BIO 2, Lecture 3
THE CHEMISTRY OF LIFE I:
ATOMS, MOLECULES,
AND BONDS
–
O

H
+
H
H2O

+
• Matter is made up of elements
• A substance that cannot be broken down
to other substances by chemical reactions
• 92 naturally-occurring elements (periodic
table)
• A compound is a substance consisting
of two or more elements in a fixed
ratio (e.g. NaCl, MgCl2)
• A compound has characteristics different
from those of its elements
Sodium
Chloride
Sodium
Chloride
About 25 of the 92
naturally-occurring
elements are
essential to living
organisms on Earth
Dwarfing of plants due to
nitrogen deficiency
Goiter due to iodine
deficiency
• An element’s chemical behavior and
properties depend on the structure of
its atoms
• Each element consists of unique atoms
• An atom is the smallest unit of matter
that still contains the behavior and
properties of an element
• Atoms are composed of a nucleus
containing protons (+) and (usually)
neutrons, and electrons (-) that inhabit
defined energy shells around the nucleus
Cloud of negative charge
(2 electrons)
Electrons
Nucleus
(a)
(b)
• Atoms of the various elements differ in
number of subatomic particles they
contain
• An element’s atomic number is the
number of protons in its nucleus
• An element’s mass number is the sum of
protons plus neutrons in the nucleus
• Atomic mass, the atom’s total mass, can
be approximated by the mass number
(since electrons are so light)
• All atoms of an element have the same
number of protons but may differ in
number of neutrons
• Isotopes are two atoms of an element
that differ in number of neutrons
• Radioactive isotopes decay
spontaneously, giving off particles and
energy
Isotopes of hydrogen:
Symbol Name
# protons
# neutrons
Half-life
1H
1
1
1
1
1
1
1
0
1
2
3
4
5
6
Stable
Stable
12.3 yrs
Very low*
Very low*
Very low*
Very low*
2H
3H
4H
5H
6H
7H
Protium
Deuterium
Tritium
Lab only
Lab only
Lab only
Lab only
* less than 10-22 seconds
• Some applications of radioactive
isotopes in biological research are:
– Dating rocks and fossils
– Tracing atoms through metabolic processes
to learn about those processes
– Diagnosing medical disorders
Parent Isotope
Stable Daughter
Product
Currently Accepted
Half-Life Values
Uranium-238
Lead-206
4.5 billion years
Uranium-235
Lead-207
704 million years
Thorium-232
Lead-208
14.0 billion years
Rubidium-87
Strontium-87
48.8 billion years
Potassium-40
Argon-40
1.25 billion years
Compounds including
radioactive tracer
(bright blue)
Human cells
1 Human
cells are
incubated
with compounds used to
make DNA. One compound is
labeled with 3H.
2 The cells are
placed in test
tubes; their DNA
is isolated; and
unused labeled
compounds are
removed.
Incubators
1
10º
C
4
25º
C
7
40º
C
2
15º
C
5
30º
C
8
45º
C
3
20º
C
6
35º
C
9
50º
C
DNA (old and new)
3 The test tubes are placed in a scintillation counter.
Counts per minute
( 1,000)
30
20
Optimum
temperature
for DNA
synthesis
10
0
10
20 30 40
Temperature
(ºC)
50
Cancerous
throat
tissue
• Energy is the capacity to do work (fight
entropy)
• Atoms have mass and therefore have
potential energy; E = mc2
• Part of this energy is stored in the
nucleus of the atom and part is stored in
the energy levels of the electrons
• An electron’s state of potential energy is
called its energy level, or electron shell
(a) A ball bouncing down a flight
of stairs provides an analogy
for energy levels of electrons
(b)
Third shell
(highest energy level)
Second shell
(higher energy level)
Energy
absorbed
First shell
(lowest energy level)
Energy
lost
Atomic
nucleus
• The chemical behavior of an atom is
determined by the distribution of
electrons in electron shells
• The periodic table of the elements shows
the electron distribution for each
element
• Valence electrons are those in the
outermost shell, or valence shell
• Elements with filled valence shells are
inherently stable and don’t readily
combine with other elements
Hydrogen
1H
Atomic mass
First
shell
Lithium
3Li
Beryllium
4Be
Sodium
11Na
Magnesium Aluminum
12Mg
13Al
Boron
5B
