Topic 3:

Atoms and Bonding

BIOL-107
What do all of these things have in common?
They are ALL made up of chemical elements
 What is an Element?
• Elements are substances that cannot be broken
down into simpler substances by chemical reactions
(i.e. non-nuclear reactions)

• Elements are identified by chemical symbols

O = oxygen ; H = hydrogen; C = carbon

*Some elements have scientific names different from their

common names:
sodium
Na = natrium
gold
Au = aurum
 Elements
• A list of elements can be found on the
Periodic Table
• There are currently 118 unique elements
• ~25 are found commonly in biological
molecules
• Of those, only 6 elements make up 95% of an
organism. These are known as the CHNOPS
elements:
 The Atom
An atom is the basic building block of all matter and is
the smallest unit of matter that has the properties of a
chemical element.

Carbon Graphite Carbon Graphite Carbon Atom

#2 Pencil Molecule
 The Atom

Atoms are made up of 3 subatomic particles:

1. Protons: positive charge
2. Neutrons: neutral charge
3. Electrons: negative charge
 Protons
NUCLEUS
Neutrons

Electron
(Orbit in shells outside the nucleus)
 Subatomic Particle Summary
Particle Mass Charge Location

Proton 1 amu Nucleus

Neutron 1 amu Neutral Nucleus

(No charge)
9x10-31 amu Shells
Electron orbiting
(Negligible)
nucleus
 Atomic Mass
• The mass of an atom of an element is called its
atomic mass
– Mass of an electron is so small it’s considered
negligible
– Atomic mass = Number of Protons + Number of Neutrons
=#P+#N

*Unit of mass = amu (atomic mass units)

 How are Elements Identified?
• Elements are identified by the number of
protons within an atom.
– All atoms of an element have the same number of
protons
– Atoms of an element many have different number
of electrons or of neutrons (isotopes)

• The number of protons is constant - Best identifier

Atomic number = the number of protons

 Primary elements in living things
carbon hydrogen oxygen
C H O
Atomic number 6 Atomic number 1 Atomic number 8

nitrogen phosphorus sulfur

N P S
Atomic number 7 Atomic number 15 Atomic number 16
 Elements are identified by their
atomic number (number of protons)

6 protons 6 protons 6 protons 7 protons

6 neutrons 7 neutrons 8 neutrons 7 neutrons
carbon carbon carbon nitrogen
12
C
13
C 14
C 14
N

Isotopes
 Practice Problems:
What is the atomic mass of a carbon atom
(atomic number 6) that contains 7 neutrons?

13 amu (Atomic mass = #P + #N)

 Practice Problems:
If an atom of sodium (atomic number 11) has
an atomic mass of 23, how many neutrons does
it contain?

12 neutrons (Atomic mass - #P =#N)

 Practice Problems:
An atom of fluorine has a mass of 20 amu and
contains 11 neutrons. What is the atomic
number of fluorine?

9 (# P or Atomic #= Atomic mass - #N)

Periodic Table
 Periodic table of elements
Elements are listed in order of atomic number
1 2
H He
1.01 4.0

3 4 5 6 7 8 9 10
Li Be B C N O F Ne
6.94 9.01 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 24.30 26.98 28.09 30.97 32.07 35.45 39.95

19 20
K Ca
39.10 40.08

The “atomic mass” is at the bottom

Why are the atomic masses on the periodic
table not whole numbers?
• The “atomic mass” (i.e. atomic weight) on
periodic table is the weighted average of the
atomic masses of the different isotopes of an
element.
Isotope 12
C 13
C 14
C
Atomic Mass 12 amu 13.003 amu 14 amu
Percentage 98.89 % 1.11% ~10-12 %
98 . 89 1 .11
𝑥 12 . 00 𝑎𝑚𝑢+ 𝑥 13 . 003 𝑎𝑚𝑢=𝟏𝟐 . 𝟎𝟏𝟏 𝒂𝒎𝒖
100 100
 Isotopes
• Atoms of an element with the same number
of protons, but different number of neutrons
(they have different atomic masses)

Example: 1H is Hydrogen (0 neutrons)

2
H is Deuterium (1 neutron)
3
H is Tritium (2 neutrons)
 Radioactive Isotopes
• Isotopes are stable when it has a balanced
number of neutrons or protons.
• Isotopes that are not stable and emit radiation
are called radioactive isotopes.
– A radioisotope undergoes spontaneous decay and
emits radiation (energy) as it decays to try and
become more stable
3
1H
32
15P 14
6 C
tritium Phosphorus-32 Carbon-14
*Most isotopes are NOT radioactive
 Radioisotopes
• Used in various scientific research and clinical
applications
• Autoradiography: a technique that detects the
decay of radioisotopes
• Used in:
– Dating fossils
– Tracing biochemical pathways
– Sequencing DNA
– Diagnostics and treatment
• PET (fluorine-18)
 PET Scan
• Positron emission tomography (PET scan), is
a type of nuclear medicine imaging using
autoradiography.

