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Superset

The Chemical Context
of Life

2

Figure 2
...
1

matter consists of chemical
elements in pure form and in
combinations called compounds

2
...
3

the formation and function of
molecules depend on chemical
bonding between atoms

2
...
Wood ants live in colonies of hundreds or thousands, and the colony as a
whole has a particularly effective way of dealing with enemies
...
1)
...
For quite a few ant species, the formic acid isn’t shot
out, but probably serves as a disinfectant that protects the ants against microbial
parasites
...

Research on ants and other insects is a good example of how relevant chemistry is to the study of life
...
Biologists specialize
in the study of life, but organisms and their environments are natural systems to
which the concepts of chemistry and physics apply
...

This unit of chapters introduces some basic concepts of chemistry that apply to
the study of life
...
This chapter focuses on the chemical
components that make up all matter
...

interview with Deborah Gordon: investigating ant behavior

28

Get ready for this Chapter

COnCEpT

2
...
* Matter exists in many forms
...


elements and Compounds
Matter is made up of elements
...
Today, chemists recognize 92 elements occurring in
nature; gold, copper, carbon, and oxygen are examples
...

Some symbols are derived from Latin or German; for instance,
the symbol for sodium is Na, from the Latin word natrium
...
Table salt, for
example, is sodium chloride (NaCl), a compound composed
of the elements sodium (Na) and chlorine (Cl) in a 1:1 ratio
...

When chemically combined, however, sodium and chlorine
form an edible compound
...
These are simple examples of organized matter having
emergent properties: A compound has characteristics different from those of its elements (Figure 2
...


Figure 2
...
The
metal sodium combines with the poisonous gas chlorine, forming the
edible compound sodium chloride, or table salt
...
The essential elements are similar among organisms, but there is some variation—for example, humans need
25 elements, but plants need only 17
...
Calcium (Ca), phosphorus (P), potassium (K), sulfur (S),
and a few other elements account for most of the remaining
4% or so of an organism’s mass
...
Some trace elements, such as iron (Fe), are needed by all forms of life; others
are required only by certain species
...
A daily
intake of only 0
...
An iodine deficiency
in the diet causes the thyroid gland to grow to abnormal size,
a condition called goiter
...
Relative amounts of all the
elements in the human body are listed in Table 2
...

Some naturally occurring elements are toxic to organisms
...
In some areas of the
world, arsenic occurs naturally and can make its way into the
groundwater
...
Efforts are under way to
reduce arsenic levels in their water supply
...
1

elements in the human Body
Symbol

Oxygen

O

65
...
5%

Hydrogen

H

9
...
3%

Calcium

Ca

1
...
0%

Potassium

K

0
...
3%

Sodium

Na

0
...
2%

Mg

0
...
Mass is the amount of matter in an object, whereas the
weight of an object is how strongly that mass is pulled by gravity
...
However, as long as we are earthbound,
the weight of an object is a measure of its mass; in everyday language, therefore,
we tend to use the terms interchangeably
...
3%

u 3
...
01% of mass): Boron (B), chromium (Cr), cobalt (Co),
copper (Cu), fluorine (F), iodine (I), iron (Fe), manganese (Mn), molybdenum (Mo),
selenium (Se), silicon (Si), tin (Sn), vanadium (V), zinc (Zn)

inTERpRET THE dATA Given the makeup of the human body, what
compound do you think accounts for the high percentage of oxygen?

CHAPTeR 2

The Chemical Context of Life

29

Figure 2
...
These plants are
growing on serpentine soil, which contains elements that are usually
toxic to plants
...

This specially-adapted species is found only on this one hill in Tiburon,
a peninsula that juts into San Francisco Bay
...
2

an element’s properties depend
on the structure of its atoms
Each element consists of a certain type of atom that is different from the atoms of any other element
...
Atoms are so small that it would take about a million
of them to stretch across the period printed at the end of this
sentence
...
For
example, the symbol C stands for both the element carbon
and a single carbon atom
...
Serpentine is a jade-like
mineral that contains elevated concentrations of elements
such as chromium, nickel, and cobalt
...
3)
...
Researchers
are studying whether serpentine-adapted plants could be
used to take up toxic heavy metals in contaminated areas,
concentrating them for safer disposal
...
Using high-energy
collisions, physicists have produced more than 100 types of
particles from the atom, but only three kinds of particles are
relevant here: neutrons, protons, and electrons
...
Each proton has one
unit of positive charge, and each electron has one unit of
negative charge
...

