NSC 223 MEDICAL BIOCHEMISTRY 1

COURSE
GUIDE

NSC 223
MEDICAL BIOCHEMISTRY I

Course Team
Dr. O Emma-Okon&Dr. J.O. Areola (Course Writers)
Dr. O.O. Irinoye&Dr. T.O. Oladogba (Course Editors)
Dr. S.A Isa, Dr. M.S Enaji & Dr. S. Rabiu (Course Reviwers)

NATIONALOPEN UNIVERSITY OFNIGERIA

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NSC 223 MEDICAL BIOCHEMISTRY I

National Open University of Nigeria

Headquarters
University Village
Plot 91, Cadastral Zone,
Nnamdi Azikiwe Expressway
Jabi Abuja

Lagos Office
14/16 Ahmadu Bello Way
Victoria Island, Lagos

EMAIL: nursingdepartment@[Link]

URL: [Link]

Published by
National Open University of Nigeria

Printed 2015

ISBN: 978-058-886-4

All Rights Reserved

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NSC 223 MEDICAL BIOCHEMISTRY 1

CONTENTS PAGE

Introduction................................................................................. iv
Course Aims................................................................................ iv
Course Objectives........................................................................ iv
Working through the Course....................................................... iv
Course Materials.......................................................................... iv
Study Units.................................................................................. v
Reference Textbooks................................................................... vi
Equipment and Software Needed to Access Course.................... vi
Number and Places of Meeting................................................... vi
Discussion Forum........................................................................ vii
Course Evaluation....................................................................... vii
Grading Criteria........................................................................... vii
Grading Scale.............................................................................. viii
Schedule of Assignments with Dates.......................................... viii
How to Get the Most from this Course........................................viii

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NSC 223 MEDICAL BIOCHEMISTRY I

INTRODUCTION

This course is medical biochemistry. Medical biochemistry is a subset of

general biochemistry. The course is designed to introduce beginners to
the concepts of biochemistry which deal with the chemical reactions in
biological systems. In this course, you will learn the biochemical
activities that occur inside the cell and how these activities determine
our state of health and what happens in disease. The reason why we fall
sick and the root causes of disease will be clearer to you at the end of the
course. Take a second look at yourself in the mirror; note the shape of
your face, the shape of your nose, ear and lips. Examine your
complexion, your height and the colour of your hair. Now look at your
mother carefully, how many of these features do you share with her? Do
the same to your father. Do you observe any features not shared with
either of your parents? If there is any, it may be the feature you inherited
from your grandparents. Scientific basis for this simple experiment will
be explained to you in this course. Diseases can be caused by micro-
organisms, what we eat, drink and by our lifestyle; it can also be
inherited from our parents. You will be in a position to explain the
source or cause of a particular disease and the mechanism of its
treatment if you understand the biochemistry of human body. The
knowledge that will be acquired in this course will assist you in
understanding the effects of drugs on the body and the effects of our
body on the drugs we use for therapeutic purposes. The concluding
aspects of this course highlight the roles of biocatalysts as mediators of
cellular reactions and the importance of vitamins in maintaining life
processes.

COURSE AIM

The aim of this course is to build your foundation for application of the
understanding of the basic chemical processes of the body in health and
diseases.

COURSE OBJECTIVE

At the completion of this course, you should be able to:

• explain the context of medical biochemistry in health and disease

conditions. .

WORKING THROUGH THIS COURSE

The course will be delivered adopting the blended learning mode, 70%
of online but interactive sessions and 30% of face-to-face during
laboratory sessions. You are expected to register for this course online
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NSC 223 MEDICAL BIOCHEMISTRY 1

before you can have access to all the materials and have access to the
class sessions online. You will have hard and soft copies of course
materials, you will also have online interactive sessions, face-to-face
sessions with instructors during practical sessions in the laboratory. The
interactive online activities will be available to you on the course link on
the Website of NOUN. There are activities and assignments online for
every unit every week. It is important that you visit the course sites
weekly and do all assignments to meet deadlines and to contribute to the
topical issues that would be raised for everyone’s contribution.

You will be expected to read every module along with all assigned
readings to prepare you to have meaningful contributions to all sessions
and to complete all activities. It is important that you attempt all the
Tutor-Marked Assignment (TMA) and other Self-Assessment Questions
(SAQ) at the end of the Module or Units to help your understanding of
the contents and to help you prepare for the in-course tests and the final
examination. You will also be expected to keep a portfolio where you
keep all your completed assignments.

STUDY UNITS

This course is the first of two courses that you will take and divided into
3 Modules of 14 study units.

Module 1 General Introduction to Medical Biochemistry

Unit 1 Introduction to Physiological and Pathological Chemistry
Unit 2 Cell Structure and Functions 1
Unit 3 Functions of the Cell Membrane and the Organelles

Module 2 Chemistry of Biomolecules

Unit 1 Chemistry of Carbohydrates

Unit 2 Chemistry of Carbohydrates (II)
Unit 3 Water, Acids, Bases and Buffer
Unit 4 Chemistry of Amino Acids and Proteins (I)
Unit 5 Chemistry of Amino Acids and Proteins (II)
Unit 6 Chemistry of Lipids
Unit 7 Chemistry of Nucleic acids I
Unit 8 Chemistry of Nucleic acids II

Module 3 Basic Enzymology

Unit 1 Introductory Enzymology

Unit 2 Enzyme Kinetics I
Unit 3 Enzyme Kinetics II

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NSC 223 MEDICAL BIOCHEMISTRY I

Bibliography
Murry, R. K., Bender, D. A., Bothan, K.M., Kennelly, P. J., Rodwell, V.
W. and Well, P. A.(2015). Harper’s Illustrated Biochemistry (30th
Edition) McGraw-Hill Medical.

Nelson, D. L. and Cox, M. M. (2012). Lehninger Principles of

Biochemistry (6th edition) WHFreeman.

Pamela, C. C., Richard, A. H. and Denise, R. F. (2013). Lippincott’s

Illustrated Reviews Biochemistry (6th edition) Lippincott Williams &
Wilkins.

Marks' Essentials of Medical Biochemistry: A clinical approach. 2nd

Edition Copyright 2007 Lippincott Williams & Wilkins.

Garrett and Grisham Biochemistry, 2nd Edition. Harcourt College Pub

Lippincott Biochemistry Fourth Edition (2010).

Robert K. Murray, MD, PhD. ‘Harper’s Illustrated Biochemistry’.

Twenty-Eighth Edition. 2009

Devlin T.M. (2010) Textbook of Biochemistry with Clinical Correlation

7thEdition. JohnWiley&SonsInc.

Davis, Jack. 2019. An Introduction to Enzyme Kinetics. News-

Medical, viewed 25 August 2021, [Link]
[Link]/life-sciences/An-Introduction-to-Enzyme-
[Link].

Factors Affecting Enzyme Activity: 6 Factors ([Link])

retrieved August 28, 2021

[Link] Editors. “Animal Cell.” Biology Dictionary,

[Link], 19/08/2021,
[Link]

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NSC 223 MEDICAL BIOCHEMISTRY 1

COURSE REQUIREMENTS AND EXPECTATIONS OF

YOU

Attendance of 95% of all interactive sessions, submission of all

assignments to meet deadlines; participation in all CMA, attendance of
all laboratory sessions with evidence as provided in the log book,
submission of reports from all laboratory practical sessions and
attendance of the final course examination. You are also expected to:

1. Be versatile in basic computer skills

2. Participate in all laboratory practical up to 90% of the time
3. Submit personal reports from laboratory practical sessions on
schedule
4. Log in to the class online discussion board at least once a week
and contribute to ongoing discussions.
5. Contribute actively to group seminar presentations.

EQUIPMENT AND SOFTWARE NEEDED TO ACCESS

THIS COURSE

You will be expected to have the following tools:

1. A computer (laptop or desktop or a tablet)

2. Internet access, preferably broadband rather than dial-up access
3. MS Office software – Word PROCESSOR, Power point,
Spreadsheet
4. Browser – Preferably Internet Explorer, Moxilla Firefox
5. Adobe Acrobat Reader.

NUMBER AND PLACES OF MEETING (ONLINE, FACE-

TO-FACE, LABORATORY PRACTICALS)

The details of these will be provided to you at the time of

commencement of this course.

DISCUSSION FORUM

There will be an online discussion forum and topics for discussion will
be available for your contributions. It is mandatory that you participate
in every discussion every week. You participation link you, your face,
your ideas and views to that of every member of the class and earns you
some mark.

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NSC 223 MEDICAL BIOCHEMISTRY I

COURSE EVALUATION

There are two forms of evaluation of the progress you are making in this
course. The first are the series of activities, assignments and end of unit,
computer or Tutor-Marked Assignment, and laboratory practical
sessions and report that constitute the continuous assessment that all
carry 30% of the total mark. The second is a written examination with
multiple choice, short answers and essay questions that take 70% of the
total mark that you will do on completion of the course.
Students’ evaluation: you will be assessed and evaluated based on the
following criteria:

• In-course examination
In-course examination will come up in the middle of the
semester. This would come in form of Computer Marked
Assignment. This will be in addition to one compulsory Tutor-
Marked Assignment (TMA) and three Computer Marked
Assignment that comes as specified after the modules.
• Laboratory practical: Attendance, record of participation and
other assignments will be graded and added to the other scores
form other forms of examinations.
• Final examination: The final written examination will come up
at the end of the semester comprising essay and objective
questions covering all the contents covered in the course. The
final examination will amount to 60% of the total grade for the
course.

• Learner-Facilitator evaluation of the course

This will be done through group review, written assessment of
learning (theory and laboratory practical) by you and the

GRADING CRITERIA
Grades will be based on the following percentages
Tutor- Marked Assignments 10%
Computer- marked Assignment 10%
Group assignments 5% 40%
Discussion Topic participation 5%
Laboratory practical 10%
End-of-Course examination 60%

GRADING SCALE
A = 70-100

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B = 60 - 69
C= 50 - 59
F = <49

HOW TO GET THE MOST FROM THIS COURSE

i. Read and understand the context of this course by reading
through this Course Guide paying attention to details. You must
know the requirements before you will do well.
ii. Develop a study plan for yourself.
iii. Follow instructions about registration and master expectations in
terms of reading, participation in discussion forum, end of unit
and module assignments, laboratory practical and other directives
given by the course coordinator, facilitators and tutors.
iv. Read your course texts and other reference textbooks.
v. Listen to audio files, watch the video clips and consult websites
when given.
vi. Participate actively in online discussion forum and make sure you
are in touch with your study group and your course coordinator.
vii. Submit your assignments as at when due.
viii. Work ahead of the interactive sessions.
ix. Work through your assignments when returned to you and do not
wait until when examination is approaching before resolving any
challenge you have with any unit or any topic.
x. Keep in touch with your study centre and School of Health
Sciences’ website as information will be provided continuously
on this site.
xi. Be optimistic about doing well.

SUMMARY
The Course NSC 223 (Medical Biochemistry I) is a compulsory course
for Nursing Science students. The course content is prepared in modules
and units as well as related practicals. It covers the basic requirements
for teaching medical biochemistry to Nursing Science students. It is
expected that the foundation provided in NSC 223 would find relevance
as students advance in their course of study. The minimum pass grade is
50% made up of assignments and examination components

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NSC 223 MEDICAL BIOCHEMISTRY I

MAIN
COURSE

CONTENTS PAGE

Module 1 General Introduction to Medical

Biochemistry.................................................... 1

Unit 1 Introduction to Physiological and Pathological

Chemistry.......................................................... 1
Unit 2 Cell Structure and Functions .......................... 5
Unit 3 Membrane structure abd organisation ................ 15

Module 2 Chemistry of Biomolecules............................. 21

Unit 1 Chemistry of Carbohydrates.............................. 21
Unit 2 Chemistry of Carbohydrates (II)........................ 29
Unit 3 Water, Acids, Bases and Buffer........................ 33
Unit 4 Chemistry of Amino Acids and Proteins (I).... 38
Unit 5 Chemistry of Amino Acids and Proteins (II)... 50
Unit 6 Chemistry of Lipids..................................... 60
Unit 7 Chemistry of Nucleic Acids I…………………… 69
Unit 8 Chemistry of Nucleic Acids II……………. 75

Module 3 Basic Enzymology............................................ 80

Unit 1 Introductory Enzymology..................................... 80
Unit 2 Enzyme Kinetics I............................................... 91
Unit 3 Enzymes Kinetics II........................................... 96

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NSC 223 MEDICAL BIOCHEMISTRY 1

MODULE 1 GENERAL INTRODUCTION TO

MEDICAL BIOCHEMISTRY

Unit 1 Introduction to Physiological and Pathological Chemistry

Unit 2 Cell Structure and Functions
Unit 3 Functions of the Cell Membrane

UNIT 1 INTRODUCTION TO PHYSIOLOGICAL AND

PATHOLOGICAL CHEMISTRY

CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Definition of Biochemistry
3.2 Breakthrough in Biochemistry
3.3 Relevance of Medical Biochemistry to other Life Sciences
3.4 Branches of Biochemistry
4.0 Conclusion
5.0 Summary
6.0 Tutor-Marked Assignment
7.0 References/Further Reading

1.0 INTRODUCTION

This unit introduces you to medical biochemistry with some

explanations of the relevance of the course to Nursing Science. You
will also be exposed to different branches of biochemistry.

2.0 OBJECTIVES

At the end of this unit, you should be able to:

• Define medical biochemistry

• Mention the major breakthrough in the field of biochemistry
• Explain the relevance of biochemistry to nursing, medicine and
other health sciences
• Describe different branches of biochemistry.

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NSC 223 MEDICAL BIOCHEMISTRY I

3.0 MAIN CONTENT

3.1 Definition of Biochemistry

Biochemistry is the study of chemical processes in living organisms. It

can also be defined as the application of chemistry to the study of
biological processes in living organisms. Biochemistry is both a life
science and a chemical science; it explores the chemistry of living
organisms and the molecular basis for the changes occurring in living
cells.

Medical biochemistry can be described as a branch of General

biochemistry; its scope is not as broad as general biochemistry. Medical
biochemistry is defined as the study of biochemical processes that occur
within the human body in relation with their application in the field of
medicine. Millions of complex chemical reactions are going on in the
human body at any given time, ranging from the balance of the
endocrine system to the storage and utilization of fuel molecules such as
glucose. By studying and understanding these highly complex reactions,
medical biochemists have found better ways to fight infections and
diseases at the molecular level. Since an Engineer cannot repair a
vehicle if he does not understand how it works, so a Nurse must
understand how human body works before she can treat her patient
effectively.
Much of biochemistry deals with the structures and functions of cellular
components such as proteins, carbohydrates, lipids and nucleic acids
collectively known as biomolecules. The main focus of medical
biochemistry is in understanding how biological molecules give rise to
the processes that occur within living cells, which in turn relates greatly
to the study and understanding of the whole organism (human being).

3.2 Breakthrough in Biochemistry

Our present knowledge of human body came from series of experiments

and research conducted several years ago. Transfer of genetic
information from one generation to the next was not thoroughly
understood until the major breakthrough of 1953/54. One of the major
breakthroughs in medical biochemistry was the discovery of an accurate
model of DEOXYRIBONUCLEIC ACID (DNA) by James Watson and
Francis Crick in 1953. This discovery opened up possibilities in the
realm of medical biochemistry that had been inaccessible until that time.

The human genome was mapped completely in 2003 as a result of the 13

year Human Genome project (HGP). Since then, medical biochemists
have had access to vital genetic information which has allowed for

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NSC 223 MEDICAL BIOCHEMISTRY 1

manipulation within the cell nucleus. They are also finding ways to
isolate harmful traits within human DNA, and have found methods of
sometimes causing them to completely shut down prior to manifestation.
Intense effort on the parts of the scientific and medical communities
applied to biochemical research has led to the discovery of many
vaccines, anti-depressants and other useful medicinal drugs. These drugs
often work hand-in-hand with the chemical makeup of the human
anatomy. Without medical biochemistry, much of modern medicine
would not be practiced as it is known today.

3.3 Relevance of Medical Biochemistry to Other Health

Sciences

Medical Biochemistry provides foundation for other health sciences

such as medicine, Nursing, pharmacy, microbiology etc. Various
methods are used by Biochemists to isolate, purify, characterise and
study the reactions of all cellular components. Biochemists have
contributed greatly to the discovery of new drugs to treat chronic
diseases such as cancer, viral infections and metabolic disorders. They
are able to do this because they have thorough understanding of what
happens at the molecular level i.e. inside the cell.

3.4 Branches of Biochemistry

i. Toxicology: This field studies the adverse effects of toxic or

foreign chemical substances on the organisms. Environmental
and food toxicology also fall under this branch of biochemistry.
ii. Enzymology: The study of enzymes, their functions, deficiency
and the consequence of such deficiency in diseases.
iii. Molecular biology and Biotechnology: This field evolved directly
from Nucleic acid biochemistry and it involves manipulation of
DNA to improve drug research and solve health problems. It has
wide applications in other fields of science which includes
cancer research.
iv. Lipid and carbohydrate biochemistry: These fields study the
biochemical basis of metabolic disorders such as diabetes, obesity
and Cardiovascular diseases.
v. Natural products biochemistry: This is a new area of research in
biochemistry; it evolved as a result of interest of scientists across
the world in searching for new drugs from plants. Quinine and
Artesunate (anti-malaria drugs) were isolated from plants.
vi. Bioinformatics: Bioinformatics is a shortened form of “Biological
informatics”. It is ofte focused on obtaining biologically oriented
data such as nucleic acid and protein sequence, structures,
functions, pathways ad their interactions.

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NSC 223 MEDICAL BIOCHEMISTRY I

Self-Assessment Exercices

Hihglight the roles of Medical Biochemistry to Nursing Sciences.

4.0 CONCLUSION

This introductory unit has shown that biochemistry as a study of the

chemical processes in the body has made many breakthroughs that is
helping in better understanding and planning of care for people. The five
main branches of biochemistry presented have different dimensions to
the discourse of health and health care.

5.0 SUMMARY

In this unit, you have learnt about the following:

• Definition of Biochemistry
• Breakthrough in Biochemistry
• Relevance of Medical Biochemistry to other health Sciences
• Branches of Biochemistry.

6.0 TUTOR-MARKED ASSIGNMENT

1. What is biochemistry?
2. Why is it important for nursing students to study biochemistry?
3. Assuming there were no biochemists in the world up till year
2010, do you think medicine and nursing sciences will be
practiced the way they are practiced today? Explain your answer.
4. Mention 3 branches of biochemistry and explain the area of
biochemistry they study.

7.0 REFERENCES/FURTHER READING

Nelson, D. L. and Cox, M. M. (2012). Lehninger Principles of

Biochemistry (6th edition) WHFreeman.

Marks' Essentials of Medical Biochemistry: A clinical approach. 2nd

Edition Copyright 2007 Lippincott Williams & Wilkins.

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NSC 223 MEDICAL BIOCHEMISTRY 1

UNIT 2 CELL STRUCTURE AND FUNCTIONS

CONTENTS

1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 The Definition and Structure of Animal Cell
3.2 Differences between Prokaryotes and Eukaryotes Cells
3.3 Types, Classification and Life -Span of Animal Cells
3.4 The Chemical Composition of Plasma Membranes
4.0 Conclusion
5.0 Summary
6.0 Tutor-Marked Assignment
7.0 References/Further Reading

1.0 INTRODUCTION

The living cells we are discussing here is not different from the cell you
learnt in Biology when you were in secondary school. Cells are the
monomeric unit through which the complex human body was
constructed; my body and your body contain several billion cells!
Biochemical arrangement of cells and how these cells interact to
perform various functions in man are not only fascinating but also very
interesting. Imagine the sensitivity of cells responsible for taste;
different region of your tongue detects different taste.

Some cells are replaced every 72 hours in our body while some spend up
to ten years before they die. Also some cells remained in our body
throughout our lifetime. It is important to understand the importance of
compartmentalization in cells and the functions of various organelles
present in the cells. This knowledge will help you in subsequent
modules; most biochemical reactions take place inside the cell but in
different organelles; for example, energy generation takes place inside
the mitochondria. Thorough understanding of cell structure will help
you to understand the root causes of many diseases and the biochemical
mechanisms of their treatment. These mechanisms will also be relevant
in other physiological courses you are going to offer.

2.0 OBJECTIVES

At the end of this unit, you should be able to:

• Define a cell and draw the structure of a typical animal cell

• Differentiate between prokaryotic and eukaryotic cells

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NSC 223 MEDICAL BIOCHEMISTRY I

• Describe the types, classification and life span of animal cells

• Describe the chemical composition of plasma membranes.

3.0 MAIN CONTENT

3.1 The Definition and Structure of Animal Cell

A living cell is defined as the fundamental unit of life and it is the

smallest unit capable of exhibiting the characteristics of life. Cell was
accidentally discovered in 1665 by Robert Hooke while examining a
thin slice of cork under his new crude microscope. He observed
numerous porous structures (dead cells made of cellulose found in
plants) and named them CELLS (Latin, cellula means little room or
small chamber). Further research later confirmed that all living things
are composed of cells.

Fig. 1: Structure of Animal Cell (source: Google images)

Animal cells have different shapes and sizes; some are circular,
spherical, cylindrical, Fibrous etc. Red blood cells called erythrocytes
are one of the smallest animal cells while ova are among the largest. In
terms of length, nerve cells are the longest. For ease of representation,
circular structure is commonly used to illustrate the structure of animal

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NSC 223 MEDICAL BIOCHEMISTRY 1

cells. Study the structure of animal cell (Figure 2.1); take note of the
organelles shown in the structure (mitochondria, ribosome, Golgi,
endoplasmic reticulum, and lysosome). These organelles have different
functions they perform in the cell; the functions will be discussed in
subsequent section. A cell can be subdivided into 3 parts namely:
i. The plasma membrane- The plasma membrane is also called the
cell membrane, is the outer membrane common to all cells. The
plasma membrane defines the internal environment of the cell. It
is the thin cover that separates a cell from its environment, it also
protect the components of the cell from leaking. It prevents the
fluid outside the cell called extracellular fluid (ECF) from mixing
with the fluid inside the cell called intracellular fluid (ICF).
Plasma membranes regulate the materials that enters or leaves the
cell, for this reason, it is said to be semi-permeable. In addition,
the plasma membrane has some glycoproteins and glycolypids on
its surface; these molecules serve as signal molecule between
cells.
ii. The cytoplasm: This is the fluid-like space between the plasma
and nuclear membrane. Cytoplasm is the cavity where the
organelles are found. It provides space for the movement of
synthesised products from one compartment to another for further
processing. The organelles are suspended in the cytoplasm by
cytoskeleton network that resemble nets.
iii. Nucleus: The nucleus is the control center of the cell surrounded
by two membranes – the outer and inner nuclear membrane
envelopes. The outer membrane is continuous with the
endoplasmic [Link] is the most important part of the cell;
the nucleus is always centrally located. Nucleus is very important
to the cell because it contains the genetic materials (DNA and
RNA) that control all the activities of the cell. Nucleus regulates
the rate and time of cell division. It also determines the materials
that enter or exit the cell.
iv. Endoplasmic reticulum (ER) - This is a network of tubular and
flat vesicles. The tubules and vesicles are interconnected. There
are two basic regions of endoplasmic reticulum: the smooth and
the rough endoplasmic reticulum. The rough endoplasmic
reticulum contains ribosomes. The major function of the
ribosomes on the rough endoplasmic reticulum (RER) is the
biosynthesis of proteins for export to the outside of the cells and
enzymes to be imported into cellular organelles such as the
lysosomes. The major function of the smooth endoplasmic
reticulum (SER) is the biosynthesis of lipids and steroid
hormones.

