An ntodetto

wIs N A have seen the emegene of romatbalilu new tur mbwjws that ta1n yy
f nen uga n he tueatmet of dineane, alles the Heete makeup f plants and
Amals,and maduve harterla in hel clean up tox wasteus, ieyes in the histn y
the wnlt have buvlog al mganinnn leen o valualde t is as n d t that
w ght and aolt What han hapened to make thia evluton prvssihyjwt om
ni)
a t t t ou peisonal livesi What might it do to ouI soety
The noar utue holds the prompect of wondrous new medical diagyu8tix
pro
durs, suth that people can be dlagnoned as having cances or Huntingnts diwaw

Mafical di4gnsis can even be pertormed on undividual human eys that asr serti

ad n v r , or outsiule the
body. Fertilized eggs that do o t cary such dederts ca
then be mplanted in the womb to develop into fetuses. Crops will be engjneered
thet
quire less tertilizer or pesticide. Previously untreatable diseases will yield to new
pnducts and new procedures, sometimes through replacement or repair of dele
tie genetic material. ln short, the biological world is full of what are now extremely
valuable commodities, from naturally occurring products with medicinal properties
found in certain plants to oil-degrading bacteria that can be used to clean up tozic
wastes to pieces of genetic material that might be used to cure disease or treat obesity
But the development of such products and practices is not without potential
harm. Should individuals, even fetuses and eggs, be diagnosed and deemed dete
tive Who should determine this? Should genetic material be altered in individuals?
What will be the environmental effects of spreading genetically altered crops or ani-
mals As with any newly developing technology, biotechnology has both positive
and negative aspects. Would we choose, in retrospect, to avoid developing the atomic
bomb and nuclear technology? Is it possible to choose whether or not new technolo-
gies are developed and applied? Would the myriad developments that arose from nu-
clear technology, particularly medical advances, outweigh the negative aspects? Who
makes these decisions, and how? What is an acceptable risk, and how is the nsk of
an unknown technology estimated?

1
 IuNGN

HAPTERI 4N INTND ON TOININ

Hte lppy, inn a t

ot e
partaulai npu
These questions ane
l e l h n d well bent aud
botechnology developnents
involve mn WI
some b u e h u p t . sl0l ey
because some ot the more dine comequewes of
to ink abou. the
wwuld be long lastng This is au issur
tat a vllen ltfu ull
dld othetn, tlut ihe lug tesm ellets on
herent risks topopulations, both human
environment are otlen tar Ieoved nom our eveiyla exejle'j(e, Maybe it maliau
sense, then, to consider the various pers0nal tiki we alieauly eulue anl are famt
ar with and tuy to build a moe enpaus(ve vlew ol k AähenHel rom thia Vantdu
lage
point. At the conclusion of this chapter, we will retn lo the lople of rlsk and teclh

nological development.
Technology is the application of seientific kuowledgr, nkilla, nalelals, lahor,
and wealth tor a practical purpose. The tremendoua aulvaneen in biologlcal know
edge have allowed the extensive utilization ot living thinga an tools and resourcea
Biotechnology. then, is the application of biological principles, organlsms, and prod
ucts to practical purposes. As such, biotechnology is as old as civilization. Humans
have been making bread, wine, and eheese for centuries, as well as breeding denir
able plants and animals. These processes all use living things or materlals from
liv.
ing things. But biotechnology is also a brand new sclence, since many of its most
powerful tools and techniques have been developed only within the past several
decades. Many of these developments have occurred as a result of
different sci
ences-biology, chemistry, physics, and others-coming together in order to
particular problem. solve a
One of the goals of this book is to
provide a useful understanding of biotechnol
ogy and its underlying principles. Another
cussion of issues that you as individuals
goal is to apply this knowledge to the dis
and we as a society face as a result of
new technology. To the
help attain these goals, each chapter interweaves
us
with a wide variety of social,
political, princtples
issues that involve the science. philosophical, legal, economic, and religious
The end result should be not
entific facts but an awareness of the just knowledge of scl
inevitable result of using scientific
and an ability to make
informed decisions. Many knowledge
and its impact, remain
unanswered. It is these questions, about both the sclence
intriguing. questions
that we hope you find most
Since biotechnology involves the manipulation of
tant that you
develop a firm living things, it is very impor
chapter highlights a numberunderstanding of certain basic
of topics related to principles of life. This first
material may be review, it how living
how organisms function. should provide you with a framework
things work. While sone
for understandng

THE CELLULAR BASIS OF LIFE

Such
to
a
bewildering variety of life is found on
imagine that all the earth
organisms actually share many that t is sometimes
all
iving organisms
must share some common features. diticu"
nonliving things, such as rocks or characteristics that make them different
water
Fundamen
characteristics that all living or tennis
balls. We would like to no
organisms have and ideny
nonliving things do not.
 ORCANIZATION OF CELLS 3

Living things
have the ability to reproduce
vang things have the ability to extract energy from the environment.

ENactly how organisms accomplish these feats will be the focus of future chap-
S Sut both oi these characteristics point toward fundamental similarities in living
nings Do these twO properties result in any other common features, say, 50me or
anizatonal principle that all living things adhere to that helps both of these things
happen?
ne second properry. the extraction of energy from the environment, actually de
termines a great del about how life must be organized. Energy provides the means
Ot accomplishing work. which is, after all, what living things need to do to stay alive.
In order to extract energr irom materials in the environment, the organism must
sOmehow separate itseli irom the environment. This allows the accumulation of the
energy necessary to periorm useful work. It is easy to see how large animals like hu-
mans separare themselves: we have skin that covers our body. Howeve, we must
look deaper to t and the organizational impact of this necessary separation, ifor
even the most minute organism must be separated from its environment in order to
maintain the energvy differences that allow useful work to be done.
Al living things utilize the same basic organizational principle of being con-
structed from smaller units. Each unit of life." the material that serves as the fun-
damental basis for living things. is an entity unto itself. We call these basic living
enities cells. Cells are the smallest units of life. In their simnplest form, they consist
of an interior called the cytoplasm surrounded by a barrier called a cell membrane.
Inside the cell occur all the chemical reactions that serve to extract energy from the
environment. as well as al the reacions that make organisms grOW, move. repro-
duce, and do everything else that they must do. Since much of biotech ogy deals

with what happens inside cells. we need to establish a ffrm understanding of the
structural organization of cells