Protons and neutrons are packed together tightly in a dense
core, or atomic nucleus, at the center of an atom; protons
give the nucleus a positive charge
...
Figure 2
...
4 Simplified models of a helium (He) atom
...

Two electrons (yellow) exist outside the nucleus
...

Cloud of negative
charge (2 electrons)

Electrons
Nucleus

COnCEpT CHECK 2
...
MAKE COnnECTiOnS explain how table salt has
emergent properties
...
1
...
is a trace element an essential element? explain
...


(b) In this more simplified model,
the electrons are shown
as two small yellow spheres
on a circle around the nucleus
...
WHAT iF? in humans, iron is a trace element required
for the proper functioning of hemoglobin, the molecule
that carries oxygen in red blood cells
...
MAKE COnnECTiOnS explain how natural selection
might have played a role in the evolution of species that
are tolerant of serpentine soils
...
2
...


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UNiT ONe

The Chemistry of Life

two commonly used models of the structure of the helium
atom as an example
...
7 * 10-24 gram (g)
...
Thus, for atoms and subatomic particles
(and for molecules, too), we use a unit of measurement called
the dalton, in honor of John Dalton, the British scientist who
helped develop atomic theory around 1800
...
) Neutrons and protons have masses
close to 1 dalton
...


atomic number and atomic mass
Atoms of the various elements differ in their number of subatomic particles
...
This number of protons, which is unique to that element, is called the atomic
number and is written as a subscript to the left of the symbol for the element
...
Unless otherwise indicated, an atom is neutral in
electrical charge, which means that its protons must be balanced by an equal number of electrons
...

We can deduce the number of neutrons from a second
quantity, the mass number, which is the total number of
protons and neutrons in the nucleus of an atom
...
For example, we can use this shorthand to write an
atom of helium as 42He
...
In our example, the helium atom 42He has 2 neutrons
...

These different atomic forms of the same element are called
isotopes of the element
...
As an example, the element carbon,
which has the atomic number 6, has three naturally occurring isotopes
...
The
isotope 126C has 6 neutrons
...

A third, even rarer isotope, 146C, has 8 neutrons
...
Although the isotopes of an element
have slightly different masses, they behave identically in
chemical reactions
...
Thus carbon
has an atomic mass of 12
...
)
Both 12C and 13C are stable isotopes, meaning that their
nuclei do not have a tendency to lose subatomic particles,
a process called decay
...
A radioactive isotope is one in which
the nucleus decays spontaneously, giving off particles and
energy
...
For example, when an atom of
carbon-14 (14C) decays, it loses a proton, becoming an atom
of nitrogen (14N)
...


æ

æ

Mass number = number of protons + neutrons
= 23 for sodium
23
Na
11

Neutrons and protons each have a mass very close to 1 dalton,
so the mass number is close to, but slightly different from, the
total mass of an atom, called its atomic mass
...
9898 daltons
...

Because the contribution of electrons to mass is negligible,
almost all of an atom’s mass is concentrated in its nucleus
...
Cells can use radioactive atoms just as they would
use nonradioactive isotopes of the same element
...
For
example, certain kidney disorders are diagnosed by injecting
small doses of radioactively labeled substances into the blood
and then analyzing the tracer molecules excreted in the
urine
...
5 A pET
scan, a medical use for
radioactive isotopes
...
The bright yellow
spot marks an area
with an elevated level
of radioactively labeled
glucose, which in turn
indicates high metabolic
activity, a hallmark of
cancerous tissue
...
5)
...
The
severity of this damage depends on the type and amount of
radiation an organism absorbs
...
The doses of most isotopes used in medical diagnosis,
however, are relatively safe
...
Fossils provide a large body
of evidence for evolution, documenting differences between
organisms from the past and those living at present and giving us insight into species that have disappeared over time
...
This is where radioactive isotopes come in
...
Each
radioactive isotope has a characteristic half-life that is not
affected by temperature, pressure, or any other environmental
variable
...
Half-life values range from
very short for some isotopes, measured in seconds or days,
to extremely long—uranium-238 has a half-life of 4
...
5 billion years old, similar to the estimated age of Earth
...
(Figure 25
...
)

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The Chemistry of Life

The simplified models of the atom in Figure 2
...
If an atom of helium were the size of a typical football
stadium, the nucleus would be the size of a pencil eraser in
the center of the field
...
Atoms are mostly
empty space
...
Of the three subatomic particles we have discussed,
only electrons are directly involved in chemical reactions
...
Energy is defined as the capacity to cause change—
for instance, by doing work
...
For
example, water in a reservoir on a hill has potential energy
because of its altitude
...
Because energy has been expended, the water
has less energy at the bottom of the hill than it did in the reservoir
...
To restore the potential energy of a reservoir,
work must be done to elevate the water against gravity
...
6)
...
6 Energy levels of an atom’s electrons
...

