BIOS1167 - Discipline of Biomedical Science, University of Sydney

‘Key Concepts of Body Chemistry’ – revision notes

Human biochemistry is the study of the nature of the matter in our bodies. The
transformation of small simple particles of this matter into large complex substances allows
our bodies to function as an organic whole. The breakdown of complex substances in the
body into simple particles provides the energy for body function. In order to understand how
this happens, we must first have an introduction to some basics of chemistry itself.

BASIC CHEMICAL PRINCIPLES

Elements are the basic structures from which everything is made. When we talk about
“everything” in the universe we can call everything “matter”

Some examples of common elements in our body are sodium, chlorine, carbon, hydrogen and
oxygen.

QUESTION: “what are elements made of?”

The answer is that elements are made of atoms.

A useful definition of atoms is that they are the:

“Smallest unit of matter making up an element which still retains the
chemical properties or characteristics of the element”.

Common salt (sodium chloride, NaCl) is an example of matter. It is made up of the elements
sodium and chlorine. Water (H2O) is another example of matter. It is made up of the
elements hydrogen and oxygen. What do you think this tells us about the role of the different
elements in giving matter its particular form?

It is the elements present in matter which give it its particular form. When different elements
are present, matter will take on different forms.

QUESTION
Remember that elements have the structure of an atoms. Given that different
elements give matter different form, do you think that all elements (and therefore
all atoms) are the same?

ANSWER:
All the elements are different – there are over 100 different elements listed in the
Periodic Table. The atoms of each Element are:
• chemically distinct
• differ from those of any other element
 BIOS1167 - Discipline of Biomedical Science, University of Sydney

We’ve now identified some of the basic facts regarding elements. There are two more
important things we need to know.

These are:
1. elements are pure substances.

2. elements cannot be broken down (remember elements are the fundamental building blocks
of matter)

Because elements are so important, they each have a name and symbol.
eg. Carbon C
iodine I
calcium Ca
oxygen O

There are more than 100 different elements found in the universe - some are very common,
some are very rare. Think of an element like platinum which is very rare – (that is why
platinum jewellery is so expensive – more expensive than gold!)

QUESTION
Do you think that all elements would be present in equal amounts in the body?
ANSWER:
The answer to this question is no - not all elements are equally represented.

This is because:

1. some elements are common while some are rare

2. the body has a particular form - particular elements are needed to give it that form
(remember - the elements present give matter its form, and the body is just another
example of matter)
3. many elements may actually damage the body if they are present - for example Uranium
or Arsenic or Lead or Mercury
4. Relatively few elements make up the human body.
 BIOS1167 - Discipline of Biomedical Science, University of Sydney

Let’s look at the elements which are most common in the body:

Elemental Composition of the Body

Element Symbol % Composition by
Body Mass
THE BIG FOUR
oxygen 0 65
carbon C 18
hydrogen H 10
nitrogen N 3

THE NEXT SEVEN

calcium Ca 1.5
phosphorous P 1.0
Magnesium Mg 0.1
Potassium K 0.4
Sodium Na 0.2
Sulfur S 0.3
Chlorine Cl 0.1

TRACE ELEMENTS
copper Cu
Iron Fe
Zinc Zn
Cobalt Co
Manganese Mn
Selenium Se
Iodine I

These elements are found in a variety of important molecules and serve a variety of functions.
For example:
• calcium and phosphorus help to give the bone its strength
• carbon, oxygen, hydrogen and nitrogen are all found in proteins
• carbon, hydrogen and oxygen are the main elements also found
in fats (lipids), sugars (carbohydrates)

The elements in the body do not have to exist independently of each other. They are
combined together to do specific jobs. The same elements can be doing different jobs
So what makes this possible - how can the same elements be doing different things? The way
in which they are combined determines the jobs they can do.
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We now need to think about the ways in which this combination of elements can occur.

Molecules and compounds

In the previous section, we saw:

1. that elements could not be broken down by substances eg acids
2. that elements can be combined to form molecules

When we are thinking about the combination of elements, we need to recognise that elements
can combine with:
1. identical elements or with
2. other elements.

