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Essentials of

Biology
Sylvia S. Mader
Michael Windelspecht

Chapter 2
The Chemical
Basis of Life
Lecture Outline

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2.1 Atoms and Atomic Bonds
Matter
 Refers to anything that takes up space and
has mass
 Can exist as a solid, liquid, or gas
 Composed of elements
• Element—substance that cannot be broken down
into another substance by ordinary chemical
means
• Only 92 naturally occurring elements
• Four elements make up about 96% of the body
weight of most living organisms—carbon,
hydrogen, oxygen, and nitrogen
Figure 2.1 Elements in
living organisms.
• Atomic structure
 Atomic theory states that elements consist of
atoms
 Atomic symbol—name of the atom or element
• H for hydrogen or Na for sodium
 Subatomic particles
• Neutrons—no electrical charge, found in nucleus
• Protons—positive charge, found in nucleus
• Electrons—negative charge, found outside of
nucleus
 Mass number is equal to sum of protons and
neutrons—electrons have about zero mass
• Atomic weight changes with gravity
Figure 2.2 Two models of helium (He).
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+ = proton = neutron – = electron

inside nucleus outside nucleus

+ +
– nucleus
+ +


a. b.
• Atomic number
 All atoms of an element have this same
number of protons
 Also gives number of electrons if an atom is
electrically neutral
• Periodic table
 Elements’ chemical and physical
characteristics recur in a predictable manner
 Atoms are arranged in periods (rows) and
groups (columns)
Figure 2.3 A portion of the periodic table.
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Groups

1 2
H He
1.008 4.003
3 4 5 6 7 8 9 10
Li Be B C N O F Ne
6.941 9.012 10.81 12.01 14.01 16.00 19.00 20.18
11 12 13 14 15 16 17 18
Na Mg Al Si P S Cl Ar
22.99 24.31 26.98 28.09 30.97 32.07 35.45 39.95
19 20 31 32 33 34 35 36
Periods

K Ca Ga Ge As Se Br Kr
39.10 40.08 69.72 72.59 74.92 78.96 79.90 83.60
• Isotopes
 Atoms of the same element that differ in the
number of neutrons
 Isotopes have the same number of protons
but a different number of neutrons (different
mass numbers)
 Unstable and may decay, emitting radiation
 Radioactive isotope behavior is essentially the
same as a stable isotope of same element
• Can be used as tracer—PET scan
• Can cause damage to cells leading to cancer
• Can be used to sterilize medical equipment
Figure 2.4 PET scan.
Figure 2.5 High levels of
radiation.
• Arrangement of electrons in an atom
 Electrons are constantly moving.
 Useful to construct models of atoms with energy
levels or electron shells
 Each shell contains a certain number of electrons.
 For atoms up through number 20
• 2 electrons fill first shell
• 8 electrons fill each additional shell
 Octet rule for valence shell
• Valence shell—outermost shell
• If an atom has more than 2 shells, the outer shell is most
stable with 8 electrons
• Atoms can give up, accept, or share electrons to have 8
 Chemical properties of atoms are largely determined
by the arrangement of their electrons.
Figure 2.6 Atoms of the six important elements.
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inner shell
electron
electron
shell P
H nucleus C N O

outer
Hydrogen (valence)
1 shell
H
1 Carbon Nitrogen Oxygen Phosphorus
6 7 8 15
C N O P
12 14 16 31

Sulfur
16
S
32
• Types of chemical bonds
 Molecule—group of atoms bonded together
• O2, H2O, C6H12O6, N2
 Compound—molecule containing atoms of
more than one element
• H2O, C6H12O6
 2 types of bonds
• Ionic—attraction between opposite charges
• Covalent—sharing electrons to complete outer
shell
• Ionic bonding
 Forms when 2 atoms are held together by the
attraction between opposite charges
 Sodium has 1 electron in valence shell
• Usually gives up an electron
 Chlorine has 7 electrons in valence shell
• Usually accepts an electron from another atom
Figure 2.7a Formation of sodium chloride.