(a) A ball bouncing down a flight
of stairs can come to rest only
on each step, not between steps
...

Third shell (highest energy
level in this model)
Second shell (higher
energy level)

First shell (lowest energy
level)

Energy
absorbed

Energy
lost

Atomic
nucleus
(b) An electron can move from one shell to another only if the energy
it gains or loses is exactly equal to the difference in energy between
the energy levels of the two shells
...

Figure Walkthrough

Calibrating a Standard Radioactive
Isotope Decay Curve and
Interpreting Data
How Long Might neanderthals Have Co-Existed with
Modern Humans (Homo
(Homo sapiens)?
sapiens)? Neanderthals (Homo
(Homo
neanderthalensis) were living in europe by 350,000 years ago and
may have coexisted with early Homo sapiens in parts of eurasia for
hundreds or thousands of years before Neanderthals became extinct
...
They used carbon-14 dating to determine the age of a
Neanderthal fossil from the most recent (uppermost) archeological
layer containing Neanderthal bones
...
The age will help you approximate the
last time the two species may have coexisted at the site where this
fossil was collected
...
C is present
in the atmosphere in small amounts at a constant ratio with both
13
C and 12C, two other isotopes of carbon
...
These proportions
remain the same in the tissues of an animal that eats the plant
...
Once an
organism dies, it stops taking in new 14C but the 14C in its tissues continues to decay, while the 12C in its tissues remains the same because
it is not radioactive and does not decay
...
The fraction of 14C
in a fossil compared to the original fraction of 14C can be converted
to years because we know that the half-life of 14C is 5,730 years—in
other words, half of the 14C in a fossil decays every 5,730 years
...
0078 (or, in scientific
notation, 7
...
The following
questions will guide you through translating this fraction into the
age of the fossil
...
A standard curve of radioactive isotope decay is shown at the
top of the right column
...
Recall that a half-life is the amount of time it takes for half
of the radioactive isotope to decay
...

Draw an arrow to the data point for half-life = 1 and write the

electrons are attracted to the positively charged nucleus
...
Unlike the continuous flow of
water downhill, changes in the potential energy of electrons
can occur only in steps of fixed amounts
...
0

neanderthal
fossils

0
...
8
0
...
6
0
...
4
0
...
2
0
...
Pinhasi et al
...
doi 10
...
1018938108

fraction of 14C that will remain after one half-life
...
Convert
each fraction to a decimal number and round off to a maximum
of three significant digits (zeros at the beginning of the number
do not count as significant digits)
...

2
...
To calibrate the x-axis
for 14C decay, write the time before present in years below each
half-life
...
The researchers found that the Neanderthal fossil had approximately
0
...
(a) Using
the numbers on your graph, determine how many half-lives have
passed since the Neanderthal died
...
sapiens) became
established in the same region as the last Neanderthals approximately 39,000–42,000 years ago
...
Carbon-14 dating works for fossils up to about 75,000 years old;
fossils older than that contain too little 14C to be detected
...
5 million years ago
...
(b) Radioactive uranium-235 has
a half-life of 704 million years
...

instructors: A version of this Scientific Skills exercise
can be assigned in MasteringBiology
...
6a)
...
Similarly, an electron’s potential
energy is determined by its energy level
...