We’ll begin by thinking about what happens when identical elements combine.

The simplest structure which can be formed by combining elements is known as a

molecule or compound. You could think of a molecule as a tightly bound group of
atoms.

We can define a molecule as the:

“Smallest unit of matter that can exist independently and still retain
the properties of that element”.

A good example is the oxygen molecule, which consists of 2 oxygen atoms joined together to
form O2

QUESTION
From what you know so far, how would you describe a simple molecule or compound?
ANSWER
A molecule or compound is a group of atoms which are stuck (bonded) together.

Many important elements exist as molecules

H2 – hydrogen - (the most abundant in the universe!)
N2 - nitrogen
O2 – oxygen - (the most abundant – of total body mass – in the body!)
I2 – iodine

Other examples of molecules

C6H12O6 - glucose
H2O = water
etc etc etc

So far we have seen that:

1. elements are made up of atoms and
2. molecules and compounds are made up of elements (atoms) which are stuck together
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What is it that holds the atoms together in a molecule or compound?

To answer this, we need to think about the structure of atoms.

Internal Structure of the atom:

The way we talk about atoms makes them sound like they are a solid structure, but they are
not.

We can imagine an atom to be something like a peach. At the centre of the peach is the seed,
and at the centre of the atom is the nucleus.

Inside the Nucleus:

Protons: + (positive) charged particles

Neutrons: particless with No charge

The protons and neutrons actually have a mass (commonly also called weight), so we can see
that the number of protons in the nucleus is important because:
• it determines the positive charge (and therefore the number of electrons surrounding the
nucleus)
• it determines (together with the neutrons) the weight of the atom.

Outside the nucleus

Electrons - (negative) charged particles

Electrons effectively have no mass (is negligible), in other words are considered weightless.

_________________________________________

Because there are so many elements, we find it useful to list and categorise in a table form.
The table of elements is known as the Periodic Table - copy included as final page of this
file.

The number of protons in the nucleus of an atom determines the position of an element on the
periodic table. Each element is listed in the table by their atomic number which is equal to
the number of protons in its nucleus.

In other words, if you know the atomic number of any element you also know a number of
important facts about that element:
 BIOS1167 - Discipline of Biomedical Science, University of Sydney

Atomic Number = Number in the Periodic Table

= Number of Protons
= Number of Electrons

ACTIVITY
Look at a periodic table - copy included as final page of this file.

The Horizontal rows are called Periods

The Vertical columns are called Groups

Note: on most versions of the Periodic Table show the elements divided into metals and
nonmetals.

From looking at the table, and the atomic numbers (the number of protons), you can see that
the entire classification system of elements is based on the number of protons present in the
atoms that make them up. Remember, it is the number of protons is what defines the atom of
that element; if an element has 6 protons, it must be Carbon

We know that the nucleus also contains neutrons, which add mass, but don’t affect the
electrical charge (or the number of electrons).

Although
QUESTION: the number of protons and electrons in the nucleus is specific for a particular
element, the number
Does every atom ofof neutrons can
a particular vary. have to have an identical mass?
element
ANSWER:
Because the nucleus of an element can contain different numbers of neutrons, not all atoms of
a particular element must have the same mass (but they must have the same number of
protons).
Because the mass of the atoms of a particular element may be variable, we need to specify
mass in addition to the number of protons. We do this by measuring the Atomic Mass
Number.

Atomic Mass Number = Number of Protons + Number of Neutrons

The mass of the nucleus is important for more than simply descriptive reasons. When we have
elements with different nuclear masses, the different forms are known as isotopes.

Isotopes:
We can define isotopes as “Atoms which have the same Atomic Number but different Atomic
mass number(s)”.
We can therefore say that they differ only in the number of neutrons.
For example, carbon atoms exist in three forms. They can have
• 6 protons and 6 neutrons
• 6 protons and 7 neutrons
 BIOS1167 - Discipline of Biomedical Science, University of Sydney

• 6 protons and 8 neutrons

There must always be 6 protons (otherwise the atom would not be carbon).