ORGANIZATION OF CELLS
cells
There are many different kinds of organisms made of many difierent types of
there are really only rwo types of cells found
bur in terms of basic cellular sTucTure
prokaryvtic (Figure I.1) andeukaryotic (Figure 12). The only organisms
n narure:
cells are the bactenia. single-celled organisms found in vir
hat consist of prokaryoic
organisms, even other single-celled or-
rually every environment
on earth. AL otner

r e Eukaryouc. The primary difference berween

ganisms such veasts and agae.
as
how the ntenor oi the cell is organized
the rwo cell types is in
suTOunded by a membrane. This serves several purposes,
Each vpe oi cell is
barmEr berwee the inside and the outside. We
which is to act as a selecave
one of barmer Prokaryoic cells
the membrane serves so nicely as a
wllsee shortly why
tne cytopiasm Eukaryoic cells. on the other
have only internal compartment.
one
EaCn compartment is surrounded bv its
internal comparmenS
hand, have manv SOme of which are indicated in

membrane,and eacn n s Specine uposes.

DWn
 THIN(s
CHAPTERI AN INTRODUCTION TO LIVIN

> Fimbriae

Ribosomes

Cell wall

Cell
membrane

Nucleoid

(a) Flagella (b)

0.5 um
Figure II A typical
prokaryotic cell. (a) Most prokaryotic cells
rounded by a cell wall. There have a cell membrane sur-
are no internal
compartments, and the DNA occupies a region of
the cytoplasm called the nucleoid.
Ribosomes are responsible for
vide movement. Fimbriae protein synthesis. Flagella pro-
help cells attach to each other or to surfaces.
prokaryotic cel. (b) A photograph of a

Figure 1.2. The

compartment we will mention the most in this
the compartment enclosed book is the nucleus,
mation used by the cell as it
by the nuclear membrane that
stores the
While the existence of
goes about its
business. biological infor
internal compartments is
karyotic cells, there are other differences the most
as well. Bear telling feature of eu-
ferences are in mind that most
generalizations; there are exceptions. For
your blood are eukaryotic cells, but
of these dif
they have no internal example, red blood cells in
development of these cells, the internal compartments. During the
form without compartments. membranes are dissolved to yield the
Eukaryotic cells are larger than hna
such as many prokaryotic cells, often ten times the diameter.
Some eukaryotic cells,
out using a eggs, are so large that
microscope-although
grow more slowly and such cells are not
common.
you can see them
wit
reproduce
surprising since they are usually so less frequently Eukaryotic
than prokaryotic
cells als0
large. cells. This is not
produce fewer than twenty minutes
in Some
prokaryotic cells
given ideal conditions, can grow and re
whereas the average
 ORCANIZATION OF CELLS

DT
take w e n - 0
numan
cel even under the best oi circumssances might
reproduce
Eukaryoic cells often speciahzed. meaning they have deveTI
are
sgec
of cels such s
pabilitieS. This is certainly true in organisms made many
functions withan our bodieS. Such as T s
pecialized cells serve thousands of
in the red biod e s
SIon ot electical impulses bv nerves and transport of oxvgen
un order to de
Tnis implies that a vanety of cells must be property organized
Uur v c
Tor all the functions necessary to an organism. and thiss indeed the case
es are organized into functional units called tissues Liver cells. tor exmg
specialized to periorm all the functions of the iver. These functions diter d n
requn s
cally trom those of a sin cell Specialized cells often have speciahzed
cells. on he ocher
ecialized
including the need to have particular neighbors. No

Miochondron

S
Fagellu

Nucea
emoe NUCLES
Chrometn

Roug
enounaSme

Rcsomes

Lvsosome

Cel

Smoh enooiasmic
reticulum

N the maor ntemai compartens

Figure I.2 Eukaryoic cell. oica eukanotc cel. showinS Ome n

T,oca anma c e l e DNA S OC

w*ir he nucieus Mtaxnomuannes AP
Piatand anmal cels (a) anc e c c e maremas I e andondiasmc e t e m s u t a
he enerz curency for the cel Lysosomes degrae
cels
tenspor SYStem for moiecues wthn
 CHAPTEM AN INTROD 1ON ) LIVI NG T95NE g

Atr vr
Central
vacuole

Nuclear
membrane
NUCLEUS
Chromatin

Rough Chloropla
endoplasmic
reticulum

Smooth
endoplasmic
reticulum

Ribosomes
Cell wall
(b)
Cell membrane

Figure I.2 (b) A typical plant cell. Plant cells

vacuoles, large fluid-filled compartments; and generally have a rigid cell wall and contain at least two
compartments:
chloroplasts, involved in light-energy capture.

hand, are more self-sufficient and can often exist alone.

There are many other dif-
ferences as well; we will discuss
many of them at more appropriate
the book. in points

BIOMOLECULES
Molecules arechemical compounds that under normal
ken into smaller units while circumstances cannot be bro-
ent molecules make
maintaining their original characteristics.
Many differ
up our cells, from lipids that make
which stores genetic information; from up cell membranes to DNA,
stream and elicit special
hormones that travel through the blood-
responses to chlorophyll, which absorbs
Studying these molecules, their structures, and how light in plants.
biochemistry. Fortunately, it is possible to classify mostthey function is the domain ot
of the molecules used in
logical systems into only a few categories,
making an appreciation of their structurebio
and function much easier.
SIOMOiECULES

e we discuss each tvie of biomolecule in more detail. it s wOrth noting that

an t them shane a common feature Thev are polymers Most of vOu have un

ai heard of polvmers. probably in coniunction with plastic maternals. What

Omer? lt is simpl a chain of small molecules. generally called monommeTs.
CemicalN lnked to torm a larger one. A metal chain is a sort of polymer ot individ
S - t h e chain is the hnal product. but it is made of links ioined so that they
hot nomallh conme apart. The links are the building blocks that make up the hina
n t h e metal chain analogv is especially good for biological polymers, because
e nss in a chain
almost alwavs appear end to end, in a linear fashion. Each link is
Onnected to onlv two others, head to tail. Biological polymers are usually made ot
building blocks attached end to end (Figure 1.3).
You can see how this linked structure makes it easy to manufacture metal chains.
Wth a
large supply of the individual building blocks (the links), on hand, any de-
Sared chain, of any
length or thickness, can be quickly made by using the same ma-
chinerv. The
machinery only has to be designed to accept different building blocks
in order to
become a "universal" maker of virtually any chain
that manyv biomolecules are
imaginable. The fact
linear polymers makes sense. If the cell can maintain a
steady supply of the appropriate building blocks, then one kind of cellular machine
might be able to construct many different molecules depending on the instructions
fed to the machine.

