Chapter 2
Life’s Chemical
Basis
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2.1 Mercury Rising
• Mercury
– Naturally occurring toxic metal
– Most located in rocky minerals
– Released into the atmosphere by volcanic
activity and burning coal
– Combines with carbon to form methylmercury
• Methylmercury
– Ends up in the tissues of aquatic organisms
– Large predatory fish contain large amounts
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The Effects of Mercury
• Humans who eat fish and shellfish ingest
mercury
• Mercury damages the nervous system,
brain, kidneys, and other organs
– Takes months or years to be cleared from the
body
– Can build up if small amounts are ingested
regularly
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2.2 Start With Atoms
• Atoms consist of:
– Positively charged protons in nucleus
– Uncharged neutrons in nucleus
– Negatively charged electrons orbiting the
nucleus
• Charge
– Electrical property
– Like charges repel; opposite charges attract
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The Characteristics of an Atom
• All atoms have protons
– Most have about the same number of electrons
as protons
• Atomic number
– The number of protons in the nucleus
– Determines the type of atom, or element
• Elements
– Pure substances
– Consist only of atoms with the same atomic
number
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The Periodic Table
• Number of protons, neutrons, and electrons
– Used to predict how elements will behave
• Periodic table
– Arrangement of the elements by atomic number
– Invented by Dmitry Mendeleyev
– Each element is represented by a symbol
typically related to its Latin or Greek name
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Atoms and Elements
A atoms consist of electrons
moving around a nucleus of
protons and neutrons. models
such as this one do not show
what atoms look like. electrons
move in defined, threedimensional spaces about
10,000 times bigger than the
nucleus.
B example of an
element.
proton
+
–
–
neutron
electro
n
C
element
symbol
mass
number
elemental
substance
element
name
1
carbon
H
–
6
atomic number
12
2
He
3
4
5
6
7
8
9
10
Li
Be
B
C
N
O
F
Ne
11
12
13
14
15
16
17
18
Na Mg
19
20
21
K
Ca
Sc
37
38
39
22
Al
Si
P
S
Cl
Ar
28
29
30
31
32
33
34
35
36
Co
Ni
Cu
Zn
Ga
Ge
As
Se
Br
Kr
45
46
47
48
49
50
51
52
53
54
23
24
25
26
27
Ti
V
Cr
Mn
Fe
40
41
42
43
44
Rb
Sr
Y
Zr
Nb
Mo
Tc
Ru
Rh
Pd
Ag
Cd
In
Sn
Sb
Te
I
Xe
55
56
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
Cs
Ba
Lu
Hf
Ta
W
Re
Os
Ir
Pt
Au
Hg
Tl
Pb
Bi
Po
At
Rn
87
88
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
Fr
Ra
Lr
Rf
Db
Sg
Bh
Hs
Mt
Ds
Rg
Cn Uut
Fl
57
58
59
60
61
62
63
64
65
66
67
68
La
Ce
Pr
Nd
Pm Sm
Eu
Gd
Tb
Dy
Ho
Er
89
90
91
92
93
94
95
96
97
98
99
100
101
102
Ac
Th
Pa
U
Np
Pu
Am Cm
Bk
Cf
Es
Fm
Md
No
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Uup Lv
69
70
Tm Yb
Uus Uuo
Isotopes and Radioisotopes
• All atoms of an element have the same
number of protons
– Can differ in number of other subatomic
particles
• Isotopes
– Differ in number of neutrons
• Mass number
– The total number of neutrons and protons in the
nucleus of an isotope
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Carbon 12 and 14
• Carbon 12 (12C)
– Most common Carbon isotope
– Contains six protons and six neutrons
• Carbon 14 (14C)
– Example of a radioactive isotope (radioisotope)
– Naturally occurring
– Unstable nucleus breaks up spontaneously
• Emits radiation (radioactive decay)
– Decay occurs at a predictable rate
• Basis of carbon dating
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Tracers and Radioisotopes
• Tracers
– Substances with a detectable component
– Radioisotopes are often used
– Widely used in research
• Medical application of radioisotopes
– PET (positron-emission tomography)
• Allows us to see a process within a person’s body
using a radioactive sugar or other tracer
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2.3 Why Electrons Matter
• Electrons
– Have mass but no size
– Move fast but never collide
– Gain energy by absorbing only the amount
needed to boost it to the next energy level
– Emits energy in precise amounts
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A The first shell corresponds to the first
energy level, and it can hold up to 2
electrons. Hydrogen has one proton, so
it has 1 electron and 1 vacancy. A
helium atom has 2 protons, 2 electrons,
and no vacancies. The number of
protons in each model is shown.