The most commonly found form of carbon is the one that has 6 protons and 6 neutrons in its
nucleus

Isotopes of Carbon % Abundance

12
C 98.89

13
C 1.11

14
C trace

Atomic Mass:

QUESTION:
Do you think the atomic mass of carbon found in nature will be exactly 12? Remember,
there are three isotopes of carbon found in nature.

ANSWER:
The answer is no. Remember that there are three isotopes of carbon - carbon can have three
different weights. Each of these isotopes may be present in naturally occurring carbon. When
determining the atomic weight of carbon we need to take into account
• the different isotopes
• their different masses
• their relative abundance.
• The Atomic mass (or weight) of naturally occurring Carbon = 12.01 a.m.u. This is the
average of the masses of all the carbon atoms (the various isotopes) which exist on the earth.
• Now look back on your Periodic Table - you can see that most relative atomic mass as
listed on the table are not given as an exact number. This is because most atoms have more
than one isotope and the atomic weight given is an average of all the occurring isotopes.
 BIOS1167 - Discipline of Biomedical Science, University of Sydney

Electron Configuration

Remember there are also electrons surrounding the nucleus of atoms. We can imagine them
orbiting like planets around the sun. However, the orbiting electrons are restricted to orbiting
in particular places which occur at certain distances from the nucleus. In addition, we can
only have a certain number of electrons orbiting at each distance.

Electrons found only certain distances from the nucleus; these are known as “Principal
Energy Levels” or Shells

These levels are labelled 1, 2, 3 etc. in order of increasing distance form the nucleus.
Each Level may contain a certain maximum of electrons before the electrons must be put in
the next level

The maximum number of electrons in given by a very simple formula (you do not have to
remember this). The maximum number of electrons that can be found at any particular
energy level is 2 n2 electrons (where n = number of level)
for example:

Level 1 has 2 x 12 = 2 electrons

Level 2 has 2 x 22 = 8 electrons
Level 3 has 2 x 32 =18 electrons and so on

Most elements important in body chemistry have electrons accommodated in the first 4
levels

Now let us think again about the Periodic Table remembering that:
• electrons are arranged in shells around the nucleus
• each shell has a limit to the number of electrons it can hold.

The Periodic Table shows elements in order of increasing Atomic Number and corresponds
to the number of electrons.

QUESTION: Why does the Atomic Number also equal the number of electrons?

Answer: Remember, the Atomic number tells us the number of positively charged
protons present in the nucleus. Within an atom, the positive proton attracts a negative
electron to towards the nucleus. This means the atoms of elements have the same number
or protons and electrons.
 BIOS1167 - Discipline of Biomedical Science, University of Sydney

VALENCY

Chemical Reactions involve only those electrons in the outer level (all underlying levels are
closed shells).

Therefore, in chemical terms, when thinking about chemical bonds, you are only ever
concerned with the electrons in the outer level or shell. This means that if you know an
element has only one electron in its outer level, you can predict that it will react by losing this
electron (it doesn’t matter if it has either 20 or 80 electrons underneath the outer level)

Outer shell electrons are known as Valence Electrons and can be defined as “electrons which
take part in chemical reactions”.

Groups - (downward columns) in the Periodic Table have the same number of electrons in
their outer levels and therefore tend to have similar chemical characteristics.

These generalisations about elements in the periodic Table will help us to predict how
will behave when they interact with other atoms ie. when they enter into chemical
reactions

1. Atoms which do not have 8 electrons in their outer shell, try to get 8 when they enter into
chemical reactions; this is known as the octet rule.

2. When atoms with one or two electrons in their outer shell react, they will tend to lose
electrons and atoms with 6 or 7 electrons will tend to gain electrons to achieve an octet.

3. Other atoms, especially those with 4 electrons in their outermost level may attain a
complete octet by sharing electrons with other atoms.