Lipids
Consider an oil with which you are familiar, such as
if you add some to water? The oil, which
cooking oil. What happens
may originally disperse into tiny drop-
lets, eventually comes together in larger droplets, or pools, generally on the surface of
the water. Why? Oil and water don't
mix. The chemical way of describing this is that
the oil molecules are hydrophobic, or
water-hating. Fats and oils, known as lipids,

Figure .3 Biological poly

Unlinked mers. Polymers are assembled
monomer from individual building blocks or
monomers.

Short polymer Enzyme

(catalyst)

Longer polymer
 8 CHAPTER 1 AN
INTRODUCTION TO LIVING THINGS

preter not to be in contact with water. Their

surrounded by other lipid molecules-or even
chemistry is mnore "satistied" it they are
by air-rather than by water. That is
why all of the small droplets coalesce into a
the contact between the oil and the water.
large one on the suriace. This minimizes
Such hydrophobic
forces are a
portant part of the chemistry of living
very im
things, in large part because they are respon-
sible for the formation of membranes.
Theparticular lipids involved in cell membrane formation actually have two
chemicaly distinct sides, one that is hydrophobic and another that is not and preferS
to be in water. The latter is referred to as
hydrophilic (Figure 1.4a). Imagine adding
lipid molecules of this sort onto a water surface. Initially, a lip1d monolayer forms on
the water'ssurface, with the hydrophilic ends sticking in the water and the hy-
drophobic ends poking into the air. Adding more lipid molecules could cause them
to congregate around one another, forming a micelle (Figure 1.4b). As more and
more lipid molecules are added, they eventually will form a spherical structure
nown as a bilayered vesicle. In this way, the hydrophobic parts of the lipid mole
cules are most satisfied, since they are in contact with other hydrophobic parts of
lipids and not water. The hydrophilic parts of the lipid molecules are also satisfied,
since they are in contact with water. You can see that a vesicle is essentially a sphere
made of two layers of lipids (Figure 1.4b). This bilayering of lipid molecules in sheet
like form is the basic structure of cell membranes.
Imagine such a membrane surrounding a cell. One of the important properti
of the membrane is to act as a selective or differential barrier. In order for cells
carry on their business, the internal contents of the cell must be separated from the
external environment. Yet the external environment is the source of water, nutri
cells somehow, whie waste
ents, and other raw materials that must be able to enter
of a lipid
products generated inside cells must be able to leave. The bilayer structure

I4 Lipids and their interactions with

Figure
water. (a) Representation of lipids involved in the
membranes. The head groups Surface of liquid
formation of biological
with water. The
arehydrophilic; they prefer contact
be in contact with
hydrophobic tails prefer not to
water. The basis of membrane formation in
(b) form
water. As lipids are added to water, they initially
surface of the water. As more
a monolayer on the

lipids are added, micelles form, allowing hydrophobic

tails to interact with one another and not the water. Aicelle
As more lipids are added, bilayered vesicles eventually
internal Hydrophilic head
form, containing two layers of lipids and an
compartment of water. The hydrophobically
con-

the basic structure of bio-

nected lipid bilayers form
logical membranes.

Hydrophobic tails

(hlStructuresformed in water
BIOMOLECULES

membrane establishes a barrier that prevents the movement of most, but not all, sub-
stances. Such a semipermeable membrane is a vital part of the cell.
t iseasy to see how such a membrane might serve as a semipermeable barrier.
imagine some toxic molecules traveling through the blood. In order for these mole
cules exert their toxicity, they must enter a cell and disrupt some aspect of that
cell's function. But the toxic molecules are hydrophilic; they much prefer to be in a
water-based environment such as blood. How easy is it for these molecules to gain
entrance to a cellular cytoplasm by crossing a cell membrane? In order to cross, they
must move through what is essentially a water-free zone-the inside of the bilayer,
wncn is hydrophobic. This simply cannot happen. Very few hydrophilic molecules
can freely cross membranes, and the few that can (such as water and carbon diox
ide) are very smal. The cell membrane, simply by having a structure based on lipids
that are hydrophilic at one end and hydrophobic at the other, can serve as a protec-
tive device, determining which molecules can freely enter cells.
There are many hydrophobic molecules that are not repelled by the lipid bilayer
and can freely cross a cell membrane. An example is estrogen, one of many hy
rophobic hormones secreted into the bloodstream. Hormones are usually produced
in response to a particular need, travel through the circulatory system to particular
target cells, and then cross the cell membrane, causing changes in the cell's activity.
If membranes are semipermeable and only a few hydrophilic molecules can en-
ter or exit cells freely, how do all the necessary nutrients get into cells? Most of the
nutrients the cell needs are very hydrophilic. There must be a way of getting these
molecules into the cel1. This leads us to the next group of biomolecules, the proteins.

Proteins
Proteins are the most diverse class of biological polymers. They can serve as trans-
porters in a variety of ways, moving molecules such as oxygen and cholesterol
through the blood, or sugar and salt across a cell membrane. They can also function
as structural elements (hair is made of protein, as is the lens of the eye). But one of
the primary functions of proteins is to perform and control the innumerable chemi-
cal reactions that occur within cells as materials are processed and made into vari-
ous products. It is in this role that we will become most familiar with proteins.
How does one group of molecules perform such a diverse set of functions? The
answer lies in the variety of available building blocks. The metal chains we used as
examples of "polymers" are always constructed from a single type of building block-
a link of a particular size, made of a particular metal, and having a certain color and
strength-to suit the intended application. In contrast, proteins can be made from
twenty different building blocks that can be attached in any order. These building
blocks (monomers), called amino acids, provide the raw material for all protein pro
duction in all organisms.
Each of the twenty amino acids has several chemical groups that we will learn
more about later. Some of these groups are involved in linking amino acids to each
other in the protein chain; each amino acid has two ends that can join to other amino
acids. Unlike the links of a metallic chain, each amino acid also has a particular
chemical group that lends the amino acid its identity. No matter what order the amino
 INH 4N N
WAPAk

