3.

1 Biological Elements
STUDENT NOTES
OCR Y1 / AS Level Biology A
Module 2 Foundations in Biology
Chapter 3 Biological Molecules
Saturday, 19 January 2019 Turn to pages 40 and 41
in the OUP Textbook

3.1 Biological Elements

Lesson Objectives:
To be able to:
• Describe the chemical elements that make up
biological molecules
• Describe the bonding process in many biological
compounds
• Describe the function of key ions in biological
processes
 Atoms
• All matter is made up of atoms
• Each atom is made of three types of particle:
– neutrons, with no charge
– protons, with a positive charge
– electrons with a negative charge
• The neutrons and protons form the nucleus
• The electrons orbit around the nucleus
• In an atom, the number of protons is the same as the
number of electrons (so no overall charge)
A sodium atom
 How are electrons arranged?
Electrons are not evenly spread but exist in layers called
shells. (The shells can also be called energy levels).
The arrangement of electrons in these shells is often
called the electron configuration.

1st shell

2nd shell

3rd shell

Note that this diagram is not drawn to scale – the atom is

mostly empty space. If the electrons are the size shown,
the nucleus would be too small to see.
 How many electrons per shell?
Each shell has a maximum number of electrons that it can
hold. Electrons will fill the shells nearest the nucleus first.
1st shell holds
a maximum of
2 electrons

2nd shell holds

a maximum of
8 electrons

3rd shell holds

a maximum of
8 electrons

This electron arrangement is written as 2,8,8.

 Why do atoms form bonds?
Bonds involve the electrons in the outer shells of atoms.

Each shell has a maximum number of electrons that it can

hold. Electrons fill the shells nearest the nucleus first.

1st shell holds a

maximum of 2 electrons

2nd shell holds a

maximum of 8 electrons

3rd shell holds a

maximum of 8 electrons

Filled electron shells are very stable.

 Why do atoms form bonds?
The atoms of noble gases have completely
full outer shells and so are stable.

This makes the noble gases very unreactive

and so they do not usually form bonds.

The atoms of other elements have

incomplete outer electron shells
and so are unstable.

By forming bonds, the atoms of these

elements are able to have filled outer
shells and become stable.
 Stability of atoms

• Each atom has one or more orbitals of electrons

• Atoms are more stable if their outer orbital is full
• Stability is achieved by either gaining or losing electrons
from the outer orbital
A sodium ion is formed when a
sodium atom loses the electron
from its outer orbital
 What is a covalent bond?
Non-metal elements usually just need one or two electrons
to fill their outer shells. So how do they form a bond?

incomplete
Cl outer shells Cl

The two non-metal atoms cannot form a bond by transferring

electrons from one to another. Instead, they share electrons.

Each atom now

Cl Cl has a full, stable
outer shell.
The shared electrons join the atoms together.
This is called a covalent bond.
 How is a covalent bond drawn?
A covalent bond consists of a shared pair of electrons.

Cl Cl
covalent bond
Only outer shells of electrons are involved in bonding, so the
inner shells do not always have to be included in diagrams.
Two common ways to represent a covalent bond are:

simplified Cl –Cl
dot and solid
Cl Cl
cross line Cl – Cl
diagram
 Covalent bonding in water
Compounds can contain more than one covalent bond.
Oxygen (2.6) needs 2 more electrons, but hydrogen [1] only
needs 1 more. How can these three elements be joined by
covalent bonding?
The oxygen atom shares 1
electron with 1 hydrogen
atom, and a second O
electron with another H H
hydrogen atom.

What is the name of the molecule that is formed?

H2O (or H–O–H) is water.

What are simple covalent structures?
Covalent molecules that contain only a few atoms are
called simple covalent structures.
Most substances that contain simple covalent molecules
have low melting and boiling points and are therefore liquids
or gases at room temperature, e.g. water, oxygen, carbon
dioxide, chlorine and hydrogen. Why?
The covalent bonds within these molecules are strong but
the bonds between molecules are weak and easy to break.

weak bonds
strong bonds
between
within
molecules
molecules
Important Biological Molecules
 Ions are formed when an atom
gains, or loses, electrons
• If an atom loses one or more electrons, it becomes a
positively charged ion
• If an atom gains one or more electrons, it becomes a
negatively charged ion
• If placed in an electric field, ions will migrate to the
electrode with the opposite charge
– Negatively charged ions migrate to the positive
electrode (anode), so are called anions
– Positively charged ions migrate to the negatively
charged electrode (cathode), so are called cations
 Representing ions

• A sodium ion still has 11 protons but having lost one

electron it only has 10 electrons, ie it has a positive
charge
• Na (atom) – 1 electron = Na+ (sodium ion)
• Some atoms gain electrons
• If a chlorine atom gains one electron it becomes a
negatively charged chloride ion
• Cl (atom) + 1 electron = Cl– (chloride ion)
 A cation and anion can share
electrons
• When they do, their opposite charges attract
each other forming an ionic bond
 Useful Biological Ions
Anions Required for

Cations Required for

Nitrate (NO3-) • Amino Acid
formation
Calcium (Ca2+) • Nerve Impulses
• Muscle Hydrogen • Maintain blood pH
Contractions Carbonate
(HCO3-)
Sodium (Na+) • Nerve Impulses
• Kidney Function Chloride (Cl-) • Balance sodium
and potassium ions
Potassium (K+) • Nerve Impulses in cells
• Stomata Phosphate • Cell Membranes
(PO43-) • Nucleic Acids and
Hydrogen (H+) • Catalysts
ATP formation
• pH Determination
• Bone formation
Ammonium • Needed to make Hydroxide • Catalysts
(NH4+) nitrate ions (OH-) • pH determination
Complex Biological Molecules
Review Questions