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NSC 223 MEDICAL BIOCHEMISTRY I

v. Mitochondria - The mitochondria are the cell’s power plant where

energy is produced. The basic structure of the mitochondrion is
composed of two lipid bilayer-protein membranes: an outer and inner
membrane. The inner membrane is highly folded resulting in a
surface area 3 to 5 times that of the outer membrane. The inner
membrane is impermeable to ions and most [Link] aqueous
space enclosed by the inner membrane is called the mitochondrial
matrix. The major metabolic pathways involved in the oxidation of
carbohydrates, lipids, amino acids, and special biosynthetic pathways
involving urea and heme synthesis are located in mitochondrial
matrix. Mitochondria also contain specific DNA containing genetic
information for synthesis of some mitochondrial proteins.

vi. Lysosomes - These are single membrane vesicles with an internal

fluid environment that is highly acidic (pH 2) containing a variety of
enzymes that catalyze the breakdown of cellular macromolecules and
also digest large particles such as retired mitochondria and bacterial
cells ingested by the cell.
vii.

3.2 Differences between Prokaryotes and Eukaryotes Cells

The electron microscope allowed classification of cells into two major

groups, prokaryotes and eukaryotes based on the presence and absence
of the true nucleus. Eukaryotes have nucleus which is covered by
nuclear membrane; Animals, plants and fungi belong to the eukaryotes.
Prokaryotes have no typical nucleus (no true nucleus), bacteria and blue
green algae belong to the prokaryotes. Eukaryotic cells are much larger
than prokaryotes, they also have a variety of other membrane bound
organelles in their cytoplasm, and example includes mitochondria,
lysosomes, endoplasmic reticulum (ER) and Golgi complexes.

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3.3 Types, Classification and Life -Span of Animal Cells

There are about 210 distinct human cell types and there are between 50
and 100 trillion cells in adult human body. Animals grow as a result of
cell division and cell enlargement. All animals begin their existence as a
simple cell i.e. fertilized egg. This cell divides into 2, 4, 8, 16, 32 etc. to
produce a body consisting of numerous cells. Ovum is the largest cell
cell in man while red blood cell is the smallest.

Multi-cellular organisms are able to specialise cells to perform specific

functions. A group of such cells is a tissue and in animals these occurs
as four basic types namely epithelium tissues, nervous tissues, muscle
tissues and connective tissues. Several types of tissues work together as
an organ to produce a particular function such as the pumping of blood
by the heart. This pattern continues to a higher level with several organs
functioning as an organ system to allow for reproduction, digestion etc.
Mult-icellular organisms consist of several organ systems.
Cells within the human body have different lifespan based on the type
and function of that cell. Although some types of cells are short lived,
others remain in person’s body for months, years or throughout life.
Taste receptor cells in the mouth live for 10 days, one month for the skin
cells, 15 years for muscle cells and a lifetime for nerve cells.
Normal red blood cell lives for about 3-4months while sickle shaped red
blood cells live for only 10-20 days. White blood cells live for about a
year and sperm cells have a lifespan of about 3 days.

3.4 The Chemical Composition of Plasma Membranes

Plasma membrane mainly compose of lipids and proteins. There is a

wide variation in lipid-protein ratio between different cell membranes.
The functions performed by cell and the location determine the quantity
of proteins and lipids present in their membranes. Here are some
examples of cell membranes and their percentage protein-lipid ratio:

Table 1: Protein-Lipid ratio of some plasma membranes

Membrane Protein (%) Lipid (%)

Erythrocyte 49 41
Liver 60 40
CNS myelin 20 79
Outer mitochondria 50 46
Inner mitochondria 75 23

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NSC 223 MEDICAL BIOCHEMISTRY I

Membrane Lipids

Lipid composition of membranes influences membrane fluidity in terms

of length, unsaturation and presence of cholesterol.
There are several types of membrane lipids. The fundamental building
blocks of cell membranes are the phospholipids. Other lipids present in
the cell membranes are cholesterol and glycolipids. Membrane lipids are
amphipathic molecules (they have both hydrophilic and hydrophobic
ends, hydrophilic means “water loving”; this part readily associates with
water while hydrophobic ends means “water hating”; they tend to move
away from water). Formation of bilayers is another common property
shared by all membrane lipids (Figure 1.2).

Fig. 2: Simplified Structure of Plasma Membrane Bilayer (source- google images)

(a) Phospholipids are the most abundant membrane lipids. They have
a polar head group and two hydrophilic hydrocarbon tails. The
tails are usually fatty acids and they can differ in length (20-24
carbon atoms. One tail usually has one or more double bonds
(unsaturated) while the other tail may not contain double bond
(saturated). Each double bond creates a bend or kink in the tail.
Lipid molecules spontaneously aggregate to bury their
hydrophobic tails in the interior and expose their hydrophilic
heads to water. Depending on their shape, they can do this in
either of two ways; they can form spherical micelles, with the
tails inward or they can form bilayers with the hydrophobic tails
sandwiched between the hydrophobic head groups. The same
forces that drive phospholipids to form bilayers also provide a
self-healing property for the cell membrane. A lipid bilayer has
other characteristics beside its self-healing properties that make it
an ideal structure for cell membranes. One of the most important
of these is its fluidity which is crucial to many membrane
functions.

A shorter chain length and the presence of double bonds (unsaturated

fatty acids) in fatty acid components of phospholipids promote fluidity
at low temperature and vice versa. In animals, cholesterol is the key
regulator of membrane fluidity

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NSC 223 MEDICAL BIOCHEMISTRY 1

Fig. 3: Three Different Ways of Representing Phospholipid Orientation in the

Plasma Membranes (source: Google images)

Fig. 4: Three Dimensional Structure of Plasma Membrane Showing the Two Bilayers
(source: Google images)

The major phospholipids predominate in the plasma membrane of many

mammalian cells are; phosphatidyl choline, phosphatidyl ethanolamine
and phosphatidyl serine. Only phosphatidyl serine carries a negative
charge, the other two are electrically neutral at physiological pH. Some
phospholipids, such as the inositol phospholipids are present in smaller
quantities. They are usually referred to as phosphoglycerides.

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NSC 223 MEDICAL BIOCHEMISTRY I

(b) Sphingomyelin is another group of phospholipids; it contains a

sphingosine back bone rather than glycerol to which fatty acids
and phosphoryl choline are attached. It is electrically neutral at
physiological pH; they are prominent in myelin sheaths.
The Asymmetry of the Lipid Bilayer

Membrane asymmetry refers to the non-identical nature of the two sides

of a membrane. For example phosphatidyl serine (a phospholipid) is
predominantly found on the inner surface of human red blood cells.
Most (but not all) phosphatidyl choline occurs in the outer monolayer of
membranes.
The lipid compositions of the two monolayer of the lipid bilayer in all
membranes are quite different. In the human red blood cell membrane,
almost all phospholipids that have choline (phoshphotidyl choline and
sphingomyelin) are in the outer monolayer, whereas phospholipids
molecules that contain primary amino group (phosphatidyl ethanolamine
and phosphatidyl serine) are in the inner monolayer. Glycolipids and
glycoprotein are found on the outer monolayer. Animals exploit the
phospholipids asymmetry of their plasma membrane to distinguish
between live and dead cells. When animal cells undergo apoptosis,
phosphatidyl serine which is normally confined to the cytosolic
monolayer of the plasma membrane rapidly translocates to the
extracellular monolayer. The phosphatidyl serine exposed on the cell
surface serves as a signal to induce the macrophages to ingest and digest
the dead cell.

Cholesterol

Cholesterol is another important membrane lipid found almost

exclusively in the plasma membrane of mammalian cells. It provides
stability to the membrane, and it is neutral at physiological pH. In the
erythrocyte membrane, the outer membrane leaflet is a rigid four-ringed
molecule with a tiny hydrophilic end (hydroxyl group).

Glycolipids

Glycolipids are sugar-containing lipids, like sphingomyelin, the

glycolipids in animal cells are derived from sphingosine. In glycolipids,
one or more sugars rather than phosphoryl choline are attached to this
group. The simplest glycolipid is called cerebroside and it contains a
simple sugar residue, either glucose or galactose. More complex
glycolipids such as gangliosides contain a branched chain of as many as
seven sugar residues. Glycolipids are oriented in such a way that the
sugar residues are always on the extracellular side of the membrane.

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NSC 223 MEDICAL BIOCHEMISTRY 1

Lipid vesicle or Liposome

The ability of phospholipids to form lipid bilayer has been used to create
an important clinical tool called liposome or lipid vesicle. Liposome is
an aqueous compartment enclosed by a lipid bilayer (Figure 2.5). The
liposome can be used to deliver drugs to target cells or DNA to specific
cells for gene therapy. This liposome fuse with the plasma membrane of
target cell, introducing the drugs or chemicals it contains into the cell.
The selective fusion of lipid vesicle with particular kinds of cells is a
promising means of controlling the delivery of drugs to target cells.
Research is ongoing on the use of liposome for cancer chemotherapy.

Fig. 5: The Structure of a Cross Section of Liposome (source: Google images)

Membrane Proteins

Membrane proteins perform most of the specific functions of the

membranes. They give each stype of membrane in the cell its
characteristic functional properties. The amount and types of proteins in
a membrane also varies, for example, in the myelin membrane, which
serves mainly as electrical insulator for nerve cells, less than 25% of the
membrane mass is protein. In the mitochondria, 75% of the membrane
component is protein due to the presence of many enzymes and electron
pumps.

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NSC 223 MEDICAL BIOCHEMISTRY I

Membrane proteins can be classified as being either peripheral or

integral on the basis of their association with the membrane lipids.
Integral membrane proteins interact extensively with the hydrocarbon
chains of membrane lipids; in fact, most of them span the lipid bilayer,
protruding at both ends. They have high percentage of non-polar amino
acids and represent about 70% of total membrane proteins. Examples are
membrane enzymes, hormone receptors, pumps and channels. In
contrast, peripheral proteins are bound to the surface of lipid bilayer
primarily by electrostatic and hydrogen bonds. Many peripheral
membrane proteins are bound to the surfaces of integral proteins, on
either the cytosolic or extra cellular side of the membrane. Examples
include cytochrome c and acetyl choline esterase.
Glycoproteins in blood typing

Carbohydrate groups are covalently attached to many different proteins

to form glycoprotein. Many glycoproteins are components of cell
membranes, where they play a variety of roles in processes such as cell
adhesion, receptors for hormones, responsible for negative charges on
many cell surface and binding of sperm to eggs. The carbohydrates of
glycoprotein determine the blood group antigens that have been used in
blood typing. Carbohydrates are attached to glycoprotein and glycolipids
on the surface of red blood cells. For one type of blood group one of the
three different structures termed A, B and O may be present. These
structures have in common oligosaccharide foundation called the “O”
antigen. Those people that belong to blood group A have one extra
monosaccharide called N-acetylgalactosamine in addition to the
common oligosaccharide present in all humans. People in blood group B
contain an extra monosaccharide called galactose, through an α-1,3
linkage to a glactose moiety of the common oligosaccharide present in
all humans.

4.0 CONCLUSION
The organelles of the basic cell, through the chemical structure perform
different functions.

5.0 SUMMARY
In this unit, you have learnt about the following:
• The definition and structure of Animal cell
• Differences between Prokaryotes and Eukaryotes cells
• Types, Classification and life -span of animal cells
• The chemical components of plasma membranes

6.0 TUTOR- MARKED ASSIGNMENT

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NSC 223 MEDICAL BIOCHEMISTRY 1

1. Draw a well labelled diagram of a typical animal cell.

2. List three differences between prokaryotic and eukaryotic cells,
give two examples of each.
3. Give an example of a cell that live for (a) Less than 5 days (b) 10
days (c) 1 month (d) 1 year (e) 15 years (f) Life time.
4. What are the major composition of the plasma membranes?
5. List 2 functions for each of the following organelles:
a. (a) Nucleus (b) Mitochondria (c) Rough endoplasmic reticulum
(d) Peroxisomes

7.0 REFERENCES/FURTHER READING

Devlin, T.M. (2010). Textbook of Biochemistry with Clinical

Correlation. (7th ed.) JohnWiley& Sons Inc.

[Link] Editors. “Animal Cell.” Biology Dictionary,

[Link], 19/08/2021,
[Link]

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NSC 223 MEDICAL BIOCHEMISTRY I

UNIT 3 FUNCTIONS OF THE CELL MEMBRANE

CONTENTS

1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Membrane structure and Organisation
3.2 The Functions of Plasma membranes
3.3 Endocytosis and Exocytosis
4.0 Conclusion
5.0 Summary
6.0 Tutor- Marked Assignment
7.0 References/Further Reading

1.0 INTRODUCTION

The cell membrane and the organelles carry out all the functions
performed by living cells. The cell or plasma membrane can be referred
to as ‘the wall of a city’ it protects the components of the cell and also
regulates what enters or leaves the cell. The plasma membrane is very
important to all cells; the cell owes its survival to intact and functional
cell membrane. If there is injury to the cell membrane, the whole cell
may be destroyed. The organelles are the various mini-cells found inside
the cell, they help the cell to perform its diverse functions such as
synthesis, storage, energy generation and excretion of waste materials.
Most of them contain a separate membrane that encloses their individual
contents. The presence of separate membrane prevents the destructive
activities of degrading enzymes present in the lysosome. The pH of fluid
in the lysosome is also different from the pH of the cytoplasmic fluid.
The collective functions of the plasma membrane and the organelles are
referred to as the cell functions.

2.0 OBJECTIVES

At the end of this unit, you should be able to:

• Describe the basic organisation of the cell membranes

• Describe the various functions of the cell membrane.
• List the factors that regulate the movement of materials across the
membranes.

3.0 MAIN CONTENT

3.1 Membrane structure and Organisation

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NSC 223 MEDICAL BIOCHEMISTRY 1

i. Biological membranes are composed of phospholipid bilayer

structure in which protein molecules are either partially or wholly
embedded. Phospholipids spontaneously arranged themselves
into two layers (bilayer): the hydrophilic (water loving) polar
head of the phospholipid molecules face the outside and inside of
the cell where water is found. The hydrophobic (water hating)
non polar tails face each other.
ii. Based on location, cell membrane proteins are divided into two:
integral and peripheral proteins. The integral proteins are found
within the membranes and have hydrophobic regions embedded
within the membranes while the hydrophilic regions project
outwards from both surfaces of the bilayer. Peripheral proteins
occur either on the outside or the inner surface of the membrane.
Based on functions, membrane proteins can also be classifiedinto
three: structural proteins, enzymes and carrier proteins. The
structural proteins form part of the membrane; the carrier proteins
are involved in transport across membranes while enzymes
perform catalysis.

Summary of general features shared by membranes from different

organelles or cells:
1. Impermeability to polar molecules or ions except through a
specific transporter for that molecule or ion
2. Flexible, non-rigid to allow for cellular or organellar changes
in shape and size
3. Durability; usually resistant to damages or remarkable ability
to reseal quite quickly and surviving for the lifetime of the
cell
4. A trilaminar appearance of two dark lines separated by a
lighter space when viewed with an electron microscope
Presence of proteins – peripheral and integral proteins are not
only structural but have a variety of other functions including
enzyme activity, signaling, receptors or as transporters.

3.2 The Functions of Plasma Membranes

i. Protection: The plasma membrane protects the cytoplasm and the
organelles present in the cytoplasm. It is responsible for the
maintenance of shape and size of cells. The most important
function of cell membrane is transportation and regulation of
materials across the membrane.
ii. Transportation of materials across the cell membrane: The cell
membrane act as semi permeable membrane which allows only
some substances to pass through it and act as a barrier for other

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NSC 223 MEDICAL BIOCHEMISTRY I

substances. For example, small hydrophobic molecules such as

CO2, O2 and small lipids dissolve in the membrane and pass
through readily. Tiny polar molecules such as H2O and alcohol
can also slip between the phospholipids molecules. Ions and most
nutrient molecules do not move freely through the membrane, but
are often carried by the transport protein channels, either with or
without the use of energy.
Gradients are important in moving materials through membranes both
passively (without the use of energy by the cell) and actively (transport
requiring cell energy).

Fig 6: Passive Transport - Passive Transport in Cells Involves the Process of

Diffusion, the Diffusion can be simple or facilitated

Factors that affect passive diffusion across membranes

1. Concentration gradient across membrane
2. Electrical potential across the membrane
3. Permeability coefficient of the substances for the membrane
4. Hydrostatic pressure gradient across the membrane
5. Increase in ambient temperature

Simple diffusion – In terms of cellular activity, the rate of simple

diffusion can be affected by temperature, molecular size, concentration
of the gradient. Materials that are moved through membranes by simple
diffusion include: water, carbon dioxide, oxygen, some lipid soluble
molecules such as alcohol.
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NSC 223 MEDICAL BIOCHEMISTRY 1

Facilitated diffusion – Most molecules cannot move freely through the

membrane, but do cross membranes with the help of membrane
transport proteins, which temporarily bind to the substance to be moved
through the membrane, a process called facilitated diffusion or passive
transport. No energy is involved in the process; both carrier proteins and
channel proteins are involved in facilitated diffusion. Materials that pass
through membranes by facilitated diffusion include glucose, amino acids
and many small ions. The movement of water through membranes also
involves facilitated diffusion, the special protin channel used for this is
called aquaporins, and it facilitates the movement of water at a rate
needed for cell activities.
Facilitated diffusion process may be coupled to the movement of other
molecules in the same direction or opposite direction. In co-transport;
the transport of one molecule depends on sequential transfer of another
molecule. Co-transport may be symport or antiport. A symport moves
two molecules in the same direction e.g. sodium-glucose transporter.
Antiport system moves two molecules in opposite direction, it is also
known as counter transport e.g. sodium-potassium transporter.

Fig. 7: Active Transport - Energy Requiring Transport across Membranes

All cells need to move some substances through membrane in a

direction counter to the gradient or move substances that are too large or
bulky with the use of cell energy. Cells have a number of ways to
transport materials across the cell membrane with the use of energy.
Some transport proteins (carrier proteins) can move substances through
the membrane against the concentration gradient. Active transport
typically requires two carrier protein active sites. One recognizes the
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NSC 223 MEDICAL BIOCHEMISTRY I

substances to be carried while the other releases ATP to provide energy

for the protein carrier. In some cases, concentration gradients of ions
typically (H+) protons or (Na+) sodium ions can be used to provide the
energy needed to move molecules through the membranes.
Active transport is classified into two types according to the source of
energy used. Primary active transport derives its energy directly from
the hydrolysis of ATP while the secondary active transport uses an
indirect energy of an electrochemical gradient or membrane potential
produced originally by primary active transport. An example of primary
active transport is sodium-potassium pump (Na+-K+ ATPase). It is the
protein or enzyme responsible for the transportation of Na+ and K+
across the cell membrane. The enzyme is known as sodium-potassium
Adenosine triphosphatase.
The energy required for the transportation of sodium and potassium ions
are derived from the hydrolysis of ATP. For every three Na+ pumped out
of the cell, two K+ are released into the cytosol. Physiological
importance of Na+- K+ gradient in animal cells are: the control of cell
volume, it renders neurons and muscle cells electrically excitable and It
drives the active transport of sugars and amino acids.

3.3 Endocytosis and Exocytosis

Vesicle mediated transport-Transportation of large substances may

require changes in membrane shape and the fusion of the plasma
membrane with vesicles containing the substances to be moved. Such
changes in membranes occur throughout the life time of the cell.
Movement of materials of the cell involving changes of the membrane
and formation of vesicles is called exocytosis while the movement of
materials into the cell is called endocytosis.

Exocytosis- Materials can be exported from the cell by fusing vesicles

with the plasma membrane. For example, insulin made inside the cells
of the pancreas is released to the blood stream by exocytosis.
Endocytosis- There is a variety of endocytosis processes in the cell,
examples includes pinocytosis, receptor mediated endocytosis and
phagocytosis.

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Fig.8: Endocytosis and Exocytosis

4.0 CONCLUSION
Biological membranes separate the internal environment from the
external environment of a cell. Membrane controls movement of
substances in and out of the cell by selective permeability. Membranes
play important roles in energy production and cell signaling.

5.0 SUMMARY
In this unit, you have learnt about the organisation of cell membranes..
We have also related the structure of the cell membrane to the different
forms of mechanism of transportation of material across different media
with explanation of factors that drive such exchange.

6.0 TUTOR- MARKED ASSIGNMENT

1. Using illustrated diagram, explain the passive mechanism of

transportation across the cell membrane.
2. Differentiate between the active and passive methods of
transportation.
3. List the various factors that can affect passive diffusion across
membranes.
4. Explain with a well labelled diagram the mechanism of
endocytosis and exocytosis.

7.0 REFERENCES/FURTHER READING

Lippincott Biochemistry Fourth Edition (2010).

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NSC 223 MEDICAL BIOCHEMISTRY I

Robert K. Murray, MD, PhD. ‘Harper’s Illustrated Biochemistry’.

Twenty-Eighth Edition. 2009

Lehninger Principles of Biochemistry, Fourth Edition (2006).

[Link] Editors. “Animal Cell.” Biology Dictionary,

[Link],19/08/2021,
[Link]

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NSC 223 MEDICAL BIOCHEMISTRY 1

MODULE 2 CHEMISTRY OF BIOMOLECULES

Unit 1 Chemistry of Carbohydrates I

Unit 2 Chemistry of Carbohydrates (II)
Unit 3 Water, Acids, Bases and Buffer
Unit 4 Chemistry of Amino Acids and Protein (I)
Unit 5 Chemistry of Amino Acids and Proteins (II)
Unit 6 Chemistry of Lipids
Unit 7 Chemistry of Nucleic Acids I
Unit 8 Chemistry of Nucleic Acids II

UNIT 1 CHEMISTRY OF CARBOHYDRATES

CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Definition by Classification of Carbohydrates
3.2 Isomers of Glucose
4.0 Conclusion
5.0 Summary
6.0 Tutor-Marked Assignment
7.0 References/Further Reading

1.0 INTRODUCTION
Biochemistry is concerned with the chemical components of the human
body- their properties, functions, synthesis, transport and degradation.
These are called biomolecules. Major classes of these molecules include
carbohydrates, lipids, proteins and Nucleic acids. The building blocks of
these compounds are the simple sugars, fatty acids, amino acids and
mononucleotides. Carbohydrates (CHOs) are compounds containing C,
H and O and having the general formula CnH2nOn Carbohydrates are
widely distributed in plants and animals where they play important
structural and metabolic roles. Glucose is the most important
carbohydrate.
Most dietary CHO is absorbed into the bloodstream as glucose formed
by the hydrolysis (breakdown) of dietary starch and disaccharides. Other
sugars are also converted to glucose in the liver. Glucose is the major
metabolic fuel of mammals and a universal fuel of fetus. It is the
precursor for the synthesis of all other CHOs in the body, including
glycogen for storage , ribose and deoxyribose in nucleic acids ,
galactose for synthesis of lactose in milk, in glycolipids and in

33
NSC 223 MEDICAL BIOCHEMISTRY I

combination with proteins in glycoproteins and proteoglycans. Diseases

associated with CHO metabolism include Diabetes Mellitus,
Galactosemia, Glycogen storage diseases and Lactose intolerance.