e I.S Kakling a chan of amno actts. (a) Ageonetri iepresentation of an amino acid chain
a N et a s e h a n a h m alg n p that extenh hom the indivihual anino acids that
Aee te a han avvabe wntera tivs between ndivitual anvino acid sicde chains dictate howthe
w*
A Nm qe htera tins tis type determne thhe structure of individual proteins

i t s aae comnovtat in, the individual chemical groups of the amino acids, called side
a t s . are und extending ton the sides of the
protein chain (Figure 1.5a). All of
these cheunial grvups can interact with nearby
neighbors
or with those farther
awaythe prten chain can be quite tlexible
(Figure 1.5b). For example, a chemical
Tup tht possesses a negative charge might interact with a
nearby group having
a sitne
charye. Since negative and positive charges attract each other, the two
groups will be pullend eloser together. Or hydrophobic side chains can be
forced to-
ether Thus, unike u r metal lnks, the individual building blocks of the
chain are not inert. Each retains a chemieal protein
identity and can perform a chemical func
tion even within the
protein chain. It is the collection of amino acid chemical
and the sequence in which they are groups
three
arranged that ultimately gives a protein its final
dimensional shape and its particular function.
How ditterent proteins can potentially be
many
ent amino acids: Consider an
formed from the twenty differ-
average-size
acids linked into one chain. Since each of the
protein, which might consist of 300 amino
300 positions of this chain could be
illed with any one oft the twenty amino
acids, there are 20 00
an extremely
large number! Clearly, the number of possible combinations,
ture, however, uses only a limited possible proteins is very large. Na-
subset of all
The sequence of amino acids possible protein chains.
determines the relative
ual chemical groups of each
building block, which in large positioning of the individ
groups interact with each other and thus the final part determines whicn
ecule. instance, consider a hypothetical transport
For structure and function of the mo
in the membrane but in
contact with both the protein that is found embedde
ments. Molecules outside the cell external and the internal environ
that are being
groups present on the outside t the protein. The brought in will react to the chemica
brane must contain hydrophobic part of the protein within the
regions that can exist within men
the lipid bilayer. 1n
 11
CHEMICAL FORCESs IMPORTANT TO BlOMOLECULES

must be hydrophilic and

con-
region of the protein exposed on the inside of the cell
tain the proper chemical groups for internal
interactions.
Ihus, of primary importance to understanding the nature of a particular protein
what function
Knowing its amino acid sequence, sincethis sequence determines
1s
the proten will perform in the cell. Some of the fundamental biological questions
we

Will deal with in future chapters are how the information for the
amino acid se-

quences of proteins is stored in a usable fashion in cells and how

this information is
used by the cell to construct actual proteins.

Nucleic Acids
Nucleic acids are primarily responsible for the storage and transmission of biologi-
cal information. Nucleic acids, like proteins, are linear polymers, built from building
blocks called nucleotides. Four different primary nucleotides are found in each of the
two kinds of nucleic acid molecules, DNA and RNA. Nucleotides are successively
linked to each other in a particular manner, yielding a final "chain" of nucleotides
Like the amino acids of proteins, each nucleotide possesses a unique chemical
8roup-a nitrogenous base-that extends from the nucleotide chain. The particular
structures assumed by nucleic acid molecules, partieularly DNA, are the subject of
more elaborate description in the next chapter.

Carbohydrates
Carbohydrates, also known as sugars and starches, comprise a large and diverse
group of molecules that serve several functions. Some carbohydrates are purely
structural elements, such as the cellulose that provides much of the strength and
rigidity of plant tissues. Others serve a role in communication or recognition,
such as
the molecules that determine your ABO blood type. Some carbobydrates are used as
building blocks; the nucleotides described above all contain a carbohydrate compo-
nent. But the most prevalent role of carbohydrates is as a source of energy in cells.
Carbobydrates are the preferred source of energy in most cells. We will have more to
say about the role of carbohydrates in providing energy later in this chapter.

CHEMICAL FORCES IMPORTANT

TO BIOMOLECULES

What holds the various building blocks together in a biomolecule? Exactly what
kinds of chemical forces operate to give a protein or a nucleic acid its final structure
Such forces are key to understanding how cells work-not only do they determine
thestructure and function of individual molecules, but they also govern molecular
interactions. We will start by describing the forces responsible for holding individual
atoms together and work our way up through larger and larger molecules until we
can understand some of what is necessary to maintain the structure of large biomole-
cules and ensure their proper functioning.
Molecules are made of atoms, the smallest chemical entities. Only a handful of
 THINGS
INTRODUCTION TO LIVING
CHAPTER 1 AN

different atoms are important to our understanding biological molecules. Car

of most biological molecula.

bon plays a central role in almost all biological

certain
molecules because of
chem
cal properties it possesses: It can bond
to many different kinds of ms, and
atoms, and
stable under conditions found inside the cell, Ovveese these
bonds are generally quiteand
drogen, nitrogen, sulfur, phosphorous are the other prominent atoms in hia biomol-
ecules. Each atom brings with it particular chemical properties.
Atoms can react with each other in many ways, sometimes forming stable int.
actions called bonds. These bonds take many forms, but three of the mostimportan
nter
in biological systems are the ionic bond, the covalent bond, and the hydrogen bond

lonic Bonds
lonic bonds form between an atom that easily gives up one of its electrons and an-
other atom that readily accepts that electron. One of the atoms becomes positively
charged, and the other becomes negatively charged. Charged atoms are called ions,
A classic example of a solid crystal compound formed by ionic bonds is sodium chlo-
ride (table salt). The sodium and chlorine atoms are present in salt in a one-to-one
ratio: For every sodium atom there is a corresponding chlorine atom. A sodium atom
readily donates an electron to a chlorine atom. However, the structure of sodium
chloride is such that there is no direct connection between each pair of atoms even
though the sodium ion has a positive charge and the chloride ion has a negative
one. Rather, they are arranged in a three-dimensional pattern of alternating sodium
and chloride ions. Every sodium ion is surrounded by chloride ions, and every
chlo
ride ion is surrounded by sodium ions (Figure 1.6). Thus, in the crystal cf sodium
chloride, each positive charge (sodium ion) is surrounded by a "shield" of negative
charges (chloride ions), and each of these negative charges is surrounded by a cor-
responding "shield" of positive charges. Overall, each positive charge is negated, or
balanced by a negative charge, such that overall the sodium chloride crystals have no
net charge.
An interesting thing happens to most ionic compounds when they are put into
water, for example, when table salt is dissolved in water. One of the unique proper
ties of water is that it can form its own "shields" around charges. As a salt crystal1is
placed in water, individual ions begin to come out of the crystal structure. As the ions
move out of the crystal, they become surrounded and shielded
by water molecules
Figure I.6 The crystal structure of sodium
chloride. Within a crystal of sodium chloride-
table salt-each atom of sodium (Na") or chiorine
(C)is surrounded by six of the opposite atoms.
Na
 B1OMOLECULES
CHEMICAL FORCES IMPORTANT TO

