Principles of Biochemistry

(Part 1)
SPS505 Exercise Biochemistry
 Learning outcomes
At the end of the lesson, students should be able to
1. Identify the main chemical elements in the human body
2. Describe and draw the basic atomic structure
3. Differentiate between atomic number and atomic mass
4. Identify the differences between atoms, ions,
molecules, compounds and isotopes
5. Differentiate between ionic and covalent bonds
6. Differentiate between molecular formula and molecular
mass
7. Differentiate between organic and inorganic substances
 Matter
• Matter is anything
that has mass and
occupies space
• Matter can be
classified according
to
1. Physical state Which state of matter can be compressed?
• Gas
• Liquid
• Solid
2. Composition
• Pure
substance
• Mixture
 Matter is anything that
occupies space and has mass

A substance A substance that contains A mixture with A mixture that is

that consists of two or more elements uniform not uniform in
only one type that are chemically appearance and appearance and
of atom bonded together composition composition
 Elements
• All matter (living and non-living things) is composed of
elements
• Only ~25 of the 92 naturally occurring elements are
important to living things
• In the human body, 4 main elements account for ~96%
of the total mass
 Main elements in the human body
Oxygen (65%)
• Component of water and most organic molecules
• Required for cellular respiration

Carbon (18%)
• Backbone of organic molecules

Hydrogen (10%)
• Component of water and organic molecules

Nitrogen (3%)
• Component of proteins and nucleic acids
 What are elements?
• Elements are substances that cannot be broken down into
simpler substances by chemical reactions
• An element is a liquid, solid or gas that contains only one
type of atom
Carbon
• E.g.

Oxygen
Hydrogen

Nitrogen
 What is an atom?
• Atom : the smallest unit of an element that
1. retains the physical and chemical properties of that
element
2. can take part in chemical reactions
• Atom is the smallest functional unit of matter
• Atoms are made up of three types of subatomic particles
1. Protons
2. Neutrons
3. Electrons
 Atom
• The mass of an atom is concentrated in the nucleus
• The protons and neutrons account for >99.9% of the atom’s mass

• Atoms are electrically neutral due to the equal numbers

of electrons and protons
Draw the structure of an atom
and label the subatomic
particles inside the atom
 Atoms of different elements
Lithium Carbon Oxygen Neon
Symbol Li C O Ne
Atomic number 3 6 8 10
Melting point (°C) 181 3550 -219 -249
Boiling point (°C) 1330°C 3825 -182 -246
Flammable yes yes no no
Metal, solid Non-metal, solid gas gas

n:4 n:6 n:8 n : 10

ATOMIC NUMBER p:3 p:6 p:8 p : 10
e:3 e:6 e:8 e : 10
 Standard representation for an atom
Atomic mass number (A)
• The mass of an atom of an element
• Equivalent to the total number of protons and neutrons

Atomic number (Z)

• Number of protons in its nucleus
• Each element has its own atomic number
• Since atoms are neutral, the proton number is also the number of
electrons in the atoms
 copper fluorine beryllium

barium chlorine radon

For each element, state :-
1. the atomic mass number
2. the atomic number
3. the number of protons
4. the number of neutrons
5. the number of electrons
 Electronic structure of an atom
• Electrons orbit the nucleus in the shells of an atom
• Because electrons are constantly moving, their precise
position at any one time is unknown
• Electrons can be thought of as occupying one or more
spherical clouds of negative charge around the nucleus
called shells
 Electronic structure of an atom
• Each shell can accommodate certain number of electrons
• The diagram below indicates the maximum number of
electrons for the first 20 elements
• The way in which the electrons are arranged in an atom is
called the electron arrangement

2.8.8

• The electrons in the outermost shell are known as

valence electrons
DRAW THE ELECTRONIC STRUCTURE
OF THESE ATOMS
 The periodic table

• The periodic table shows all known elements in order of

increasing atomic number
• The table also organizes elements into groups based on
the number of valence electrons
 The Periodic Table

• All the elements of a group have the same number of

valence electrons and similar chemical properties
 The octet rule
• When the electron arrangement of an atom is a
duplet or an octet, the atom is chemically very stable
and non-reactive