Fig. 8: Biomolecules

2.0 OBJECTIVES

At the end of this unit, you should be able to:

• Define the terms monosaccharide, disaccharide, oligosaccharide

and polysaccharide.
• Explain the different ways in which the structures of glucose and
other monosaccharides can be represented,
• Describe the occurrence of isomerism in sugars.

3.0 MAIN CONTENT

3.1 Definition and Classification of Carbohydrates
Carbohydrates can be defined as optically active polyhydroxyaldehydes
or polyhydroxyketones or substances that yield one of these compounds
upon hydrolysis.

Functions of carbohydrates

Structural component of cells

Major source of energy

Storage substances of potential energy

Regulation of fat metabolism

Protein sparing function

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NSC 223 MEDICAL BIOCHEMISTRY 1

Role in gastrointestinal function

Cell recognition

Supportive function

Anticoagulants

Carbohydrates are classified according to the number of sugar units in

the molecule as follows:
Monosaccharides: These are sugars that contain one sugar unit and thus
cannot be further hydrolyzed. They represent the end product of CHO
digestion in the human body. They may be classified as trioses, tetroses,
pentoses, hexoses or heptoses, depending upon the no of C atoms, and
as aldoses and ketoses depending on whether they have an aldehyde or
ketone group.

Fig. 9: Aldose vs Ketose

Disaccharides : These are condensation products of 2 monosaccharide

units e.g lactose (galactose + glucose) ,maltose (2 glucose) and sucrose (
glucose + fructose)
Oligosaccharides: Condensation products of 3-10 monosaccharides.
Most are not digested byhuman enzymes. Rather, they play structural
roles.

Polysaccharides: Condensation products of > 10 monosaccharide units.

Example starch and Dextrin, which may be linear or branched polymers.
Food also contains a wide variety of other polysaccharides, collectively
known as non starch polysacchs, they are not digested by human
enzymes and are the major components of dietary fibre Examples
include Cellulose (a glucose polymer from plant cell walls) and Inulin (
a fructose polymer which the storage CHO in some plants.

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NSC 223 MEDICAL BIOCHEMISTRY I

Table 1: Classification of Sugars

Aldoses Ketoses
Trioses (C3H6O3) Glyceraldehyde Dihydroxyacetone
Tetroses (C4H8O4) Erythrose Erythrulose

Pentoses (C5H10O5) Ribose Ribulose

Hexoses (C6H12O6) Glucose Fructose

Heptoses (C7H14O7) - Sedoheptulose

Fig. 10: Sugars with different no of Carbon Atoms

Structure of Glucose

The straight chain structural formula of glucose can account for some of
its properties, but a cyclic structure, formed by a reaction between the
aldehyde group and an OH group is thermodynamically more favoured
and accounts for other properties. The cyclic structure results from the
reaction between the aldehyde group in C1 and the OH group in C5,
forming a hemiacetal linkage and producing either of 2 stereoisomers.
The structure can also be represented in form of a chair, with the 6
membered ring containing one oxygen atom.

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NSC 223 MEDICAL BIOCHEMISTRY 1

Fig. 11: Structures of Glucose

Straight chainHaworth projectionChair form

3.2 Isomers of Glucose

Isomerism is the occurrence of compounds with the same chemical

formula but different structural formula. The important types of
isomerism found in glucose are D and L isomerism. The designation of
a sugar isomer as the D form or of its mirror image as the L form is
determined by its spatial relationship to the parent compound of the
carbohydrates, [Link] orientation of the –H and –OH
groups around the c atom adjacent to the terminal primary alcohol
carbon determines whether the sugar belongs to the D or L series (when
the –OH grp on this C is on the right, the sugar is the D isomer, when it
is on the left, it is the L-isomer) Most of the naturally occurring
monosaccharide are D sugars. The presence of asymmetric c atom also
confers optical activity on the compound. When a beam of plane-
polarised light is passed through a solution of an optical isomer, it
rotates either to the right (dextrorotatory, +) or to the left, (levorotatory -
)

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NSC 223 MEDICAL BIOCHEMISTRY I

Fig.12: D and L forms of Glucose

Pyranose and Furanose ring structures: Most monosaccharide

spontaneously form ring structures in which the aldehyde or keto group
forms a bond with one of its OH groups. If the ring contains 5 atoms, it
is called a furanose ring; if it contains 6 atoms, it is called a pyranose
ring. For glucose in solution > 99% is in the pyranose form.

Fig.13: Furanose vs Pyranose Rings

Alpha and Beta Anomers:Anomerism is the formation of rings that

result in the creation of an assymetric carbon, called the anomeric
carbon. If the –OH group on the anomeric carbon lies to the right of the
carbon chain, it is considered to be in the α- configuration, and in β
configuration if it lies to the left of the chain.(One of 2 stereoisomers of
a cyclic saccharide that differs only in its configuration at the
hemiacetal carbon, a hemiacetal is formed by combination of an
aldehyde and an alcohol group).

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NSC 223 MEDICAL BIOCHEMISTRY 1

Fig. 14: Anomeric forms of Glucose

Epimers: These are isomers differing as a result of variations in

configurations of the –OH and –H on C atoms 2,3 and 4 of glucose. The
most important biological isomers of glucose are mannose (C2) and
galactose C4).

Fig. 15:Epimers of Glucose

Aldose-Ketose Isomerism: Fructose has the same molecular formula as

glucose but differs in its structure. Since it has a keto grp in position 2
whereas there is an aldehyde group in position 1 of glucose.

Fig 16: Aldose and Keto forms of Carbohydrates

MUTAROTATION - D-glucose really exists in three different forms—

an acyclic aldehyde and two cyclic hemiacetals- all of which are in
equilibrium. Each cyclic hemiacetal can be isolated and crystallized

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NSC 223 MEDICAL BIOCHEMISTRY I

separately, but when any one compound is placed in solution, an

equilibrium mixture of all three forms results. This process is called
mutarotation.
At equilibrium, the mixture has 36% of the α anomer, 64% of the β
anomer, and only a trace amount of the acyclic aldehyde. The three
forms of the D-glucose are shown below

Figure 17: Mutarotation of D-glucose

Reducing and Non-Reducing Sugars - When the anomeric carbon of a

sugar is not attached to any other structure, the sugar can act as a
reducing agent and is termed a reducing sugar. Such sugars can react
with chromogenic agents (for example, Benedict's reagent or Fehling's
solution) causing the reagent to be reduced and colored. The anomeric
carbon of the sugar becomes oxidized to a carboxyl group. In some
disaccharides e.g. sucrose both of the carbonyl groups are involved in
glycosidic bond formation, so there are no free carbonyl groups. Such
sugars are called non-reducing sugars. They do NOT reduce Benedict’s
reagent.

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NSC 223 MEDICAL BIOCHEMISTRY 1

6 CH 2OH 6 CH 2OH

5 O 5 O
H H H H
H H
1 4 1
4 OH H OH H
OH O OH
3 2 3 2

H OH maltose H OH
Sucrose
Figure 18: Reducing and non reducing carbohydrates

Activity – draw the chemical structures of the different forms of glucose

over and over again until you become conversant with the chemical
composition

4.0 CONCLUSION
In this unit, you have learnt about the following:
i. The meaning of the terms monosaccharide, disaccharide,
oligosaccharide and polysaccharide.
ii. The different ways in which the structures of glucose (the most
important carbohydrate) and other monosaccharides can be
represented.
iii. The types of isomerism found in sugars.

5.0 SUMMARY
Carbohydrates are widely distributed in cells. Most carbohydrates
utilize by the body are synthesize from from amino acids, but
most animal carbohydrate is derived ultimately from plants.
Carbohydrates perform several important functions in the body.
Some of the important properties of carbohydrates include
isomerism, mutarotation and anomerism.
.

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NSC 223 MEDICAL BIOCHEMISTRY I

6.0 TUTOR-MARKED ASSIGNMENT

1. Explain the types of isomerism found in glucose.
2. Give 2 examples each of Monosaccharides, Oligosaccharides and
Polysaccharides found in nature.
3. Explain the following properties of carbohydrates
i. Anomerism
ii. Epimerism
iii. Mutarotation

7.0 REFERENCES/FURTHER READING

Murray, R.K., Bender, D.A., Botham, K. M., Kennelly, P.J., Rodwell
V.W. & Well, P.A., (2012). Harper’s Illustrated Biochemistry.
(29th ed.). McGraw-Hill Medical.

Devlin T.M. (2010). Textbook of Biochemistry with Clinical

Correlation. (7th ed.). John Wiley & Sons Inc.

Nelson, D.L. & Cox, M.M. (2009). Lehninger Principles of

Biochemistry. (4th ed.).

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NSC 223 MEDICAL BIOCHEMISTRY 1

UNIT 2 CHEMISTRY OF CARBOHYRATES (II)

CONTENTS

1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Glucose, Galactose, Fructose and Mannose
3.2 Roles of Carbohydrates in Cell Membranes
3.3 Reactions of Carbohyrates
4.0 Conclusion
5.0 Summary
6.0 Tutor-Marked Assignment
7.0 References/Further Reading

1.0 INTRODUCTION

The previous study session has provided information on the basic

chemistry of different types of Sugars. In this session, you will learn
more about these sugars and their physiological relevance. You will also
get to know about some derivatives of these sugars and their functions.
The important reactions of carbohydrates will also be discussed.

2.0 OBJECTIVES

At the end of this unit, you should be able to:

• State the composition and give examples of disaccharides,

oligosaccharides and polysaccharides found in biological
systems.
• Describe the roles of carbohydrates in cell membranes and
lipoproteins.
• Describe the reactions of carbohydrates.

3.0 MAIN CONTENT

3.1 Glucose, Galactose, Fructose and Mannose

Glucose, galactose, fructose and mannose are physiologically the most

important hexoses. Pentoses are important in nucleotides, nucleic acids
and several coenzymes. Derivatives of trioses, tetroses, and pentoses are
also formed as metabolic intermediates in some pathways of CHO
metabolism (glycolysis and pentose phosphate pathway).Carboxylic acid
derivatives of glucose are also important. They include D-glucuronate,
L-iduronate and L-gulonate. Deoxy sugars are those in which one OH

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NSC 223 MEDICAL BIOCHEMISTRY I

group has been replaced by H e.g deoxyribose in DNA. Amino sugars

include D-glucosamine, D-galactosamine and D-mannosamine.

Physiologically important disaccharides include maltose, sucrose and

Lactose. Starch and glycogen are storage polymers of glucose in plants
and animals respectively. Starch is the major source of energy in the
diet. It forms an α-glucosidic chain, called a glucosan or glucan. The 2
main constituents are amylose (13-20%), which has a non-branching
helical structure, and amylopectin (80-87%) which consists of branched
chains composed of 24-30 glucose residues with α1→4 linkages in the
chains and by α1→6 linkages at the branch points. The glycemic index
of a starchy food is a measure of its digestibility, based on the extent to
which it raises the blood concentration of glucose compared with an
equivalent amount of glucose.

Table 1: Disaccharides

Sugar Composition Source

Sucrose Glucose , Fructose Cane sugar, sorghum,
some fruits and
vegetables
Lactose Galactose, Glucose Milk
Maltose 2 Glucose units( in α-1→4 Enzymatic hydrolysis of
linkage) starch
Lactulose Galactose, Fructose Heated Milk
Trehalose 2 Glucose units ( in α-1→1
linkage)

Table 2: Pentoses

Sugar Source
D-Ribose Nucleic acids and metabolic
intermediate
D- Ribulose Metabolic intermediate
D- Arabinose Plant gums
D- Xylose Plant gums, Proteoglycans
L-Xylulose Metabolic intermediate

Table 3: Hexoses

Sugar Source Biochemical

importance
D-Glucose Cane sugar, Fruit Main metabolic fuel
juices, starch, maltose
and Lactose
D-Fructose Fruit juices, honey, Readily metabolised
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NSC 223 MEDICAL BIOCHEMISTRY 1

Inulin via glucose

D-Galactose Lactose Readily metabolised to
glucose. Synthesised in
mammary gland for
synthesis of lactose
D-Mannose Plant gums Constituent of
glycoproteins

3.2 Some Carbohydrates of Physiological importance

Glycogen is the storage polysaccharide in animals. It is a more highly

branched structure than amylopectin. Muscle glycogen granules are
made of up to 60,000 glucose residues. Inulin is a polysaccharide of
fructose while dextrins are intermediates in the hydrolysis of starch.
Cellulose is the chief constituent of plant cell walls. It is insoluble and
consists of ofglucopyranose units linked by β 1→4 bonds to form long,
straight chains strengthened by cross-linking H bonds. Mammals lack
any enzyme that hydrolyzes the β 1→4 bonds, and so cannot digest
cellulose. It is an important source of bulk in the diet, and the major
component of dietary fibre. Chitin is a structural polysaccharide in the
exoskeleton of crustaceans and insects and also in mushrooms.
Glycosaminoglycans are complex CHOs containing amino sugars and
uronic acids. They may be attached to a protein molecule to form a
proteoglycan. Proteoglycans provide the ground or packing substance
of connective tissue Examples include hyaluronic acid, chondroitin
sulphate and heparin. Glycoproteins (mucoproteins) are ptoteins
containing branched or unbranched oligosacc chains. They occur in cell
membranes and include serum albumin. Approximately 5% of the
weight of cell membranes is CHO in glycoproteins and glycolipids.

S tarc h
C e llu lo s e

M u c o p r o t e in s

Fig 1: Structures of cellulose, Starch and Mucoproteins

3.3 Some Reactions of Carbohydrates

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NSC 223 MEDICAL BIOCHEMISTRY I

1. Esterification: Monosaccharides have alcoholic groups which can

participate in esterification reactions with carboxylic groups from
other compounds.

2. Oxidation: Oxidation of monosaccharides with an oxidizing agent

such as hypobromous acid lead to the oxidation of the aldehyde
group to carbonyl group to produce either aldonic, uronic or sacharic
acid.

3. Reduction: Reduction is the chemist’s term for electron gain. A

molecule that gains an electron is thus “reduced”. A molecule that
donates electrons is called “reducing agent”. A sugar that donates
electrons is called a “reducing sugar”. The electron is donated by the
carbonyl group. Reaction of monosaccharides (glucose, mannose,
and fructose) with reducing agents such as sodium amalgam Na(Hg)
reduces the aldehyde or keto group to produce the corresponding
alcohol.

4. Dehydration: When treated with concentrated H2SO4

monosaccharides undergo dehydration with elimination of three
water molecules. Six carbon sugars give hydroxymethyl furfurals
while five carbon sugars give furfurals

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NSC 223 MEDICAL BIOCHEMISTRY 1

4.0 CONCLUSION

Important monosaccharides in the body are glucose, galactose, fructose

and mannose. These carbohydrates have important roles carbohydrates
in cell membranes. Carbohydrates can undergo several reactions that
important in health and disease conditions.

5.0 SUMMARY

In this unit, you have learnt about distinguishing between glucose,

galactose, fructose and mannose. You have also learnt about the roles of
carbohydrates in cell membranes.

6.0 TUTOR- MARKED ASSIGNMENT

1. Using structures only, distinguish between the 3 epimers of
glucose.
2. State the components of the following sugars and the types of
linkage: sucrose, lactulose, trehalose and maltose.
3. Draw a table showing the generic name, ketose and aldose forms
of sugars with 3,4, 5 and 6 carbon atoms.

7.0 REFERENCES/FURTHER READING

Murray, R.K., Bender, D.A., Botham, K. M., Kennelly, P.J., Rodwell

V.W. & Well, P.A., (2012). Harper’s Illustrated Biochemistry.
(29th ed.). McGraw-Hill Medical.

Devlin, T.M. (2010). Textbook of Biochemistry with Clinical

Correlation. (7th ed.). JohnWiley& Sons Inc.

Nelson, D.L. & Cox, M.M. (2009). Lehninger Principles of

Biochemistry. (4th ed.).

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NSC 223 MEDICAL BIOCHEMISTRY I

UNIT 3 WATER, ACIDS, BASES AND BUFFER

CONTENTS

1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 The Properties of Water
3.2 Biological Importance of Water
3.3 Acid, Base and Buffer
4.0 Conclusion
5.0 Summary
6.0 Tutor- Marked Assignment
7.0 References/Further Reading

1.0 INTRODUCTION

Water is the most abundant matter on earth and also in all living
creatures. Typically, organisms are constituted of 70 to 90 % water.
Water must be present before any metabolic activity can take place in
the cell. It is referred to as a weak electrolyte because it can undergo
partial dissociation to two ions made up of a proton (H+) and hydroxyl
ion (OH-).

Acids and Bases are defined with respect to their ability to gain or loss
protons. Buffer is a solution that resists change in the pH of a solution
when proton or hydroxyl ions are suddenly added. Concentration of
these ions determines the degree of acidity or alkalinity of solutions,
including body fluids.

2.0 OBJECTIVES

At the end of this unit, you should be able to:

• Explain the properties of water

• Describe the importance of water as the major component of
living organisms.
• Define acid, base and buffer
• Calculate the pH, pOH and pka of a given solution
• Explain the biological importance of buffer.

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NSC 223 MEDICAL BIOCHEMISTRY 1

3.0 MAIN CONTENT

3.1 The Properties of Water

Water is one of the most important substances on earth. It is the basic

molecule of life. In Biochemistry water is the predominant chemical
component of living organisms. The human body is about 70% water. It
plays a role in transportation of materials to and from the cells. It is the
aqueous solution for biochemical reactions. It acts as solvent for
biochemical reactions in the body and help in maintaining the
temperature of the body.
Water exists in three different forms: vapour/steam, solid and liquid.
Above 100oC as vapour, below 0oC as solid, between 0oC and 100oC as
liquid.

Some important properties of water are discussed below:

Polarity - In a water molecule two hydrogen atoms form single polar

covalent bonds with an oxygen atom. This gives water more structure
than other liquids. Because oxygen is more electronegative, the region
around oxygen has a partial negative charge. The region near the two
hydrogen atoms has a partial positive charge. Thus, water molecule is a
polar molecule with opposite ends of the molecule with opposite
charges.

Universal solvent – water is regarded as universal solvent, meaning

many compounds can dissolve in it. Because of its high polar nature,
water is an excellent solvent for polar and ionic (hydrophilic) substances
such as salt and non ionic but polar substances such as sugars. Water is
poor solvent for non-polar (hydrophobic) substances.

Hydrogen bond – hydrogen bond hold water molecule together. The

region around oxygen has a partial negative charge while the region near
the two hydrogen atoms has a partial positive charge. The slightly
negative regions of one molecule are attracted to the slightly positive
regions of nearby molecules, forming a hydrogen bond. Each water
molecule can form hydrogen bonds with up to four neighbors. Each
water molecule can form a maximum of 4 hydrogen bondsThe hydrogen
bonds joining water molecules are weak, about 1/20th as strong as
covalent [Link] form, break, and reform with great frequency.

High specific heat – Specific heat of a substance is the amount of heat

required to raise/change its temperature by 1oC. The amount of heat
energy (calories) required to raise the temperature of one gram of water
from 15oC to 16oC is known as specific heat of water. Water with its

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NSC 223 MEDICAL BIOCHEMISTRY I

high specific heat helps to maintain the constant temperature of living

organisms in the varying environmental temperature.

High heat of vaporization – Heat of vaporization is defined as the no

of calories required to change one gram of liquid into vapour.
Vaporization is commonly called evaporation. When water evaporates
from the surface of the skin, it absorbs a great deal of heat from the body
thus evaporation has a cooling effect. Thus high heat of vaporization
helps to regulate body temperature and prevent organisms from
overheating.

Biological Importance of Water

• A molecule with electrical charge distributed unequally

about its structure is referred to as a dipole. H3O = H+ +
OH-
• The strong dipole and high dielectric constant of water
enables it to dissolve large quantities of charged
compounds.
• Presence of hydrogen bond also enables water to dissolve
many organic molecules that contain functional groups.
• Water provide environment for macromolecules to achieve
stable structure in solution

Acid, Base and Buffer

• Acid is a compound that dissociates in aqueous solution to

produce proton (H+) and a conjugate base (A-).
HA = H + A
• Acid may dissociate partially (weak acid) or completely
(strong acid) in solution. In solution, weak acid establishes
equilibrium between the proton and its conjugate base.
• The equilibrium constant is called the acid dissociation
constant (Ka) where K is the constant and a is the acid.
Ka = [H+] [A-]
[HA]
• Base is a compound that accepts proton in aqueous
environment, for example ammonia reacts with a proton to
produce an ammonium ion.

Calculation of pH, pOH and pKa

The pH of a solution is simply defined as the negative logarithm

of hydrogen ions concentration,
pH = - log [H+] and
pOH = - log [OH-].

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NSC 223 MEDICAL BIOCHEMISTRY 1

Most living cells have a very narrow range of tolerance for pH, i.e. [H+].
The [H+] concentration will be important (either explicitly or implicitly)
for many other topics in biology. [H+] is controlled in all biological
organisms, and in virtually all biochemical experiments. Each pH unit
represents a factor of 10 differences in [H+].

The pH of some body fluids must occupy a very narrow range. For
example, a healthy individual has a blood pH in the range of 7.35–7.45.
Maintaining this pH is crucial to the life of the individual. The pH of
other fluids can be more variable. Urine has a pH anywhere from 4.6–
8.0, depending on an individual’s recent diet and exercise.

The pH scale is a way of expressing the strength of acids and bases.

Instead of using very small numbers, the negative power of 10 on the
molarity of the H+ (or OH-) ion is used. On the pH scale, values below 7
are acidic, value of 7 is neutral, while values above 7 are basic
(alkaline).

Figure 12: The pH scale

As with the hydrogen ion concentration, the concentration of the

hydroxide ion can also be expressed logarithmically as pOH. The pOH
of a solution can though be defined as the negative logarithm of the
hydroxide ion concentration.
pOH = -log[OH-]

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NSC 223 MEDICAL BIOCHEMISTRY I

The pOH scale is similar to the pH scale in that a pOH of 7 is indicative

of a neutral solution. A basic solution has a pOH of less than 7, while an
acidic solution has a pOH value greater than 7. The pOH can be use to
determine the hydroxide ion concentration from a solution with a known
pH. Thus, pH and pOH are related as follows:

pH + pOH = 14

Example 1: If the H+ concentration of a solution is 4.2 x 10-3 calculate

the pH of the solution.