B The second shell corresponds to
the second energy level, and it can
hold up to 8 electrons. Carbon has 6
protons, so its first shell is full. Its
second shell has 4 electrons, and
four vacancies. Oxygen has 8
protons and two vacancies. Neon has
10 protons and no vacancies.
first shell
second shell
C The third shell, which corresponds
to the third energy level, can hold up to
8 electrons. A sodium atom has 11
protons, so its first two shells are full; third shell
the third shell has one electron. Thus,
sodium has seven vacancies. Chlorine
has 17 pro tons and one vacancy.
Argon has 18 protons and no
vacancies.
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1 proton
1
1 electron
hydrogen (H)
2
helium (He)
6
8
carbon (C)
oxygen (O)
11
17
sodium (Na)
chlorine (Cl)
10
neon (Ne)
18
argon (Ar)
Stepped Art
Shell Models
A t h e fi r s t s h e l l corresponds to the first
1
one proton
energy level, and it can hold up to 2
electrons. Hydrogen has one proton, so it
has 1 electron and 1 vacancy. a helium atom
has 2 protons, 2 electrons, and no
vacancies.
2
one
first
l
hydrogen electron
(H)
helium
(He)
B t h e s e c o n d s h e l l corresponds to the
6
second
shell
carbon
(C)
11
third
shell
sodium
(na)
8
oxygen
(o)
17
chlorine
(Cl)
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10
neon
(ne)
18
argon
(ar)
second energy level, and it can hold up to 8
electrons. Carbon has 6 electrons, so its first
shell is full. its second shell has 4 electrons
and four vacancies. oxygen has 8 electrons
and two vacancies. neon has 10 electrons
and
no vacancies.
c t h e thi rd s h e l l corresponds to the
third energy level, and it can hold up to 8
electrons. a sodium atom has 11 electrons,
so its first two shells are full; the third shell
has one electron. Thus, sodium has seven
vacancies. Chlorine has 17 electrons and
one vacancy. argon has 18 electrons and no
vacancies.
The Shell Model and Stability
• Shell model
– Used to help visualize how electrons populate
atoms
• Shells are filled from the innermost shell
outward
• When atom’s outer shell filled with electrons
– In a stable state
– Examples: helium, neon, argon
• Stable atoms have little tendency to interact
with other atoms
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Vacancies and Free Radicals
• When atom’s outer shell has a vacancy
– Has room for another electron
– Tends to get rid of electrons by interacting with
other atoms
– Chemically active
• Free radicals
– Atoms with unpaired electrons
– Very unstable
– Dangerous to life
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electron loss
electron gain
Sodium
atom
Chlorine
atom
11p+
11e–
17p+
17e–
charge: 0
charge: 0
Sodium
ion
Chloride
ion
11p+
10e–
17p+
18e–
charge: +1
charge: –1
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Stepped Art
electron gain
electron loss
17
11
17
11
Sodium
atom
Sodium
ion
Chlorine
atom
Chloride
ion
11p+
11e– 0
charge:
11p+
–
10e
charge:
+1
17p+
–
17e
charge:
0
17p+
–
18e
charge:
–1
A a sodium atom (na) becomes a positively charged sodium
ion (na +) when it loses the single electron in its third shell. The
atom’s full second shell is now its outermost, so it has no
vacancies.
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B a chlorine atom (Cl) becomes a negatively charged chloride
ion (Cl–) when it gains an electron and fills the vacancy in its
third, outermost shell.
Ions
• Atoms with unequal number of protons and
electrons
• Carry a net charge
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2.4 Chemical Bonds: From Atoms to
Molecules
• Chemical bond
– Attractive force arising between two atoms
when their electrons interact
• Molecules
– Formed when atoms interact
– Held together by chemical bonds
• Compound
– Molecule consisting of two or more elements
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Ionic Bonds and Polarity
• Ionic bonds
– Atoms are held together by mutual attraction of
opposite charges
– Can be quite strong
– Example: table salt (NaCl)
• Polarity
– Separation of charge
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Electronegativity and Covalent Bonds
• Electronegativity
– Measures atom’s tendency to pull electrons
away from another atom
• Covalent bonds
– Occur when electrons from different atoms
share a space in a shell
– Can be stronger than ionic bonds
• But not always stronger
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Structural Formulas
• Line between two atoms indicates a single
covalent bond
• Double line indicates a double bond
– Two atoms sharing two pairs of electrons
– Stronger than a single bond
• Triple line indicates a triple bond
– Two atoms sharing three pairs of electrons
• Stronger than a double bond
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Covalent Bonds in Molecules
• Insert Table 2.1 without the title and split up
into two, placed side by side
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Structural Models
• Structural models
– Balls connected with sticks
– No distinction between single, double, and triple
bonds
• Polar covalent bond
– Atoms share electrons unequally
– One side slightly more electronegative than the
other
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M o l e c u l a r H y d r o g e n (H—H)
1
Two hydrogen atoms, each
with one proton, share two
electrons
in
a
nonpolar
covalent bond.