We have now begun to see some patterns emerge about how atoms behave in a chemical
reaction and have introduced the idea of
• losing or gaining electrons (to form charged particles called ions)
• sharing electrons

Remember a very important rule:

atoms have the same number of protons and electrons;
that is the same number of positive and negative charges
Therefore: Atoms are neutral particles

If atoms lose or gain an electron they are losing or gaining a negative charge and will become
a charged particle

The name for a charged particle is an ion,

 BIOS1167 - Discipline of Biomedical Science, University of Sydney

ION FORMATION

Atoms can gain or lose electrons. Let s look at what happens when this occurs:

If an atom loses an electron (we abbreviate an electron as e-) the atom will have a positive
charge (it will have one more proton than the total number of electrons). Because it is
charged, the electron is an ion. We call a positive ion a Cation.

If an atom gains an electron (e-) it takes on a negative charge and is a negative ion. We call
negative ions Anions.

Note: on most versions of the Periodic Table show the elements divided into metals and
non-metals.

Metals in the Periodic table have a tendency to lose electrons and form Cations:

For example: Na→ Na+ (sodium ion) + e-

Non-metals have a tendency to gain electrons and form Anions:

For example: Cl + e- → Cl- (chloride ion)

Both these ions are examples of simple ions, they consist of one atom with a +ve or -ve
charge. Sometime a group of atoms bound together chemically will have a charge; these
particles are known as Polyatomic Ions:

Definition of Polyatomic Ions

Groups of atoms which are bound chemically and which carry an overall charge due to an
excess or deficiency of electrons on the group.

These ions behave as one particle in solution. In other words, when dissolved in water, the
various atoms present in the polyatomic ion remain bound together.

Both Simple and Polyatomic Ions have very important roles in the body
 BIOS1167 - Discipline of Biomedical Science, University of Sydney

Some important simple ions in the body

Name Symbol
Sodium Na-
Chloride Cl-
Potassium K+
Mg Mg2+
Calcium Ca2+

Some important polyatomic ions in the body

Name Symbol
Carbonate CO32-
Sulphate SO42-
Phosphate PO43-
Ammonium NH4+
Bicarbonate HCO3-

IONIC COMPOUNDS (salts)

When two or more charged particles (ions) come together they form a compound called an
ionic compound.

We know that chemical compounds have mass, and that an ionic compound such as salt
(NaCl) will have mass.

The mass (weight) of any compound is simply: the sum of the atomic masses (or weights)
of the elements (remember that we can find the mass of each of the atoms present in the
Periodic Table)

For example: the atomic mass of common old table salt (sodium chloride, NaCl) is 23 + 35.5
= 58.5.

The type of compounds which make up our bodies are important. If we know the type of
compound we can tell, for instance, if this substance will dissolve in our cell fluid and help
conduct nerve messages. The easiest way to do this is to know how the atoms in the
compounds are held or “bonded” together.
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Chemical Bonding is essentially of two types:

1. IONIC BONDS

When a compound is made up of ions - with positive and negative

Charges - the oppositely charged ions will attract each other. This attraction holds the ions
together - and thus forms the compound. This is called an Ionic Bond.

We can define an ionic bond as the “Electrostatic attraction between positive and negative
ions”. In an ionic bond, electrons are lost or gained (transferred) between atoms.

For example:

NaCl (sodium chloride, common salt) is an ionic compound. Ionic compounds are also
called Salts. Salts are very important in our bodies

NaCl (salt) will dissolve in water ! and dissociate into 2 ions: Na+ + Cl -

Salts in a water solution (also called electrolytes) have many important medical uses eg
physiological saline is a commonly used in intravenous drips)

MOLECULAR COMPOUNDS (Molecules)

1. COVALENT BONDS

Elements which do not lose or gain electrons easily must try to achieve the stable number of 8
electrons in their outer shell by another means; they do this by sharing electrons with other
atoms.

Carbon is the element on which our life system is built.