Solution:

pH = - log [H+] , log[4.2 x 10-3] = log 4.2 + log 10-3 = 0.62 -3 = -

2.38. Substitute for log [H+] in the equation.
pH = -(-2.38), the two negative values cancelled out, pH = 2.38

Example 2: Calculate the [H+], [OH-] and pH of 0.01M ethanoic acid,

given that ( Ka = 1.76 x 10-5).

Solution:

Note that ethanoic acid is a weak acid, it dissociates partially in

solution, therefore HA = H+ + A- , if the conjugates are represented by
x, then HA = 0.1- x ≈ 0.1( value of x is negligible)

Ka = [H+] [A-]
[HA]
Ka = 1.76 x 10-5 = x2/0.1
x2 = 1.76 x 10-6 , x is equal to the square root of 1.76 x 10-6
this is equal to 1.33 x 10-3, therefore,
[H+] = 1.33 x 10-3

pH = -log 1.33 x 10-3 = 0.12-3, if you take away 3 from 0.12, this will
give you a negative value ( -2.88).
pH = 2.88 .

To calculate the pOH, the dissociation of pure water will be considered.

H3O = H+ + OH-,
[H+] + [OH-] = 1.0 x10-14,
[OH-] = 1.0 x 10-14/ [H+]
= 1.0 x 10-14/1.33 x 10-3,
[OH-] =7.52 x 10-12.
But pOH = -log 7.52 x 10-12

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NSC 223 MEDICAL BIOCHEMISTRY 1

This is equal to 0.88 – 12,

pOH = 11.12

Buffers

A buffer is a solution that can resist changes in pH upon addition of acid

or basic components. Buffers are able to neutralize small amount of
added acid or base to maintain the pH of the solution relatively stable.
Most buffers are solutions composed of approximately equal amounts of
a weak acid and salt of its conjugate base. Buffers help organisms
maintain the pH of body fluids within the narrow range necessary for
life. They work by accepting H+ from solutions when they are in excess
and by donating H+ when they have been depleted.
Body fluids such as blood, cerebrospinal fluid, saliva etc. have constant
pH under normal physiological conditions. This is possible due to the
presence of buffer in these fluids. Hydrogen and hydroxyl ions are
constantly added to the body fluids as products of metabolism.
Characteristics of a buffer
i. It has a definite pH value
ii. Its pH value doesn’t change even with the addition of a small
amount of strong acid or base.
iii. Its pH value doesn’t change on keeping for a long time.
iv. Its pH value doesn’t change on dilution.
v.

Table 2.1: Approximate pH values of some body fluids.

BODY FLUID PHYSIOLOGICAL pH

Saliva 5.8-7.1

Pancreatic juice 7.5-8.8

Blood 7.4

Gastric juice 1.6 – 1.8

Urine 4.6-8.0

Physiological Buffers

Physiological buffers are chemical substances used by the body to

prevent large changes in the pH of the body fluids.

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NSC 223 MEDICAL BIOCHEMISTRY I

The four types of physiological buffers are the bicarbonate, phosphate,

hemoglobin and protein buffer systems. The bicarbonate buffer is the
major regulator of blood pH. The phosphate buffer regulates the
cytosolic pH. [CO2] and [HCO3] are much higher than [PO4] in blood;
the reverse is true in the cytosol, [PO4] is much greater than [HCO3].

The bicarbonate CO2 system works as follows: If hydrogen ions enter

the blood, then they combine with base (HCO3) to form carbonic
respiration to exhale more CO2. If a large amount of an acid is added to
the blood, the quick compensation is an excretion of CO2 with a
reduction in the plasma bicarbonate: the slower compensation is that the
acid is excreted by the kidneys which replace bicarbonate in the blood.
Removal of hydrogen ions from blood—as for example, following HCl
secretion into the stomach—is compensated for by retaining CO2 and
forming more base (in the short term). In both cases, the respiratory
system makes rapid buffering possible; the renal system supplies the
long-term buffering.

Figure 13: conversion of carbon dioxide to bicarbonate

Blood Bicarbonate and Metabolic Acidosis

The bicarbonate blood buffer in a normal adult maintains the blood pH

at around 7.40. If the blood pH drops below 7.35, the condition is
referred to as an acidosis. A prolonged blood pH below 7.0 can lead to
death. Clinically for an acidosis, the acid-base parameters (pH, [HCO3-],
[CO2]) of the patient’s blood should be monitored. The normal values
for these are pH = 7.40; [HCO3-] = 24 mM; [CO2] = 1.2 mM.

Metabolic acidosis is an electrolyte disorder characterized by

disturbance in the body’s acid-base balance mechanisms. The three
major root causes of metabolic acidosis are increased acid production,
loss of bicarbonate and reduced ability of the kidneys to excrete excess
acids. Metabolic acidosis is characterized by low concentration of
bicarbonate, which can happen with increased generation of acids such
as ketoacids or lactic acids, excess loss of bicarbonate by the kidneys or
gastrointestinal tract.

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NSC 223 MEDICAL BIOCHEMISTRY 1

Henderson-HasselbalchEquation

The Henderson-Hasselbalch equation is an equation that shows the

relationship between the pH of a solution, the pKa and the ratio of the
conjugate base and conjugate acid. The equation is useful for estimating
the pH of a buffer solution and finding the equilibrium pH in an acid-
base reaction. The equation can be use to determine the pH of different
solutions in different chemical equations as well as in the biological
systems like enzymes and other proteins.

The Henderson-Hasselbalch equation is given as follow:

Example: What would be the pH of a solution containing 0.1 M

CH3COO- and 0.9 M CH3COOH? (pKa = 4.76)
Solution: pH = pKa + Log [A-] /[HA]
CH3C00H CH3C00- + H+
pH = 4.76 + log(0.1/0.9)
pH = 4.76 + log 0.111
pH = 4.76 + (-0.95)
pH = 3.81

4.0 CONCLUSION

Water is life and a core component of all other fluids that make
chemical reactions possible in the body. Water plays very important
roles in the biological systems. These roles are as a result of the various
chemical and physical properties of water molecules. Acid base
biochemistry is also important to the biological system. Most living cells
have a very narrow range of tolerance for [Link] ions
concentration measure is important for many biochemical reactions.
Physiological buffers are chemical substances used by the body to
prevent large changes in the pH of the body fluids.

5.0 SUMMARY

• In Biochemistry water is the predominant chemical component

of living organisms.

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NSC 223 MEDICAL BIOCHEMISTRY I

• The human body is about 70% water and plays a role in

transportation of materials to and from the cells. It is the aqueous
solution for biochemical reactions.
• An Acid is a substance that can release a proton or hydrogen ion
(H+) when dissolved in water.
• A Base is a substance that can release a Hydroxyl ion when
dissolved in water.
• Physiological buffers are substances used by the body to prevent
large changes in the pH of the body fluids. The bicarbonate
blood buffer in a normal adult maintains the blood pH at around
7.40. If the blood pH drops below 7.35, the condition is referred
to as an acidosis.

6.0 TUTOR- MARKED ASSIGNMENT

1. Water is regarded as a universal solvent. Discuss.

2. Define the terms acid and base.
3. What are buffer?Discuss the role of bicarbonate buffer in the
maintenance of blood pH.
4. Calculate the pH of a solution of weak acid whose Molarity is
0.0008.
5. Calculate the [H+], [OH-] and pH of 2.5 x 10-3 M ethanoic acid,
given that (Ka = 1.48 x 10-5).
6. State the Henderson Hasselbalch equation and its importance.

7.0 REFERENCES/FURTHER READING

Murray, R.K., Bender, D.A., Botham, K. M., Kennelly, P.J., Rodwell
V.W. & Well, P.A., (2012). Harper’s Illustrated Biochemistry.
(29th ed.). McGraw-Hill Medical.

Devlin, T.M. (2010). Textbook of Biochemistry with Clinical

Correlation. (7th ed.). John Wiley & Sons Inc.

Nelson, D.L. & Cox, M.M. (2009). Lehninger Principles of

th
Biochemistry. (4 ed.).
Marks' Essentials of Medical Biochemistry: A clinical approach. 2nd
Edition Copyright 2007 Lippincott Williams & Wilkins.

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NSC 223 MEDICAL BIOCHEMISTRY 1

UNIT 4 CHEMISTRY OF AMINO ACIDS AND

PROTEINS 1
CONTENTS
1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Chemical Nature of Amino Acids
3.2 The 20 Amino Acids Found in Proteins
3.3 R Groups and the Chemical Properties of Amino Acids.
3.4 pI of Amino Acids
3.5 Formation of Peptide Bonds
4.0 Summary
5.0 Conclusion
6.0 Tutor-Marked Assignment
7.0 References/Further Reading

1.0 INTRODUCTION

Amino acids are the basic structural units of Proteins. Proteins in all
species from bacteria to humans are constructed from the same set of
twenty amino acids. Outside the formation of proteins, amino acids are
involved in neurotransmitter transport and biosynthesis. An amino acid
consists of amino group (NH2), a carboxylic group (-COOH), a
hydrogen atom (H) and a distinctive R group which is specific to each
amino acid. These 3 groups are bonded to a carbon atom, called the α-
carbon. Amino acids take part in many types of reactions, but the most
important of these is the formation of a peptide bond. This involves the
joining of the α- carboxyl group of one amino acid to the α- amino
group of another amino acid, with the loss of a water molecule. Amino
acids are grouped according to the nature of their side chains .Since
amino acids are weak acids, their strength is expressed as pKa(negative
log of ionisation constant). The net charge on an amino acid depends on
the pKa of its functional groups and the pH of the surrounding medium.
The isoelectric pH, also called pI is the pH midway between pKa values
on either side of the isoionic species.

2.0 OBJECTIVES
At the end of this unit, you should be able to:

• Describe the general structure of α- amino acids

• Identify the 20 amino acids which make up proteins
• Explain the relationship between r groups and the chemical
properties of amino acids.
• Calculate the pi of a monoamino monocarboxylic amino acid
57
NSC 223 MEDICAL BIOCHEMISTRY I

• Describe how peptide bonds are formed and peptides named.

3.0 MAIN CONTENT

3.1 Chemical Nature of Amino Acids

Amino acids are the basic structural units of proteins. An amino acid
consists of amino group, a carboxyl group, a hydrogen atom and a
distinctive R group bonded to a carbon atom, called the α- carbon. An R
group is referred to as a side chain. Amino acids in solution at neutral
pH are predominantly dipolar ions (or Zwitterions) rather than unionised
molecules. In the dipolar form, the amino group is protonated (-NH3+)
while the carboxyl group is dissociated (-COO-). The ionisation state of
an amino acid varies with pH. In acid solution e.g at pH 1, the carboxyl
group is un-ionised (-COOH) and the amino group is ionised (-NH3+).
In alkaline solution, the carboxyl group is ionised (-COO-) and the
amino group is un-ionised (-NH2). At physiologic pH, carboxyl groups
exist almost entirely as -COO- and amino groups predominantly as –-
NH3+.

pH 1 pH7 pH 11
Fig. 1a: Ionization States of an Amino Acid as a Function of pH
Twenty kinds of side chains varying in size, shape, charge, hydrogen
bonding capacity and chemical reactivity are commonly found in
proteins. All proteins in all species from bacteria to humans are
constructed from the same set of twenty amino acids. The different
range of functions mediated by proteins results from the diversity and
versatility of these twenty kinds of building blocks. The arrangement of
four different groups about the α- carbon confers optical activity on
amino acids. The 2 mirror images are called the L-isomer and the D-
isomer. However, only L-amino acids are constituents of proteins. D-
amino acids that occur naturally include free D-serine and D- aspartate
in brain tissue, D-alanine and D-glutamate in the cell walls of gram + ve
bacteria and D-amino acids in some non-mammalian peptides and
certain anti biotics. Many proteins also contain derived amino acids ,
which are usually formed by enzymatic modification of an amino acid
after it has been incorporated into a protein e.g collage n contains
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NSC 223 MEDICAL BIOCHEMISTRY 1

hdroxyproline (the –OH group serves to stabilize the collagen fibre), pro
thrombin, a clotting protein contains γ-carboxyglutamate. Defective
carboxylation of glutamate in this protein may lead to haemorrhage. The
action of some hormones is also mediated by phosphorylation and
dephosphorylation of specific serine residues in a variety of proteins.

Fig. 2 b: Absolute configurations of the L- and D- isomers of amino acids

3.2 The 20 Amino Acids found in Proteins

The simplest amino acid is glycine, which contains a hydrogen atom as

side chain. It is the only non-chiral amino acid. Alanine has a methyl
group as its side chain. Others that have hydrocarbon side chains include
valine, leucine, isoleucine and proline (proline contains a secondary
rather than a primary a7ino group and can be referred to as an imino
acid .

Serine and threonine contain aliphatic hydroxyl groups. Aromatic amino

acids include Phe, Tyr and Trp. The side chains of these amino acids are
uncharged at physiologic pH. Lysine and Arginine contain + vely
charged side chains at neutral pH, while His is either +vely charged or
neutral depending on its local environment. These 3 are called basic
amino acids. Glu, Asp are called acidic [Link] and are –vely charged at
physiol. pH. The uncharged derivatives of Glu and asp are glutamine
and asparagine. They contain a terminal amide group rather than a
carboxylate. Two amino acids with sulfur containing side chains are
methionine and cysteine. Cys plays a special role in some proteins by
forming disulfide cross-links.

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NSC 223 MEDICAL BIOCHEMISTRY I

Table 1: The 20 Amino Acids

Amino acid Three –letter abbreviation One-letter symbol

Alanine Ala A

Arginine Arg R

Asparagine Asn N

Aspartic acid Asp D

Cysteine Cys C

Glutamine Gln Q

Glutamic acid Glu E

Glycine Gly G

Histidine His H

Isoleucine Ile I

Leucine Leu L

Lysine Lys K

Methionine Met M

Phenylalanine Phe F

Proline Pro P
Serine Ser S

Threonine Thr T
Tryptophan Trp W
Tyrosine Tyr Y
Valine Val V

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NSC 223 MEDICAL BIOCHEMISTRY 1

Gly Ala Val

LeuIleu Pro
Amino acids with Hydrocarbon side chains

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NSC 223 MEDICAL BIOCHEMISTRY I

SerThr
Amino acids with side chains containing hydroxyl (OH) groups.

Phe Tyr Trp

Amino acids with aromatic side chains.

Lys Arg

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NSC 223 MEDICAL BIOCHEMISTRY 1

His
Basic Amino acids

Glu Asp
Acidic amino acids

GlnAsn

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NSC 223 MEDICAL BIOCHEMISTRY I

Amino acids with carboxamide groups

Met Cys
Sulphur-containing amino acids.
Fig. 3b: Structures of Amino Acids

Essential and Non-essential Amino Acids

Essential amino acids (EAA) are those amino acids that cannot be
synthesized by the human body, and therefore have to be supply by the
diet. EAA are also known as indispensable amino acids. On the other
hand, those amino acids that can be synthesized by the body are called
non-essential amino acids (dispensable amino acids). Out of the 20
common amino acids, 10 are essential while the other 10 are non-
essential. Daily adult intake of amino acids is approximately 0.8g/Kg.
This will be higher for a child or pregnant woman. Animal proteins are
often low in certain important amino acids e.g methionine and lysine.
Legumes are low in methionine. Grains are low in lysine. Corn is low in
tryptophan and lysine. Dietary proteins cannot be absorbed directly from
the intestine. They must be hydrolyzed by a group of enzymes
(proteases and peptidases) to amino acids.

ESSENTIAL AMINO ACIDS NON ESSENTIAL AMINO ACIDS

Histidine* Alanine
Isoleucine Arginine
Leucine Asparagine
Lysine Aspartate
Methionine Cysteine
Phenylalanine Glutamate
Threonine Glutamine
Tryptophan Glycine
Valine Proline

Table 1: Essential and Non-essential amino acids (*some adults can

synthesize it on their own).

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NSC 223 MEDICAL BIOCHEMISTRY 1

3.3 R Groups and the Chemical Properties of Amino Acids.

The charged functional groups of some amino acids ensure that they are
readily soluble in polar solvents such as water and ethanol but insoluble
in nonpolar solvents such as benzene or ether. Similarly, the high
amount of energy required to disrupt the ionic forces that stabilize the
crystal lattice account for the high melting poits of amino acids. Amino
acids do not absorb visible light and are therefore colourless. However,
Tyr,Phe and Trp absorb high wavelength UV light. They contribute
majorly to the ability of most proteins to absorb light in the region of
280nm. The respective R groups of amino acids determine their
properties e.g the hydrophobic R groups of Ala, Val, Leu and Ileu as
well as the aromatic R groups of Phe, Tyr and Trp typically occur in the
interior of cytosolic proteins. The charged R groups of basic and acidic
amino acids stabilise specific protein conformation via ionic interactions
or salt bonds. Each functional group of an amino acid exhibits all its
characteristic chemical reactions. For carboxylic acid groups, such
reactions include formation of esters, amides and acid anhydrides while
those for amino groups include acylation, amidation and esterification.
Optical activity - In all amino acids, α-carbon atom is asymmetric (4
different groups) with exception of glycine. Hence, they exhibit optical
activity and they rotate the plane-polarized light to the right or left. As a
result, they exist in two optical isomers, D (+) or L (-). The D and L
isomers are mirror images of each other. In nature L-amino acids are
more common and therefore called Natural amino acids. All amino acids
found in proteins are of the L-configuration.
Asymmetry - most amino acids have one asymmetric carbon atom. Two
amino acids Threonine and Isoleucine have 2 asymmetric carbon and
therefore have 4 optical isomers (2n = 22 = 2x2 = 4).

Figure 14: L and D isomers of amino acids

D- amino acids that occur naturally include free D-serine and D-

aspartate in brain tissue, D-alanine and D-glutamate in the cell walls of
gram positive bacteria and D-amino acids in some non-mammalian
peptides and certain antibiotics.

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Many proteins also contain derived amino acids , which are usually
formed by enzymatic modification of an amino acid after it has been
incorporated into a protein. For example, collagen contains
hdroxyproline (the –OH group serves to stabilize the collagen fibre).
Prothrombin, a clotting protein contains γ-carboxyglutamate. Defective
carboxylation of glutamate in this protein may lead to haemorrhage. The
action of some hormones is also mediated by phosphorylation and
dephosphorylation of specific serine residues in a variety of proteins.

Acid Base Properties of Amino Acids

Ampholytes or Amphoteric Nature of Amino acids - All amino acids
contain at least two ionizable groups the α-amino group and the α-
carboxyllic group, some contain an additional acidic or basic group in
their side chain , which are responsible for the amino acids , acid- base
behaviour.
As a result of their ionizability the following equilibrium reaction can
be written;

R-COOH R-COO- + H+
R-NH2 R-NH3 +

Since the above reactions are reversible this indicates that amino acids
can act as acids (as demonstrated by the forward reaction) or as bases (as
demonstrated by the reverse reaction). Thus compounds with such
behavior are called Ampholytes or Amphoteric compounds. They are
capable of donating or accepting protons.

Zwitterions - Amino acids behave as Zwitterions. A zwitterion is a

dipolar ion containing negative and positive charges. All neutral amino
acids are present in the Zwitterions form. At physiological pH (around
7.4) the carboxyl group will be unprotonated and the amino group will
be protonated..

3.4 pI of Amino Acids

The net charge on an amino acid i.e the sum of all the +vely and –vely
charged groups present depend on the pK values of its functional
groups and the PH of the surrounding medium. Altering the charge on
amino acids and their derivatives by varying the pH facilitates the
physical separation of amino acids, peptides and proteins. The iso
electric pH , called the pI is the pH midway between pK values on either
side of the isoelectric species. For an amino acid such as alanine that has
only 2 ionisable groups, the isoelectric pH is
pI= Pk1 + pK2/2= 2.35+ 9.69/2= 6.02

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For polyfunctional acids, pI is the pH midway between the pka values

on either side of the isoionic species e.g for aspartic acid, pI = 2.09+
3.96/2, = 3.20
Table 3: Pk Values of some Amino Acids
pK values at 25oC
AminoΑ- α- Side
acid COOHNH3+ Chain
group group

Valine 2.3 9.6

Aspartic acid 2.0 10.0 3.9
Glutamic acid 2.2 9.7 4.3
Histidine 1.8 9.2 6.0
Cysteine 1.8 10.8 8.3
Tyrosine 2.2 9.1 10.9
Lysine 2.2 9.2 10.8

Arginine 1.8 9.0 12.5

Fig. 4b: Determination of Isoelectric Point of Ala and Lys

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Diss ociatio n o f Lys in e

3.5 Formation of Peptide Bonds

The most important reaction of amino acids is the formation of a peptide

bond. This involves the joining of the α- carboxyl group of one amino
acid to the α- amino group of another amino acid, with resultant loss of a
water molecule. The biosynthesis of peptide bonds requires an input of
free energy, whereas their hydrolysis is thermodynamically favourable.
Many amino acids (usually > 100) are joined by peptide bonds to form a
polypeptide chain

Fig. 5a: Formation of Peptide Bond

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An amino acid unit in a polypeptide is called a residue. A PP chain has

different ends- the α-amino and the α- carboxyl groups. The amino end
is taken to be the beginning of the chain e.g in the tripeptide ala-gly-trp,
alanine is the amino-terminal residue and trp is the carboxyl terminal
residue. A PP chain consists of a regularly repeating part, called the
main chain (also called the backbone), and a variable part comprising
the distinctive side chains. In some proteins, a few side chains are cross-
linked by disulfide bonds. These cross links are formed by the oxidation
of cysteine residues. The resulting disulfide is called cystine. Amino
acids present in peptides are called aminoacyl residues and are named by
replacing the-ate or –ine suffix of free [Link] with ---yle.g aspartyl, alanyl
etc. Peptides are then named as derivatives of the carboxyl terminal
aminoacyl residue e.g Lys-Leu-Tyr-Gln is called Lysyl-Leucyl-Tyrosyl-
Glutamine. This indicates that the α- carboxyl group of glutamine is not
involved in peptide bond formation. Many proteins consist of a single
polypeptide chain e.g myoglobin. Others contain 2 or more chains
which may be either identical or different [Link] is made up of
2 chains of one kind and 2 of another kind of pp chain (α and β) , held
together by non covalent forces. The PP chains of some multichain
proteins are linked by disulfide bonds e.g insulin.

4.0 CONCLUSION

In this unit, you have learnt about the chemical nature of amino acids,
the 20 amino acids found in proteins, the R Groups and the chemical
properties of amino acids, the pI of Amino acids as well as formation of
peptide bonds.

5.0 SUMMARY

In this unit, you have learnt about the chemical nature of amino acids,
the 20 amino acids found in proteins, the R Groups and the chemical
properties of amino acids, the pI of Amino acids as well as formation of
peptide bonds.

6.0 TUTOR- MARKED ASSIGNMENT

1. Describe the general structure of α- amino acids.
2. Identify the 20 amino acids which make up proteins.
3. Explain the relationship between R groups and the chemical
properties of amino acids.
4. Calculate the pI of a monoamino monocarboxylic amino acid.
5. Describe how peptide bonds are formed and peptides named.

