Biochemistry

of life

2 Atoms, Isotopes & Ions

• Matter is made up of elements
• An element is a substance that cannot be broken down
to other substances by chemical reactions
• A compound is a substance consisting of two or more
elements in a fixed ratio
• A compound has characteristics different from those of
its elements

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3 Atoms, Isotopes & Ions
• About 20–25% of the 92
elements are essential to life
• Carbon, hydrogen, oxygen, and
nitrogen make up 96% of living
matter
• Most of the remaining 4%
consists of calcium, phosphorus,
potassium, and sulfur
• Trace elements are those
required by an organism in
minute quantities

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4 Atoms, Isotopes & Ions

An atom is the smallest unit of matter that still retains the

properties of an element
• Atoms are composed of subatomic particles
• Relevant subatomic particles include
Neutrons (no electrical charge)
Protons (positive charge)
Electrons (negative charge)

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5 Atoms, Isotopes & Ions
• Neutrons and protons form the atomic nucleus
• Electrons form a cloud around the nucleus
• Neutron mass and proton mass are almost identical and
are measured in daltons
Electrons
Nucleus
Cloud of negative
charge (2 electrons)

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6 Atoms, Isotopes & Ions

• Atoms of the various elements differ in number of
subatomic particles
• 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

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7 Atoms, Isotopes & Ions

• 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

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8 Electrons and Bonding

• Energy is the capacity to cause change

• Potential energy is the energy that matter has because
of its location or structure
• The electrons of an atom differ in their amounts of
potential energy
• An electron’s state of potential energy is called its
energy level, or electron shell

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9 Electrons and Bonding
Third shell (highest energy
level in this model)
Third shell (highest energy
Energy
level in this model)
absorbed

Third shell (highest energy

level in this model)
Energy
lost
Atomic
nucleus

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10 Electrons and Bonding

Valence electrons are in the outermost shell, or valence
shell
• The chemical behavior of an atom is mostly determined
by the valence electrons
• Elements with a full valence shell are chemically inert
• “Octet rule”

First shell
Neon, with two filled
Shells (10 electrons)
Second shell

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11 Electrons and Bonding
• Atoms with incomplete valence shells can share or transfer
valence electrons with certain other atoms
• These interactions result in atoms staying close together held
by attractions called chemical bonds
• A bond is a union between the structures of 2 or more atoms
based on the difference in electronegativities* between their
nuclei
* the pull 1 nucleus has on its own and another nucleus’ electrons

• If electronegativity difference is
• 0.0 – 0.2 pure covalent bond
• >0.2 – 1.6 polar covalent bond
•
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>1.8
November 2015
ionic bond

12 Electrons and Bonding

IONS
Are atoms that have lost or gained electron(s) from their
valence shell
• A cation is a positively charged ion
• An anion is a negatively charged ion

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13 Electrons and Bonding

IONIC BONDS
Electrostatic attraction between 2 ions of opposite
charge
An ionic bond is an attraction between an anion and a
cation

Na+ Cl–
Sodium ion Chloride ion
(a cation) (an anion)

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Sodium chloride (NaCl)

14 Electrons and Bonding

IONIC BONDS
Not common in Biological systems
85% - 99% H2O
Ionic bonds would dissociate

Found rarely, and only in places where large molecules

(e.g. proteins) can create a hydrophobic environment
to protect the bond from dissociation.

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15 Electrons and Bonding

COVALENT BONDS
Electronegativity difference <1.8
Can not remove electron from weaker atom share
The shared electrons count as part of each atom’s
valence shell
Covalent bonds can form between atoms of the same
element or atoms of different elements

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16 Electrons and Bonding

Pure Covalent Bonds
Electrons are shared equally
O2, H2, N2

Hydrogen (H2)

Oxygen (O2)

Methane (CH4)
C-H bond is apolar
(no charge)
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17 Electrons and Bonding

Polar Covalent Bonds

Involve unequal sharing of electrons
Result: bond has areas of slight “+” or “-” charge
Typical of the water molecule δ–
stronger Oxygen pulls Hydrogen’s electrons
closer to its own nucleus
These bonds impact the chemical
properties of the macromolecules

δ+ δ+
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18 Electrons and Bonding

