Module 1 Building Blocks of Biochemistry 1 of 6

BMOL2201/6201
Biochemistry: An Introduction

Shoba Ranganathan
Dept. of Molecular Sciences, 4WW (F7B), Room 121
T: 02 9850 6262; E: [email protected]
What is Biochemistry ?
• The study of life: chemistry of biomolecules
 overlaps other disciplines, including cell and molecular
biology, chemistry, genetics, immunology, microbiology,
pharmacology, and physiology
• Key questions
1. What are the structures of biological molecules?
2. How do biological molecules interact with each other?
3. How does the cell synthesise and degrade biological
molecules?
4. How is energy conserved and used by the cell?
5. What are the mechanisms for organizing biological
molecules and coordinating their activities?
6. How is genetic information stored and processed?
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BMOL2201/6201
 Building blocks of key biomolecules: nucleic acids,
proteins, sugars and lipids
 Biochemical signalling: how does the cell know what
to do and when? (Cell Biology)
 Metabolism: making biomolecules from their building
blocks as well as breaking them down
 How do we get energy?
 How are biomolecules organized into teams for
coordinating their activities?

Eat healthy and avoid metabolic diseases such as

obesity and diabetes!
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Learning Objectives of this unit

1. Overall biochemical and cell biology knowledge

2. Capacity to define key concepts
3. Connecting protein structure with function
4. Identify, quantify and separate biomolecules
5. Tracking enzyme reactions and biochemical
signalling
6. Metabolic pathway mapping
7. Data analysis

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Learning Objectives of this unit
1. Overall biochemical and cell biology knowledge:
 define the differences between eukaryotic and prokaryotic
cell structure;
 relate the biochemical processes required for growth and
energy; and
 understand controls mechanisms involved in the synthesis
and breakdown of important biomolecules.
2. Capacity to define key concepts: to define and relate
 the key concepts of compartmentation of biochemical
processes;
 the thermodynamic principles of enzyme catalysis;
 the major biological systems involved in metabolism and
energy production pathways in the living cell; and
 the concept of cell-cell communication as related to
metabolic control.

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Learning Objectives of this unit
3. Connecting protein structure with function:
 define the protein structure-function paradigm; and
 describe, in qualitative and quantitative terms, the relationship
between structure and function of proteins.
4. Identify, quantify and separate biomolecules:
 utilize appropriate experimental methods to characterise,
quantify and separate different types of biomolecules.
5. Tracking enzyme reactions and biochemical
signalling:
 identify the factors influencing the rate of an enzyme-catalysed
reaction;
 measure rates of enzyme reactions to determine basic kinetic
parameters of an enzyme; and
 understand how external changes are communicated to the
interior of cells and organelles.
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Learning Objectives of this unit
6. Metabolic pathway mapping:
 relate the flow of metabolites via metabolic pathway mapping;
 identify the interactions between different metabolic pathways;
 understand pathways involved in energy metabolism.

7. Data analysis:
 collect experimental data using biochemical techniques; and
 sort, graph, analyse and present the experimental results in a
biochemical context.

These learning objectives will be delivered via lectures, practical

exercises (in the laboratory) and tutorial questions (in tutorial sessions).

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Content delivery
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 Login: MQ Student ID (8 numbers)
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Textbook
https://www.youtube.com/watch?list=PLXfe2hpW_gSIDc_VPFgG_ObYFx5MePstn&v=Cj69EB-pqjE

Fundamentals of Biochemistry: Life at the

Molecular Level, 5th Edition by Donald Voet,
Judith G. Voet, and Charlotte W. Pratt( Wiley)

http://www.wileydirect.com.au/buy/fundamentals-of-
biochemistry-5th-edition/.
Module 1: Building Blocks of Biochemistry
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Brushing up your Chemistry and
Biology fundamentals
• Revision materials on iLearn
• Check out Chapters 0-2 in the textbook

Tips on doing well

• You’ll need to work steadily, because new
material is based on earlier material.
• You will not be able to leave mastering the
content until the last few weeks.
• Direct correlation between lecture/tutorial
attendance and student performance.
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Objectives

Introduction to the Chemistry of Life: VVP5: Chap. 1

1. What are biomolecules made of?
2. Cellular architecture
3. Thermodynamics (basics)
4. Water: the medium of life: VVP5: Chap. 2

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Living matter consists of a few
elements!
• Water makes up ~70%
of humans and most
living organisms
• Trace amounts of many
other elements are also
essential
• Organic molecules
arose from simple
inorganic molecules

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Common functional groups and
their role in biochemistry - 1

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Common functional groups and
their role in biochemistry - 2

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 Complex self-replicating molecules
arose from simple molecules
• Simple molecules polymerise to make biopolymers

• Polymerization is usually via

condensation (reverse reaction is
hydrolysis): e.g. carboxylic acid and
amine
 Condensation FORMS water
 Hydrolysis USES UP water
• Different monomers combined into a
polymer lead to chemical versatility
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Complementarity in biochemistry
• Macromolecules containing complementary
groups can pair-up:

• This is the principle behind

extended self-replication

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Introduction to the Chemistry of Life
Summary VVP5: Chap. 1
• Biological molecules are constructed from a limited
number of elements.
• Certain functional groups and linkages characterize
different types of biomolecules.
• During chemical evolution, simple compounds
condensed to form more complex molecules and
polymers.
• Self-replicating molecules persist due to natural
selection.