CHAPTeR 2

The Chemical Context of Life

33

An electron’s energy level is correlated with its average
distance from the nucleus
...
In diagrams, shells can be represented by
concentric circles, as they are in Figure 2
...
The first shell
is closest to the nucleus, and electrons in this shell have the
lowest potential energy
...
An electron can move from one shell to another,
but only by absorbing or losing an amount of energy equal
to the difference in potential energy between its position
in the old shell and that in the new shell
...
For example, light energy can excite an electron
to a higher energy level
...
You’ll learn more about photosynthesis in
Chapter 10
...
For example, sunlight

excites electrons in the surface of a car to higher energy
levels
...
This thermal energy can be transferred to the air or to your hand if you touch the car
...
Beginning
with hydrogen, the simplest atom, we can imagine building
the atoms of the other elements by adding 1 proton and 1 electron at a time (along with an appropriate number of neutrons)
...
7, a modified version of what is called the periodic
table of the elements, shows this distribution of electrons for the
first 18 elements, from hydrogen (1H) to argon (18Ar)
...
The left-to-right
sequence of elements in each row corresponds to the sequential addition of electrons and protons
...
)

Figure 2
...

In a standard periodic table (see Appendix B), information for each element is presented as shown for helium
in the inset
...
These diagrams are a convenient way to picture the distribution of an atom’s electrons
among its electron shells, but these simplified models do not accurately represent the shape of the atom
or the location of its electrons
...
As electrons are added, they occupy the lowest available shell
...
003

Helium
2He

Element symbol
Electron
distribution
diagram

Lithium
3Li

Beryllium
4Be

Boron
5B

Carbon
6C

Nitrogen
7N

Oxygen
8O

Fluorine
9F

Neon
10Ne

Sodium
11Na

Magnesium
12Mg

Aluminum
13Al

Silicon
14Si

Phosphorus
15P

Sulfur
16S

Chlorine
17Cl

Argon
18Ar

Second
shell

Third
shell

ViSUAL SKiLLS Looking at the depictions of atoms in this chart, what is the atomic number of magnesium?
How many protons and electrons does it have? How many electron shells? How many valence electrons?

34

UNiT ONe

The Chemistry of Life

animation: electron Distribution
Diagrams

Hydrogen’s 1 electron and helium’s 2 electrons are located
in the first shell
...
In an atom, this
state is in the first shell
...
In an atom with
more than 2 electrons, the additional electrons must occupy
higher shells because the first shell is full
...
Two of these electrons fill the first
shell, while the third electron occupies the second shell
...
Neon, at the
end of the second row, has 8 electrons in the second shell,
giving it a total of 10 electrons
...
We call those outer
electrons valence electrons and the outermost electron
shell the valence shell
...

Atoms with the same number of electrons in their valence shells
exhibit similar chemical behavior
...
2)
...
At the
far right of the periodic table are helium, neon, and argon, the
only three elements shown in Figure 2
...
These elements are said to be inert, meaning chemically
unreactive
...
7 are chemically
reactive because they have incomplete valence shells
...
8 Electron orbitals
...
An electron distribution
diagram is shown here for a neon atom, which has a total of 10
electrons
...


First shell

Second shell

y

x

1s orbital

2s orbital

z
Three 2p orbitals

(b) Separate electron orbitals
...
Each orbital
holds a maximum of 2 electrons
...
The second
shell, on the right, has one larger s orbital (designated 2s for
the second shell) plus three dumbbell-shaped orbitals called
p orbitals (2p for the second shell)
...
Each 2p orbital is outlined here in a different color
...
It is still convenient
to use two-dimensional concentric-circle diagrams, as in
Figure 2
...

However, you need to remember that each concentric circle
represents only the average distance between an electron in
that shell and the nucleus
...
In reality,
we can never know the exact location of an electron
...
The three-dimensional space where
an electron is found 90% of the time is called an orbital
...
Figure 2
...
You can think of an orbital as a component of an electron shell
...
To reveal the complete
picture of the electron orbitals of neon, we superimpose the 1s
orbital of the first shell and the 2s and three 2p orbitals of the
second shell
...
(The third shell
and other higher electron shells also have s and p orbitals, as
well as orbitals of more complex shapes
...
The
first electron shell can therefore accommodate up to 2 electrons
in its s orbital
...
The four
orbitals of the second electron shell can hold up to 8 electrons,
CHAPTeR 2

The Chemical Context of Life

35

2 in each orbital
...

The reactivity of an atom arises from the presence of
unpaired electrons in one or more orbitals of the atom’s
valence shell
...
When they
do so, it is the unpaired electrons that are involved
...
2
1
...
What is its
mass number?
2
...
A radioactive isotope
of nitrogen has 8 neutrons
...

3
...

