful for the input from a number of colleagues during the preparation of
this third edition, most notably colleagues at Oxford Brookes University, Dr Caroline
Gri 忏iths , Dr Peter Grebenik, Dr Alwyn Griffiths, and Professor David Fell, who all con -
tributed with helpful discussion and scrutiny of parts of the text. We also thank those
reviewers who provided critical feedback on the second edition, which shaped many
of the changes we have made for this third edition:
It goes without saying that any mistakes or errors that remain are solely our
responsibility.
We also received valuable help with the preparation of some artwork for the book.
We thank Dr James Keel 凹, U niversity of Cambridge, for preparing the orbital images
that appear in Chapters 2, 3, and 8; and to Professor Peter Atkins, University of Oxford,
for providing the electrostatic surface plots that appear in Chapters 3 and 4.
Chemical structures were prepared using a combination of ChemDraw Standard
12.0 and Chem3D Ultra 9.0. Biological structures were generated using the open -
source software PyMOL (Delano, W. L. The PyMOL Molecular Graphics System (2002)
on the World Wide Web at http://www.pymol.org/ ), using data from the Protein
Data Bank (http://www.rcsb.org/ pbd/ ).
We'd also like to gratefully acknowledge those individuals at Oxford University Press
who have steered the third edition through to completion. We thank Sarah Lodge for
her valuable support, and our production editor, Suzy Armitage, for her careful atten -
tion throughout the production process. We also thank Julian Thomas and Heather
Addison, our copy-editor and proofreader respectively, from whose eagle eyes the
book has doubtless benefited greatly.
Finally, we give grateful thanks to our families, friends, and colleagues who have
continued to offer encouragement and support, despite the neglect they have expe-
rienced in the face of the self-imposed solitary confinement with a laptop that book-
writing demands.
JWC, Oxford
TKB Oxford
June2013
e1co 门丁 e to emist or tne
. .
1osc1ences
We ’ve written this book to try to make learning the essentials of chemistry as easy
and enjoyable as possible. You might be asking yourse lf 'Why should I bother with
chem istry at all?' We've devoted Chapter 1 to answering this question; take a look at
that chapter before you start reading the rest of the book.
1mponant part of science 1s being able to share ideas and bon, twelve atoms of hydrogen. and s, be able to understand chemistry. 丁hese skil ls, which apply
_
icate complicated information ma transparent, rel ia- its molecular formula ,s C6H 吃06. Whe
formula , we follow two other convent10, to topics covered throughout the book, are presented in
CHEMIC A飞仙e
\and 咀us创 toe
……
,ee inSecti。n 2.1 I飞ow chemical symbols are used
,dent,ty of the ch I el Asim, • We list the composite elements ,
rather than according to the numbe the Chemical Toolkits. We include five Chemical Toolkits in
1s ,s called the cl、emical f。rmula. }
ment that a目 present. So. for exam
nic compound accurately we need to iden- rather than C606H,2.
this edition:
• If the molecule contains a single
也 x.'9 :o c.. you master key numerical and data-handling skills. Look
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a 沃 b 辛 c..
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b3- out for the QR code images in the text, scan the code
A fU A with your smartphone, and go straight to the video that
relates to the topic you ’re studying. Alternatively, you'll find
We i ζom e to Chemist印 for the Biosciences XXI
our videos o n Yo uTube· fo ll ow the link from our O nl ine The chemical bond: bridging the
Resource Ce ntre. W efi ~cf'sut more 如UI the Just as \Ve use glue to holdcv,o objectst·
differ!点ways in which to one another tohelpthem associate in
chemicalbonds form later in that holdsatoms together.Justas\Ve h
the chapter. different types of rnaterial, so bondst1
Yo u can fi nd th e Online Resource Centre at different ,vays.Butwhatgives riseto th
Valenceelectrons holdthe key to c
http://www.oxfordtextboo ks.co.u k/orc/ andredistribution of valenceelectrons
act in astableway-to 'bondtoone an ’
crowe3e/ We fi nd飞}) Ut m to drive chemicalbonding.Figure3.1 sh
diffe rirl't ways i occupythevolurneoftheatorn furth四
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chem ical bon requisite forbondingto occur. You can’i
coming intocontact; similarly, abond;
atomsaren tsufficiently close toone an
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Margin comments Anatornsprotonsandneutrons, ,vit
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tionofcompoundsand arentinvolved ’
Yo u'l l see two types of comment in the margi n as yo u read dothecoreelectrons(which occupysh
thro ugh the book.