Referring
to
hydrogen
& helium
only

• Elements in Group 8 (noble gases) exist as monoatom

in nature
• They are inert and do not react with any other
elements or themselves to form any chemical
compounds
 The octet rule
• Atoms in other groups which are not in duplet/octet
tend to react with other atoms in various ways to
achieve a stable electron arrangement
• The tendency of an atom to achieve an octet
arrangement of electrons in the outermost shell is
called the octet rule
• Atoms can achieve duplet or octet electron
arrangement in 3 ways:
1. throw away the excess electron(s)
2. receiving electron(s) from other atom
3. sharing electron(s)
 Chemical bonds
• Atom forms chemical bonds in order to achieve a stable
electron arrangement
• The bonding can occur in 2 ways:
1. transferring of valence electrons to form ionic bond
2. Sharing of pairs of electrons to form covalent bond
• A group of two or more atoms that are chemically
bonded together is called a molecule
• If a molecule consists of two or more elements, it is
called a compound
WILL FORM CATIONS WILL FORM ANIONS

n : 12 n : 12 n : 14 n : 16 n : 16 n : 18
p : 11 p : 12 p : 13 p : 15 p : 16 p : 17
e : 11 e : 12 e : 13 e : 15 e : 16 e : 17
 Ion
• An ion is formed when an atom receives or releases one
or more valence electrons
• An ion is an atom or a molecule with electrical charge
• When an atom donates one or more valence electron, it
becomes a cation (a positively charged ion, e.g. Na+)

Sodium atom Sodium ion

 Ion
• An ion is formed when an atom receives or releases one
or more valence electrons
• An ion is an atom or a molecule with electrical charge
• When an atom gains one or more valence electron, it
becomes an anion (a negatively charged ion, e.g. F-)

Fluorine atom Fluoride ion

 Ionic bonds
• Ionic bond is formed through the transfer of valence
electrons from metal atoms to non-metal atoms to
achieve stable electron arrangement
• Metal atoms from Groups 1, 2 and 3 tend to donate all
their valence electrons to form cations
• Non-metal atoms from Groups 5, 6 and 7 tend to gain
electrons to form anions
• The formation of cations and anions will create a strong
electrostatic attractive force that pull oppositely charged
ions together to form an ionic compound
 Ionic bonds
• An ionic compound is electrically neutral
• Total number of positive charges = total
number of negative charges
 Covalent bonds
• Covalent bonds are formed through the sharing of pairs of
electrons to achieve stable electron arrangement

• Non-metal atoms from Groups 4, 5, 6 and 7 and hydrogen

atoms tend to form covalent bonds by sharing electron
pairs with
1. Atoms of the same elements (e.g. H2, O2, N2, Cl2)
2. Atoms of different elements (e.g. H2O, CO2, NH3, HCl)
 Covalent bonds
• Each atom contributes an equal number of electrons for
sharing
• Single covalent bond – 1 pair of electrons is shared

• Double covalent bond – 2 pairs of electrons are shared

• Triple covalent bond – 3 pairs of electrons are shared

• The shared paired of electrons forms the covalent bond

between the two atoms
 Covalent bond Ionic bond
Occur through the interaction of neutral Occur through the interaction between
atoms cations and anions
Electron pairs are shared between Electrostatic attraction between cations
atoms and anions
Usually exists between non-metal atoms Usually exists between metal and non-
metal atoms
The bond can be single, double or triple No multiplicity
 Isotopes
• Isotopes are atoms of the same element with the same
number of protons but different number of neutrons

Carbon-12 Carbon-13 Carbon-14

Properties of Isotope
Same or different?
No. of proton
No. of neutron
Chemical properties
Physical properties
 Molecular formula
• Molecular formula shows the types and number of
atoms of each element in a molecule
• Molecular formula of water is H2O

Molecular mass
• Molecular mass is the sum of the atomic masses of the
elements that make up the molecule
• Measured in daltons (Da)
Atomic mass of H = 1
Atomic mass of O = 16
Molecular mass of water (H2O) = (1 X 2) + 16
= 18 Da
 Structural Formula
• Structural formula shows the arrangement of atoms and
bonds in a molecule

Molecular Molecular Structural

Substance
formula mass formula

Water H2O 18 Da

Methane

Carbon dioxide
 Carbon
• Carbon is relatively rare in the natural
world (<0.03% of Earth’s crust) but
living organisms actively accumulate
it
• Carbon accounts for ~18% of body
weight in humans
• Carbon is an the common building
block of all organic molecules
because of the many ways it can form
strong covalent bonds with other
atoms
 Carbon
• The natural tendency of carbon to form four covalent
bonds with other molecules makes it an ideal structural
component, one that can branch in a multiple directions
• There is almost no limit to the size of organic molecules
derived from carbon
• Some macromolecules can consists of thousands or even
millions of smaller molecules
 Classes of biological substances
• Studying of biochemistry is facilitated by dividing
biological substances into 2 classes