Eventually, all
associated with the others.
ions no longer need to be
individual
ne no crystal left.
This is what happens
oI the ions move into the water, and there is
and torms ny
wnen compounds dissolve: Water breaks apart
the normal structure
dration shells around the individual components. consider-
of ionic bonds by
we can begin to get an idea of the relative strength
salt and put them onto a regular table
ing an example. Take a few crystals of table
Ihen put another spoon on top. Using your
thumb, try to crush the crystals
Spoon. will find is that you can take
in the first spoon by grinding down on them. What you
break them into smaller
the relatively uniform salt crystals found in salt shakers and

crystals without much effort. This should not be too

surprising-nothing in the struc
1adie
a particular size.
ture of the sodium chloride crystal suggests a preference for
Salt is packaged and sold as very uniform crystals of useful
size; it would be rather
a 2-foot-by-2-1oot crystal
unwieldy at the table to add salt by chiseling off a bit from
in the middle of the table! The point is this: When you
break a crystal into smaller
or
ones, you are breaking ionic bonds. It doesn't take
much input of energY (a bit
thumb power will easily do it) to break the ionic bond between
sodium and chloride.
Some ionic bonds are stronger than others. The basic point, however, remains true
lonic bonds are relatively weak bonds, especially in water. The fact that salt crystals
notion.
break apart into individual ions when they are put into water supports this
is
Thus, ionic bonds can be characterized (in biological systems, where everything
in water) as relatively weak bonds occurring between atoms that can easily become
charged.

Covalent Bonds
Covalent bonds, on the other hand, can be relatively strong. Covalent bonds Occur
when atoms come together and, instead of completely donating electrons, share
them. In contrast to what happens when atoms form ionic bonds, the electrons in co-
valent bonds are not garnered by one of the participating atoms and lost by the other.
Instead, they are more equally shared, acting as a part of both atoms (Figure 1.7a,
b). Thus, there are no ions, and the result can be a much stronger bond. Depending
on the individual atoms involved, covalent bonds can be difficult to break, requiring8
a significant input of energy. Most compounds formed from covalent bonds do not
ionize in water unless the covalent bonds are very weak. Still, they can dissolve in

Figure 1.7 Covalent bonds. Atoms engaged in covalent bonding

0 0 share electrons. (a) A representation of a covalent bond. The lines repre-
sent pairs of electrons being shared. (b) A more graphical representation
(a) (b) of a covalent bond, showing the electron "cloud sumounding the two
atoms. Note that, since the atoms are identical, the cloud is shared
8 equaly between the two. (c) A representation of a polar covalent bond
c 0 C O (d) In this polar bond, oxgen has a greater affinity for electrons than
does carbon; therefore, it attracts them to a greater extent. This is illus-
trated by the electron cloud being more concentrated around the oxy-
c) (d) gen atomthan around the carbon atom. This unequal distribution of
electrons results in the partial charges indicated by 8" and 8".
 T H I N G S

L I V I N G

TO
INTRODUCTION

C H A P T E R
1 AN
shell
around he enti
the entire moleecu
14
create a
hydration
by
by aa host
host o
ofw
f
Hy
molecues
molecule

molecules
of a
if the
water enveloptments
other interaction
tion. AC
water
complete irom any
molecule

shells are ability to .

t o
dration
shield the
enclosed

covalent
bonds? An atom's attract i o n i ean
ela
eleç
that effectively
ofatoms
form
it will form
covalent o r
nicnbonds,
d
What kinds of
whether
ot the of an
ability of an
Iatom
measure

the shareda good ota

measure
tract
tron provides
electrons in like!lihood
a covalentas
bond,
a or the electronegativitybetween one
express
this
both. Chemists
electronegativities,
that is, hot..
different
atoms with very and ther atom
another atom that rread
are formed by for an
electron
at&Veg
attraction
one of the
substituent
atom that has a great when at least
are formed electronegativitu DPe
Covalent bonds intermediate
up.
and thus has
one an

fers to share the

electron
chlorine are quite different.
raf
gainecting
of sodium and
ample, the
electronegativities of chlorine
and of chlorine to readily gain
the tendency of sodium
to easily lose an electron
forms covalent
t torms
that it
one
bond,
middle, meaning
in the bonde
Carbon has an electronegativity
covalent bonds. For instance, not all cou
almost exclusively.
There are some fine points involving
if a carbon shares an electron with another
lent bonds are the same. For example, in the bond have equal ele.
two atoms participating
carbon, all else being equal the
should therefore be equally shared. On the other
tronegativities, and the electron
with an oxygen atom, the two atoms have
hand, if a carbon atom shares an electron
different electronegativities. Oxygen has a much greater tendency to accept an elec-
tron, so the electron is not equally shared but spends more of its time associated with
the oxygen atom. Thus, a partial negative charge is associated with the oxygen atom.
There must also be an equal and opposite partial positive charge associated with the
carbon atom. Since there is not a complete loss of the electron by the carbon, the re
sult is not an ionic bond, but the bond has a partial ionic character. The bond is said
to be polar (Figure 1.7c, d). It might be compared to a bar magnet, with one end be
ng north and the other south. The bond acts like a bar magnet of charge, with
negative charge at one end, around the oxygen, and some positive charge at the other
some
end, around the carbon.
Even though this bond is not ionic, it will act
ties. In other words, should a
according to its electronic proper
strong negative charge come near the bond, the
atom will be attracted to it, and the carbo
oxygen atom will be repelled. In this way, p0d
bonds can play a significant role in
establishing the shape and function of biolo8ca
molecules. Many of the amino acids, for
while others have side chains that can example,
have side chains with polar bonds,
in participate ionic bonds.