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7.0 REFERENCES/FURTHER READING

Murray, R.K., Bender, D.A., Botham, K. M., Kennelly, P.J., Rodwell
V.W. & Well, P.A.. (2012). Harper’s Illustrated Biochemistry.
(29th ed.). McGraw-Hill Medical.

Devlin, T.M. (2010). Textbook of Biochemistry with Clinical

Correlation. (7th ed.). John Wiley & Sons Inc.

Nelson, D.L. & Cox, M.M. (2009). Lehninger Principles of

Biochemistry. (4th ed.).

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UNIT 5 CHEMISTRY OF AMINO ACIDS AND

PROTEINS (II)
CONTENTS
0.0 Introduction
1.0 Objectives
2.0 Main Content
2.1 Functions and Classification of Proteins
2.2 Purification of Proteins
3.3 Roles of Proteins in Biological Processes
4.0 Conclusion
5.0 Summary
6.0 Tutor-Marked Assignment
7.0 References/Further Reading

1.0 INTRODUCTION
We continue with our study of amino acids and proteins. In this session,
you will learn the various methods of determining the amino acid
components of peptides and proteins and the principles on which these
methods are based. You will also learn how amino acids in a given
sample can be quantified. A man called Fredrick Sanger was the first
scientist to determine the amino acid sequence of a protein. He
determined the amino acid sequence of insulin in 1953 and was given
the 1958 Nobel Prize in chemistry in recognition of his work. Today,
methods for this procedure have been automated and made simple. The
amino acid sequence of many proteins is now known and this has
assisted Biochemists in tracing molecular events in evolution.
Alterations in amino acid sequence can produce abnormal function and
diseases. For instance, sickle cell anaemia results from replacement of a
single amino acid, Glu with Val in the B chain of Haemoglobin. The 4
levels of protein structure are also discussed as well as the various
functions of proteins in biological systems.

2.0 OBJECTIVES
At the end of this unit, you should be able to:

• Explain the process of protein purification

• Discuss how amino acid composition is determined
• Discuss how amino acid sequence is determined
• Explain the different levels of protein structure
• State the roles of proteins in biological processes
• Explain how amino acid sequence of a protein is determined.

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3.0 MAIN CONTENT

3.1 Functions and Classification of Proteins

Proteinsare macromolecules composed of one or more polypeptide
chains possessing a characteristic amino acid sequenceProteins are
essential constituents of living cells making up about 12% of the
protoplasm. They contain carbon, nitrogen, hydrogen, oxygen and
sometimes [Link] are constructed largely of amino acids.

Functions of proteins
• Enzymes catalysts
• Transport
• Storage
• Contraction/Movement
• Mechanical support
• Immune protection
• Blood clotting
• Hormonal action

Classification of proteins
Proteins are classified in two ways:
1. On the basis of their solubility or shape as Globular or Fibrous
Proteins.
Globular proteins are spherical in shape. They are soluble in
water and are highly branched. Examples are Enzymes, protein
hormones, Antibodies, Hemoglobin etc
Fibrous proteins are linear and [Link] are insoluble in
water. They are in form of fibres and are highly resistant to
digestion by proteolytic enzymes. Examples include Collagen,
Elastin, Keratin, Actin and Myosin, etc

2. On the basis of increasing complexity of structure as Simple,

Conjugated or Derived proteins.
Simple proteins yield amino acids or their derivatives on
hydrolysis e.g albumins and globulins. Conjugated proteins are
proteins united with non-protein substances. The non-protein
substances linked to proteins are called prosthetic group while the
protein part is called apoprotein. The prosthetic group and
apoprotein are together called Holoproteins. Thus on hydrolysis
they yield amino acids and non-protein substances. E.g
Glycoproteins, Phosphoproteins, and Lipoproteins. Derived
proteins are the intermediate products formed from natural
proteins when they are hydrolyzed by heat, acids, alkalis or
enzymes. [Link], metaproteans, proteoses, peptones etc

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3.2 Purification of Proteins

Each protein has a unique, precisely defined amino acid sequence. In

1953, Frederick Sanger determined the amino acid sequence of insulin.
Since then, hundreds of other proteins have been sequenced. This is an
important procedure as it provides insight into its biological activity and
function. Much of the evolutionary history of the protein can also be
known from its aa sequence and composition as proteins resemble one
another in their amino acid sequences only if they have a common
ancestor. Consequently, molecular events in evolution can be traced
from amino acid sequences. Alterations in amino acid sequence can
produce abnormal function and diseases. For instance, cell anaemia
results from replacement of a single amino acid, Glu with Val in the
chain of Hae. The first step is to purify the protein, after which its amino
composition is determined
A protein must be purified prior to determination of its chemical
composition, structure and function. The first task is to develop an assay
procedure for the protein. This utilizes specific properties of the protein
such as the rate of transformation of substrate to product (in the case of
an enzyme), antibody-antigen reaction or a physiological response that
gives a quantitative measure of activity per unit protein concentration.
This is known as the protein’s specific activity. The purpose of a
purification procedure is to increase a protein’s specific activity to the
value expected for the pure protein. Initial purification of a soluble
cellular protein involves disruption of the cell membranes, followed by
differential centrifugation in a density gradient to isolate the protein
from sub cellular particles and high molecular weight aggregates.
Further purification may utilise selective precipitation by inorganic salts
(salting out) or by organic solvents. Final purification includes a
combination of techniques that separate based on molecular charge,
molecular size, affinity or a combination of two or more of these..
Techniques based on charge include electrophoresis, isoelectric focusing
and ion exchange chromatography. Those based on molecular mass or
size includes ultracentrifugation, molecular exclusion
chromatography/gel filtration while affinity chromatography is based on
the affinity of the protein for its substrate, membrane receptors or
antibodies. Polyacrylamide gel electrophoresis is based on size and
charge.

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Ion Exchange column

Running a protein through a column

Fig. 1: Tools for Protein Purification

Determination of amino acid composition of a peptide/ protein

The peptide is hydrolyzed into its constituent amino acids by heating it

in 6N HCl at 110oC for 24 hours. The amino acids in the hydrolysate are
separated by ion exchange chromatography on a column of sulfonated
polystyrene. The separated amino acids are detected by the colour
produced when they are heated with ninhydrin: α- amino acids give an
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intense blue colour while imino acids such as proline give a yellow
colour. The quantity of amino acids is proportional to the optical
absorbance of the solution after heating it with ninhydrin. Fluorescamine
can also be used, which reacts with its α- amino group to form a highly
fluorescent product. The identity of the amino acid is revealed by its
elution volume, i.e the vol of buffer used to remove the amino acid from
the column. The chromatographic pattern of the hrdolysate is then
compared with that of a standard mixture of amino acids.

FluorescamineNinhydrin
Fig. 2: Reagents for Quantifying Proteins

Determination of Amino Acid Sequence of a Peptide/Protein

Sequencing of a protein was first carried out by Frederick sanger in

1953. He determined the amino acid sequence of insulin. Mature insulin
consists of the 21-residue A chain and the 30-residue B chain linked by
disulfide bonds. Fred Sanger reduced the disulfide bonds using
performic acid and thus separated the 2 chains. He then cleaved each
chain into smaller peptides using trypsin, chymotrypsin and pepsin. The
resulting peptides were then precipitated with 6N HCl to hydrolyze
peptide bonds and generate peptides with as few as two or three amino

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acids. He then reacted each peptide with 1-fluoro-2,4-dinitrobenzene

(Sanger’s reagent) which derivatives the exposed α amino group of
amino acid residues. Working backwards to larger fragments enabled
Sanger to determine the complete sequence of Insulin. Dansyl Chloride
is also used to identify amino-terminal residues. It reacts with amino
groups to form highly fluorescent and stable sulfonamide derivatives.
Although the DNP and Dansyl methods are powerful, they cannot be
used repetitively on the same peptide because the peptide is totally
degraded in the acid-hydrolysis step. Pehr Edman introduced
Phenylisothiocyanate (Edman’s reagent) to selectively label the amino-
terminal residue of a peptide. This generates a PTH (
phenylthiohydantoin) derivative . in contrast to the Sanger’s reagent,
the PTH derivative can be removed under mild conditions to generate a
new amino terminal residue. Successive rounds of derivatisation with
Edman’s reagent can therefore be used to sequence many residues of a
single sample of peptide. Edman sequencing has been automated, using
a thin film or solid matrix to immobilise the peptide and HPLC to
identify PTH amino acids. The Edman method determines the first 20-
30 residues of a peptide. Since most pps contain several hundred aas, it
is necessary to first cleave the pp into small peptides prior to Edman
sequencing. Reagents for the chemical or enzymatic cleavage of proteins
include CNBr, Trypsin etc. Following cleavage, the resulting peptides
are purified and sequenced.

Phenyl
isothiocyanate
(Edman’s Dansyl
Reagent) chloride
1-fluoro 2,4-
dinitrobenzene
Fig. 3: Reagents used for Sequencing Proteins/Peptides. They Label the exposed α-
Amino Group of Amino Acid Residues

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Fig. 4: Amino Acid Sequence of Insulin

Table 1: Reagents used in the Cleavage of Polypeptides

Reagent Cleavage site
Chemical cleavage
Cyanogen Bromide Carboxyl side of Met residues
Hydroxylamine Asparagine-glycine bonds
2-Nitro-5-thiocyanobenzoate Amino side of cysteine residues
Enzymatic cleavage
Trypsin Carboxyl side of Lys and Arg
Clostripain Carboxyl side of Arg residues
Staphylococcal protease Carboxyl side of Asp and Glu

3.2 Proteins Structure

There are 4 levels of protein structure:

Primary structure refers to the sequence of amino acids and location of

disulfide bridges if there are any. It is a complete description of the
covalent connections of a protein.
Secondary structure refers to the steric relationship of amino acid
residues that are close to one another in the linear sequence. Some of
these relationships are of a regular kind, giving rise to a periodic
structure. The α helix, the β- pleated sheet and the collagen helix are
examples of 20 structure. The helix is a rod like structure. The tightly

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coiled polypeptide main chain forms the inner part of the rod, and the
side chains extend outward in a helical array. The stability of an α helix
arises primarily from hydrogen bonds formed bw the NH and CO
groups of the main chain. The Co group of each amino acid is hydrogen
bonded to the NH group of the amino acid that is situated 4 residues
ahead in the linear sequence. Each residue is related to the next one by a
translation of 1.5 Å along the helix axis and a rotation of 100o, which
gives 3.6 amino acids per turn of helix. Thus [Link] that are spaced 4-5
apart in the linear sequence are spatially close to one another in an α
helix while those 2 apart in the linear sequence are situated on opposite
sides of the helix and so are unlikely to make contact. The pitch of the α
helix is 5.4 Å (the product of the translation and no of residues per
turn).The α helix can be right handed (clockwise) or left-handed
(anticlockwise). Only right handed helices are found in proteins. Since
the peptide bond of proline lacks a H atom to contribute a H bond,
proline can only be stably accommodated within the first turn of an α
helix. When present elsewhere, proline disrupts the conformation of the
helix, producing a bend.. Because of its small size, glycine also often
induces bends in α helices. The β sheet differs markedly from the α helix
in that it is a sheet rather than a rod. The pp in the β pleated sheet is fully
extended rather than being tightly coiled. The axial distance bw adjacent
amino acids is 3.5Å. The β sheet is stabilised by hydrogen bonds bw NH
and CO groups in different pp strands, whereas in the α helix, the H
bonds are bw NH and CO groups in the same PP chain.
The collagen helix is responsible for the high tensile strength of
collagen, the major component of skin, bone and tendon.
Tertiary Structure

This refers to the entire 3-dimensional conformation` of a protein. It is

the steric relationship of amino acid residues that are far apart in the
linear sequence. It includes the geometric relationship between distant
segments of primary structure and the positional relationship of the side
chains with one another. It indicates, in 3- dimensional space how
secondary structural features (Helices & sheets) assemble to form
domains.

Quartenary Structure

This refers to the arrangement of polypeptide chains in a multichain

protein. The subunits in a 40 structure are associated non-covalently. It
should be noted that a protein having only 1 pp chain e.g myoglobin , as
well as one in which the PP chains are covalently bonded together e.g
chymotrypsin cannot have 40 structure. Each PP chain in a protein with
40 is referred to as a subunit e.g. Hae has 4 pp chains(α2β2) held
together non covalently in a specific conformation as required for its

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function. A protein domain refers to a compact, semi- independent

globular unit of protein structure. It is a section of protein structure
capable of performing a particular chemical or physical task.30 and 40
structures are stabilized by non covalent interactions which include
hydrophobic interactions, hydrogen bonds, salt bridges and intra
polypeptide disulfide bonds.

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Collagen helix
Fig. 5: Levels of Protein Structure

3.3 Roles of Proteins in Biological Processes

Proteins play crucial roles in virtually all Biological processes. Some of
these roles include

Enzymatic catalysis: Nearly all chemical reactions in Biological

systems are catalyzed by [Link] transformations rarely
occur at perceptible rates in vivo in the absence of [Link] known
enzymes are proteins. Thus, proteins play the unique role of determining
the pattern of chemical transformations in biological systems.

Transport and storage: Many small molecules and ions are transported
by specific proteins [Link] transports oxygen in erythrocytes while
myoglobin transports oxygen in muscle. Transferrin carries iron in the
plasma of blood to the liver where it is stored as a complex with ferritin,
another protein.
Co-ordinated motion: proteins are the major components of muscle.
Muscle contraction is accomplished by the sliding motion of two kinds
of protein filaments. On the microscopic scale, coordinated motion such
as the mvmt of chromosomes in mitosis and the propulsion of sperm by
their flagella are also produced by contractile assemblies consisting of
proteins.
Mechanical Support: The high tensil strength of skin and bone is due
to the presence of collage, a fibrous protein
Immune protection: Antibodies are highly specific proteins that
recognize and combine with foreign substances such as viruses, bacteria
and cells from other organisms.

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Generation and transmission of nerve impulses: The response of

nerve cells to specific stimuli is mediated by receptor proteins e.g
rhodopsin is the photoreceptor protein in retinal rod cells.
Control of Growth and Differentiation: Controlled sequential
expression of genetic information is essential for the orderly growth and
differentiation of cells. Repressor proteins are important control
elements that silence specific segments of the DNA of a cell. Nerve
growth factor, a protein complex serves to guide the formation of neutral
networks in higher organisms.

3.0 CONCLUSION
Proteins are essential nutrients for tissue growth, repairs and
replacement. They are macromolecules composed of one or more
polypeptide chains possessing a characteristic amino acid sequence.
Proteins are essential constituents of living cells making up about 12%
of the protoplasm. They contain carbon, nitrogen, hydrogen, oxygen and
sometimes [Link] are constructed largely of amino acids.

5.0 SUMMARY

All protein polymers are constructed from the same set of 20 monomers,
amino acids. A protein consists of one or more polypeptides folded and
coiled into a specific conformation.
Four levels of protein structure are primary, secondary, tertiary and
quarternary structures.

6.0 TUTOR- MARKED ASSIGNMENT

1. Explain the process of protein purification.

2. Discuss how amino acid composition is determined.
3. Discuss how amino acid sequence is determined.
4. Explain the different levels of protein structure.
5. State the roles of proteins in Biological processes.

7.0 REFERENCES/FURTHER READING

Murray, R.K., Bender, D.A., Botham, K. M., Kennelly, P.J., Rodwell
V.W. & Well, P.A., (2012). Harper’s Illustrated Biochemistry.
(29th ed.). McGraw-Hill Medical.

Devlin, T.M. (2010). Textbook of Biochemistry with Clinical

Correlation. (7th ed.). JohnWiley& Sons Inc.

Nelson, D.L. & Cox, M.M. (2009). Lehninger Principles of

Biochemistry. (4th ed.).

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Marks' Essentials of Medical Biochemistry: A clinical approach. 2nd

Edition Copyright 2007 Lippincott Williams & Wilkins.

Garrett and Grisham Biochemistry, 2nd Edition. Harcourt College Pub

Lippincott Biochemistry Fourth Edition (2010).

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UNIT 6 CHEMISTRY OF LIPIDS

CONTENTS

1.0 Introduction
2.0 Objectives
3.0 Contents
3.1 Biological Functions of Lipids
3.2 Classification of Lipids
3.3 Lipoproteins
4.0 Conclusion
5.0 Summary
6.0 Tutor-Marked Assignment
7.0 References/Further Reading

1.0 INTRODUCTION

Lipids are another important class of macro molecule found in all living
cells. They are the only macromolecule without a specific monomeric
units. The word lipid was derived from Greek word lipos, the meaning
of lipos in greek is fats. This is why lipid and fat are used
interchangeably in many literatures. Lipids are described as a group of
heterogeneous compounds that are not readily soluble in water or polar
solvents but are readily soluble in organic solvents such as chloroform,
hydrocarbons etc. Examples of lipids include fats, oils steroids, waxes
and related compounds. Lipids are usually hydrophobic or amphipathic
molecules, the most common lipids in nature consist of fatty acids
linked by an enter bond to glycerol or to other alcohol such as
cholesterol. In addition to fatty acids and alcohol they may contain other
compounds such as phosphoric acid, organic bases and carbohydrates.
All the components of lipids can be released or separated by various
hydrolytic procedures.
The study of lipid biochemistry is important for thorough understanding
of causes, effects and management of metabolic disorders of lipid
metabolism such as obesity and cardiovascular diseases. Measurement
of lipoproteins and cholesterol in the blood can serve as early warning
for impending danger to our health.

2.0 OBJECTIVES

At the end of this unit, you should be able to:

• List the biological functions of lipids

• Classify lipids to different groups based on their chemical
composition
• Describe the classes of lipoproteins.

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3.1 Biological Functions of Lipids

Lipids have various important functions in animals, some of the

functions are:

i. Lipids are important dietary constituents of food and have high

energy value.
ii. Dietary lipids are the sources of fat soluble vitamins and essential
fatty acids. They also help in transportation of many water
insoluble molecules.
iii. Lipids serve as energy stores, fats stored in animals as
triacylglycerol or triglyceride in the adipose tissue is a potential
source of energy.
iv. Fats present in the subcutaneous tissues act as an insulating
material.
v. Lipids are important component of plasma membranes.
vi. Lipids are involved in various intra and intercellular signaling
processes.

3.2 Classification of Lipids

Lipids are classified into three groups based on the number and types of
components present in the lipid. The three groups are simple lipids,
complex or compound lipids and derived lipids.

Simple Lipids

They are the simplest form of lipids and the ester of fatty acids with
various types of alcohols. When simple lipids are hydrolysed, they yield
just two types of products. (Fatty acids and alcohol or glycerol).
Examples of simple lipids are fats, oils and waxes.

(a) Fats – Fats are solid at room temperature because their fatty acids
are saturated. Fats are obtained naturally from animal sources;
example of natural fats is lard. Butter and margarine are artificial
fats produced by hydrogenation of oils (conversion of
unsaturated).

Fats play vital role in maintaining healthy skin and hair, insulating body
organs against shock and maintaining body temperature. In animals, fats
are stored in the white adipose tissue, or fatty tissue. Adipocyte store fat
derived from the diet and those derived from metabolism in the liver.
Visceral fat is located within the abdominal wall i.e. beneath the wall of
abdominal muscle) whereas subcutaneous fat is located beneath the
skin.

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(b) Oils- Oils are liquid lipids at room temperature due to the
presence of unsaturated fatty acids. Oils are obtained from plant
seeds or through the melting of animal fats.
(c) Waxes - They are also solid at room temperature due to the
presence of saturated fatty acids and high molecular weight
monohydric alcohol.

Complex Lipids

Complex lipids contain other amphipathic compounds in addition to

fatty acids and alcohol present in simple lipids. The compounds include
phosphoric acid, various sugars, sphingosine, ethanolamine and serine.
Generally, complex lipids yield three or more primary products when
they are hydrolysed. Examples of complex lipids include phospholipids,
glycolipids and sphingolipids. Sphingophospholipids are made up of
fatty acids, sphingosine, phosphoric acid and choline.

Sulpholipids (sulphur containing lipids), and lipoproteins also belong to

the group of complex lipids.

Derived Lipids

These lipids are derived from the hydrolysis of simple and complex
lipids. They are mainly fatty acids, glycerols and steroids or sterols.

Fig. 1: Chemical Structures of Fatty Acids (Source Google Images)

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Fatty Acids

Fatty acids are the carboxylic acids with a long hydrocarbon chain. Fatty
acids in animals occur mainly as esters in natural fats and oils (they exist
as components of triglycerides)

Fatty acids occur as free fatty acids in the plasma where it acts as
transporter of various biological molecules, especially plasma albumin.
Fatty acids that occur in natural fats usually contain an even number of
carbons between 11 and 24 carbon atoms. The 16 and 18 carbon fatty
acids are the most common FA in animals. They may be saturated or
unsaturated.

(a) Saturated fatty acids

Saturated fatty acids are the fatty acids without double bonds,
examples of such fatty acids are palmitic acid (C16), stearic acid (C18)
and arachidonic acid (C20). Palmitic acid, myristic acid and stearic acid
are the most abundant saturated fatty acids in human. Lauric acid (C12)
is present in coconut oil.

Unsaturated fatty acids are the FA that contains one or more double
bonds. Unsaturated FA can be divided into three groups based on the
number of double bonds present. Most naturally occurring unsaturated
FAs have a cis-configuration i.e. the hydrogen atoms are on the same
side of the chain while FAs containing trans-double bonds (hydrogen
atoms are on the opposite sides) are found in small amounts in natural
fats and in greater amounts after processes involving catalytic
hydrogenation.

1. Monounsaturated Fatty Acids (MUFA): They contain only one

double bond. Oleic acid is the most abundant monounsaturated
FA in nature, Palmitoleic acid is another example of MUFA, and
it is present in nearly all fats.

2. Polyunsaturated fatty acids (PUFA) – These are the FAs obtained

from plant seeds. They usually contain 2 or more double bonds.
In PUFA, double bonds are usually separated by a methylene
(CH2) group. PUFA are present in oils such as soyabean oil,
groundnut oil, sunflower, benin-seed oil etc. Examples of PUFA
are linoleic and linolenic acids; they are also called omega 6 and
omega 3 FAs respectively. These two PUFA are also referred to
as essential PUFA (EFA). They are essential because animals
cannot synthesize them, therefore they must be supplied to the
body in the diet.

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3. Linolenic acid– it is known as omega-3 fatty acid (ω3): Why are

these two PUFAs essential to animals? Linoleic and linolenic
fatty acids are the biosynthetic precursors of 20 and 22 carbons
polyunsaturated FAs, with 3 to 6 double bonds. Enzymes which
insert double bonds into unsaturated fatty acids are known as
desaturases. Desaturases in animals can insert a double bond on
the carboxyl side of existing double bonds only, they are called
∆9 desaturases. ∆9 desaturases are the only desaturase present in
animals; hence they can synthesize only oleic acid and members
of its family. The FAs derived from linoleic acid, especially
arachidonic acids, are the precursors of the prostaglandins and
steroids.

