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Chapter 2

The Chemical Context of Life

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Matter
• Takes up space
and has mass
• Exists as elements
(pure form) and in
chemical
combinations
called compounds

2
Properties of Matter
• An element’s properties depend
on the structure of its atoms
• Each element consists of a
certain kind of atom that is
different from those of other
elements
• An atom is the smallest unit of
matter that still retains the
properties of an element

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Four Elements make up about
96% of matter (wet weight
percentage) in the human body.

• Oxygen O 65.0
• Carbon C 18.5
• Hydrogen H 9.5
• Nitrogen N 3.3

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Other Elements
• A few other elements Make up the remaining
4% of living matter

Table 2.1 5
Deficiencies
• If there is a deficiency of an essential
element, disease results

Figure 2.3
(b) Iodine
(a) Nitrogen deficiency
deficiency (Goiter)

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Trace Elements
• Trace elements Are
required by an
organism in only
minute quantities
• Minerals such as Fe
and Zn are trace
elements
• And metals such as:

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Elements
• Can’t be broken down into simpler
substances by chemical reaction
• Composed of atoms
• Essential elements in living things
include carbon C, hydrogen H, oxygen O,
and nitrogen N making up 96% of an
organism

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Compounds
• Are substances consisting of two or more
elements combined in a fixed ratio
• Have characteristics different from those
of their elements

Figure 2.2
Sodium Chloride Sodium Chloride 9
Subatomic Particles

• Atoms of each element Are composed


of even smaller parts called subatomic
particles
• Neutrons, which have no electrical
charge
• Protons, which are positively charged
• Electrons, which are negatively charged

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Subatomic Particle Location

• Protons and
neutrons
– Are found in the
atomic nucleus
• Electrons
– Surround the
nucleus in a “cloud”

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Simplified models of an Atom
Cloud of negative Electrons
charge (2 electrons)

Nucleus

Figure 2.4

(a) This model represents the (b) In this even more simplified
electrons as a cloud of model, the electrons are
negative charge, as if we had shown as two small blue
taken many snapshots of the 2 spheres on a circle around the
electrons over time, with each nucleus.
dot representing an electron‘s
position at one point in time.

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Atomic Number
•Is unique to each element and is used to
arrange atoms on the Periodic table
•Carbon = 12
•Oxygen = 16
•Hydrogen = 1
•Nitrogen = 17

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Atomic Mass
• Is an approximation of the atomic mass
of an atom
•It is the average of the mass of all
isotopes of that particular element
•Can be used to find the number of
neutrons (Subtract atomic number from
atomic mass)

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Atomic Number & Atomic Mass

• Atoms of the various elements Differ in


their number of subatomic particles
• The number of protons in the nucleus =
atomic number
• The number of protons + neutrons =
atomic mass
• Neutral atoms have equal numbers of
protons & electrons (+ and – charges)

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Isotopes
• Different forms of the same element
• Have the same number of protons, but
different number of neutrons
• May be radioactive spontaneously giving
off particles and energy
• May be used to date fossils or as medical
tracers

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Periodic table
– Shows the electron distribution for all
the elements
Helium
Hydrogen 2 Atomic number
He 2He
1H Element symbol
Atomic mass 4.00
First Electron-shell
shell diagram

Lithium Beryllium Boron Carbon Nitrogen Oxygen Fluorine Neon


3Li 4Be 3B 6C 7N 8O 9F 10 Ne

Second
shell

Sodium Magnesium Aluminum Silicon Phosphorus Sulfur Chlorine Argon


11 Na 12 Mg 13 Al 14 Si 15 P 16 S 17 Cl 18 Ar

Third
shell

igure 2.8

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Other uses
– Can be used in medicine to treat tumors

Cancerous
throat
tissue

re 2.6

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APPLICATION Scientists use radioactive isotopes to label certain chemical substances,
creating tracers that can be used to follow a metabolic process or locate the substance
within an organism. In this example, radioactive tracers are being used to determine the
effect of temperature on the rate at which cells make copies of their DNA.
TECHNIQUE
Ingredients including
Radioactive tracer Incubators
(bright blue)
1 2 3
10°C 15°C 20°C
Human cells
Ingredients for 4 5 6
25°C 30°C 35°C
1 making DNA are
added to human cells. One 7 8 9
ingredient is labeled with 3H, a 40°C 45°C 50°C
radioactive isotope of hydrogen. Nine dishes of
cells are incubated at different temperatures.
The cells make new DNA, incorporating the
radioactive tracer with 3H.
The cells are placed in test
2 tubes, their DNA is DNA (old and new)
isolated, and unused
2 3 4 5 6 7 8
ingredients are removed. 1
9