• Small amounts of radioactive material

(fluorine-18) are injected to diagnose or treat
disease and other abnormalities within the
body.
How many electrons does an atom have?

• The number of electrons usually EQUALS the

atomic number
• Example:
– Carbon: 6 protons
6 electrons
• Electrons are contained within energy shells
– 1913 Niels Bohr developed the idea that electrons
orbiting an atomic nucleus can only occupy certain
energy levels
 Electrons
• Electrons determine how an - -

atom will interact with other

- -
atoms. - - -

• The movement and - -

configuration of electrons is - -

determined by electron shells -

- -
- -
– The amount of potential
energy in a given atom is
determined by the distance an - -
electron is from the nucleus
Protons give the identity, electrons the personality
 Electron Shells
• Most biological elements
have 2-3 electron shells - -
– 1, 2 and 3
- -
• Each shell can hold a - - -

maximum # of e-
–1=2 - 1 2 3 -
- -
–2=8
– 3 = 8 (for elements up to - - -
-
-
20amu – larger atoms get
additional subshells)
- -
• The outermost shell with e -

is called the valence shell

 Using the Periodic Table
The vertical column (Group) tells you how many e- are in the
valence shell.

The horizontal
row tells you
how many shells
an element has
and what the
valence shell is.

Carbon is in row 2 and column IV (4). It has two e- shells (1 and 2)

and there are 4 e- in the valence shell (2).
 Practice Questions

• How many e- shells does oxygen have?

Oxygen: 2 electron shells (1 and 2)
• How many valence e- does oxygen have?
Oxygen: 6 e- (Column- VI) in its valence shell 2
 Practice Questions

• How many e- shells does phosphorus have?

P: 3 electron shells (1, 2, and 3)
• How many valence e- does phosphorus have?
P: 5 e- (Column- V) in its valence shell 3
 Electron Placement Exercise
• Draw 4 circles on a sheet of paper like below:
 Using the following information and your cheerios
set up the electron configuration for each of the
following elements within your drawn circles.
*Remember to always start with the inner circle (shell 1) and work outward.

Element Atomic Number Vertical Column Group

1. Carbon 6 IVA

2. Oxygen 8 VIA

3. Phosphorus 15 VA

4. Chlorine 17 VIIA

5. Potassium 19 IA
 Inert or reactive?
• Atoms behave as though they “want” to have a
full outer shell

• Atoms with full outer shells are non-reactive

or inert

• Atoms that do not have full outer shells will

interact with other atoms to fill those shells.
They are reactive
 “Happiness” is a full electron shell!
• Which of the following atoms is “happy” or
inert and which is “not happy” and reactive?

1 Shell – 2 e- 2 Shell – 6 e- 2 Shell – 8 e-

 Practice Questions
Will an atom with 9 protons be reactive or inert?
1. How many electrons does this atom carry? 9
2. How many electrons in the first (1) shell? -2

3. How many electrons in the next (2) shell? 7

4. Is the 2nd shell full? NO

5. Is the atom reactive or inert? Reactive

 Practice Questions
Is an electrically neutral atom with 18 protons
reactive or inert?
18
-2
16
Shell 3: 8 e- -8
Shell 1:Shell
2 e- 2: 8 e-
8
-8
0
Is the outer (3) shell full? Yes

Is the atom reactive or inert? Inert

 Ions
• Ions are atoms with an electrical charge: positive
or negative

• An atom becomes an ion (charged) when it

either gains or losses electrons
 Ions
• Positively-charged ion are called cations
– When an atom has 1, 2 or 3 e- in its
outermost shell, it will tend to lose those
electrons and become + charged
 Ions
• Negatively-charged ion are called anions
– Atoms with 5, 6 or 7 e- in their outermost
shell will tend to gain electrons and become
___charged
Biologically Important Cations
Name Formula Charge
Sodium Na+ +1
Potassium K+ +1
Hydrogen H+ +1
Magnesium Mg2+ +2
Calcium Ca2+ +2
Iron Fe2+ or Fe 3+ +2 or +3
Biologically Important Anions
Name Formula Charge
-
Chlorine Cl -1
-
Iodide I -1
-
Fluoride F -1
-
Hydroxide OH -1
 Chemical Bonds
• Chemical bonds allow atoms to achieve
stability by creating arrangements to fill the
outer shell of each atom.