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Na Cl

sodium atom (Na) + chlorine atom (Cl)


a.
 Ions—charged atoms

• Sodium has 1 more proton than electrons: now Na+

• Chlorine has 1 more electron than protons: now Cl-

• Ionic compounds often called salts


Figure 2.7a Formation of sodium chloride, continued

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Na Cl

sodium atom (Na+) chlorine atom (Cl–)


a.
= sodium chloride (NaCl)
• Covalent bonding
 2 atoms share electrons
 2 hydrogen atoms can share electrons to fill
their outer shell—orbitals overlap.
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H H

Hydrogen gas (H2)

 Structural formula—uses straight lines H-H


• 1 line indicates 1 pair of shared electrons.
 Molecular formula—simply shows number of
atoms involved H2
• Double covalent bond—sharing 2 pairs of
electrons
 Oxygen gas O2 or O=O
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Oxygen gas (O2)


• Triple covalent bond—sharing 3 pairs of
electrons
 Nitrogen gas N2 or N≡N
• Single atom may form bonds with more than one
atom
 May be represented by ball-and-stick models or
space-filling models
Figure 2.8 Shapes of covalently bonded molecules.
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Methane (CH4)

H
H C H H C H
H
b. Structural model

a. Electron model showing covalent bonds

hydrogen H

covalent bond

carbon C
H
H
109°
H
d. Space-filling model
c. Ball-and-stick model
• Chemical formulas and reactions
 Reactants—molecules that participate in reactions
• Shown to the left of the arrow
 Products—molecules formed by reactions
• Shown to the right of the arrow
 Equation is balanced if the same number of each type of atom
occurs on both sides of the arrow.
• An overall equation for photosynthesis
Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

6 CO2 + 6 H2O C6H12O6 + 6 O2


carbon water glucose oxygen
dioxide

• Molecular formula for glucose


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one molecule
C6H12O6

indicates indicates indicates


6 atoms 12 atoms 6 atoms
of carbon of hydrogen of oxygen
Quick Question
Q) What is the general structure of an atom?
A) The nucleus us a small dense center with
the protons and neutrons packed tightly into
it. There are concentric orbitals around the

nucleus with electrons.
proton
+
nucleus neutron
+
electron
orbital

Quick Question
Q) Can you create a summary table showing
the mass, location, and charge of the three
subatomic particles?
A)
Quick Question
Q) How does the arrangement of electrons
relate to the location on the periodic table?
A) “Period” tells me how many orbitals or
rings of electrons there are around the
nucleus, “group” tells me how many
electrons are in the outer orbital
Example: period 2 group 6 is Oxygen (O),
and period 4 group 1 is Potassium (K)
Quick Questions
Q) How does the placement of elements on the periodic
table relate to their bonding with each other?
A) Things close together form covalent bonds* and
things far apart form ionic bonds

Q) What are isotopes, and how/why are they useful?


A) The have the same number of protons and electrons,
but different neutrons. This makes them chemically the
same, but physically different, so they (or their decay)
can be tracked and measured. This is useful in
radiometric dating, and medical treatments or
procedures
Quick Question
Q) Contrast ionic and covalent bonding
A) Ionic bonding involves the transfer of electrons,
occurs from elements far apart on the periodic table,
name ends in “ide”*, have high melting points, will
conduct electricity, and generally involves only a
handful of elements. Covalent bonds involves the
sharing of electrons, occur between elements close
together on the periodic table, have a variety of
endings, low melting points, won’t conduct electricity,
and can be large or small.
EX: NaCl – sodium chloride, is ionic
CO2 – carbon dioxide is covalent
Quick Questions
Q) Can you identify the products and the reactants in
the two equations below, and describe the
relationship of the two equations?

A) The reactants go in; they are to the left of the


arrow. The products come out; they are to the
right of the arrow.
In this case, the reactants of one are the product of
the other
2.2 Water’s Importance to Life
• Life began in water
• Single most important molecule on Earth
• All organisms are 70–90% water
• Water has unique properties that make it a
life-supporting substance
• Properties stem from the structure of the
molecule
• The structure of water
 Polar covalent bond
• Atoms do not share electrons equally.
• Oxygen is more electronegative than hydrogen.
• Electrons spend more time around the oxygen
nucleus than the hydrogen nuclei.
• Oxygen end becomes slightly negative/hydrogens
become slightly positive—NOT an ionic bond or
ions
 Hydrogen bond—slightly positive hydrogen of
one water molecule attracted to the slightly
negative oxygen in another water molecule
Figure 2.9 The structure of water.