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A solution called scintillation
fluid is added to the test
3 tubes and they are placed in
a scintillation counter. As
the 3H in the newly made
DNA decays, it emits
radiation that excites
chemicals in the scintillation
fluid, causing them to give
off light. Flashes of light
are recorded by the
scintillation counter.
The frequency of flashes, which is recorded as counts per minute,
RESULTS
is proportional to the amount of the radioactive tracer present, indicating the
amount of new DNA. In this experiment, when the counts per minute are plotted
against temperature, it RESULTS
is clear that temperature affects the rate of DNA
synthesis—the most DNA was made at 35°C.
Optimum
Counts per minute

30 temperature
for DNA
(x 1,000)

20 synthesis
10
0
10 20 30 40 50
Temperature (°C)

Figure 2.5
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Energy Levels of Electrons
Electron Arrangement
• An atom’s electrons Vary in the amount
of energy they possess
• Electrons further from the nucleus
have more energy
• Electron’s can absorb energy and
become “excited”
• Excited electrons gain energy and move
to higher energy levels or lose energy
and move to lower levels

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Energy
• Energy
– Is defined as the capacity to cause change
• Potential energy
- Is the energy that matter possesses
because of its location or structure
• Kinetic Energy
- Is the energy of motion

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Electrons and Energy
• The electrons of an atom
– Differ in the amounts of potential energy
they possess

(a) A ball bouncing down a flight


of stairs provides an analogy
for energy levels of electrons,
because the ball can only rest
on each step, not between
Figure 2.7A steps.

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Energy Levels
• Are represented by electron shells
Third energy level (shell)

Second energy level (shell) Energy


absorbed

First energy level (shell)

Energy
lost
Atomic
nucleus

(b) An electron can move from one level to another only if the energy
it gains or loses is exactly equal to the difference in energy between
the two levels. Arrows indicate some of the step-wise changes in
Figure 2.7B potential energy that are possible.

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Electron Configuration and
Chemical Properties
• The chemical behavior of an atom
– Is defined by its electron configuration and
distribution
– K (2e-)
– L-M (8e-)

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Question
• What is the electron configuration of
these atoms?
• Carbon
• Nitrogen
• Sulfur

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Why do some elements react?
• Valence electrons
– Are those in the outermost, or valence shell
– Determine the chemical behavior of an
atom

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Electron Orbitals
• An orbital
– Is the three-dimensional space where an
electron is found 90% of the time

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Electron Orbitals
• Each electron shell
– Consists of a specific number of orbitals

Electron orbitals.
Each orbital holds
up to two electrons. x Y

Z
1s orbital 2s orbital Three 2p orbitals 1s, 2s, and 2p orbitals
Electron-shell diagrams.
Each shell is shown with
its maximum number of
electrons, grouped in pairs.

(a) First shell (b) Second shell (c) Neon, with two filled shells
(maximum (maximum (10 electrons)
Figure 2.9 2 electrons) 8 electrons)

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Chemical Bonding

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Ions
• An anion
– Is negatively
charged ions
• A cation
– Is positively
charged

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Ionic Bonds
• In some cases, atoms strip electrons
away from their bonding partners
• Electron transfer between two atoms
creates ions
• Ions
– Are atoms with more or fewer electrons
than usual
– Are charged atoms

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Ionic Bonding
• An ionic bond
– Is an attraction between anions and cations
1 2 Each resulting ion has a completed
The lone valence electron of a sodium
atom is transferred to join the 7 valence valence shell. An ionic bond can form
electrons of a chlorine atom. between the oppositely charged ions.

+ –

Na Cl Na Cl

Na+ Cl–
Sodium on Chloride ion
Na Cl
(a cation) (an anion)
Chlorine atom
Figure 2.13 Sodium atom
(an uncharged (an uncharged
atom) atom)
Sodium chloride (NaCl)

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Ionic Substances
• Ionic
compounds
– Are often
called salts,
which may
form crystals

Na+
Cl–
Figure 2.14

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Covalent Bonds
• Sharing of a
Hydrogen atoms (2 H)

pair of valence 1 In each hydrogen


atom, the single electron

electrons is held in its orbital by


its attraction to the
+ +
proton in the nucleus.

• Examples: H2
2 When two hydrogen
atoms approach each
other, the electron of
each atom is also + +
attracted to the proton
in the other nucleus.

3 The two electrons


become shared in a
covalent bond,
forming an H2 + +
molecule.
Hydrogen
Figure 2.10 molecule (H2)

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Covalent Bonding
• A molecule
– Consists of two or more atoms held together
by covalent bonds
• A single bond
– Is the sharing of one pair of valence
electrons
• A double bond
– Is the sharing of two pairs of valence
electrons

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Multiple Covalent Bonds
Name Electron- Structural Space-
(molecular shell formula filling
formula) diagram model

(a) Hydrogen (H2).