• The formation of a chemical bond results in a

new molecule, which may have different
properties from the original atoms.

• A molecule is group of two or more atoms

– Atoms can be of the same and/or different
elements
 Chemical Bonds
• Two basic types of chemical bonds:
– Ionic Bonds
• Form when one or more electrons are
transferred between atoms
– Covalent Bonds
• Formed when electrons are shared
between atoms
 Ionic Bonds: Electrons Transferred
Involves the attraction of opposite electrical charges

• One atom donates an e-

– Gains a + charge

• One atom accepts an e-

– Gains a – charge
*Atoms with a charge are called
ions Ionic bond in table salt
• Opposite charges attracts ions to each other
• Ionic bonds are most stable as crystals – e.g. salt
Ionic Bonds: Electrons Transferred
11Na + Cl
17 -

Na+ + Cl- NaCl

Covalent Bonds: Electrons Shared
• Form between two atoms when they share
electrons

• The number of electrons

shared varies
– Depends on how many
atoms needs to fill its
outermost electron shell
Covalent Bonds: Electrons Shared
Example: Methane (gas)
H
1H 6C
1

H
1
1H
CH4
 Covalent Bonds
Can be either:
• Non-polar covalent bonds:
– Equal sharing of electrons

• Polar covalent bonds:

– Unequal sharing of electrons
 Electronegativity
• Attraction for e- by a nucleus is called the
atom’s electronegativity

– Electronegativity will influence the type of bonds

an atom is likely to form when it interacts with
other atoms.

• The Pauling Scale rates the electronegativity

of different atoms.
 Electronegativity Rates
High: more likely to get e-

Low: more likely to give-up e-

 Electronegativity and Bonds
• The difference in electronegativity between two atoms
will dictate what type of bond they are likely to form:
Electronegativity difference Type of Bond Formed
0 – 0.4 Non-polar covalent
0.5 – 1.9 Polar covalent
2.0 + Ionic
• Example: E.N. Difference = largest – smallest
– E.N. Fluorine (F) = 4.0 E.N. Difference = 4.0 - 1.0
– E.N. Lithium (Li) = 1.0 = 3.0
(ionic bond!)
 Non-Polar Covalent Bonds
• Electrons are shared equally between atoms
• Atoms have similar or the same electronegativity

Electronegativity:
• Carbon (C): 2.5
• Hydrogen (H): 2.1
– Similar electronegativity
(E.N. Difference is 0.4)
– e- of H not pulled as
much by C
 Polar Covalent Bonds
• Electrons are pulled toward the element with
the higher electronegativity
• This unequal pull on electrons results in
partial charges in the atoms
– The one that ‘spends more time’
with the e- has a partial negative
charge
– The on that ‘spends less time’ with
electrons will have a partial
positive charge
 Polar Covalent Bonds
Electronegativity:
• Oxygen (O): 3.5
• Hydrogen (H): 2.1

– E.N. Difference = 1.4, so they

form a polar covalent bond.
– e- are pulled more towards the O
(more electronegative atom) and
away from the H

*Partial charges resulting from a

polar covalent bond are indicated
The polarization of water molecules
causes them to clump together!

We’ll discuss this

more next topic!
 Chemical Reactions
• When atoms or molecules react to form new
molecules, we call it a chemical reaction

• The reaction is the process of building and/or

breaking chemical bonds
• All chemical reactions have at least 2 parts:
2H2 + O2 2H2O
Reactants Product
• Reactants: atoms or molecules that are interacting
• Product(s): the result of that interaction
 REACTANTS PRODUCT
S + O2 SO2
sulfur oxygen sulfur dioxide
 Oxidation and Reduction
• This is a special class of reactions that is
important in biology
• Involves the transfer of either hydrogen atoms or
electrons
– OXIDATION is the loss of electrons or hydrogen
atoms (OIL; Oxidation Is Loss)
– REDUCTION is the gain of electrons or
hydrogen atoms (RIG; Reduction Is Gain)

• Oxidation-reduction reactions always occur

together - > shortened to REDOX reactions
 Example

Na + Cl Na+Cl-
Is Na being reduced or oxidized?
Oxidized because it must have LOST an electron
to acquire a + charge (OIL)
Is Cl being reduced or oxidized?
Reduced because it must be GAINING an electron
to acquire a – charge (RIG)
 We can tell if electrons are moving by
looking at the movement of hydrogen

FAD + H2 FADH2
•Is FAD being oxidized or reduced?
Reduced
It gained a hydrogen so it must have gained
electrons! (RIG)

*Keep in mind this is only half a reaction as there is also

a component that needs to be oxidized!
Remember

OIL RIG
Oxidation is loss
Reduction is gain