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Oxygen is slightly negative (–)

b. hydrogen bond
O
H H
a.

Hydrogens are slightly positive (+)


• Properties of water
 Solvency
 Cohesion and adhesion
 High surface tension
 High heat capacity
 High heat of vaporization
 Varying density
• Water is a solvent
 Due to polarity and H-bonding, water
dissolves many substances
 Hydrophilic—molecules attracted to water
 Hydrophobic—molecules not attracted to
water
 Water causes NaCl to dissociate
• Cohesion
 Ability of water molecules to cling to each other due to
hydrogen bonding
• Adhesion
 Ability of water molecules to cling to other polar
surfaces
• Allows water to be excellent transport system
both in and outside of living organisms
• Contributes to water transport in plants
Figure 2.10 Cohesion and adhesion of water molecules.
• Water has a high surface tension
 Water molecules at the surface cling more
tightly to each other than to the air above.
 Mainly due to hydrogen bonding
• Water has a high heat capacity
 The many hydrogen bonds linking water
molecules allow water to absorb heat
without greatly changing its temperature.
 Temperature of water rises and falls slowly
• Heat of vaporization
 Takes a great deal of energy to break H
bonds for evaporation
 Heat is dispelled as water evaporates.
Figure 2.11 Heat of vaporization.
• Ice is less dense than water
 Unlike other substances, water expands as it
freezes.
 Ice floats rather than sinks.
 It makes life possible in water.
 Ice acts as an insulator.
Figure 2.12 Properties of ice.
The Biological Significance of
Ice Floating
– When water molecules get cold enough, they
move apart, forming ice.
– A chunk of ice has fewer molecules than an
equal volume of liquid water.
– Ice floats because it is less dense than the liquid
water around it.
The Biological Significance of Ice Floating
•This change in density allows for bodies of water to
“turn over”, a process that helps circulate water
between the top and bottom twice a year.
Quick Questions
Q) What properties of water make it so unique, and
important to life?
A) Polar covalent bonds between O and H create high
solvency, Cohesion and adhesion, High surface
tension, High heat capacity, High heat of
vaporization, Varying density

Q) Why is hydrogen bonding so important?


A) Allows water to dissolve lots of stuff and therefor be a
good transport medium, allows adhesion and cohesion,
high heat capacity, high heat of vaporization, and allows
ice to be less dense than water.
2.3 Acids and Bases

• Water dissociates into an equal number of


hydrogen ions (H+) and hydroxide ions (OH–)
Acidic Solutions (High H+ Concentration)

• Lemon juice, vinegar, and coffee


• Acids release hydrogen ions
Basic Solutions (Low H+ Concentration)

• Milk of magnesia and ammonia


• Either take up hydrogen ions or release
hydroxide ions
• pH and the pH scale
 Mathematical way to indicate the number of
hydrogen ions in solution
 pH scale ranges from 0 to 14
• pH below 7 is acidic—more [H+] than [OH–]
• pH above 7 is basic—more [OH–] than [H+]
• pH of 7 is neutral—[H+] equal to [OH–]
Figure 2.13 The pH scale.
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hydrochloric acid (HCI) 0

Increasing [H+]
stomach acid 1

lemon juice 2

Acid
Coca-Cola, beer, vinegar 3
[H+]
tomatoes 4

black coffee 5
normal rain water
urine 6
saliva
pure water, tears [H+] =
7 neutral pH
human blood [OH–]
seawater 8

baking soda, stomach antacids9

Increasing [OH–]
Great Salt Lake10
milk of magnesia [OH–]
household ammonia11

Base
bicarbonate of soda 12

oven cleaner13

sodium hydroxide (NaOH)14


• Buffers and pH
 Chemical or combination of chemicals that
keeps pH within normal limits
 Resists pH change by taking up excess H+ or
OH–
 pH of blood is about 7.4—maintained by
buffer
Figure 2.14 Acidosis.
Quick Questions
Q) Contrast the characteristics of an acid
with a base

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