Biotech 2:
Atoms and Molecules
OS Text Reading – pp. 36-48
Electron cloud
Protons
2e– Nucleus
Electrons
Mass number = 4
Neutrons
2
2
2
Electron cloud
Protons
6e–
Nucleus
Electrons
Mass number = 12
Neutrons
6
6
6
Helium
Carbon atomic number =
# of protons
mass number =
# of neutrons & protons
Atoms &
Subatomic
Particles
Atoms of the same element having different numbers of
neutrons are referred to as different isotopes, some of
which are unstable and thus radioactive.
Isotopes
• radioactive emissions are of different types
depending on the isotope
*
• each radioactive isotope has a characteristic half-life
Neon, with two filled
Shells (10 electrons)
First shell
Second shell
First shell Second shell
1s orbital 2s orbital Three 2p orbitals
(a) Electron distribution diagram
(b) Separate electron orbitals
(c) Superimposed electron orbitals
1s, 2s, and
2p orbitals
x y
z
Electron
Orbitals
• orbitals are geometrically
arranged regions of
space around an atomic
nucleus in which
electrons are found
• orbitals are arranged
in groups at distinct
energy levels called
electron shells
• each orbital can hold no
more than 2 electrons
(a) A ball bouncing down a flight of stairs provides an analogy for energy levels of electrons
Third shell (highest energy level)
Second shell (higher energy level)
Energy absorbed
First shell (lowest energy level)
Atomic nucleus
(b)
Energy lost
Energy Shells
First
shell
Second
shell
Third
shell
Hydrogen
1H
Lithium
3Li
Sodium
11Na
Beryllium
4Be
Magnesium
12Mg
Boron
5B
Aluminum
13Al
Carbon
6C
Silicon
14Si
Nitrogen
7N
Phosphorus
15P
Oxygen
8O
Sulfur
16S
Fluorine
9F
Chlorine
17Cl
Neon
10Ne
Argon
18Ar
Helium
2He 2
He
4.00 Mass number
Atomic number
Element symbol
Electron
distribution
diagram
The Periodic Table • elements in the same column have the same number of
valence electrons, and similar chemical properties
Hydrogen atoms (2 H)
Hydrogen molecule (H2)
The Formation of
Molecules
2 or more atoms connected
by a chemical bond(s)
constitute a molecule
• chemical bonds involve
unpaired electrons from each
atom involved in the bond
• covalent bonds involve the
sharing of such electrons
• jonic bonds involve the
donation/acceptance of
such electrons
(a) Hydrogen (H2)
(b) Oxygen (O2)
(c) Water (H2O)
Name and
Molecular
Formula
Electron
Distribution
Diagram
Lewis Dot
Structure and
Structural
Formula
Space-
Filling
Model
(d) Methane (CH4)
Representing
Molecular
Structure
Polarity in Covalent Bonds
–
+ + H H
O
H2O
The sharing of electrons in covalent bonds is not
necessarily equal, depending on the electronegativity
of the atoms involved in the bond:
• non-polar bonds occur between atoms of the same or
similar electronegativities due to equal sharing of e-
• polar bonds occur between
atoms with significantly
different electronegativities
due to unequal sharing of e-
Non-polar Molecules
• electrons are shared equally between identical atoms since
their attraction for electrons (electronegativity) is the same
Polar Molecules
• elements tend to
vary in their
electronegativities
• if atoms sharing
electrons differ
significantly in
electronegativity,
the electrons are
shared unequally
and the bond is
polar
NON-POLAR
POLAR
C & H electronegativies
are ~ the same
O & H electronegativities
are significantly different
+
+
+
+
+
water (H2O)
ammonia (NH3)
Hydrogen bond
Polarity & Hydrogen Bonds Hydrogen bonds are weak interactions that occur
between atoms involved in polar covalent bonds,
one of which is a hydrogen atom:
+ H atom bound
to a more
electronegative
atom (e.g., N or O)
- charge on atom
of another
molecule or
chemical group
+ –
Na
Sodium atom Cl
Chlorine atom
Na+
Sodium ion
(a cation)
Cl–
Chloride ion
(an anion)
Ionic bond
Electronic
transfer
forms ions
Ions and Ionic Bonds
Na+
Cl–
sodium chloride (NaCl)
crystal
opposing ions
form neutral salts
Reactants Reaction Products
2 H2 O2 2 H2O
Chemical Reactions
Covalent bonds in reactant molecules break and
the atoms form new covalent bonds in the products
• all atoms from reactants end up in products
• chemical reactions are reversible, direction depends on
conditions, concentrations of products vs reactants