Hydrogen Bonds
Weak electrostatic attractions between polar areas of a
molecule and/or bond
Analogy:
Gulliver waking up on the beach of the Lilliputians island
He is tied down by their tiny ropes
BUT, many ropes and he can’t break their collective
strength

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19 Electrons and Bonding
δ+
Hydrogen Bonds δ–

Water (H2O)

δ+
Hydrogen bond δ–
(shown with dotted or
dashed line)

Ammonia (NH3)

δ+ δ+

Meg O’Mahony November 2015 δ+

20 Electrons and Bonding

Van der Waals Interactions

If electrons are distributed asymmetrically in molecules
or atoms (as a result of their random movement in the
electron cloud), they can result in “hot spots” of positive
or negative charge

Van der Waals interactions are attractions between

molecules that are close together as a result of these
very weak temporary charges

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21 Electrons and Bonding

Hydrophobic Interactions (London forces)

Apolar molecules (neutral; charge)
result of pure covalent bonds Source: Wikipedia commons

hydrocarbon groups
Apolar molecules move away from charged or polar
molecules and towards areas of neutral (no) charge
In figure, notice how the polar balsalmic vinegar, forms
spherical balls in the apolar olive oil
Spherical shape presents smallest possible surface area

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22 Functional Groups

In Biology, certain atoms tend to travel together much of

the time
Like a group of Best Friends

R represents Rest
of the molecule

whimsyworkshop.blogspot.com

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23 Functional Groups

Functional Groups give molecules many of their typical

Chemical properties
Physical properties

Chemical reactions form between the functional groups

to form recognized “linkages” or bonds

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24 Functional Groups

There are 7 common functional groups in Biology.

Hydroxyl
Carboxyl
Carbonyl
Amino
Sulfhydryl
Phosphate
Methyl, Ethyl (Hydrocarbon)

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 CHEMICAL Hydroxyl Carbonyl Carboxyl
GROUP

STRUCTURE

EXAMPLE

Acetone Acetic acid

Ethanol

Propanal
Organic Acid
H donor

Nonionized Ionized

Amino Sulfhydryl Phosphate Methyl

CHEMICAL Amino Thiols Phosphates Methyl
GROUP

STRUCTURE

EXAMPLE

Glycine Cysteine Glycerol phosphate 5-Methyl cytidine

Organic Base
H acceptor

Nonionized Ionized
27 Linkages: Ester

occurs between a carboxyl group (which, as an organic

acid, donates its proton, H+) and a hydroxyl group.

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28 Linkages: Ether
Forms between 2 hydroxyl groups
In sugars (where it is called a glycosidic linkage)

SUGAR
POLYMERIZATION

+
O

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29 Linkages: Peptide

Forms between a carboxyl group and an amino group

Characteristic linkage in proteins

PROTEIN
Meg O’Mahony November 2015 PRIMARY STRUCTURE

30 Linkages: Anhydride

forms between 2 carboxyl groups; 2 phosphate groups;

a phosphate group and a carboxyl group
Important linkage in ATP; important in thermodynamic
transformations

H + H H

CELLULAR
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31 Linkages: Disulphide

forms between 2 sulfhydryl groups

Important in stabilizing 1o and 2o structures in proteins

H
+ 2 H+

PROTEIN
STRUCTURAL STABILITY
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32 Types of Reactions : Condensation

(Dehydration Synthesis)

A reaction in which 2 molecules are joined with the loss of

a water molecule.

These “building up” reactions are anabolic.

LINKAGES
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33 Types of Reactions : Hydrolysis

These reactions break bonds by the addition of a molecule

of water.

These “catabolic” reactions break molecules apart.

DIGESTION
Meg O’Mahony November 2015 (grade 11 Bio)

34 Types of Reactions : Neutralization

Reactions in which an acid and base react together to form

a salt and water.
NOTE: In Biology, we use the Brönsted-Lowry definition of
Acids/Bases.
+

HOMEOSTASIS
UNIT
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35 Types of Reactions : Redox
In these reactions, electron (pairs)* are lost or gained.
OIL RIG LEO the Lion says GER

ENERGETICS
UNIT

*The loss/gain of H+ is incidental.

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36 Types of Reactions : Phosphorylation

Reactions in which an inorganic phosphate is added to a

molecule

First reaction of Glycolysis. CELLULAR

Meg O’Mahony November 2015 THERMODYNAMICS