1
8
Molecular Oxygen
(O=O)
8
Two oxygen atoms, each with
eight protons, share four
electrons in a double covalent
bond.
W a t e r (H—O—H)
1
8
1
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Two hydrogen atoms share
electrons with an oxygen atom in
two covalent bonds. The bonds
are polar because the oxygen
exerts a greater pull on the
shared electrons than the
hydrogens do.
2.5 Hydrogen Bonds and Water
• Water has unique properties
– Molecule has no overall charge
– Oxygen atom carries slight negative charge
– Hydrogen atoms carry slight positive charges
– Polarity attracts them to one another
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The Hydrogen Bond Explained
• Attraction between a covalently bonded
hydrogen atom and another atom taking part
in a separate polar covalent bond
• Not a chemical bond
• Forms and breaks more easily than covalent
or ionic bonds
• Collectively quite strong
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Hydrogen Bonds and Water
• Extensive hydrogen bonding gives liquid
water special properties
– Makes life possible
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slight negative
charge
–
A polarity of the water
molecule. each of the
hydrogen atoms in a water
molecule bears a slight
positive charge (represented
by a blue overlay). The
oxygen atom carries a slight
negative charge (red
overlay).
O
H
H
+
+
Slightpositvecharge
a hydrogen bond
B a hydrogen bond is
an attraction between
a hydrogen atom and
another atom taking
part in a separate
polar covalent bond.
c The many
hydrogen bonds that
form among water
molecules impart
special properties to
liquid water.
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H
H
O
H
O
H
Water’s Special Properties: Hydrophilic
• Water is an excellent solvent
– Other substances can easily dissolve in it
• Hydrophilic
– Water-loving
– Hydrophilic substances dissolve easily in water
• Solution
– Uniform mixture
– Example: salt dissolved in water
– Proportions of substances in a solution can vary
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Water’s Special Properties:
Hydrophobic
• Concentration
– Amount of solute dissolved in a given fluid
amount
• Hydrophobic
– Water-dreading
– Hydrophobic substances do not interact with
water
• Example: oils
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Water’s Special Properties: Cohesion
and Evaporation
• Cohesion
– Hydrogen bonds collectively exert a continuous
pull on individual water molecules
– Plays a role in surface tension
• Evaporation
– Water molecules escape from liquid water
surface as vapor
– Resisted by hydrogen bonding
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Temperature
• Temperature
– Measure of the energy of motion of atoms and
molecules
• Water stabilizes temperature
– Hydrogen bonding keeps water molecules from
moving as much as they would otherwise
• Temperature stability
– Important part of homeostasis
– Molecules of life function within certain range of
temperature
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2.6 Acids and Bases
• pH
– A measure of the number of hydrogen ions in a
water-based fluid
• Pure water has a neutral pH of 7
• Lower pH fluids have more hydrogen ions
than higher pH fluids
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Acids
• Acids
– Substances that give up hydrogen ions in water
– Have pH below 7
– Example: lemon juice (pH 2)
• Acids range from weak to strong
– Gastric fluid inside stomach is strongly acidic
(pH 1-2)
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Bases
• Accept hydrogen ions from water
• Have pH above 7
• Example: baking soda dissolved in water
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Carbonic Acid and Buffers
• Carbonic acid
– Forms when carbon dioxide gas dissolves in
blood plasma
– A weak acid
– Gives up a hydrogen ion in water
• Becomes a bicarbonate
• Buffer
– Set of chemicals that act to keep pH stable
– Example: carbonic acid and bicarbonate
together
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The Bicarbonate Buffer System
• Carbonic acid
– When base is added, carbonic acid gives up
hydrogen ions to become bicarbonate
• Hydrogen ions replace those that base removed from
the system
– When acid is added, hydrogen ions released by
the acid combine with the bicarbonate
– pH remains stable, between 7.3 and 7.5
– Addition of too much acid or base can
overwhelm the system
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Issues with Breathing
• When breathing is impaired:
– Carbon dioxide gas accumulates in tissues
– Too much carbonic acid forms in plasma
– If excess acid reduces blood pH below 7.3
• Coma results
• When hyperventilation occurs:
– Body loses too much carbon dioxide
– Blood pH increases
– Prolonged muscle spasm or coma may occur
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Burning Coal and Fossil Fuels
• Burning coal and fossil fuels
– Releases sulfur and nitrogen compounds
– Affects the pH of rain
– Rain is not buffered, so addition of acid has
dramatic effects
• Causes corrosion
• Affects pH of soils, lakes, and streams and the
organisms living there
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Points to Ponder
• Water is the “universal solvent” on Earth
– Do you know of any other compound that would
serve as well or better?
– If life existed on a remote waterless planet,
could another substance replace it as an
effective solvent?
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