Maths tools
Many students fi nd th e use of mathematics in bio logy to be
hugely intimidating. Howeve r, mathematical and nu meri -
cal too ls are amongst some of the most useful too ls at the
bio logist's d isposal - he lpi ng us, for example, to analyse MATHS TOOL 1 Rearranging equations
and make sense of data. In fac t - and desp ite fi rst impres- an equation, we typically ,.vant to get an
we 陀arrange Solution
sions - maths can actually help to simplify the biological term (the variable we’re to calculate) by itself
Lrγ1ng
of the equation, and any known terms (the vari- 专 x Jf
wo rl d, by helping us to mode l and describe processes and dv know the value of) on the other side of the
MATHS TOO、 ,
日
BOX2.2 of plants:
Thew。rid ah。由ed ofdiscriminati。n Boxes
We m1gh1 of a
1hink 出3i ISOI。pes sin田e e阳ne时 are 回回叩 slowly than ’ico,w11h,n the chloroplasts; nco,gets t。wt回re
1hat 1hey arev,rtually
SI 阳lar Does adiffer-
,nd剧nguishable IIos needed m。requ,ckl机 and s。 is prefcren11ally metabolized Each chapter features a number of boxes that supp le -
sognificance? To plants, at
旦nee of 。ne neutron 陪ally 臼叫 any ofplam discriminate agamst 1ico,to
D,ffere,it 可pes d,ff,田-
to be
,ns•、咀" appears 'ye正 eMdegre目。 h。W趴剧 Plants can bed,v,ded ,nto <hree differem ment the main text. In some cases, these boxes pro -
te the,r own food supph白 byphot,。syn由血’去 group,,wh,ch a附 dosongu曲时 by 由e 叩peof pho<o叩n由es1s
from the
,carb。n d,。x,de and
atm。sphere, thatoccurs w11h,n 由自n c,. C... and CAM Resea优h hasfomd
the sugar glucose Thos pro-
itogene咀te that c,plants d,scrim,nate against to agreater degree
' ℃07
vide a little more detail about a concept being covered
organelles
,ropl苗盹 specialized wt由m than c. plants, and 白马 pl朋ts abs。rb less "CO, than C,
BOX 2.2 ,owered by absorbed by the ene咆y plants Thos d,他町、cein 1飞 upta陆can tel interesting
uss。me
things.For example,sucrose (table sugar) comes from either which isn ’t central to your grasping the subject matter,
,ox,de (CO,)contains two ,soto阳sof sugar beet (a C, sugai cane {a C,plant). If
plant)。r a 臼mple
9% "Cand
l咱p。ruo时93 11 伊一飞(It of sucro臼 containsarelauvely amount ol "Cthen we
h唱h
but wh ich you might find interesting. Most often, how-
0.000000000 1%)
n,onof 飞 -JυSt can d时υce 仙at ucame from sugar cane and not beet sυgar
e mie:ht t hiL'阳p:~nts d,scnm川…?州飞and (because C,plants abso巾 13( (as 13CO边 toa g陪ater deg附e
- ,ome elements can exhibit different valenci肘, and therefore contribute to Self-c heck qu estions
different numbers of covalent bonds.
•a ge ref臼-ence:
O nli ne q u izzi ng
ge 陀
Key points or cwo-lerter chemical symbols that act as al>l:>reviattons for their full names.
Similarly, each element has two numbers associated with it which enable us to
iclemify at a glance the number of protons, eleccrons and neutrons it contams -
Key points appear throughout many chapters, and state that 1s, its atomic composition. These two numbers are che atomic number and
mass number.
the mai n take-home messages of the sections in which • Theatom
The atontic number (s。metimes called the proton n umber) cells us the mun -
ber of protons within the atom. By implication, this number also indicates the
number of electrons in the atom (Remember for an atom to bea neutral particle
they appear. If yo u don’t quite grasp the key points, then electrons i ic must conta111 exact!}’ the same number of protons and electrons.)
The mass number indicates the total number of prc)tons and neutrons that the
atom conrains. To de阻rmine the number of neutrons 111 an atom, we merely sub-
try re-readi ng the section. • The mαSS tract the atomic number (number of protons) from the mass number (number of
protons+ neutrons)
neutrons
Checklists of key concepts • Thea 阳m,c number is equal to both the number of protons and the number of
electrons in a neutral atom of a giνen element.