Symptoms of essential fatty acids deficiency

When essential fatty acids (omega-3 and omega-6 fatty acids) are not
present in our diets, our body will not be able to produce prostaglandins
and sterols (this is just one of many functions of these FA). We know
that hormones are very important for reproduction in man and woman,
deficiency of material required to synthesise them will result in
inadequate or complete absence of the hormones. The result is infertility.
So, foods that are rich in essential fatty acids are good for our health,
examples of such foods are fish, poultry products, fruits, vegetables, nuts
(especially walnuts), legumes (especially soyabeans), beef etc. The
symptoms of essential fatty acids deficiency are:

i. Growth retardation
ii. Poor wound healing
iii. Dermatitis, and hair loss
iv. Kidney and liver diseases
v. Infertility
vi. Depression

The most noticeable symptoms of EFA deficiency are skin disorders

such as scaly dermatitis. It can show up another on the body, but usually
occur on the hands, shoulders, forearms and face. When EFA are
included in the diets, these symptoms disappear within 7days.

Eicosanoid

The third group of unsaturated FA is the family of PUFA known as

eicosanoids. The eicosanoids are a complex family of bioactive lipid
messengers, generated by oxygenation of 20-carbon polyunsaturated
fatty acids, primarily arachidonic acid. Eicosanoids are local-acting
hormones that stimulate cells adjacent to their site of synthesis. In
general, eicosanoids have a short half-life, usually on the order of

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minutes. They are not stored in cells but instead are released as soon as
they are synthesized. Eicosanoids fall into two main classes;

i. Prostanoids that have a ring structures including prostaglandins,

thrombaxanes and prostacyclins.
ii. Linear eicosanoids consisting of leukotrienes, lipoxins and
hydroxyl eicosatetraenoid acids (HETE).

Prostaglandins

Prostaglandins exist in virtually every mammalian tissue. They are

synthesized from arachidonic acid. Prostaglandins act to modulate many
physiological functions including blood pressure, contraction of uterus,
and inflammatory signals. Prostaglandins are designated PGA, PGD,
PGE and PGF based on the functional groups on the cyclopentane ring.
Prostaglandin H2 and prostacyclin are synthesized from PG H2.

Leukotrienes and lipoxins are linear eicosanoids unlike the prostanoids,

which contain a ring in their structure, the leukotrikenes are linear
molecules. The terms leukotriene was derived from their cell of origin
(Leukocytes) and the fact that their structures contain three carbon-
carbon double bonds in conjugation. The most important Leukotrienes
in humans are: LTA4 and LTB4.

Triacylglycerols

Fig. 2: Structure of Triacylglycerol

Triacylglycerols are esters of the alcohol called glycerol and fatty acids.

They represent the major form of fat found in nature and their primary
function is to provide energy for the cell. The cell degrades fatty acids to
Co2 and water at the expense of molecular oxygen. One gram of fatty
acid liberates about 9 kilocalories (38 KJ) of energy, this is about 2.5
times higher than that of the other foodstuffs i.e. protein and
carbohydrate which yield about 4 kilocalories/g (17KJ) when
catabolized. The human body stores large amounts of fatty acids as
triglyceride in adipose tissue, and this is the storage form of energy in all

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animals. Fatty acids in the form of triglycerides are in anhydrous form,

whereas, carbohydrates and proteins are stored in an aqueous
environment. It is evident that, in terms of the energy to mass ratio, fat is
a much more efficient means of storing energy than carbohydrate or
protein. Mammalian tissues also contain some diglycerides and
menoglyceriles, but they occur in very small quantity when compared
with triglycerides.

Naturally occurring fats and oils develop unpleasant smell and taste if
stored for long under moist conditions, the chemical reaction responsible
for the odour and taste as called rancidity. Rancidity is due to partial
hydrolysis of TAG and the subsequent oxidation of the hydrolysed fatty
acids to aldehyde and ketone

Steroids

Cholesterol is a monohydric alcohol; it is classified as a devived lipid

because it is a component of other complex lipids. It is also a precursor
of two important classes of molecules; bile acids and steroid hormones;
cholesterol is probably the best-known steroid because of its association
with atherosclerosis and heart disease.

All steroids have a similar cyclic nucleus resembling phenanthrene

(rings A, B and C) to which a cyclopentane ring ∆ is attached.

The five classes of steroids are

i. Glucocorticoids ]
ii. Minerals corticoids ] 21- carbon structures
iii. Progesterone
iv. Testosterone ] 19 carbon structure
v. Androgens ]

Bile acids or bile salts play a major role in the digestion and absorption
of triacylglycerols and cholesterolyl esters. Formation of bile salts
represents the only significant metabolic mechanism for eliminating
excess cholesterol from the body.

3.3 Lipoproteins

Lipids are not soluble in aqueous solution such as the blood. Since lipids
are not soluble in water, how are they transported in the body? This
problem was solved by the presence of a lipid carrier called lipoproteins.
Lipoprotein is made up of lipid and protein in such a way that the lipids
components are packed at the center while the protein components serve
as the coat. The lipoprotein coat also contains amphipathic molecules

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such as phospholips, cholesterol, and specially synthesized protein

called apoproteins. The polar ends of the amphipathic lipids face the
surface of the particles, while the hydrophobic portions are oriented
towards the centre of the particle.

Fig. 3: Effects of LDL and HDL on the Artery (Source: Google Images)

Classification of lipoproteins
i. High Density Lipoprotein (HDL): The most dense lipoprotein
class is called high density lipoprotein. It contains about 50%
lipids and 50% protein. The major function of HDL is to collect
cholesterol from peripheral tissues and transport it back to the
liver where it is converted to bile acids and excreted. This
function is referred to as reverse cholesterol transport (RCT).
HDL is usually referred to as good cholesterol because of its
ability to reduce the body’s cholesterol content; high
concentration of HDL in the blood is good for the prevention of
cardiovascular diseases.
ii. Low Density Lipoproteins (LDL): They are cholesterol rich
particles, LDL carries about 75% of the total cholesterol in
human plasma. Its major function is the transport of cholesterol to
various extrahepatic tissues. They are usually referred to as bad
cholesterol because of their role in cholesterol distribution to
body cells. So, low concentration of LDL in the plasma is
beneficial to the body than high concentration.
iii. Very low Density lipoprotein (VLDL): They are secreted to the
blood plasma by the hepatocytes. Only 50-60% of their mass is
triacylglycerols and they contain relatively more cholesterol
esters than the chylomicrons.
iv. Chylomicrons: These particles have the lowest density among the
lipoproteins. About 90% of their mass is made up of triglyceride,
cholesterol esters and free cholesterols.

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Physical Properties of lipids

• Lipids are soluble in non-polar solvents, such as ether, alcohol,

chloroform, acetone, and benzene.
• Lipids are insoluble in water.
• Lipid molecules have no ionic charges.
• Pure fats and oils are colorless, odorless, and tasteless.
• Lipids are considered hydrophobic or amphiphilic small
molecules.
• Lipids are greasy in texture and stored in adipose tissues inside
the body.
• Lipids are either liquid or non-crystalline solid at room
temperature.
• Lipids can either be present in saturated (having only single
bonds) or unsaturated (having one or more double bonds)
structural form.

Chemical Properties of lipids

• Hydrolysis - Triacylglycerols undergo stepwise enzymatic

hydrolysis to finally liberate free fatty acids and glycerol. The
process of hydrolysis, catalyzed by lipases is important for
digestion of fat in the gastrointestinal tract and fat mobilization
from the adipose tissues.

• Saponification - The hydrolysis of triacylglycerols by alkali to

produce glycerol and soaps is known as saponification.

• Rancidity - Rancidity is the term used to represent the

deterioration of fats and oils resulting in an unpleasant taste. Fats
containing unsaturated fatty acids are more susceptible to
rancidity.

• Lipid Peroxidation - In the living cells, lipids undergo oxidation

to produce peroxides and free radicals which can damage the
tissues. The free radicals are believed to cause inflammatory
diseases such as cancer, artherosclerosis, ageing etc.

• Halogenation - Unsaturated fatty acids, whether they are free or

combined as esters in fats and oils, react with halogens by
addition at the double bond(s). The reaction results in the
decolorization of the halogen solution.

4.0 CONCLUSION

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Lipids are heterogeneous compounds that are insoluble in water,

but soluble in organic solvents (example, ether, benzene, acetone,
chloroform). These include any group of organic compounds like fats,
oils, steroids, waxes and related compounds. The three major
classification of lipids are Simple, Compound and Derived lipids.

5.0 SUMMARY

• In this unit, you have learnt about the biological functions of

lipids, classification of Lipids and lipoproteins.
• Triacylglycerol are most abundant group of lipids that primarily
function as fuel reserves of animals. The fat reserve of normal
humans is sufficient to meet the body’s caloric requirements for
2-3 months.
• Chemical properties of lipid include saponification, rancidity,
hydrolysis, halogenation and peroxidation.
• The essential functions of fatty acids to the structure and function
of human body has been discussed. Essential and non essential
fatty acids and their roles in human nutrition has been discussed.

6.0 TUTOR- MARKED ASSIGNMENT

1. Describe the group of macromolecules called lipids and give 3

examples
2. Lipids are classified to 3 groups, name them and give 2 examples
of each group
3. Describe the biological importance of lipids
4. Write short notes on the following : Waxes, Fats and Oils
5. Differentiate between saturated and unsaturated fatty acids, give
two examples of each
6. List the two essential fatty acids and explain the reason why they
are essential to human beings.
7. If there is deficiency of essential fatty acids, what are the
symptoms the person will feel or observe?
8. Describe the Eicosanoids and their biochemical reactions
9. Explain why the triglycerides store energy better than proteins
and carbohydrates
10. How are lipids transported in the blood bearing in mind that
lipids are not soluble in polar solution such as blood

7.0 REFERENCES/FURTHER READING

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Murray, R.K., Bender, D.A., Botham, K. M., Kennelly, P.J., Rodwell

V.W. & Well, P.A., (2012). Harper’s Illustrated Biochemistry.
(29th ed.). McGraw-Hill Medical.

Devlin, T.M. (2010). Textbook of Biochemistry with Clinical

Correlation.(7th ed.). John Wiley & Sons Inc.

Marks' Essentials of Medical Biochemistry: A clinical approach. 2nd

Edition Copyright 2007 Lippincott Williams & Wilkins.

Lippincott Biochemistry Fourth Edition (2010).

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UNIT 6: CHEMISTRY OF NUCLEIC ACID I

CONTENTS

1.0 Introduction
2.0 Objectives
3.0 Contents
3.1 Nucleic Acids
3.2 The Nucleotides
3.3 Types of Nucleotides
4.0 Conclusion
5.0 Summary
6.0 Tutor-Marked Assignment
7.0 Reference/Further Reading

1.0 INTRODUCTION

Nucleic acids are the most important macromolecules in all living things
because it is the genetic material responsible for the transfer of genetic
information from one generation of organisms to another. The traits we
shared with our parents are due to the genes inherited from them. These
include but not limited to physical appearance, colour of skin, size of
eye balls, intelligence etc.

2.0 OBJECTIVES

At the end of this unit, you should be able to:

• describe the chemical components of nucleic acids

• describe the formation of nucleosides
• describe the formation of nucleotides
• describe deoxyribonucleic acids (dna)
• describe ribonucleic acids (rna)
• explain the following terms:
a. (a) Replication (b) Transcription (c) Translation (d)
DNA Denaturation and Renaturation
• State the importance of some synthetic nucleotidesand the
chemical components of nucleic acids

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3.0 MAIN CONTENT

3.1 Nucleic Acids

Nucleic acids are linear polymers of nucleotides i.e. nucleotides are the
monomeric units of nucleic acids. Each nucleotide has three
components: a five-carbon monosaccharide, a nitrogen-containing cyclic
compound (base) and a phosphate group.

Five carbon Sugars – The five carbon sugars are known as pentoses.
Two different five-carbon sugars are employed in the construction of
nucleic acids; they are ribose and deoxyribose sugars. The only
difference between them is the absence of oxygen on the 2’carbon atom
of deoxyribose sugar. The structure shown in figure 10.1 is ribose sugar
while the structure in figure 10.2 is deoxyribose sugar.

Fig.1: The Structure of Ribose Sugar (Source: Google Images)

Fig. 2: The Structure of Deoxyribose Sugar (Source: Google Images)

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1. Nitrogenous bases – The nitrogenous bases employed in the

construction of nucleic acids are members of two classes of
nitrogen containing compounds known as purines and
pyrimidines. Purine has 2 derivatives in nucleic acids (Adenine
and Guanine) usually represented by letters A and G. Pyrimidine
has 3 derivatives in nucleic acids (cytosine, uracil and thymine)
usually represented by capital letters C,U,T. Thymine is present
only in DNA molecules while uracil is present only in RNA.
Adenine, Gnanine and cytosine bases are present in both DNA
and RNA.

These nitrogenous bases are the key components of nucleic acid because
genetic information is stored in the sequence of bases along the DNA
strands. Every time a cell divides, the information is passed along to the
new cells.

Fig. 3: The Structures of Purine and Pyrimidine bases (Source Google Images)

2. Phosphate Group – It is a very important component of nucleic

acids. It serves as the link between 2 sugar molecules or
nucleotides in polynucleotides. The phosphate group is a strong
acid in solution; this explains why DNA and RNA are called
acids. It is also responsible for the negative charges on DNA and
RNA at physiological pH.

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Fig. 4: The Phosphate Group (Source: Google Images)

3.2 The Nucleosides

Nucleosides – Ribose or deoxyribose Sugar +Nitrogenous Base. The

combination of ribose or deoxyriboe and one of the 5 bases produces a
nucleoside. They are linked via a covalent β-N-glycosidic bond.
Nucleosides present in RNA are Adenosine, guanosine, cytidine and
uridine.

Nucleosides present in DNA are deoxy adenosine, deoxygyanosine,

deoxycytidine and deoxythymidine or thymidine usually abbreviated as
A, G, C and T. While the nucleotides present in RNA are represented by
A, G, C, U. The structures of uridine (a representative of RNA) and
thymidine (a representative of DNA) are shown in figure 10.5

Fig. 5: The Structures of 2 Nucleosides, Uridine and Thymidine (Source: Google

Images)

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The Nucleotides

Nucleotides are phosphrylated nucleosides (nucleosides + phosphate) or

sugar + base + phosphate. Each nucleotide is a 5-monophosphate ester
of a nucleoside. The Po4 group is attached to the hydroxyl group of
pentose sugar by an ester linkage, usually OH group on carbon 5, 3 or 2.

3.3 Types of Nucleotides

i. Monophosphate – Nucleotides containing only one phosphate

molecule
a. AMP – Adenosine monophosphate
b. GMP – Guanosine monophosphate
c. UMP – Uridine monophosphate (the structure is shown in
figure 7.6)
ii. Diphosphates and Triphosphates contain two and three molecules
of phosphate respectively. Examples of diphosphate nucleotides
are ADP, GDP, UDP while ATP, GTP and UTP are examples of
triphosphate nucleotides.
iii. Cyclic nucleotides – In cyclic nucleotides, a Po4 molecule
esterifies two OH molecules on carbon 5 and carbon 3 or carbon
3 and 2 (RNA) small letter C is usually added to denote cyclic
nucleotide e.g. 3; 51 cAMP (31, 51 cyclic Adenosine
monophosphate),31, 51 c-GMP is called 31, 51 cyclic Guanosine
monophosphate.
iv. Polynucleotides- The 31OH of the pentose of a mononucleotide
esterifies the 51phosphoryl group of the 2nd mononucleotide to
form a dinucleotide. The bond between two nucleotides in
polynucleotides is known as 31, 51 phosphodiester bond. The next
nucleotide joins the existing polynucleotide through its free 31-
OH group.

Each end of a nucleotide polymer (polynucleotide) is distinct; one end

has a free 51 Phosphate while the other end has a free 31-OH group, by
convention the ncuelotides or base sequence is written in 51 to 31 -
direction, therefore polynucleotides are called directional
macromolecules.

DNA and RNA are long linear polymers called nucleic acids that carry
information in a form that can be passed from one generation to the
next. Genetic information is stored in the sequence of bases along a
nucleic acid chain.

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Fig. 6: Structure of Ridine Monophosphate (Source: Google Images)

4.0 CONCLUSION

Nucleic acids occur in living cells where they are not only responsible
for storage and transmission of genetic information but also translate
this information for precise synthesis of proteins characteristic of the
individual cell. Thus the biosynthesis and repair of nucleic acids is a
vital operation in living systems. Substances that inhibit or interfere with
this fundamental process may ultimately cause a cell to die.

5.0 SUMMARY

• The three basic components of nucleic acids are: a nitrogenous

base, a pentose sugar and a phosphoryl group.
• Nitrogenous bases belong to two classes: pyrimidines and
purines.
• The building blocks of nucleic acids are the nucleotides. They are
phosphoric esters of nucleosides.
• The common pyrimidine bases in nucleotides are Uracil (U)
Cytosine (C) and Thymine (T).
• Common purines found in nucleic acids are Guanine (G) and
Adenine (A).

7.0 TUTOR- MARKED ASSIGNMENT

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1. Describe nucleic acids and explain their importance to all living

organisms.
2. List the chemical components of nucleic acids and describe each
component.
3. What are nucleotides? Give 4 examples of nucleotides.

7.0 REFERNCES/FURTHER READING

Murray, R.K., Bender, D.A., Botham, K. M., Kennelly, P.J., Rodwell

V.W. & Well, P.A., (2012). Harper’s Illustrated Biochemistry.
(29th ed.). McGraw-Hill Medical.

Devlin, T.M. (2010). Textbook of Biochemistry with Clinical

Correlation. (7th ed.). JohnWiley& Sons Inc.

Nelson, D.L. & Cox, M.M. (2009). Lehninger Principles of

Biochemistry. (4th ed.).

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UNIT 8 CHEMISTRY OF NUCLEIC ACIDS II

CONTENTS

1.0 Introduction
2.0 Objectives
3.0 Contents
3.1 Structure of DNA
3.2 Description of Duplication and RNA Synthesis in Nucleic
Acid
3.3 Importance of Some Synthetic Nucleotides
4.0 Conclusion
5.0 Summary
6.0 Tutor-Marked Assignment
7.0 Reference/Further Reading

1.0 INTRODUCTION

The two major classes of nucleic acids are Deoxyribonucleic acid

(DNA) and Ribonucleic acid (RNA). The DNA is the carrier of genetic
information while the RNA is an intermediate in the expression of
genetic information and other diverse role. DNA is found in the nucleus
with small amounts in mitochondria and [Link] is found
throughout the cell.
The only significant variation in chemical structure of nucleic acids is
the type of base in each nucleotide position. The bases are not involved
in formation of the nucleotide backbone but serve as a distinctive side
chain.

2.0 OBJECTIVES

At the end of this unit, you should be able to:

• Describe the structure of DNA and RNA

• List the structural differences between DNA and RNA.
• Draw the schematic structure of DNA
• Explain the meaning of (i) transcription (ii) replication (iii)
translation
• List at least 3 biological functions of nucleotides apart from
genetic functions.

3.0 MAIN CONTENT

3.1 Structure of DNA

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Deoxyribonucleic acid (DNA) is an example of polynucleotide and it is

one of the two types of nucleic acids that made up the genetic materials.
DNA exists as a double stranded molecule (figure 11.1b) in eukaryotes
but single stranded DNA is common among the prokaryotes. The two
helical polynucleotide chains usually coil around a common axis. DNA
must undergo series of folding and super-folding to enable it fit into the
little space available inside the nucleus of cells. This continuous folding
finally give rise to a genetic material called chromosomes. Segment of a
strand that contains sequence of nucleotides capable of producing a
functional protein is refered to as a gene. The four nucleotide units
present in DNA are deoxyadenylate, deoxythymidylate, deoxyguanylate
and deoxycytidylate.

A unique characteristic of naturally occurring DNA molecules is their

very long chain of nucleotides. A DNA molecule must comprise many
nucleotides; this enables it to store sufficient genetic information
necessary for even the simplest organism. For example, the [Link]
genome is a single DNA molecule consisting of two chains of 4.6
million nucleotides. The human genome (complete genetic information
of an organism) comprises of about 3 billion nucleotides.

Fig.1: (a) Stacking of two Chains (B) Double Stranded Structure of dna (C)
Beads Representation ,of Double Stranded dna (Source: Google Images)

Ribonucleic acid is also a polynucleotide like DNA but it exist as a

single stranded molecule (Figure 11.2). It is usually produced from the
DNA in eukaryotes but it serves as the main genetic material in some
viruses, especially the retroviruses such as HIV. The sequence of
nucleotides in RNA is determined by the sequence of DNA present in
the cell. This will be clearer section in section 7.6. There are some

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differences between RNA and DNA; I have just discussed one of them.
Other differences are:

i. The sugar component of DNA is deoxyribose but in RNA we

have ribose sugar
ii. The nucleotides are also different by just one; in place of thymine
monophosphate in DNA, uridine monophosphate is present in
RNA as shown in section 10.2.

Fig. 2: The Structure of RNA, Molecule (Source: Google Images)

3.2 Description of Duplication and RNA Synthesis in Nucleic

Acid

(i) Replication (ii) Transcription (iii) Translation (iv) DNA

Denaturation and Renaturation

i. Replication: This is also known as duplication, it is the process

by which a replica or identical copy of DNA is made from the
parent copy. This process occurs whenever a cell is preparing to
divide. This process must take place so that the new cell will also
contain the same genetic information present in the old cell. This
is how the genetic information is preserved and passed from one
generation to the next.
ii. Transcription: This is the process by which the genetic messages
contained in the DNA molecule are read and copied correctly to
produce ribonucleic acid (RNA). This process occurs whenever
the cell or tissue requires a particular protein to carry out a
biochemical process; the protein required can be an enzyme,
receptor or other forms of proteins.

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iii. Translation: This is the process by which the genetic messages

carried by RNA are decoded and used to build proteins (enzymes,
receptors, hormones etc).
iv. DNA denaturation and renaturation: The process of separating the
complementary strands of duplex DNA is called denaturation. The
double stranded structure of DNA can be separated into two
component strands in solution by increasing the temperature,
decreasing the salt concentration and by extreme pH (strongly acidic
or strongly basic solution). Because of the base stacking and the
hydrogen bonding between the bases, the double stranded DNA
molecule exhibits properties of a rigid rod and in solution; it is a
viscous material that loses its viscosity upon denaturation as well as
its biological properties.

The complete separation of DNA strands occur over a temperature range

(50 range). The heating disrupts the hydrogen bonds between base pairs
thereby causes the strands to separate. This process is also called
melting of DNA. The melting temperature ™ of DNA molecule
depends on the pH and ionic strength of the solvent. Purine and
pyrimidine base composition also affect the melting temperature of
DNA; the greater the content of G and C, the higher the melting
temperature and vice-versa. There are 3 bonds between G and C while
there are 2 bonds between A and T. The melting temperature ™ is
defined as the temperature at which half of the helical structure is lost.

DNA solution absorbs maximally at a wavelength of 260mm, the

absorbance increases as the double helix is separated into single strands
(denaturation). This principle is also known as hypochronism.