Carbon has 4 electrons in its outer shell. It is hard to gain 4 electrons and hard to lose 4.
Therefore Carbon love to share electrons with other atoms to form molecules.

A Covalent Bond is defined as a bond that consists “sharing of electrons between atoms”.
Covalent bonds can be a single bond (1 pair of electrons), a double bond ( 2 pairs of
electrons) and even a triple bond (3 pairs of electrons being shared between atoms).

A molecule of GLUCOSE consists of Carbon and Hydrogen and Oxygen atoms all joined
together by covalent bonds…..ie atoms are all bonded together by sharing electrons.

GLUCOSE is therefore known as a molecular compound.

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Covalent bonds are strong and not readily broken.

Ionic bonds tend to be weaker than covalent bonds.

We can now see that very different types of compounds result from the atoms being held
together by different bonds – ionic bonds or covalent bonds.

Since our bodies are made up of 65% water, and most substances are therefore in a watery
solution in the cells and blood, what is really important to know is how these compounds
behave in solution.

Comparison of Ionic and molecular (Covalent) Compounds

Ionic
1. Ionic compounds usually water soluble
2. They consist of Neutral combinations of
positive and negative ions.
3. They separate on solution in water into
charged particles or ions, known as
“dissociation”.
4. These charged particles can carry an
electric current and are therefore known
as electrolytes.
Molecular
1. Covalent compounds may be soluble or
insoluble in water
2. They consist of uncharged molecules
with atoms joined by sharing electron
pairs.
3. They remain as discreet uncharged
particles in solution
4. Cannot carry an electric current in
solution.

The most important difference is that ionic compounds dissolved in water can an carry
electric current (hence they are referred to as electrolytes).

In the body, the electric current enables nerve messages to be carried through the body via the
nerve cells.

Polarity

The word Polar simply means charged.

Sometimes covalent bonds have the electrons shared equally between the bonding atoms:
and the bond is said to be a non-polar covalent bond. This occurs when electrons are evenly
shared between the atoms of the compound, no one atom takes on a slight charge.
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When carbon and hydrogen are bonded together, they share electrons in the bond equally, so
form only nonpolar bonds. The molecules formed by this bonding process have no charge.
Such molecules that contain main hydrogen and carbon are called hydrocarbons.

Therefore all hydrocarbons tend to be nonpolar molecules (review SOLUBILITY video).

Sometimes the sharing is unequal " and resulting bond is said to be a polar covalent bond.

This happens if the following 2 atoms are sharing electrons in a bond:

1. Oxygen and Nitrogen OR

2. Oxygen and Carbon OR
3. Oxygen and Hydrogen

Two important points to consider:

1. It is the difference in the electronegativity between the atoms in the bond sharing
electrons that will determine whether or not a covalent bond will be Polar or Non-
polar (refer to the ‘Membrane Molecules’ prac notes for a definition of
electronegativity and a description of how it is determined).

2. It will be the overall structure of a molecule and the number and position of the bonds
(polar, non-polar) that will determine whether or not a molecule is polar or non-polar
(refer to the Video – ‘Solubility’ to review polarity of molecules)

For example:

Polar bonds in a molecule (eg. water) make the molecule become “polar” or “charged”.

Imagine the water molecule H2O. Structurally, it looks like this (a bent molecule):

O
/ \
H H

There is a significant difference in the electronegativity of oxygen and hydrogen (>0.4). The
electron being shared in the bond will be more attracted to the atom with the higher
electronegativity values – in this case – Oxygen.

This means the Oxygen will be slightly negatively-charged. The Hydrogens of both bonds
also be slightly positively-charged.

NOTE: this will only be a slight charge around both oxygen and hydrogen, it is not like the
full charge that occurs in an ion.
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In fact, the ‘bent’ shape of the water molecule means, the whole molecule will be slightly
negatively-charged end (around the Oxygen) and a slightly positive-charged end (around the
hydrogens). The means the whole molecule is “polar”. Polar molecules can attract other polar
molecules – this force of attraction between polar molecules involving hydrogen atoms – is
called a Hydrogen bond.