2
He
4.0
0
Atomic number
Helium
2He
Element symbol
Electrondistribution
diagram
Carbon
6C
Nitrogen
7N
Oxygen
8O
Fluorine
9F
Neon
10Ne
Silicon
14Si
Phosphorus
15P
Sulfur
16S
Chlorine
17Cl
Argon
18Ar
Second
shell
Third
shell
• An orbital is the three-dimensional
space where an electron is found 90% of
the time
• Each electron shell consists of a specific
number of orbitals
• 1S (1 orbital; 2 electrons)
• 2S (1 orbital; 2 electrons)
• 2P (3 different oribitals; 6 electrons)
• The shell is designated by the number,
the orbitals by the letter
• Atoms seek filled shells above all else
(a) Electron-distribution
diagram
(b) Separate electron
orbitals
Neon, with two filled shells (10 electrons)
First shell
Second shell
y
x
1s orbital 2s orbital
z
Three 2p orbitals
(c) Superimposed electron
orbitals
1s, 2s, and 2p orbitals
• Atoms with incomplete valence shells can
share or transfer valence electrons with
certain other atoms
• These interactions usually result in atoms
staying close together, held by
attractions called chemical bonds
• A covalent bond is the sharing of a pair
of valence electrons by two atoms
• In a covalent bond, the shared electrons
count as part of each atom’s valence shell
Hydrogen
atoms (2 H)
Both atoms
unstable
(unfilled
valence shells)
Atoms stable,
share electrons so
both have filled
valence shells
e-
e-
e-
e-
eeHydrogen
molecule (H2)
• A molecule consists of two or more atoms
held together by covalent bonds
• A single covalent bond, or single bond, is
the sharing of one pair of valence
electrons
• A double covalent bond, or double bond,
is the sharing of two pairs of valence
electrons
Name and
Molecular
Formula
Electrondistribution
Diagram
Lewis Dot
Structure and
Structural
Formula
Spacefilling
Model
(a) Hydrogen (H2)
(b) Oxygen
(O2)
(c) Water
(H2O)
(d) Methane
(CH4)
COVALENT
BONDS
• Covalent bonds can form between
atoms of the same element or atoms
of different elements
• A compound is a combination of two or
more different elements
• Bonding capacity is called the atom’s
valence
• Electronegativity is an atom’s attraction
for the electrons in a covalent bond
• The more electronegative an atom, the
more strongly it pulls shared electrons
toward itself
• In a nonpolar covalent bond, the atoms
share the electron equally
• In a polar covalent bond, one atom is more
electronegative, and the atoms do not share
the electron equally
Unequal sharing of electrons causes a
partial positive or negative charge for
each atom or molecule (e.g. water)
–
O
+
H
H
H2O
+
The oxygen nucleus
has more protons and
attracts the shared
electrons more
strongly than the
hydrogen nuclei
• Rather than sharing electrons, atoms
sometimes transfer electrons to their
bonding partners because it fills their
valence shells (makes them stable)
• An example is the transfer of an electron
from sodium to chlorine
• After the transfer of an electron, both
atoms have charges
• A charged atom (or molecule) is called an ion
• Ions with opposite charges attract to form
ionic bonds
Na
Cl
Na
Cl
Na
Sodium atom
Cl
Chlorine atom
Na+
Sodium ion
(a cation)
Cl–
Chloride ion
(an anion)
Sodium chloride (NaCl)
IONIC BOND
• Compounds formed by ionic bonds are
called ionic compounds, or salts
• Salts, such as sodium chloride (table
salt), are often found in nature as
crystals because they stack easily
Na+
Cl–
• Most of the strongest bonds in organisms
are covalent bonds that form a cell’s
molecules
• Weak chemical bonds, such as ionic bonds
and hydrogen bonds, are also important
• Weak chemical bonds reinforce shapes of
large molecules and help molecules adhere
to each other
• A hydrogen bond forms when a
hydrogen atom covalently bonded to one
electronegative atom is also attracted
to another electronegative atom
• In living cells, the electronegative
partners are usually oxygen or nitrogen
atoms
• Hydrogen bonding is important in water,
DNA and RNA, proteins, and many other
molecules important for life

+
Water
(H2O)


HYDROGEN
BOND
+
Ammonia
(NH3)


+

+
+