How many electrons are needed to fill the valence shell?
4
...
7, if two or more elements
are in the same row, what do they have in common? if
two or more elements are in the same column, what do
they have in common?
For suggested answers, see Appendix A
...
3

the formation and function of
molecules depend on chemical
bonding between atoms
Now that we have looked at the structure of atoms, we can
move up the hierarchy of organization and see how atoms
combine to form molecules and ionic compounds
...
These
interactions usually result in atoms staying close together, held
by attractions called chemical bonds
...
(Ionic bonds in aqueous, or water-based, solutions
are weak interactions, as we will see later
...
For example, let’s consider what happens when
two hydrogen atoms approach each other
...
When the two hydrogen atoms come close enough
for their 1s orbitals to overlap, they can share their electrons
(Figure 2
...
Each hydrogen atom is now associated with
2 electrons in what amounts to a completed valence shell
...
9 Formation of a covalent bond
...


+

+

2 When two hydrogen

atoms approach each
other, the electron of
each atom is also
attracted to the proton
in the other nucleus
...


+

+

Hydrogen
molecule (H2)

or more atoms held together by covalent bonds constitute a
molecule, in this case a hydrogen molecule
...
10a shows several ways of representing a hydrogen
molecule
...
Electron sharing
can be depicted by an electron distribution diagram or by a
Lewis dot structure, in which element symbols are surrounded
by dots that represent the valence electrons (H : H)
...
A space-filling model
comes closest to representing the actual shape of the molecule
...
15
...

Two oxygen atoms form a molecule by sharing two pairs of
valence electrons (Figure 2
...
The atoms are thus joined
by what is called a double bond (O“O)
...
When the bonds form, they give the atom
a full complement of electrons in the valence shell
...
This bonding capacity is called the atom’s valence and usually equals
the number of unpaired electrons required to complete the
atom’s outermost (valence) shell
...
7
...
The situation is more complicated

Figure 2
...
The
number of electrons required to complete an atom’s valence shell
generally determines how many covalent bonds that atom will form
...

Name and
Molecular
Formula

Electron
Distribution
Diagram

(a) Hydrogen (H2)
...


Lewis Dot
Structure and
Structural
Formula

δ–
δ–
O

δ+

H
H

Because oxygen (O) is more electronegative than hydrogen (H),
shared electrons are pulled more toward oxygen
...
11 polar covalent bonds in a water molecule
...


(d) Methane (CH4 )
...


•
•

•
•
•
•

O

O

O

•
•

O

O •• H
H

•
•

•
•

H

O

O

H

H

H

H
H •• C •• H
H

H

•
•

(c) Water (H2O)
...


O •• •• O

•
•

(b) Oxygen (O2)
...


•
•

animation: nonpolar and Polar molecules

C
H

H

H
H

C

H

H
animation: Covalent Bonds

for phosphorus, in the third row of the periodic table, which
can have a valence of 3 or 5 depending on the combination
of single and double bonds it makes
...
Water, with the molecular formula
H2O, is a compound
...
Figure 2
...
(Water is so important to life that
Chapter 3 is devoted entirely to its structure and behavior
...
It takes four hydrogen
atoms, each with a valence of 1, to complement one atom of
carbon, with its valence of 4 (Figure 2
...
(We will look at
many other compounds of carbon in Chapter 4
...
The attraction of a
particular atom for the electrons of a covalent bond is called its

electronegativity
...
In a covalent bond between two atoms of the same element, the electrons are shared equally because the two atoms have the same
electronegativity—the tug-of-war is at a standoff
...
For example, the single
bond of H2 is nonpolar, as is the double bond of O2
...
This type of bond
is called a polar covalent bond
...
For example, the bonds between the oxygen and hydrogen atoms of a water molecule are quite polar (Figure 2
...

Oxygen is one of the most electronegative elements, attracting shared electrons much more strongly than hydrogen does
...
Because electrons have a negative charge
and are pulled toward oxygen in a water molecule, the oxygen
atom has two regions of partial negative charge (each indicated
by the Greek letter δ with a minus sign, δ-, “delta minus”), and
each hydrogen atom has a partial positive charge (δ+, “delta
plus”)
...


ionic Bonds
In some cases, two atoms are so unequal in their attraction for
valence electrons that the more electronegative atom strips
an electron completely away from its partner
...