• The mass number ind,cates the number of protons plus the number of
Each chapter ends with a checklist of key concepts, which neutrons that an atom of a giν·en element contains.
The chemical elements · Elements 。n the left of the penod,c 旧blehave 陪lauvely
Any feed back? · 川I mat回riscomp。坦d of a range of subs山ances called the
l。w 1on,zau。n ene喃自, and 陀ad1ly form posltl峭沪
charged ions
~ elements
· Elements on then价I of the periodic table have relatively
:(II element has a name a,、d ashor{hand
If you have any feedback on the book - did you fi nd any hrgh ronizatr刷刷饨’目, and are very unlikely to forni
positively-cha咆ed ions
叩lays all
the known chem,cal
Chemical princip les pe rvade much of t he life sciences. Indeed, a bio logica l sci-
entist can on ly effectively probe the many questions su rrounding bio logical sys-
tems th at remain unanswered if they use all the too ls at their disposal. Chem ical
tools are among the most powerfu l available to t he biological scientist; it fo l-
lows that chemica l concepts shou ld form a cent ral part of any biosciences degree
programme.
This book fi ll s th e gap betwee n texts for honours chemistry students (or ’chem is-
try majors') and th e huge range of US-o riginated freshman 'general chemistry' texts.
It is princi pal ly intended for those students wi th no more th an a GCSE in science,
and so assumes ve ry littl e in the way of prior knowledge. For those students who
have stu died chemistry beyond GCSE, however, we hope that it wil l act as a good
refres her, and wi ll fulfil an important goal of showing how chemistry is an integral
part of the stu dy of biology - someth ing perhaps not readi ly apparent from school-
level studies.
It may be that your students need to know chemistry in somewhat more depth
than that offered by this book. In essence, what we have written here is intended
as a 'spri ngboard' into the many excellent undergraduate chem istry texts that are
already avai lable. As such, it o忏ers a bridge to undergraduate-level stu dy, giving an
xxiv l Welcome to Chemistry for the Biosciences
introduction to those essential chemical concepts that life sciences students typically
need to know, with the intention that it will give students the confidence and motiva-
tion to progress to the ’mainstream' chemistry texts if they need to know more.
The book is written in a deliberately conversational style. Its focus is on getting stu-
dents to grasp the essential concepts, not on exhaustive coverage of the field (which
we believe, at this level, can only really lead to rote learning of facts). We cover some
relatively challenging concepts (for example, the notion of sigma and pi orbitals) but
do so in a qualitative way - in the case of sigma and pi orbitals, merely using them to
help provide a conceptual understanding of why molecules have the shape that they
do. Throughout the book, we are writing for the biosciences student, not the chem -
istry lecturer: we want this book to be relevant to biosciences students, so we have
shaped our presentation in a way that we hope will make them think 'Ah, so chemistry
is relevant to me after all, and I cα门 grasp what's going on'.
As is common with any book of this type, we faced a fine balance between sim -
plifying material enough for students to grasp the concepts readily, and simplifying
to the point of inaccuracy. We hope that, on the whole, we’ve got the balance right.
However, writing a book is an ongoing process of refinement; we would be glad to
know where you think we didn ’t get things right, so we can refine them in the future.
You can send us your feedback via the book's Online Resource Centre at
http://www.oxfordtextbooks.eo.uk/orc/crowe3e/.
We have used the third edition to enhance the text's coverage in a number of ways,
both in terms of content covered, and learning support o忏ered. Alongside numerous
m inor changes throughout each chapter of the text, the primary revisions include the
following.
Content
Touch Method. This method consists of dipping a small glass rod drawn to a needle-
like end to the depth of 1 mm. in the compound and then quickly touching the skin. The
method is qualitative only.
Use of Solutions. Alcohol, kerosene, olive oil, carbon tetrachloride and other solvents
may be used for the purpose of determining the lowest effective concentration of a
substance, and for the determination of the relative skin irritant efficiencies of various
compounds. Since the skin irritants were scarcely ever used in this form in the field, that
is, in solution, the method is not as satisfactory as the vapor method.
CHAPTER XXII
CHEMICAL WARFARE IN RELATION TO
STRATEGY AND TACTICS[43]