Renaturation is the opposite of denaturation, it is the process of re-

association of separated strands of DNA or any two strands of DNA that
are complementary in base pairing. This process takes place only
when the appropriate physiologic temperature and salt concentration are
achieved. Re-naturation is also called hybridization.

3.3 Importance of some Synthetic Nucleotides

Synthetic nucleotides are used in chemotherapy of cancer and viral

infectionsModified synthetic analog of purines, pyrimidines and
nucleotides have useful applications in clinical medicine. These
compounds are used to treat cancer because they can prevent DNA
synthesis due to their toxicity to the enzymes involved in DNA
synthesis.

Some of the synthetic nucleotides are also used to manage AIDS

patients, because they are toxic to an important enzyme required for

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DNA synthesis in the virus. For example Azidothymidine (AZT) is a

potent inhibitor of reverse transcriptase in HIV. Zidovudine is another
drug for HIV control, its active component is 21- Azido – 31
deoxythymidine. (AZT inhibits HIV replication). AZT is not used alone
but in combination with other drugs with different mechanism of
activity. The combined therapy is called highly active antiretroviral
therapy (HAART).

Non-Enzymic Reactions of Nucleic Acids

Alteration in base sequence in DNA and free nucleotides can occur in
their covalent structure which may result in a permanent change called
mutation.
Loss of exocyclic amino group: this non-enzymic deamination for
example can occur in cytosine transforming it to uracil. Adenine can
undergo deamination to hypoxanthine while guanine to xanthine (when
deaminated).
N-β-glycosyl bond hydrolysis in DNA: the bond between the base and
pentose can be hydrolysed and the rate of occurrence in purines is higher
than for pyrimidines. This reaction (depurination) can be accelerated by
dilute acids. Incubation of DNA at pH 3 causes selective removal of
purines resulting in the derivative called apurinic acid.
Effects of Radiation on DNA
Exposure of DNA to UV can cause condensation of 2 ethylene groups to
form a cyclobutane ring on closely stacked DNA bases. Adjacent
pyrimidine bases especially thymidine in cells form cyclobutane
dimmers by elimination of double bond existing between 5-6 positions
of both rings or formation of a 6-4 product between adjacent thymidines
in DNA
Other ionizing radiation X-rays, gamma rays etc can cause ring opening
and fragmentation of the phosphodiester backbone of nucleic acids a
reaction estimated to be responsible for 10% of all DNA damage caused
by environmental factors
Effects of Reactive Chemicals
Products and by-products of industries and other reactive chemicals can
cause DNA base pair breaks. Some of these chemicals are metabolized
into forms that become injurious to cells. Examples of such agents are:

• Nitrous acid(HNO2) or compounds that can be metabolized to

nitrous acid e.g NaNO3 NaNO2 dimethylnitrosamine
• Alkylating agents e.g. dimethyl sulphate (CH3)2SO4, dimethyl
nitrosamine, nitrogen mustard [HN(CH2CH2Cl)2], S-

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adenosylmethionine are common examples of agents that can

methylate bases thus altering the structure of DNA or
nucleotides. Dimethylsulphate for example methylates guanine at
O6 position which cannot base pair with cytosine. Some
beneficial methylation reactions include
- Preservation of DNA integrity and biological function.
This reaction is confined to certain regions of the DNA
- Defense mechanism to help cells recognize their DNA as
self
- Mask restriction sites thus protecting cutting of DNA by
restriction enzymes
- Suppression of transposon migration
Reactions that generate reactive oxygen species (ROS) e.g. superoxide
radicals, hydroxyl radicals and singlet oxygen can cause damage to
DNA however, cells are equipped with mechanisms that interfere or
avert the deleterious effects of such reactive species. For example
antioxidant enzymes (catalase, superoxide dismutase glutathione
peroxidase and other antioxidant vitamins like vitamin E, coupled also
with the ability of DNA to repair itself by screening for and removal of
mismatched base pairs (Proof reading).

4.0 CONCLUSION

In this unit, you have learnt about the structure of DNA, description of
duplication and RNA synthesis in nucleic acidand importance of some
synthetic nucleotides.

5.0 SUMMARY

• There are three basic components of nucleic acids: a nitrogenous

base, a pentose sugar and a phosphoryl group.
• Nitrogenous bases belong to two classes: pyrimidines and
purines. Pyrimidine is a single six membered ring containing two
nitrogen atoms. Purine is a pyrimidine to which a five membered
imidazole ring is fused.
• The common sugars found in nucleic acids are the ribose and
deoxyribose sugars.
• The phosphoryl group of nucleotides is most commonly
substituted on the C-5΄ -OH of the pentose sugar.

6.0 TUTOR- MARKED ASSIGNMENT

1. Describe the structures of DNA and RNA

2. What are the differences between DNA and RNA?

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3. Write short notes on each of the following: (i) Replication (ii)

Transcription (iii) Translation (iv) DNA Denaturation and
Renaturation

7.0 REFERENCES/FURTHER READING

Murray, R.K., Bender, D.A., Botham, K. M., Kennelly, P.J., Rodwell
V.W. & Well, P.A. (2012). Harper’s Illustrated Biochemistry
(29th ed.). McGraw-Hill Medical.

Devlin, T.M. (2010). Textbook of Biochemistry with Clinical

Correlation. (7th ed.). John Wiley & Sons Inc.

Nelson, D.L. & Cox, M.M. (2009). Lehninger Principles of

Biochemistry. (4th ed.).

Marks' Essentials of Medical Biochemistry: A clinical approach. 2nd

Edition Copyright 2007 Lippincott Williams & Wilkins.

Garrett and Grisham Biochemistry, 2nd Edition. Harcourt College Pub

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MODULE 3 BASIC ENZYMOLOGY

Unit 1 Itroductory Enzymology

Unit 2 Enzyme Kinetics I
Unit 3 Enzyme Kinetics II

UNIT 1 INTRODUCTORY ENZYMOLOGY

CONTENTS

1.0 Introduction
2.0 Objectives
3.0 Main Content
3.1 Enzymes as Catalysts of Biological Systems.
3.2 Cofactors
3.3 Naming and Classification of Enzymes
3.4 General Properties of Enzymes
3.5 Classes of Enzymes
4.0 Conclusion
5.0 Summary
6.0 Tutor- Marked Assignment
7.0 References/Further Reading

1.0 INTRODUCTION

This unit introduces you to important complex biological molecules

called Enzymes. Enzymes are important proteins that serve as
biological catalysts for reactions in all living organisms. Like all
catalysts, enzymes increase the rate of reactions, but they themselves
are not permanently changed in the process. Enzymes are essential to
the biological reactions that occur in the body, which would
otherwise often proceed too slowly to be of any use. In humans,
enzymes must catalyze reactions under very specific physiological
conditions, usually a pH around 7.4 and a temperature of 37 °C.

2.0 OBJECTIVES

At the end of this unit, you should be able to:

• Define the role of enzymes as catalysts of biological systems.

• Outline and distinguish the 3 types of cofactors required by most
enzymes.
• Explain how enzymes are named.
• Outline and explain the general properties of enzymes.

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• Enumerate the different classes of enzymes and the types of

reactions catalyzed by each class.

3.0 MAIN CONTENT

3.1 Enzymes as Biocatalyst

Although the phenomena of fermentation and digestion had long been

known, the first clear recognition of an enzyme was made by Payen and
Persoz when they found that an alcohol precipitate of malt extract
contained a thermolabile substance that converted starch to sugar. This
substance, now known as Amylase was at the time named diastase. The
first enzyme to be obtained in pure form was urea, crystallised from Jack
Beans in 1926. The work was carried out by James Sumner, for which
he was awarded the 1946 Nobel Prize. Since them, thousands of
different enzymes have been purified and their structures worked out.
With the exception of a few catalytic RNA molecules (ribozymes), all
enzymes are proteins. They range in size from large multiple subunit
complexes (called multimeric enzymes) to small single subunit forms.
The region within the enzyme molecule that contains the
chemical/functional groups to which the reactants (substrate) binds is
called the active site / catalytic site / substrate binding site of the
enzyme. The particular arrangement of an enzyme’s amino acid side
chains in the active site determines the type of molecules that can bind
and react there.

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The active site of an enzyme is usually found in a cleft or

pocket that is lined by amino acid residues that
participate in recognition of the substrate.
Fig. 1: Active Site of an Enzyme
3.2 Cofactors

Many enzymes have small non protein molecules associated with or

near the active site that determine substrate specificity. These are called
cofactors. A cofactor may be

i. A coenzyme- A non protein organic substance which is loosely

attached to the protein part. Coenzymes are often derivatives of
vitamins. They may or may not be modified in the reactions.
Those that are altered are also called co-substrates. The B
vitamins supply important components of numerous coenzymes
ii. A prosthetic group-An organic substance which is tightly bound
either covalently or non-covalently to the protein portion e. g
flavin coenzymes, pyridoxal phosphate, biotin.
iii. A metal ion activator. These include most divalent metal ions as
well as other ions e. g Cu2+, Zn2+, Mg2+, Ca2+, Co2+, Fe2+, Fe3+
and Mo3+. Enzymes which require a metal ion for activity are
called metal-activated enzymes. Metal ions are sometimes tightly
bound to the protein portion. Enzymes containing such are called
metalloenzymes.

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The protein portion is called the apoenzyme while the entire active
complex is called the holoenzyme [Link] + Cofactor =
Holoenzyme.

Apoenzyme + Cofactor Holoenzyme

(protein only) (active)
(inactive)

The major function of the coenzyme is that it prepares the active site of
the enzyme for catalytic activity.

Figure 14: Illustration of the function of coenzyme (© Pearson

Education Inc, 2010).

Table 1: Examples of Coenzymes, Metal ion Activators and

Non-vitamin Coenzymes

Coenzymes Vitamin Reaction Mediated

Biotin Biotin Carboxylation
Cobalamin (B12) B12 Alkylation
Coenzyme A Pantothenate Acyl transfer
Flavin coenzymes Riboflavin B2 Oxidation-reduction
Nicotinamide Nicotinamide Oxidation-reduction
coenzymes
Pyridoxal phosphate Pyridoxine B6 Amino group transfer
Tetrahydrofolate Folic acid One carbon group transfer
Thiamine Thiamine B1 Carbonyl transfer
pyrophosphate

Mg2+ ATP-dependent reactions

Zn2+ Carboxypeptidase, Alcohol dehydrogenase
K+ Pyruvate kinase
Cu2+, Fe2+ Oxidases and hydroxylases

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Non Vitamin
Coenzymes
Coenzyme Reaction Mediated

ATP Phosphate group transfer

Coenzyme Q Oxidation- Reduction
S-Adenosyl Methyl group transfer
methionine
Glutathione Oxidation-Reduction

3.3 Naming and Classification of Enzymes

Except for some of the earliest studied enzymes e.g pepsin, rennin and
trypsin, most other enzymes are known by common names obtained by
adding the suffix-ase to the name of the substrate or to the reaction that
they catalyzee.g glucose oxidase, transaminases etc. A systematic
scheme for naming/ classifying enzymes was adopted in 1972 by IUB.
In this system, each enzyme has a unique name and code number that
reflects the type of reaction catalyzed and the substrates involved. The
code number is made of 4 figures which indicate the main class, sub
class, sub sub class and the serial number of the enzyme in its sub sub
class e.g the enzyme commonly called hexokinase has the IUB
designation ATP: D- hexose-6 phosphotransferase EC [Link]. This
identifies the enzyme as a member of class 2 (tranferases), sub class
7(involves transfer of a phosphoryl group), Sub-sub class 1 (an alcohol
is the phosphoryl acceptor) . The last digit indicates that the enzyme is
the first in its sub sub class

For Example, the enzyme HEXOKINASE is named as follows:

IUB Name: ATP: D-Hexose-6 phosphotransferase EC [Link]

This identifies the enzyme as follows:

i. a member of class 2(transferase),

ii. sub-class 7 (Reaction involves transfer of a phosphoryl group
iii. Sub sub class 1 ( an alcohol is the phosphoryl acceptor)
iv. Serial No 1 (in its sub sub class)

General Properties of Enzymes

i. Enzymes possess enormous catalytic power. Most accelerate

reactions by factors of at least 1 million.

Consider the reaction catalysed by carbonic anhydrase

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CO2 + H2O H2CO3

The enzyme is responsible for effecting the transfer of CO2 from the
tissues into the blood and then to the alveoli. Each enzyme is capable of
hydrating 105 molecules of CO2 in one second. The catalysed reaction is
107 times faster than the uncatalysed reaction.

ii. They are highly specific both the reaction catalysed and t
heir choice of reactants. Four distinct types of enzyme specificity
have been identified. They include

A. Absolute specificity, where the enzyme catalyses only one

reaction.
B. Group specificity. The enzyme acts only on molecules with
specific functional groups.
C. Linkage specificity- The enzyme acts on a particular type of
chemical bond regardless of the rest of the molecular structure.
E.g Trypsin splits peptide bonds on the carboxyl side of lysine
and arginine residues only while thrombin acts only when the
side chain on the carboxyl side is arginine while the one on the
amino side is glycine.
D. Stereochemical specificity. The enzyme acts on a particular steric
or optical Isomer

iii. They do not alter reaction equilibria

The combination of substrate and enzyme creates a new reaction
pathway whose transition state energy is lower than it would be if the
reaction were taking place in the absence of an enzyme. However, in
this process, both the forward and reverse reactions are accelerated by
precisely the same factor. Thus enzymes accelerate the attainment of
equilibria but do not shift their position.

Fig. 2a: Enzymes do not Alter Reaction

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The enzyme stabilises the transition state, reducing the energy needed to
form products.

Enzymes are stable over only a limited range of Temperature

iv. Generally, a higher temperature brings about an increase in the

movement of enzyme and substrate molecules, resulting in more
collisions between the molecules and an d formation of more
products.(a 10oC rise in temperature increases the activation
energy of the molecules by about 12Kcal/Mol).However, if the
temperature rises beyond a certain point (which differs for each
enzyme), the enzyme activity levels out and then declines rapidly.

This is because the enzyme is denatured by heat. The tertiary

structure of the enzyme is altered and it can no longer function.
Human enzymes generally exhibit stability at temperatures up to
45-55oC. Thermophilic enzymes may be stable up to or above
100oC. For mammals and other homoeothermic organisms,
changes in enzyme reaction rates with temperature assume
physiologic importance only in circumstances such as fever or
hypothermia.

Fig 2b: Effect of Temperature on Reaction Rate

v. Enzymes are stable over only a limited range of Ph. Each

enzyme has an optimal pH range that help maintain its normal
configuration in the environment where it operates. Outside this
range, changes in the charges on ionizable amino acid residues
result in modification of the tertiary structure of the protein and
eventually lead to [Link] of pH optima include
the those of the digestive enzymes: Pepsin-2.0, Trypsin-10.0 and
Chymotrypsin-8.0

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Fig 2c: Effect of pH on Reaction Rate

vi. Enzymes are influenced by the concentration of substrate

At very low [S], collisions between enzyme and substrate are infrequent
and the reaction proceeds slowly. As [S] increases, reaction rate
increases proportionately as collisions become more frequent.

Rate α [A] [B]

When the enzyme begins to approach the maximum rate at which it can
combine with substrate, the effect of increasing [S] diminish. At
saturation point, the reaction is no longer affected by increase in [S].The
rate of the reaction at this point is called maximum velocity. The [S] at
which we have Vmax is called Km, (Michelis constant) for a particular
enzyme.

Fig 2d: Saturation Curve for an Enzyme Reaction showing the Relation between
[S] and Rate (v).

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3.5 Classification of Enzymes

All known enzymes belong to one of 6 main classes:

• Oxidoreductases
• Transferases
• Hydrolases
• Lyases/Synthases
• Isomerases
• Ligases/Synthetases

i. Oxidoreductases

a. They catalyse oxidation – reduction reactions. This includes

pairs of donors and acceptors such as saturated- unsaturated
carbon-carbon bonds, alcohols-aldehydes, aldehydes-acids and
amines-imines e. g alcohol dehydrogenase catalyzes the
oxidation of an alcohol to an aldehyde by the removal of 2
electrons and 2 hydrogen [Link] include oxidases,
oxygenases and peroxidases. Oxidases transfer 2 electrons
from a donor to oxygen, resulting in the formation of hydrogen
peroxide e.g glucose oxidase.
b. Glucose + O2→ Gluconolactone + H2O2
c. Oxygenases catalyse the incorporation of oxygen into a
substrate e.g monooxygenases catalyse formation of a hydroxyl
group and dioxygenases incorporate both atoms of O2 into a
substrate. Cytochrome P450 are an important group of
enzymes that use oxygen in the metabolism of xenobiotics such
as drugs and toxins. Peroxidases utilise H2O2 rather than
oxygen as the oxidant e.g catalase which utilises H2O2 as
both donor and acceptor and functions in the cell to detoxify
H2O2.
d. H2O2 + H2O2↔O2 + 2H2O.

ii. Transferases

a. Members of this class catalyse a chemical group from one

molecule to another, thus they have 2 substrates and 2 products.
The major groups transferred include amino, acyl, phosphate and
glycosyl. Subclasses include aminotransferases, kinases, glucosyl
and phosphoryl transferases and phosphomutases.
b. Aminotransferases transfer an amino group from one amino acid
to an α keto acid acceptor, resulting in the formation of a new
amino acid and a new keto acid.

c. L-Glutamic acid + pyruvic acid

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1. ↓
d. α ketoglutaric acid + L-Alanine

iii. Hydrolases

These catalyse hydrolysis reactions i.e the addition of water to cleave a

chemical bond. Examples of such bonds include C-O, C-N, O-P and C-
S. Subclasses include esterases, phosphatases and peptidases.

iv. Lyases

They catalyse reactions in which groups are either removed to form a

double bond or are added to a double bond. Subclasses include
decarboxylases and dehydratases. Some lyases require pyridoxal
phosphate as the cofactor. An example is fumarase, an intermediate of
the citric acid cycle.

v. Isomerases

Enzymes in this group are involved in moving a group or a double bond

within the same molecule. These include cis-trans and aldose- ketose
transformations. The enzyme is called a mutase when a phosphate is
moved from one carbon to another e.g conversion of 2-
phosphoglycerate to 3-phosphoglycerate by phosphoglycerate mutase.
Epimerases and racemases change the stereochemistry at a carbon atom.
The conversion of D-Lactate to L-Lactate is catalysed by a racemase
while conversion of D-xylulose 5-phosphate to D-ribulose 5-phosphate
is brought about by epimerase.

vi. Ligases

These enzymes catalyse bond formation between two substrate

molecules. Energy is required for the reaction to occur. Typically, the
energy is supplied by ATP hydrolysis. They are also called synthetases.
For example, to add CO2 to pyruvate, CO2 is incorporated into the
coenzyme biotin, which requires hydrolysis of ATP. The CO2 is
transferred to pyruvate by the same enzyme.

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Table 2: Major Enzyme Classes

First EC Enzyme class Type of reaction catalyzed

integer
1 Oxidoreductases Oxidation-reduction
2 Transferases Chemical group transfer. A-X + B→
A+B-X
3 Hydrolases Hydrolytic cleavages
4 Lyases Non-hydrolytic cleavage leaving
double bonds or addition of groups to a
double bond
5 Isomerases Change of geometric arrangement of a
molecule
6 Ligases Joining together of 2 molecules,
accompanied by ATP hydrolysis

4.0 CONCLUSION

Enzymes of different classifications are involved in different types of

chemical reactions in the body. Some factors make stability of the
enzymes possible and these must be understood to be able to ensure that
these are not contravened.

5.0 SUMMARY

In this unit, you have learnt that enzymes are catalysts of biological
systems. There are co-factors to efficiency of enzymes. Enzymes are
classified into 6 types and are involved in different types of reactions in
the body.

6.0 TUTOR- MARKED ASSIGNMENT

1. Explain the role of enzymes as catalysts of biological systems.

2. Distinguish the 3 types of cofactors required by most enzymes.
3. Explain how enzymes are named.
4. Discuss the general properties of enzymes.
5. Enumerate the different classes of enzymes and the types of
reactions catalyzed by each class.

7.0 REFERENCES/FURTHER READING

Murray, R.K., Bender, D.A., Botham, K. M., Kennelly, P.J., Rodwell

V.W. & Well, P.A., (2012). Harper’s Illustrated Biochemistry.
(29th ed.). McGraw-Hill Medical.

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Devlin T.M. (2010). Textbook of Biochemistry with Clinical

Correlation. (7th ed.). JohnWiley& Sons Inc.

Nelson, D.L. & Cox, M.M. (2009). Lehninger Principles of

Biochemistry. (4th ed.).

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UNIT 2 ENZYME KINETICS I

CONTENTS

1.0 Introduction
2.0 Objectives
3.0 Contents
3.1 Enzyme Activity
3.2 Michelis-Menten Rate Equation
3.3 Linear Forms of the Michelis-Menten Equation
4.0 Conclusion
5.0 Summary
6.0 Tutor- Marked Assignment
7.0 References/Further Reading

1.0 INTRODUCTION

Enzyme kinetics is the study of the rates of enzyme-catalysed reactions

and its role in metabolism. It also involves how the activity of the
enzyme is controlled in the cell and how some substances can inhibit its
activity. The reaction is measured and the effects of varying conditions
of the reaction are investigated.
The mode of action of the enzymes is summarized by the following
equation:

E is the enzyme, S is the substrate, and P is the product formed. This

equation shows that an enzyme and a substrate bind to form an enzyme-
substrate complex (ES). This complex then produces the product. As the
enzyme is released at the end and not used up in the reaction, it is a
catalyst.

2.0 OBJECTIVES

At the end of this unit, you should be able to:

• Define basic terms related to enzyme kinetics

• Derive the michelis- menten rate equation
• State the linear forms of the michelis- menten rate equation
• Make linear plots and deduce kinetic parameters from a given set
of data.

3.0 MAIN CONTENT

3.1 Enzyme Activity

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This can be defined as the amount of enzyme required to convert 1µmol

of substrate to product per minute under specified assay conditions.

1U-1micromole/minute. This is the international unit. The SI unit of

enzyme activity is the Katal, defined as the amount of enzyme required
to convert 1mol of substrate to product per second.

1U= 1.67X 10-8K= 16.7nK

Specific Activity: This is defined as the number of enzyme units per

milligram of protein (µmol/min/mg).
Turnover number: This is equal to the units of activity per mole of
enzyme. Also called the catalytic enzyme, it allows for direct
comparison of catalytic ability between enzymes e. g the constants for
catalase and α amylase are 5 X 106 and 1.9 X 104 respectively. This
indicates that catalase is about 2,500 times more active than α amylase.
Maximum velocity: This is the velocity obtained under conditions of
substrate saturation of the enzyme and specified conditions of pH,
temperature and ionic strength. Vmax is a constant for a given enzyme.