A positively charged ion is called a cation, while a negatively
charged ion is called an anion
...
Note that the transfer of an electron
is not, by itself, the formation of a bond; rather, it allows a
bond to form because it results in two ions of opposite charge
...
The
ions do not need to have acquired their charge by an electron
transfer with each other
...
The formula for an ionic
atom is transferred to join the 7 valence
valence shell
...

between the oppositely charged ions
...
“NaCl” by itself is not a molecule
...
For example, the
ionic compound magnesium chloride
Cl
Cl
Na
Na
(MgCl2) has two chloride ions for each
magnesium ion
...
One magnesium
Sodium chloride (NaCl)
animation: Formation of ions and ionic Bonds
cation can therefore form ionic bonds
with two chloride anions (Cl-)
...
In the salt ammonium chloride (NH4Cl), for
encounters an atom of chlorine (17Cl) (Figure 2
...
A sodium
instance, the anion is a single chloride ion (Cl-), but the catatom has a total of 11 electrons, with its single valence elecion is ammonium (NH4+), a nitrogen atom covalently bonded
tron in the third electron shell
...
The whole ammonium ion has an
of 17 electrons, with 7 electrons in its valence shell
...

is transferred to the chlorine atom, and both atoms end up
Environment affects the strength of ionic bonds
...
(Because sodium no longer
salt crystal, the bonds are so strong that it takes a hammer
has an electron in the third shell, the second shell is now the
and chisel to break enough of them to crack the crystal in
valence shell
...
If the same salt crystal is dissolved in water, however,
moves one unit of negative charge from sodium to chlorine
...
Most
electrical charge of 1+; the sodium atom has become a cation
...

now has 17 protons and 18 electrons, giving it a net electrical
(In Concept 3
...
)
charge of 1- ; it has become a chloride ion—an anion
...
We know the ionic compound
sodium chloride (NaCl) as table salt (Figure 2
...
Salts are
In organisms, most of the strongest chemical bonds are covaoften found in nature as crystals of various sizes and shapes
...
But
Each salt crystal is an aggregate of vast numbers of cations
weaker interactions within and between molecules are also
and anions bonded by their electrical attraction and arranged
indispensable, contributing greatly to the emergent properties
in a three-dimensional lattice
...
Many large biological molecules are held in their funcFigure 2
...
The attraction between oppositely
charged atoms, or ions, is an ionic bond
...


Figure 2
...
The sodium
ions (Na+) and chloride ions (Cl-) are held together by ionic bonds
...


Na+
Cl–

tional form by weak interactions
...
The reversibility of weak interactions can
be an advantage: Two molecules can come together, affect one
another in some way, and then separate
...
One is the ionic bond as it exists between ions
dissociated in water, which we just discussed
...


Hydrogen Bonds
Among weak chemical interactions, hydrogen bonds are
so central to the chemistry of life that they deserve special
38

UNiT ONe

The Chemistry of Life

Figure 2
...

δ+

δ–
δ–
O

Water (H2O)

H

H
This hydrogen bond
(dotted line) results from
the attraction between
the partial positive
charge on a hydrogen
atom of water and the
partial negative charge
on the nitrogen atom
of ammonia
...

Use simple outlines of space­filling models
...


animation: hydrogen Bonds

attention
...
This attraction between a hydrogen and an
electronegative atom is called a hydrogen bond
...
Refer to Figure 2
...


Van der Waals Interactions
Even a molecule with nonpolar covalent bonds may have
positively and negatively charged regions
...
The
results are ever-changing regions of positive and negative
charge that enable all atoms and molecules to stick to one
another
...
When many such interactions occur
simultaneously, however, they can be powerful: Van der
Waals interactions allow the gecko lizard shown here to
walk straight up a wall! The anatomy of the gecko’s foot—
including many minuscule hairlike projections from the
toes and strong tendons underlying the skin—strikes a balance between maximum surface
contact with the wall and
necessary stiffness of
the foot
...
This discovery has inspired development of an artificial adhesive called Geckskin: A patch the size of an index
card can hold a 700-pound weight to a wall!
Van der Waals interactions, hydrogen bonds, ionic bonds
in water, and other weak interactions may form not only
between molecules but also between parts of a large molecule,
such as a protein
...

(You will learn more about the very important biological roles
of weak interactions in Chapter 5
...
A molecule consisting of two
atoms, such as H2 or O2, is always linear, but most molecules
with more than two atoms have more complicated shapes
...
15)
...
15 Molecular shapes due to hybrid orbitals
...
The single s and three p orbitals of a
valence shell involved in covalent bonding combine to form four
teardrop-shaped hybrid orbitals
...