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Cells carry out metabolic reactions
• During evolution, selective advantage favoured
systems that were localised and protected by
boundaries when competing for resources.
• Compartmentation provides protection from
environmental fluctuations and maintains high
local concentrations of components.
• This increases the efficiency of polymerization
(e.g. biopolymers) and other chemical
reactions (e.g. metabolism, energy
generation).

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Eukaryotic cells: several
membrane-enclosed organelles

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Cellular architecture - Summary

• Compartmentation of cells promotes

efficiency of biochemical reactions.
• Metabolic pathways evolved to synthesise
biomolecules and generate energy.
• Specialised activities are carried out in
different cellular compartments.

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Thermodynamics:
Reaction spontaneity and G

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Relevant thermodynamics principles
• Free energy change can be calculated from
equilibrium concentrations.
 Le Châtelier’s Principle (please revise)
• Normal standard states are under conditions when
life does not exist. Hence, the biochemical standard
state has been adapted to biological conditions:
temperature of 25oC, a pressure of 1 atm, and a pH
of 7.0.
• Life obeys the Laws of Thermodynamics.
• Although potentially numerous reactions are
thermodynamically favoured, only a few actually
occur. This is because favourable paths are available
for these few reactions, with enzymes as catalysts.

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Thermodynamics Summary
• Energy must be conserved but takes various forms.
• In most biochemical systems, enthalpy is equivalent to heat.
• Entropy, measuring a system’s disorder, tends to increase.
• Free energy determines whether a reaction will occur
spontaneously or not.
• The free energy change for a reaction can be calculated.
• Biochemists define standard state conditions as a
temperature of 25oC, a pressure of 1 atm, and a pH of 7.0.
• Organisms are non-equilibrium, open systems that constantly
exchange matter and energy with their surroundings.
• Enzymes increase the rates of thermodynamically favourable
reactions.

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Water: the Medium of Life
VVP5: Chapter 2

• Water is essential for all forms of life.

• Every organism is 70-90% water!
• Normal human metabolic activity requires min. 65%
water!
• Water is an excellent solvent and is therefore the
medium of the majority of biochemical reactions.
• Water causes ionization of polar molecules, critical
for the function of:
 amino acids and proteins
 nucleotides and nucleic acids
 even phospholipids and membranes

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 Physical properties of water
• Water molecules are polar and 
can form hydrogen bonds with 
other molecules.
• The attractive forces acting on 
biological molecules include ionic 
interactions, hydrogen bonds, and 
van der Waals interactions.
• Polar and ionic substances can 
dissolve in water. Even fats and 
lipids have polar segments that 
orient themselves towards water: 
e.g. micelles and bilayers.

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Chemical properties of water

• Water dissociates to form H+ and OH– ions, with a

dissociation constant of 10–14.
• The acidity of a solution is expressed as a pH value,
where pH = –log[H+].
• An acid is a compound that can donate a proton, and
a base is a compound that can accept a proton.
• A dissociation constant varies with the strength of an
acid.

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Relationship of pH, [H+], and [OH-]

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Ionization of water & pH: a measure of
the acidity of a solution
H2O H+ + OH-
• pH = -log10 [H+]
• for pure water, [H+] and [OH-] equal 10-7 mol.L-1 (M)

For pure water, [H+] = [OH-] = 1 x 10-7 mol.L-1 & pH = 7

Importance of pH
• pH determines the viability of biochemical reactions.
• It affects ionization and hence the charge of molecules that have
acidic or basic groups (groups than can gain or lose protons).
 This can have significant effects on the biological, chemical and
physical properties of these molecules.
• pH can thus have a significant effect on the properties of amino
acids and proteins.

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pH Values of Common Substances

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Biochemical molecules are weak acids and
bases - dissociation based on pH of media
• Biochemistry is full of weak acids and bases, both of
which can affect the pH of an organelle

HA H + + A-
• Weak acids only partially dissociate, and the
equilibrium constant for this reaction is called Ka
Ka = [H+] [A-]
[HA]
• Similar to pH, Ka values are converted to the log
scale, as they are usually small:
pKa = -log10 Ka

e.g. vinegar: Ka = 1.74 x 10-5; pKa = 4.76

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Dissociation Constants and
pK Values of Some Acids

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 Buffers: Titration Curves of Weak Acids
• Sharp changes in pH at the
beginning and at the end.
• Around the pK value, the
reaction is close to
equilibrium, and resists pH
change.
• This is called “buffering” and
is most efficient within 1 pH
unit of the pK value: i.e. a
100-fold change in [H+].
• The dissociation constant
varies with the strength of an
acid.

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pH of weak acids/bases from
Henderson-Hasselbalch equation
• Taking logarithms of this equation gives us
-log [H+] = -log Ka + log ([A-]/[HA])
or
pH = pKa + log (base/acid)
• When there is an equal amount of base and
acid then pH = pKa
 also known as half-titration point
 titration is an effective way to determine the pKa
values
(Covered in CBMS107/CHEM1001 - please see revision materials)

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Titration of a Polyprotic Acid

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Water - Summary

• Water is polar and forms hydrogen bonds with itself

and other molecules.
• Water dissociates to form H+ and OH– ions, with a
dissociation constant of 10–14.
• The acidity of a solution is expressed as its pH,
where pH = –log[H+].
• pH has values from 0-14, with 7 being neutral pH.

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 Spot tests: Wed: ~1.45pm-1.55pm
Fri: ~2.45pm-2.55pm

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