Hydrogen Bonds
Now that we understand polar bonds, we can
so well. Water is see how water molecules
shield char
a
compound made up of covalent
to two
hydrogen atoms. Each of these two bonds-one oxygen atom b nded
has a much stronger tendency is but bonds covalent, the oxygen
atom

to attract
the oxygen atom becomes partially electrons than do the
negatively charged, and the hydrogens DEhal
Thus,
hydrogen atom5.
partially positively charged. The shape of the ome

low V, because of the additional water molecule is

electrons around the something like d
oxygen atom that esseentiall
 CHEMICAL FORCES IMPORTANT TO BIOMOLEcULES 15

Salt crysta

Na

lons in
solution

(a) (b) (c
Figure 1.8 Hydrogen bonding in water. (a) The shape and polarity of a water molecule. Each of the hydro-
gen-oxygen bonds is a polar covalent bond, giving rise to the indicated distribution of charge. (b) Water molecules
hydrogen-bond to each other readily. (¢) When sat crystals are added to water, the polar water molecules surround
each ion, shielding its charge and allowing it to leave the crystal.

force the hydrogen atoms toward each other (Figure 1.8a). The net result of the dis-
tribution of the partial charges over this shape is a molecule with one end partially
negatively charged and one end partially positively charged.
Interactions between two different polar covalent bonds are an incredibly im-
portant part of cellular chemistry. The charges associated with water molecules cause
them to interact with one another. The negatively charged oxygen on one water mol-
ecule will be attracted to positively charged hydrogens on other molecules (Fig
ure 1.8b). Hydrogen bonds are very weak compared to covalent bonds; they actually
consist of an attraction between partially negative oxygen atoms and partially posi
tive hydrogen atoms.
Hydrogen bonding in water results in properties such as surface tension. You
can, if you are careful, fill up a glass of water so that the water bulges over the lip of
the glass but does not spill. What prevents the water from running over the lip? Why
can water spiders scoot across the surface of ponds and rivers and not sink? The an-
swer is surface tension-a consequence of the hydrogen bonding between individual
water molecules.
The polarity of water molecules helps explain how water acts to disrupt ionic
bonds and form hydration shells: The polar nature of the water molecule results in
an organized arrangement being formed around any charged or polar atom or mole
cule that is in water (Figure 1.8c). Just think: All biomolecules inside cells are es-
sentially "dissolved" in water. There must be water interacting with the outside
surfaces of virtually all biomolecules. It is important to remember that a layer of wa-
ter surrounds every biomolecule and that this water needs to be moved out of the way
if two molecules are to interact.
16 CHAPTER I ° AN INTRODUCT1ON TO LIVING THINGS

Figure 1.9 Examples of hydrogen bonds in R

biomolecules. The diferent chemical groups illus
trated occur in all biomolecules: proteins, nucleic
acids, cartbohydrates, and lipids. All biomolecules
con
tain numerous chemical groups that can hydrogen-
bond to water or to other chemical H
groups.

H R

Hydrogen bonding is not limited to water. Whenever a hydrogen atom with a

partial positive charge can be oriented in a line with another atom
tial negative charge, possessing a par.
hydrogen bonds can form. Some other examples of hydrogen
bonds are shown in Figure 1.9. As we will see, even these
very weak hydrogen bonds
are used in nature to maintain structures and
perform functions.

Hydrophobic Forces
It is possible now for us to more precisely understand the nature of what
when lipids are placed into water. Since the
water molecules are so
happens
to have other polar, they like
polar molecules around them. Adding a nonpolar molecule, such as a
lipid, to water makes the water molecules disrupt their normal interactions
to accommodate the in order
hydrophobic molecule. If more and more hydrophobic mole
cules are added, they
eventually find one another and clump together, not because
of much innate attraction between them but
because there is less disruption of the
water if they are
together than if they are separate. This is called the
force, and as we have already seen it drives the formation of hydrophobic
membranes in cells.
Hydrophobic forces are important in biomolecules besides lipids. Recall that
teins are made of many individual amino acid pro-
amino acid chain are numerous building blocks. Extending from the
hydrophobic groups. When in water, these hydro
phobic groups are driven around by water until they find one another and clump to
gether, with the water trying to make them as unintrusive as
often gets folded and crunched as these possible. A protein chain
of the protein. For a great many proteins,
hydrophobic groups assemble in the center
a basic structure is arrived at in which
collectively referred to as globular proteins,
a protein chain
folds back on itself to create
a core
region of hydrophobic amino acid side chains surrounded by a
layer of the
tein chain that contains the more polar and
ionic side chains. This external layerpro
in contact with the water, a situation more 15
since they can then hydrogen-bond.
acceptable to the molecules
involved

THE KEY TO LIFE

Recall that one of the primary activities that
distinguishes living things from nonli
ing things is the ability to extract energy from the surrounding environment. În one
sense, different organisms accomplish this in a
great variety of ways: We eat laig
 17
T H E KEY TO LIFE

into usable pieces.

subsequently broken down (digested)
chunks of food, which are sup-
wherein they are constantly
inhabit the intestines of mammals, simi-
Many bacteria Bacteria in the soil
continues to eat.
as the host
plied with nutrients-as long around them. Plants send
out rOots into
nutrients from right
larly obtain appropriate
along the rest of the plant.
to
nutrients and send them
the soil that can then take up varies greatly in
nature. But
nutrients and raw materials
So the process of gaining inside indi
must end up
nutrients are gathered, they
ultimately. no matter how the cellular organ-
reactions that occur in living
vidual cells. We call the set of chemical reactions, there
of individual metabolic
isms metabolism. Despite the great variety
are some common chemical themes.