Two hydrogen
H H
atoms can form a
single bond.

(b) Oxygen (O2).


Two oxygen atoms
share two pairs of O O
electrons to form
a double bond.

Figure 2.11 A, B

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Compounds & Covalent Bonds
Name Electron- Structural Space-
(molecular shell formula filling
formula) diagram model

(c) Water (H2O).


Two hydrogen
atoms and one O H
oxygen atom are
joined by covalent H
bonds to produce a
molecule of water.

(d) Methane (CH4).


Four hydrogen
atoms can satisfy H
the valence of
one carbon
atom, forming H C H
methane.
H
Figure 2.11 C, D
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Covalent Bonding

• Electronegativity
– Is the attraction of a particular kind of atom
for the electrons in a covalent bond
• The more electronegative an atom
– The more strongly it pulls shared electrons
toward itself

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Covalent Bonding
• In a nonpolar
covalent bond
– The atoms have
similar
electronegativiti
es
– Share the
electron equally

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Covalent Bonding
• In a polar covalent bond
– The atoms have differing
electronegativities
– Share the electrons unequally
Because oxygen (O) is more electronegative than hydrogen (H),
shared electrons are pulled more toward oxygen.
δ –

This results in a
partial negative
charge on the
oxygen and a
partial positive
O charge on
the hydrogens.

Figure 2.12 H H
δ + δ +
H2O
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Weak Chemical Bonds
• Several types of weak chemical bonds
are important in living systems

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Hydrogen Bonds
• A hydrogen bond
– Forms when a hydrogen atom covalently
bonded to one electronegative atom is also
attracted to another electronegative atom
δ – δ +

Water H
(H2O) O A hydrogen
bond results
from the
H attraction
between the
δ + partial positive
charge on the
δ – hydrogen atom
of water and
Ammonia the partial
(NH3) N negative charge
on the nitrogen
H H atom of
δ + H δ + ammonia.

Figure 2.15
δ + 43
Van der Waals Interactions
• Van der Waals interactions
– Occur when transiently positive and
negative regions of molecules attract each
other

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Weak Bonds
• Weak chemical bonds
– Reinforce the shapes of large molecules
– Help molecules adhere to each other

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Molecular Shape and Function

• Structure determines Function!


• The precise shape of a molecule
– Is usually very important to its function in the
living cell
– Is determined by the positions of its atoms’
valence orbitals

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Orbitals & Covalent Bonds
• In a covalent bond
– The s and p orbitals may hybridize, creating
specific molecular shapes
Three p orbitals Four hybrid orbitals
Z

s orbital X

Y
Tetrahedron

(a) Hybridization of orbitals. The single s and three p


orbitals of a valence shell involved in covalent bonding
combine to form four teardrop-shaped hybrid orbitals.
These orbitals extend to the four corners of an imaginary
Figure 2.16 (a) tetrahedron (outlined in pink).
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Orbitals & Covalent Bonds
Space-filling Ball-and-stick Hybrid-orbital model
model model (with ball-and-stick
model superimposed)
Unbonded
Electron pair

O O

H H H H
Water (H2O) 104.5°

H H

C C
H H H H
Methane (CH4) H H

(b) Molecular shape models. Three models representing molecular shape are shown
for two examples; water and methane. The positions of the hybrid orbital
Figure 2.16 (b) determine the shapes of the molecules 48
Shape and Function
• Molecular shape
– Determines how biological molecules
recognize and respond to one another with
specificity

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Carbon Nitrogen
Hydrogen Sulfur
Oxygen
Natural
endorphin
Morphine

(a) Structures of endorphin and morphine. The boxed portion of the endorphin molecule (left) binds
to
receptor molecules on target cells in the brain. The boxed portion of the morphine molecule is a close
match.

Natural
endorphin Morphine

Brain cell Endorphin


receptors
(b) Binding to endorphin receptors. Endorphin receptors on the surface of a brain cell
recognize and can bind to both endorphin and morphine.
Figure 2.17
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Chemical Reactions
• Chemical reactions make and break
chemical bonds
• A Chemical reaction
– Is the making and breaking of chemical
bonds
– Leads to changes in the composition of
matter

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Chemical Reactions
• Chemical reactions
– Convert reactants to products

2 H2 + O2 2 H2O

Reactants Reaction Product

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Chemical Reactions
• Photosynthesis
– Is an example of a chemical reaction

Figure 2.18
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Chemical Reactions
• Chemical equilibrium
– Is reached when the forward and reverse
reaction rates are equal

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