The effect of this polarity, means Water is a highly polar molecule, and means that water
molecules really stick together – (refer to the special thermal properties discussed in your
Topic 2 lecture on ‘Water’).

This force of attraction that exists between water molecules is called a hydrogen bond. A
hydrogen bond is an intermolecular bond.

NOTE: A hydrogen bond is a force of attraction that is much weaker than either a
covalent bond or an ionic bond.

ACIDS and BASES

We all have some idea of what an acid is. A lemon tastes sour because of the citric acid
present.

Chemically, an acid is a substance which releases Hydrogen ions (H+ ) in solution (it is the
Hydrogen ions which give the sour taste).

Since H+ are sometimes called protons, an acid is also defined as a proton donor.

All Acids have a sour taste and turn litmus paper red.

A base is the opposite and chemically is a substance which releases Hydroxide ions (OH- ) in
solution

A base is also called a proton recipient.

Bases have a slippery feel (washing soda is a base) and turn litmus paper blue

Acidity is a measure of Hydrogen ion concentration. We abbreviate concentration using

square brackets, so when we refer to the hydrogen ion concentration, we signify it [H+]. The
concentration can be thought of as the density of protons in the solution.

The more Hydrogen ions present, the more acid the solution.

Until the acid is dissolved in water, the ionic bonds attaching the proton to the rest of the
compound will not break. Therefore the acid cannot lose its protons unless it is in solution.
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Strong acids give rise to a high concentration of H+. This is because strong acids are almost
fully dissociated in solution. By fully dissociated, we mean that almost all the ionic bonds
attaching the protons to the rest of the compound have broken - all the protons have been
released into solution.

Hydrochloric acid is a strong acid.

HCl ! H+ + Cl-
Hydrochloric acid present in the stomach is a strong acid.

Weak acids are only slightly dissociated in solution. This means that only some of the ionic
bonds are broken.

CH3COOH  CH3COO- + H+

Most metabolic acids, eg lactic acid, in the body are weak acids.

Lactic acid is the end product of anaerobic METABOLISM.

When you put acids and bases together they Neutralise each other.

The pH scale

The Hydrogen ion concentration of most biological fluids is usually very low eg 1 x 10-7. This
is the equivalent to about 1 H+ per 10 million other molecules in the body! While this seems
tiny, it is still very important.

We use the pH scale as a convenient scale to express the Hydrogen ion concentration.
Because the Hydrogen ion concentration determines acidity, we can use the pH scale to
express acidity as a number.

pH is defined as the negative log of the Hydrogen ion concentration.

Log is a mathematical way to convert numbers which are vastly different into a useable form.
For example, rather than writing 10, 100, 1000, 10000 and so forth - where each step in the
progression is large, and ever increasing, we can use a log scale to convert these numbers to 1,
2, 3, and 4.

The Hydrogen ion concentration in biological fluids is around 1 in 10 million. 10 million can
also be written as 107 (meaning 10 x 10 x 10 x 10 x 10 x 10 x 10).

pH = -log [H+]
∴[H+] of 1 x 10-7 = pH of 7
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What you need to know about the pH scale

• The pH scale is a negative log scale: the lower the number, the more acid the solution

• The pH scale – a pH of 7.0 = neutral pH; a pH of <7 is considered acidic; a pH>7 is

considered alkaline (or basic).

• For example: a pH of 3 is 10 times more acid than a pH of 4

QUESTION:
Hydrochloric acid is found in the stomach. What would you roughly guess the pH of
stomach fluid to be – would it be pH 2 or pH 8?
ANSWER:
The pH of stomach fluid is approximately pH 2 - it is a very acidic environment.

END OF REVISION NOTES

You have now finished the reviewing the topic of ‘Key concept of body chemistry’.

• Topic 1 – online module – please be sure to complete this module – it is available at all
times – complete as many times as you need to.
• Mastery Quiz #1 includes practice exam questions for this Topic.