Space-Filling
Model

Ball-and-Stick
Model

O
H

104
...
Three models representing molecular
shape are shown for water and methane
...

CHAPTeR 2
CHAP

The Chemical Context of Life

39

the orbitals in its valence shell undergo rearrangement
...
8), the single s and three p orbitals form four new
hybrid orbitals shaped like identical teardrops extending from
the region of the atomic nucleus, as shown in Figure 2
...

If we connect the larger ends of the teardrops with lines,
we have the outline of a geometric shape called a tetrahedron,
a pyramid with a triangular base
...
15b)
...
5°
...
15b)
...
Larger molecules containing multiple
carbon atoms, including many of the molecules that
make up living matter, have more complex overall shapes
...

Molecular shape is crucial: It determines how biological
molecules recognize and respond to one another with specificity
...
Consider the effects of opiates, drugs
such as morphine and heroin derived from opium
...
Why would
brain cells carry receptors for opiates, compounds that are
not made by the body? In 1975, the discovery of endorphins
answered this question
...
Opiates have shapes similar to endorphins and mimic them by binding to endorphin receptors in
the brain
...
16)
...


Figure 2
...
Morphine affects pain perception
and emotional state by mimicking the brain’s natural endorphins
...
The boxed portion of
the endorphin molecule (left) binds to receptor molecules on target
cells in the brain
...


Natural
endorphin

Morphine

Endorphin
receptors

Brain cell

(b) Binding to endorphin receptors
...

interview with Candace Pert: Discovering opiate receptors
in the brain

COnCEpT

2
...
An example is the reaction between hydrogen
and oxygen molecules that forms water:

COnCEpT CHECK 2
...
Why does the structure H ¬ C “ C ¬ H fail to make sense
chemically?

+

2
...
WHAT iF? if you were a pharmaceutical researcher, why
would you want to learn the three-dimensional shapes
of naturally occurring signaling molecules?
For suggested answers, see Appendix A
...
When we write the equation for a
chemical reaction, we use an arrow to indicate the conversion
of the starting materials, called the reactants, to the resulting
materials, or products
...
Notice that all atoms of the reactants must be
accounted for in the products
...

Photosynthesis, which takes place within the cells of green
plant tissues, is an important biological example of how chemical reactions rearrange matter
...

The following summarizes the process of photosynthesis:

Reactants
6 CO2
+
Carbon dioxide

Products
6 H2O
Water

Sunlight

C6H12O6
Glucose

+

6 O2
Oxygen

The raw materials of photosynthesis are carbon dioxide
(CO2) and water (H2O), which land plants absorb from the air
and soil, respectively
...
17)
...
Matter has simply been
rearranged, with an input of energy provided by sunlight
...
For example, hydrogen and nitrogen
molecules can combine to form ammonia, but ammonia can
also decompose to regenerate hydrogen and nitrogen:

Figure 2
...
Elodea, a freshwater
plant, produces sugar by
rearranging the atoms of
carbon dioxide and water in
the chemical process known
as photosynthesis, which is
powered by sunlight
...
Oxygen
gas (O2) is a by-product of
photosynthesis; notice the
bubbles of O2 gas escaping from
the leaves submerged in water
...


The same holds true for products
...
Eventually, the forward and reverse reactions occur
at the same rate, and the relative concentrations of products
and reactants stop changing
...

This is a dynamic equilibrium; reactions are still going on in
both directions, but with no net effect on the concentrations
of reactants and products
...

The reaction involving ammonia reaches equilibrium when
ammonia decomposes as rapidly as it forms
...

We will return to the subject of chemical reactions after
more detailed study of the various types of molecules that
are important to life
...


COnCEpT CHECK 2
...
MAKE COnnECTiOnS Consider the reaction between
hydrogen and oxygen that forms water, shown with balland-stick models at the beginning of Concept 2
...
After
studying Figure 2
...


3 H2 + N2 L 2 NH3

2
...

One of the factors affecting the rate of a reaction is the
concentration of reactants
...


3
...
Add energy as another product
...
Describe this equation in words
...