Oxidation-Reduction Reactions
materials (nutrients foods)? Cells need
or
How does the cell obtain energy from raw

from growing larger to signaling their neighbors,

energy to do virtually everything,
have evolved.
and very elaborate methods of obtaining this energy homes in the
extraction: how we heat our
Let's begin with an example of energy differ-
materials on which people in
winter. Oil, gas, coal, and wood are all organic
In certain parts of the United
States, people
ent parts of the world depend for fuel.
use it to
wood from our environment and
burn wood to warm their homes. We take
source of the energy?
provide heat energy. But what is the exact
fire is hot, and heat is a form
We know that burning wood or gas releases heat;
heat is given off-but at what expense?
of energy. When we burn a log, a great deal of
and smoke that has gone up the
Afterward, there is no log, only some ashes, soot,
mean in chemical terms? Burning
is a kind of
chimney. What precisely does burning
chemical reaction called oxidation. Chemists tell us that oxidation is the loss of elec-
contains
trons from a material. A burning log
needs air to burn. Why? Because air
such
in the burning process. Large polymers
oxygen, which is the real requirement and
as cellulose, which make up the
bulk of the wood, react chemically with oxygen
are transformed into carbon dioxide and water vapor during burning.
oxidation. Remember what
In the fire, the carbons from the cellulose undergo
a carbon atom is chemically
the chemists say. In the fire, as an example of oxidation,
other formerly bound to the car
attacked by oxygen, which replaces all the two
atoms

bon. The most stable end product consists of oxygens bound to one carbon, or
react anymore with oxygen; it cannot be
carbon dioxide. Carbon dioxide cannot
more of its electrons. Therefore, the carbon
further oxidized, that is, it cannot share
atom is fully oxidized; it has
two of its electrons pulled toward oxygen atoms-a
loss" of electrons.
The oxygen atoms, on the other hand, have been reduced, the opposite of being
atom "gaining" an electron (from the
oxidized. We can visualize this as each oxygen
carbon atom). Whenever there is an oxidation reaction, there must be an accompa-
Before
reduction. burning, the carbon in the wood was reduced but then be-
nying
came fully oxidized, and concurrently
the atmospheric oxygen (O,) started out as
concern ourselves with oxidation and reduc-
fully oxidized but was reduced. Why
tion? Very often, oxidation gives off energy. Oxidizing the carbons in burning wood
gives off heat energy.
 TO LIVING THING
CHAPTER 1 AN INTRODUCTION

stove, we
purposefully
control the
fire analogv.
In a
slowly by restricting
rate the.
Let's continue our wood-
allowedoxygen
it burn very
(closing the damper): if we open
at which the wood burns. We
make
canthe damper, too much oxygen will be sed. will
allowe
So we con
to re
will be released. So
and stifling heat
trol the rate at will
which carbon
burn m o r e quickly.
atoms are oxidized and release heat energy
lerive energy
act, the wood
p r o c e s s to
der
Back to biology: Cells use
in
the s a m e
essence,

fuels. What fuels do

[Link] rom
cells use
carbon-containing
the environment-oxidation of organic food, can use a
M those that need preformed
Most heterotrophic organisms,
six-carbon sugar. glucose. As previously [Link]
ot fuels, including the which is tound in man
Vvanety molecules, as is starch, any
lulose [Link] entirely of glucose
plants, including potatoes. or starch)
and other reduced carbon com.
glucose
S ocells use (from cellulose as heat: for livina
to release energy
as energy sources. Cells
oxidize glucose
pounds is captured by a compound
cells, the remaining energy released
during oxidation or
ATP actsenergy intermediate,
as an energy
caled adenosine triphosphate, or ATP. reactions.
oxidation
released from the
and can transfer energy the rate at which their
Currency, cells must regulate
Just as with our wood-fire example, How do living cells regulate
fuel is burned to capture some of
the released energy.
Carbons are not completelyoxi
oxidation? Cellular oxidations occur
in little steps.
a number of intermediate steps,
are taken through
dized immediately; instead they
oxidized until it becomes fully oxidized, re
in which a reduced carbon is gradually the oxidation
At several steps during
in the formation of carbon dioxide.
sulting being released is partially re-
oxidation reactions occur, the energy
partial
process, as
covered as ATP carbons and two hydro-
Consider a particular carbon that
is joined to two other
atom can become oxidized
common structure found
in biomolecules. This
an oxygen, next the other
gens, a
First one hydrogen gets replaced by
through several steps: carbons are replaced by
removed, and then the bonds to the other two
hydrogen is oxidized. Each step oxi-
second oxygen. This carbon is now completely
bonds to
oxidized as CO2. During a wood
a
carbon bit more until it became fully
dized the a
ordered and
occur almost instantaneously.
In cells, they are more
fire. these steps
controlled.

Activation Energy
burn spontaneously.
wood stove gets started. Logs do not
Consider how a fire in a To get
the stove, and it will sit there indefinitely, not burning.
You can put a log in in the pants, as
it
must set fire to it-giving it an energetic kick
the log burning, you other fashion
using a smaller flame obtained in some
were. Usually you
do this by add a bit ot
to burn, you initially have to
(match, lighter, and so on). To get the log
the en
energy
This energy is called the activation energy (Figure 1.10a). It represents
don't
Oxidation reactions a
to the chemical reaction under way.
get instantiy
ergy necessary did, fuel materials would disappear
spontaneously; if they of en*
ways happen or other fuels inside cells requires
an input

Like burning logs, burning

glucose be crossed.
an input of energy to
view this as a barrier that requires
[Link] can
 19
T H E KEY T0 LIFE

Activetion
energy barrier

(b

putting "jumping beans" into a wel.

Figure I.10 Activation energy. (a) Imagine situation is
to jump out of the well. This
They will rarely have the energy necessary
unable to react and form prod-
insufficient energy being
analogous to molecules with lowers the activa-
eaction is the activation energy.(b) A catalyst
ucts. The bamer to reactants. This makes it much
the barrier for the
tion enery, essentially lowering them will react.
therefore, many more of
easier for the molecules to react;

than
the activation energy
different approach to overcoming
However, cells use a
analogy falls apart. Light-
wood-burning
wood. This is where our to the system to
do people burning adds just enough energy
a smaller fire to
the wood in the stove
energY,
ing barrier. Cells, instead of adding the necessary
overcome the activation energy to solving the problem.
activation energy-a completely different approach lowered?
lower the activation energy barrier
be
now becomes: How can an
The question