1. Contain Carbon bonded 1. Substances made from

to hydrogen single elements
2. Contain 2 or more 2. Include salts, metals and
elements any other compounds
that do not contain
carbon bonded to
hydrogen
 ARE THESE ORGANIC OR
INORGANIC SUBSTANCES?
A. GLUCOSE B. ALANINE C. TRIGLYCERIDE

D. WATER E. CALCIUM F. VITAMIN A

J. Nucleic acid
G. CARBON H. CARBON DIOXIDE
Principles of Biochemistry
(Part 2)
SPS505 Exercise Biochemistry
 Learning outcomes
At the end of the lesson, students should be able to
1. Describe and draw the basic nucleotide structure
2. Differentiate between DNA and RNA
3. Describe the central dogma of molecular biology
4. Describe the principles of the genetic code
5. Describe the basic cell structure with particular
emphasis on the plasma membrane, nucleus,
cytoplasm, ribosome and mitochondria
6. Differentiate between prokaryotes and eukaryotes
7. Describe the levels of structural organisation in the
human body
8. Describe the characteristics of life
4 classes of important macromolecules
Carbohydrate/Polysaccharide
Protein
Lipid
Nucleic acid
(Large molecules made of many smaller
molecules of the same kind)
 Nucleic acids
• Nucleic acids are macromolecules containing carbon (C),
hydrogen (H), oxygen (O), nitrogen (N) and phosphorus
(P)
• The monomers of nucleic acids are nucleotides
• Each nucleotide consists of 3 parts:
1. A pentose sugar
2. A phosphate group
3. A nitrogenous base
 Nucleic acids
• Nucleic acids store and transmit genetic information
• 2 types of nucleic acids are found in cells:
1. Deoxyribonucleic acid (DNA)
2. Ribonucleic acid (RNA)
Nucleic acids
 DNA or RNA? DNA or RNA?
Double stranded Single stranded
Forms a double helix Does not form a double helix
Sugar deoxyribose Sugar ribose
Has thymine Has uracil
Store genetic information Copies information for protein
synthesis
Cannot travel in and out of nucleus Can travel in and out of nucleus
Found in nucleus, chloroplast and Found in nucleus, cytoplasm and
mitochondria ribosome
The central dogma of molecular biology
• The central dogma of molecular biology states that DNA
makes RNA makes proteins

• Replication is the process of producing 2 identical DNA

molecules from 1 original DNA molecule
• DNA replication is
essential for cell
division during
growth or repair of
damaged tissues
The central dogma of molecular biology
• Transcription is the
process of making a RNA
copy of a DNA sequence
• This copy, called a mRNA,
leaves the cell nucleus
and enters the cytoplasm
where it directs the
synthesis of the protein

• Translation is the
process of translating
the sequence of a mRNA
to a sequence of amino
acids during protein
synthesis
Genetic code • Triplets of bases
(codons) code for
specific amino acids
• Specific triplets serve
for chain initiation
(AUG) and others for
termination (UAG,
UAA and UGA)
• There are 43 = 64
different possible
base triplets (> the
total number of
amino acids)
• The genetic code is
degenerate
Genetic code
 Cells structures and functions
• Cells are basic units of living organisms
• All cells are enclosed in a cell membrane

http://leavingbio.net/cell-structure/
www.sorgentegenetica.it www.coleparmer.com

• Most cells are 70-80% water

• The interior living component of a cell is called the
protoplasm (consists of cytoplasm and nucleus)
• The cytoplasm of eukaryote contains small structures called
organelles
• Each organelle is membrane-bound to maintain its internal
environment to perform specific functions
Organelles are membrane-bound structures
that maintain their internal environment to
perform specific functions
Organelles

A typical animal cell

 Cellular components of an animal cell
1. Nucleus
• Controls all activities of the cell
• Contains most of the cell’s genetic
material
• (DNA in the form of chromatin)

• A double layered membrane called

the nuclear membrane keeps the Nucleoplasm
DNA within the nucleus Chromatin Nucleolus
• The nuclear pores are too small for
DNA to pass through but allow
passage of some small proteins and
RNA
• Components of ribosomes are
synthesized in the nucleolus
Nuclear pore
Nuclear membrane
 Cellular components of an animal cell
2. Mitochondria
• Site of cellular respiration
• Enzymes in the matrix and inner
membrane are involved in
important reactions and
processes that produce energy
(ATP) for cells
• e.g. Krebs cycle, ATP
synthesis, fatty acid
oxidation
 Cellular components of an animal cell
3. Ribosome
• Site of protein synthesis
• assemble amino acids into
proteins according to a RNA
template
• Consists of 2 subunits
• Made of RNA and protein
• Free ribosomes are located in
the cytoplasm
• Bound ribosomes are attached
to the endoplasmic reticulum
 Cellular components of an animal cell
4. Endoplasmic reticulum
• Site of synthesis, storage and
transport of macromolecules
• Rough ER (RER)
• Ribosomes attached to the
RER release their proteins
into the folds
• Many of these proteins are
packaged for transfer to the
Golgi apparatus
• Smooth ER (SER)
• Packaging the proteins and
lipids for delivery to the Golgi
apparatus
 Cellular components of an animal cell
5. Golgi apparatus
• Involved in the processing, packaging
and transport of macromolecules
• Contains enzymes that further refine
the products of the ER into final form