CHAPTeR 2

The Chemical Context of Life

41

2

Chapter Review

Go to MasteringBiology™ for Videos, Animations, Vocab Self-Quiz,
Practice Tests, and more in the Study Area
...
1

Matter consists of chemical elements
in pure form and in combinations
called compounds (pp
...
gl/6u55ks

Elements cannot be broken down chemically
to other substances
...
Oxygen, carbon,
hydrogen, and nitrogen make up approximately 96% of
living matter
...
The
attraction of an atom for the electrons of a covalent bond is its
electronegativity
...

Electrons of a polar covalent bond are pulled closer to the
more electronegative atom, such as the oxygen in H2O
...
An ionic bond is the attraction
between two oppositely charged ions:
Ionic bond

Compare an element and a compound
...
2

An element’s properties depend on the structure
of its atoms (pp
...

The atomic mass is measured in daltons and is roughly equal to
the mass number, the sum of protons plus neutrons
...
Unstable isotopes give off particles and energy as
radioactivity
...
Electron distribution in shells determines the chemical behavior of an atom
...

Electrons exist in orbitals, three-dimensional spaces with specific shapes that are components of electron shells
...
Use these diagrams to explain why these elements
are chemically unreactive
...
36–40)

Single
covalent bond

UNiT ONe

The Chemistry of Life

•
•

•
•
•
•

•
•

•
•

O• • + • O• ••

•
•

H •• H

•
•

Chemical bonds form when atoms interact and complete their
valence shells
...


COnCEpT 2
...
40–41)
Chemical reactions change reactants into products while
conserving matter
...
Chemical equilibrium is reached when the forward and
reverse reaction rates are equal
...
3

H• + H•

Weak interactions reinforce the shapes of large molecules and
help molecules adhere to each other
...
Van der Waals interactions occur between
transiently positive and negative regions of molecules
...
Covalent bonds result in hybrid orbitals, which
are responsible for the shapes of H2O, CH4, and many more complex biological molecules
...


O •• •• O

Double
covalent bond

Level 1: Knowledge/Comprehension
1
...

pRACTiCE
TEST
(B) the element can be used as a label to trace
goo
...

(C) the element is very rare on Earth
...


2
...

(B) one more proton
...

(D) one more neutron
...
The reactivity of an atom arises from
(A) the average distance of the outermost electron shell from
the nucleus
...

(C) the sum of the potential energies of all the electron shells
...

4
...

(B) The atom has more protons than electrons
...

(D) The atom has more neutrons than protons
...
Which of the following statements correctly describes any
chemical reaction that has reached equilibrium?
(A) The concentrations of products and reactants are equal
...

(C) Both forward and reverse reactions have halted
...


Level 2: Application/Analysis
6
...

Which of the following represents the 18O isotope of oxygen?
(A) 7p+, 2n0, 9e(B) 8p+, 10n0, 8e(C) 9p+, 9n0, 9e(D) 10p+, 8n0, 9e-

11
...
A male hundreds of meters away can detect these
molecules and fly toward their source
...
Each filament of an
antenna is equipped with
thousands of receptor
cells that detect the sex
attractant
...
What
predictions does your
hypothesis make? Design
an experiment to test one
of these predictions
...
WRiTE ABOUT A THEME: ORGAniZATiOn While waiting
at an airport, Neil Campbell once overheard this claim: “It’s
paranoid and ignorant to worry about industry or agriculture
contaminating the environment with their chemical wastes
...
” Drawing on your
knowledge of electron distribution, bonding, and emergent
properties (see Concept 1
...

13
...
The atomic number of sulfur is 16
...
Based on the number of valence electrons in a sulfur
atom, predict the molecular formula of the compound
...
What coefficients must be placed in the following blanks so
that all atoms are accounted for in the products?
C6H12O6 S

_________

C2H6O +

(A) 2; 1
(B) 3; 1

_________

CO2

(C) 1; 3
(D) 2; 2

9
...
Determine which molecule makes
sense because each atom has a complete valence shell and each
bond has the correct number of electrons
...


H

(a)

O

H

H

C

C

H

H
O

H

(b)

C

H
H

C

O

H

Level 3: Synthesis/Evaluation
10
...
1)
are similar to the percentages of these elements found in other
organisms
...
The beetle stores two sets of chemicals
separately in its glands
...

For selected answers, see Appendix A
...
You can use them to study on
your smartphone, tablet, or computer anytime, anywhere!

CHAPTeR 2

The Chemical Context of Life

43



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