Catalysis
to react, they must
first be brought into close proxim-
two atoms or compounds activation energy
For
positions for the reaction. The
into the appropriate for a
ity and be put to achieve these particular goals
the amount of energy necessary for these
represents it much easier
reaction. Cells lower
the activation energy by making
given sort of "chemical scaf-
take the reacting compounds and, using a
steps to occur.
Cells reaction more favorable. This
and make the start of the
fold," line them up properly is something that causes
a reaction to occur
called catalysis. A catalyst
process is 1.10b). Although the catalyst
the activation energy (Figure
more readily by lowering is never permanently changed by
the reaction; at
in the reaction, it
can be
may participate
are altered, but
not the catalyst. Thus, a catalyst
reactants
the end, the two same reaction.
to catalyze the
used over and over again are in use in everyday
chemical events. The
common, and they comes in
Catalysts are You may know that epoxy
depends on catalyst.
a
hardening of epoxy glue and the other is the "hardener,"
actually a catalyst.
is the glue itself, will not harden
two tubes;
it comes out of its tube; it
one
function as a glue when
The glue does not
 CHAPTERI AN INTRodvcTION TO LIVING THINGS

or cure
properly by itselt. The chemical reactions necessary to
make it a s

donot happen spontaneously. The hardener, when it comes in contact wit

itiates the chemical reactions that will result in the formation of
permanent epoxy cement. The hardener does this by catalyzing
the hara thege
enng the activation
reactions
energy.

Enzymees
The biological catalysts cells use are called enzymes, and
tein molecules. Enzymes catalyze virtually every chemical they are nearly alwas
reaction that occurs
cells: They join
reactants in such a way that a reaction between in
favorable. them becomes nside
more
Each individual reaction that
occurs in a cell employs a
for the express speciñc
purpose of catalyzing that reaction or a group ot related enzyme ma
member our discussion of reactions R
While this may be a burning carbohydrates to yield water and carbon
simple reaction in a wood stove, in the cell it is diotite
thirty to thirty-ffve steps or ehemical more
and the final carbon reactions occur between the start of compler
dioxide product. Each step involves a this proces
tions to catalyze that
specific reaction. unique enzyme that func
Enzyme uniqueness is critical for
many reasons, of
only the proper reactants will come which we will list two. Fir
it assures that
rence of mistakes that
might result in improper, together, preventing the occur
Second, enzymes can be controlled perhaps toxic, chemical products
reaction can be by the cell, meaning that the rate
controlled by the activity of the of a particular
product, it can speed up the reactions catalyst. If a cell needs more
abundance of a product, it can leading to that product. If the cell has an of a
slow down or ove
uct. Cells control stop the reactions leading to that
enzymes sometimes by prod
more often by adjusting
changing ability of enzymes to bind
the
the amount of
enzyme present or
cell can fine-tune the or transform
various reactions in order reactants. The
ical intermediates. This is to maintain the
vital to the health of proper levels of chem
the cell; remember
ing" or oxidation of fuel goes too
energy it might need, and if it cannot quickly the cell will not be able to that if the "bu
occur recover all of the
much energy as it needs. quickly enough the cell will not
have
Catabolic and Anabolic
We have couched our
Reactions
els to obtain coverage of enzymes and
energy. Many other metabolism in terms of
divide these reactions into thosechemical reactions occur inside cells as burning u
responsible for breaking well. we ca
oxidation reactions of
glucose, and those that things down, such as he
build things up
including the reactions that form put things togene
cleotides. Reactions that break proteins from amino acidsor and
things down are called DNA fno nu
things up are called anabolic. Ina cell at any catabolic. Reactions uild
reactions are occurring: the cell is given time, both anabolic and tharic
olic
breaking down fuel and making ATP constantly dealing with its energy cata y
(catabolic
other cell components that are no longer needed. The cell
reactions) as is
demand
constantly
well repladown
as breaking a
THR EY TO LIFR

new material t Avtlh (analuoi

beme depletent and nmaking materiala atut unetu
omponents that the raw
Catallisn proviles beakilown
eactions). which reJuuirs enegv halanee of
[Link] an enqpuisitr
anabwlism Nhus, the vell e n v m e n that
energy tor the activities nf the
reartions anevontolled
by
and gnowth All ot these ott the nmal
halaee o e
we will see [Link],
throwing
catalyze the roactions As on the cell
can [Link]
disastrvs effects
alteratim in the
means, ie
tabolism, by whatever
of some
diseases a i s e [Link]
ot most
The [Link] eaearch ains to
areas of bioteehulogy
the [Link]
tabolism ot cells. Mne ot nore
disease and what
can Ie done
metabolism can cause
understamd how disniptions nn
about cella in t e n a o
to restore the pmcesses to nomal. We shuld begin thinking alleratioIs in
[Link] s e r how
rections now, so [Link] [Link] we
contnolei sets ot chemieal
this nomal balance bervme theatening

SSUES RISK AND NEW TECHNOLoGY

inherent risks of develop

At the of this chapter, we briefly discussed the
beginning of such de-
technologies. It is unfortunate, but risk is a necessary component
ing new
investors
venture capital risks taken by
velopment. It takes various forms, from the
to the personal risks assumed by individuals
who volunteer as part of a testing pro
take huge risks by investing heavily
in specific
gram for a new drug. Corporations
find their way to mar-
products and procedures, hoping that they will eventually
assume risks by agreeing to al
ket and become useful and profitable. Municipalities
harmful to the reglon. In short, the
low research to be conducted that might prove
continue to see its share of risky
development of biotechnology has seen and will
ventures Such a question is
Does this mean the technology should not be pursued?
A theme
difficult to answer, and the answer probably depends on your perspective.
individuals
that becomes apparent quite frequently during discussions of risk is that
perceive risk differently from society as a whole. What might seem to some people
to be beneficial to society as a whole is often perceived as risky by some individuals,
and vice versa. Since living in a society must be a compromise among all the indi-
viduals involved, this apparent conflict seems quite reasonable. However, it is not al
ways easy to decide, either personally or as a part of society,
what risks to assume.
Every day, we subject ourselves to numerous risks that could be avoided. Most
of us in the United States drive far more frequently than is absolutely necessary. in-
curring some level of risk. Many choose to live at high altitudes, exposing themselves
to slightly higher levels of ultraviolet radiation. Many of us live in or near large cities,
where the ait often contains potentially harmful substances. Yet we are used to all of
these risks-they are a normal part of our lives. It doesnt always matter that virtu-
ally all of us are aware of the risks of smoking or practicing unsafe sex-numerous
individuals choose to engage in these high-risk behaviors. Others will doeverything
in their power to avoid unnecessary risk. How is society to come to grips with risk
when there are so many different individual responses? Unfortunately, that is exactly