cis Face
(‘receiving’ side of
Golgi apparatus)

trans Face
(‘shipping’ side of
Golgi apparatus)
 Cellular components of an animal cell
5. Lysosomes
• Contain hydrolytic enzymes that
breakdown macromolecules and
worn-out organelles
 Cellular components of an animal cell
5. Plasma membrane
• Regulates and controls the
movement of substances in and
out of the cell
• Semi-permeable
• Consists of protein and
phospholipids
Phospholipid

Phospholipid
bilayer
 Cellular components of an animal cell
5. Plasma membrane is only permeable to:
• Small hydrophobic solutes
• e.g. fatty acids & glycerol
• Fat-soluble hormones and vitamins
• e.g. steroids, vit. A, vit. D, vit. E & vit. K
• Small neutral solutes
• e.g. respiratory gases
(CO2, O2)
• Water
 Passive transport vs active transport
Passive transport Active transport
Movement of substances Process of moving substances
across the plasma membrane across the plasma membrane
• down the concentration • against the concentration
gradient gradient
• without the use of ATP • with the use of ATP and
Pore protein Carrier protein pumps

Pump

Simple Facilitated Osmosis Active

diffusion diffusion transport
e.g. steroid e.g. e.g. e.g. sodium-potassium pump
sodium glucose
Draw a typical animal cell and label
the cellular components in the cell
 Prokaryotic cell vs eukaryotic cell
• Prokaryotes (pro- means “before” and karyote means
“nucleus”) are organisms that lack a distinct nucleus
and other organelles due to the absence of internal
membranes. e.g. bacteria

Eukaryote Prokaryote

• Eukaryotes are organisms that possesses a clearly

defined nucleus
• Eukaryotes have membrane-bound organelles
A comparison of prokaryotes and eukaryotes
Cellular Prokaryotes Eukaryotes
components
Nucleus No definite Present
nucleus
Cell membrane Present Present
(plasma
membrane)
Mitochondria None Present
Endoplasmic None Present
reticulum
Ribosome Present Present
Chloroplasts
 Cell organisation
• Unicellular organism : organisms that are made up of only
one cell

• Multicellular organisms : organisms that are made up of

more than one cell
o There are more than 200 different types of cells in the human body!
• In multicellular organisms, different cells are adapted to
carry out specific functions
Cell specialisation
A process in which cells undergo
changes and adaptations in
structures to enable them to
carry out specific function
 Levels of structural organization in the human body

Atoms

Molecules

Macromolecules

Organelles

Cells

Tissue

Organ

Organ
System
 Tissue
• A group of cells with the
same general structure
and function

Organ
• A group of several
tissue types that carry
out a specific function
 Organ system
• Two or more organs that work together to carry out
a general function (such as digestion or movement)
 The characteristics of life
• Most biologists accept the following criteria as signs of life:
1. Living things have a different molecular composition
than non-living things do
2. Living things require energy and raw materials
3. Living things are composed of cells
4. Living things maintain a relatively constant internal
environment (homeostasis)
5. Living things respond to their external environment
6. Living things grow and reproduce
7. Populations of living things evolve
 References
• MacLaren, D., & Morton, J. (2011). Biochemistry for sport
and exercise metabolism. John Wiley & Sons.
• Campbell, M., & Farrell, S. (2007). Biochemistry: Cengage
Learning
• Mougios, V. (2006). Exercise Biochemistry: Human Kinetics
• Johnson, M. D. (2012). Human Biology. Concepts and
Current Issues. Pearson Education
• Videos
• https://www.youtube.com/watch?v=l1VXM_b2KFY
• https://www.youtube.com/watch?v=URUJD5NEXC8
• https://www.youtube.com/watch?v=C1CRrtkWwu0
• https://www.youtube.com/watch?v=ruUf7ntRCk8
• https://www.youtube.com/watch?v=gG7uCskUOrA

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