3.2 Michelis-Menten Rate Equation

In 1903, French chemist Henri found that enzyme kinetics was initiated
by a bond between enzyme and substrate. His work was taken up by
Leonor Michaelis and Maud Menten. They proposed a mathematical
model of the reaction. It involves an enzyme E binding to a substrate S
to form a complex ES, which in turn is converted into a product P
represented as follows:

S+E ES→P+E (1)

At steady state, the rate of formation of the ES complex is the same as
its rate of breakdown.

Vformation = K1[S][E]
Vbreakdown= K2[ES] + K3[ES]
K1[S][E]= [ES] {K2+K3/K1} (2)

We can define the ratio of the rate constants as Km i.e Km= K2+K3/k1
Km is the Michaelis constant
[S] [E]= [ES]Km (3)

[E] is the concentration of free enzyme and is given by the difference

between the total enzyme added to the system and any enzyme in the ES
complex

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i.e [E] = {[Et] – [ES]} = [ES]Km

Dividing through by [S] gives
{[Et] – [ES]} = [ES] Km/[S]
Dividing thru by [ES] gives
[ET]/[ES] -1= Km/[S] or [ET]/[ES] = Km/[S] +1 = Km + [S]/[S] (4)

When the enzyme is saturated with substrate, all of it will be in the ES

complex
[ET] will be = [ES]
Then, the velocity observed will be the highest possible
Vmax= K3[ET]
[ET]= Vmax/ K3

When [Et] is not equal to [ES], V= K3 [ES], [ES]= V/K3

[ET]/ [ES] = Vmax/ K3 / V/K3 = Vmax/ V
Vmax/V = Km+ [S]/ [S]
Or v= Vmax[S]/ Km + [S].

This equation is called the Michaelis-menten equation

Consider the M.m equation under 3 different conditions

1. When Km>>>[S],

The equation becomes V= Vmax[S]/ Km, V= (Vmax/Km) [S]

This implies that at low substrate concentrations, the rate is directly
proportional to [S]

2. When Km = [S]

V= Vmax[S]/ 2[S] or v= Vmax/2. i.e Km is the substrate concentration at

which we have half the maximum velocity.

3. When Km<<<[S]

V= Vmaxi.e at high [S], v= Vmax.

3.3 Linear Forms of the Michelis-Menten Equation

The linear form of the equation is

1/ V= Km/ Vmax[1/S] + 1/ Vmax

A plot of 1/V vs 1/[S] yields a straight line whose slope is Km/ Vmax and
whose y-intercept is 1/Vmax. The intercept on X-axis is -1/Km.

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This linear form is called the theLineWeaver-Burk equation and the plot
the Lineweaver-Burk plot. It can be used to obtain values of the kinetic
parameters for a given enzyme reaction.

Km is an indication of the affinity of the enzyme for its substrate. Low

Km indicates high affinity and vice versa.

Other linear forms of the M.M equation are the Eadie-Hofstee equation
and the Woolf equation.

Eadie-Hofstee- V= -Km. V/[S] + Vmax

Woolf- [S]/V= 1/Vmax.[S] +Km/Vma

Fig. 1 Lineweaver-Burk plot

Fig 2: Eadie-Hofstee Plot

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Fig. 3 Woolf Plot

Factors affecting Enzymes Activity

Enzymes are stable over only a limited range of Temperature

Velocity of an enzyme catalyzed reaction increases with increase in
temperature up to a maximum and then decline. Generally, a higher
temperature brings about an increase in the movement of enzyme and
substrate molecules, resulting in more collisions between the molecules
and and formation of more products. A 10oC rise in temperature
increases the activation energy of the molecules by about 12Kcal/Mol.
However, if the temperature rises beyond a certain point (which differs
for each enzyme), the enzyme activity levels out and then declines
rapidly. This is because the enzyme is denatured by heat. The tertiary
structure of the enzyme is altered and it can no longer function. Human
enzymes generally exhibit stability at temperatures up to 45-55oC.
Thermophilic enzymes may be stable up to or above 100oC. For
mammals and other homoeothermic organisms, changes in enzyme
reaction rates with temperature assume physiologic importance only in
circumstances such as fever or hypothermia.

4.0 CONCLUSION

Rate of Enzyme catalyzed reactions play a significant role in

metabolism, To determine the reaction rate, the initial velocity need to
be determined. The amount of product made per unit time at the start of
the reaction is called initial velocity for that concentration. An easy way
to determine Km and Vmax is to plot a Lineweaver-Burk plot. This is a
reciprocal graph of the reaction velocity against substrate concentration.

5.0 SUMMARY

In this unit, you have learnt about the following:

• Enzyme Activity

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• Michelis-Menten rate equation

• Linear forms of the Michelis-Menten Equation

6.0 TUTOR- MARKED ASSIGNMENT

1. Define basic terms related to enzyme kinetics

2. Derive the Michelis-Menten rate equation
3. State the linear forms of the Michelis-Menten rate equation
4. Make linear plots and deduce kinetic parameters from a given set
of data.

7.0 REFERENCES/FURTHER READING

Murray, R.K., Bender, D.A., Botham, K. M., Kennelly, P.J., Rodwell

V.W. & Well, P.A., (2012). Harper’s Illustrated Biochemistry.
(29th ed.). McGraw-Hill Medical.

Devlin T.M. (2010). Textbook of Biochemistry with Clinical

Correlation. (7th ed.). John Wiley & Sons Inc.

Nelson, D.L. & Cox, M.M. (2009). Lehninger Principles of

Biochemistry. (4th ed.).

Davis, Jack. 2019. An Introduction to Enzyme Kinetics. News-Medical,

viewed 25 August 2021, [Link]
sciences/[Link].

Factors Affecting Enzyme Activity: 6 Factors ([Link])

retrieved August 28, 2021

"Enzymes: Figure 3 (Opens in a new window)," by OpenStax College,

Biology, CC BY 3.0._)

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UNIT 3 ENZYME KINETICS II

CONTENTS

1.0 Introduction
2.0 Objectives
3.0 Contents
3.1 Enzyme Inhibition
3.2 Effects of Inhibitors on Lineweaver-Burk plot
3.3 Regulation of Enzyme Activity
3.4 Clinical Applications of Enzymes
4.0 Conclusion
5.0 Summary
6.0 Tutor- Marked Assignment
7.0 References/Further Reading

1.0 INTRODUCTION

Several compounds act as inhibitors of enzyme activity. The study of

enzyme inhibitors has provided insight into the mechanism and pathway
of catalysis e.g the types of functional group found in the active site and
the roles played by these groups. Most pharmaceutical compounds are
also designed as enzyme inhibitors. The different types of reversible
inhibitors include competitive, uncompetitive and non-competitive
inhibitors. They can be distinguished by their effects on the Lineweaver-
Burk plot. Some enzymes play regulatory roles in metabolism. They
include allosteric enzymes, covalently modulated enzymes and
isozymes. Enzymes are very useful tools in clinical diagnosis.

2.0 OBJECTIVES

At the end of this unit, you should be able to:

• Outline and distinguish the different types of reversible enzyme

inhibition with specific examples and explain the use of enzyme
inhibitors in drug design
• Enumerate the effects of the different types of inhibitors on
lineweaver-burk plots
• Explain the regulatory roles of allosteric enzymes , covalently
modulated enzymes and isoenzymes
• Give examples of enzymes used in clinical diagnosis and their
diagnostic importance

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3.1 Enzyme Inhibition

Much of the basic knowledge of metabolic pathways was determined by

using inhibitors of specific enzymes. Also, through the study of enzyme
inhibitors, valuable information has been obtained on the mechanism
and pathway of enzyme catalysis, substrate specificity of enzymes, the
nature of functional groups at the active site, and the participation of
certain functional groups in maintaining the active conformation of the
enzyme molecule. Pharmaceutical compounds are also mostly designed
as inhibitors of specific enzymes. E.g. penicillin works by preventing
completion of a cross link between 2 adjacent peptidoglycan chains in
the cell wall. This process is carried out by the enzyme glycopeptide
transpeptidase. Disulfiram is a drug used for the treatment of
alcoholism. Alcohol is metabolised in 2 steps to acetic acid. The first
enzyme, alcohol dehydrogenase yields acetaldehyde, which is then
converted into acetic acid by aldehyde dehydrogenase. The latter
enzyme has an active site cysteine residue that is irreversibly modified
by disulfiram, resulting in accumulation of alcohol and acetaldehyde in
the blood. People who take disulfiram become sick because of
accumulation of acetaldehyde in blood and tissue, leading to alcohol
avoidance.

Also, NSAIDs like Aspirin inhibit cyclooxygenase activity by reversibly

blocking the channel for arachidonate in the enzyme. (compounds that
inhibit cyclooxygenase have anti-inflammatory activity). Drugs
designed to inhibit enzymes unique to a microorganism will produce
few side effects in patients [Link] drugs are used [Link] they inhibit
folic acid synthesis in bacteria, while humans do not synthesise folic
acid..

Three (3) major types of reversible enzyme inhibition are competitive,

uncompetitive and non competitive inhibition. They can be
experimentally distinguished by the effects of the inhibitor on the
reaction kinetics of the enzyme, which may be analysed in terms of the
basic Michaelis Menten rate equation.

Competitive Inhibition

Here, the inhibitor combines with the free enzyme in such a way that it
competes with the normal substrate for binding at the active site. It
reacts reversibly with the enzyme to form an enzyme-inhibitor complex
(EI), analogous to the ES complex.

E+I ↔EI

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A competitive inhibitor diminishes the rate of catalysis by reducing the

proportion of enzyme molecules that have a bound substrate.

The inhibitor constant Ki can be defined as the dissociation constant of

the EI complex i.e

Ki= [E][I]/[EI]

The classic example of competitive inhibition is the inhibition of

succinate dehydrogenase by malonate and other dicarboxylate anions.
SDH is one of the enzymes responsible for the reactions of the TCA
cycle. It catalyzes the removal of 2 hydrogen atoms from the 2
methylene carbon atoms of [Link] competitive inhibitor
malonate resembles succinate in having 2 ionised carboxyl groups at PH
[Link] malonate other dicarboxylate anions e.g oxalate and
oxaloacetate may act as inhibitors of SDH.

The effect of a competitive inhibitor can be reduced or totally overcome

by increasing [S].In this type of inhibition, Km is increased while Vmax
remains the same.

COO-

CH2 Succinate

CH2

COO=
+
Hydrogen acceptor
succinate
dehydrogenase
COO-

CH
Fumarate
HC

COO-
+
Reduced hydrogen acceptor

Fig. 1: The Succinate Dehydrogenase Reaction

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COO-

CH2

COO-
Malonate

COO-

COO-
Oxalate

COO-

CH2

C O

COO-
Oxaloacetate

Fig. 2: Other Inhibitors of Succinate Dehydrogenase

Uncompetitive inhibition
Here, the inhibitor does not combine with the free enzyme or affect its
reaction with its normal substrate. Rather, it combines with the ES
complex to give an inactive ESI complex which cannot undergo further
reaction to yield the normal product
ES+ I↔ESI
Ki= [ES][I]/ [ESI]
Both Km and Vmx decrease in this type of inhibition. It is
common in two-substrate reactions.
Non competitive inhibition
A non competitive inhibitor can combine with either the free enzyme or
the ES complex, interfering with the action of both. Non competitive
inhibitors bind to a site on the enzyme different from the active site,
often to deform the enzyme so that it does not form the ES complex, and
if formed, it does not decompose at the normal rate to yieldproducts.
These effects are not reversed by increasing the substrate concentration.
In non competitive inhibition, the reaction with the inhibitor yields 2
inactive forms- EI and ESI

E+I↔EI
ES+I↔

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For which there are 2 inhibitor constants

KEI= [E][I]/ [EI]
KESI= [ES] [I]/ [ESI] which may or may not be equal.
Vmax is decreased while Km remains constant in this type of
inhibition.
Examples include the inhibition of enzymes that require metal
ions for activity by agents capable of binding the metal e.g EDTA
reversibly binds Mg2+ and other divalent cations and thus
noncompetitively inhibits some enzymes requiring such ions for
activity

3.2 Effects of Inhibitors on Lineweaver-Burk Plot

Fig. 3:

Fig 4

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Fig 5.

Table 1: Summary of the effects of Inhibitors on Lineweaver –

Burk plots 1/V0 vs 1/[S]

Slope Y-intercept
No inhibitor Km/Vmax 1/Vmax
Competitive Km/ Vmax(1+ [I]/Ki 1/Vmax
Uncompetitive Km/Vmax 1/Vmax(1+[I]/Ki
Noncompetitive Km/ Vmax(1+ [I]/Ki 1/Vmax(1+[I]/Ki

Irreversible Inhibition

Some enzymes undergo irreversible inactivation when they are treated

with agents capable of covalently and permanently modifying a
functional group required for catalysis, making the enzyme molecule
inactive. This type of inhibition cannot be treated by M.M principles.
Often, the inhibition sets in slowly compared with the normal reaction
kinetics of the enzyme, so that the inhibition is incomplete at first but
continuously increases with time because chemical modification of an
increasing fraction of the enzyme molecule takes place. E.g alkylating
agents such as iodoacetamide irreversibly inhibit the catalytic activity of
some enzymes by modifying essential cysteine residues. Heavy metals,
such as mercury and lead salts, also inhibit sulfhydryl enzymes. Eggs or
egg-white are sometimes administered as an antidote for accidental
ingestion of heavy metals: the egg white protein, ovalbumin is rich in

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sulfhydryl groups, traps the free metal ions and prevents their absorption
from the GIT.

In many cases, irreversible inhibitors are used to identify active site

residues involved in enzyme catalysis and to gain insight into the
mechanism of enzyme action. By sequencing the protein, it is possible to
identify the specific amino acid residue modified by the inhibitor and
involved in catalysis.

3.3 Regulation of Enzyme Activity

Some enzymes possess special properties which endow them with

regulatory roles in metabolism. Such enzyme forms are called regulatory
enzymes. There are 2 major types of regulatory enzymes- allosteric
enzymes and covalently modulated enzymes.

Allosteric regulation

Here, the catalytic site of the enzyme is modulated through the non
covalent binding of a specific metabolite at a site on the protein other
than the catalytic site. Most enzymes which are subject to such
modification are rate-determining enzymes in metabolic pathways.
Metabolites that bind at the allosteric site are called allosteric effectors,
modifiers or modulators. Those that enhance the protein's activity are
referred to as allosteric activators, whereas those that decrease the
protein's activity are called allosteric inhibitors. The term allosteric
comes from the Greekallos , "other", and stereos , "solid (object)", in
reference to the fact that the regulatory site of an allosteric protein is
physically distinct from its active site. The allosteric site at which the
positive inh binds is referred to as an activator site while the negative
inh binds at an inhibitory site. When an allosteric enzyme has only one
specific modulator, it is said to be monovalent. Others which respond to
2 or more modulators, each bound to a specific site on the enzyme
molecule are polyvalent. Most allosteric enzymes are oligomerici.e they
consist of several subunits. They consist of 2 or more polypeptide chain
subunits, usually in an even number. Allosteric enzymes usually exhibit
sigmoidal (S-shaped) kinetic curves rather than simple hyperbolic
curves. Activators of allosteric enzymes shift the V vs S curve to the
left, whereas allosteric inhibitors shift the curve to the right. A
homotropic allosteric modulator is a substrate for its target enzyme, as
well as a regulatory molecule of the enzyme's activity. It is typically an
activator of the enzyme. On the other hand, a heterotropic allosteric
modulator is a regulatory molecule that is not also the enzyme's
substrate. It may be either an activator or an inhibitor of the enzyme.

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End Product inhibition

There are many instances in which the final end product of a

multienzyme metabolic pathway is an allosteric inhibitor of an enzyme
that catalyzes an early and irreversible step of the pathway. This form of
allosteric regulation prevents accumulation of additional end product
and of metabolic intermediates once a cell has sufficient supplies of that
metabolic end product. An example of this is Aspartate
transcarbomylase, the enzyme that catalyzes the first reaction unique to
pyrimidine [Link] enzyme is a multi subunit protein
complex composed of 12 subunits (C6R6) forming 2 trimers of catalytic
subunits and 3 dimers of regulatory subunits. It is feed-back inhibited
by the end product of the pyrimidine pathway, CTP . Following
treatment with mercurials, ATCase loses its sensitivity to inhibition by
CTP but retains its full activity for synthesis of carbamoyl aspartate.
This suggests that CTP is bound at a different site from the substrate.

Fig. 6: Allosteric Regulation

Covalently modulated regulatory enzymes

Here, active and inactive forms of the enzyme are interconverted by

covalent modifications of their structure, catalyzed by other enzymes. A
typical example is glycogen phosphorylase which catalyzes the
breakdown of glycogen to yield Glucose 1 –phosphate
(Glucose)n + Pi ↔ (Glucose)n-1 + Glucose1 –Phosphate

The enzyme occurs in 2 forms- phosphorylase a, the more active form

and Phosphorylase b, the less active form. A is converted to b through
hydrolytic removal of phosphate groups attached to 4 serine residues
contained in each of its subunits, brought about by the action of
phosphorylase phosphatase. The b form can be reactivated to a form by
the enzyme phosphorylase kinase. Thus, the activity of the enzyme is
regulated by the action of 2 enzymes that shift the balance bw its active
and inactive forms. Generally, many protein kinases regulate the activity
of enzymes and other proteins by phosphorylation-dephosphorylation of
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serine, threonine or tyrosine residues on the proteins. Other groups

including sulphate and acetate can also be added to an enzyme to alter
its activity. Covalent modification is an effective and rapid way of
controlling the activity of a protein or enzyme.

Another way by which enzyme activity is regulated is the enzyme-

catalyzed activation of inactive precursors of enzymes (zymogens) to
yield the catalytically active forms as is found in the digestive enzymes
pepsinogen, trypsinogen and chymotrypsinogen. These enzymes are
converted into their active forms by the selective hydrolytic cleavage of
one or more specific -`peptide bonds in the zymogen molecule as
follows.

Pepsinogen→ Pepsin + Peptides (catalyzed by pepsin)

Trypsinogen →Trypsin + hexapeptides (catalyzed by enterokinase)
Chymotrypsinogen→ Chymotrypsin + 2dipeptides (catalyzed by
trypsin)

This type of covalent regulation proceeds in only one direction i.e the
enzymes cannot be converted back to their respective zymogens.

3.4 Clinical Applications of Enzymes

Many tissues produce enzymes that are relatively cell-specific. Because

these enzymes are released into the circulation as a result of tissue
damage, assays of the levels of certain enzymes in blood can provide
useful diagnostic [Link] example, ALT and AST are present in
high concentrations in hepatocytes. When these cells are injured e.g by
viral hepatitis or drug overdose, ALT and AST are released into the
blood. Several other enzymes serve as tissue specific markers of cellular
injury.

Isozymes are also very important in diagnosis. These are multiple forms
of a given enzyme that occur within a single species of an organism or a
single cell. They differ in amino acid composition and thus in their
isoelectric properties. They can be separated from each other by
electrophoresis. They also differ in their kinetic parameters and their
physical properties. Isozymes with wide clinical applications include
Lactate dehydrogenase, creatine kinase and Alkaline phosphatase. LDH
occurs as 5 different isozymes in the tissues of vertebrates. They all
catalyze the reaction

Lactate + NAD+ ↔Pyruvate + NADH + H+

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They have the same molecular weight and all contain 4 polypeptide
chains. They consist of 5 different combinations of 2 types of PP chains
designated M and H as follows

Type

Type Composition Location

LDH1 H4 Myocardium and Rbcs
LDH2 H3M ,, ,,
LDH3 H2M2 Brain and Kidney
LDH4 HM3
LDH5 M4 Liver and skeletal muscle

Although they catalyze the same reaction, they differ significantly in

their Km and Vmax values for substrates , particularly pyruvate . M4
has a relatively low Km for pyruvate while H4 has the highest Km for
this substrate. The others have kinetic properties that are intermediate
bw those of the M4 and H4 isozymes, in proportion to their relative
content of M and H chains. These characteristics provide insight into the
function of the isozymes. Skeletal muscle and embryonic tissue tend to
utilise glucose anaerobically and break it down to form lactate. Thus, the
M4 isozyme is well adapted to convert pyruvate rapidly to Lactate.
Heart muscle on the other hand does not normally form Lactate from
[Link] isozymes are important in the diagnosis of heart and liver
disease. Normally, blood contains little LDH1, but the level increases
after a myocardial infarction. Increase in LDH5 is indicative of a
secondary liver damage in the patient. Thus, measurement of these
isozymes allows monitoring of secondary complications of heart failure.
Table 12.4 Serum enzymes used in clinical diagnosis

Serum Enzyme Major Diagnostic Use

AST Myocardial infarction,

ALT Viral Hepatitis

Α-Amylase Acute Pancreatitis

Ceruloplasmin Hepatolenticular degeneration

(Wilson’s disease)
Creatine Kinase Muscle disorders and myocardial
infarction

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γ-Glutamyl transpeptidase Various Liver diseases

LDH isozymes Myocardial infarction

Lipase Acute Pancreatitis

Acid phosphatase Prostate Cancer

Alkaline Phosphatase isozymes Various bone disorders,

obstructive liver diseases.

4.0 CONCLUSION

Many compounds can bind to enzymes and in the process, significantly

alter or destroy the activity of the enzyme. Molecules that inhibit or alter
the activity of enzymes are called inhibitors. Enzyme inhibition can be
reversible or irreversible. An inhibitor can bind to an enzyme reversibly
or irreversibly. A reversible inhibitor binds to an enzyme but then
enzyme activity is restored when the inhibitor is released. On the other
hand, an irreversible inhibitor covalently binds to an enzyme,
permanently destroying its activity. Many tissues produce enzymes that
are relatively cell-specific. Because these enzymes are released into the
circulation as a result of tissue damage, assays of the levels of certain
enzymes in blood can provide useful diagnostic information.

5.0 SUMMARY

• Enzyme inhibition can be reversible or irreversible.

• An inhibitor can bind to an enzyme reversibly or irreversibly.
• A reversible inhibitor binds to an enzyme but then enzyme
activity is restored when the inhibitor is released. On the other
hand, an irreversible inhibitor covalently binds to an enzyme,
permanently destroying its activity.
• Isozymes are also very important in diagnosis

6.0 TUTOR- MARKED ASSIGNMENT

1. Distinguish the different types of reversible enzyme inhibition

with specific examples and explain the use of enzyme inhibitors
in drug design.
2. Enumerate the effects of the different types of inhibitors on
Lineweaver-Burk plots

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3. Explain the regulatory roles of allosteric enzymes, covalently

modulated enzymes and isoenzymes.
4. Give examples of enzymes used in clinical diagnosis and their
diagnostic importance.

7.0 REFERENCES/FURTHER READING

Murray, R.K., Bender, D.A., Botham, K. M., Kennelly, P.J., Rodwell

V.W. & Well, P.A., (2012). Harper’s Illustrated Biochemistry.
(29th ed.). McGraw-Hill Medical.
Devlin, T.M. (2010). Textbook of Biochemistry with Clinical
Correlation. (7th ed.). John Wiley & Sons Inc.

Nelson, D.L. & Cox, M.M. (2009). Lehninger Principles of

Biochemistry. (4th ed.).

Davis, Jack. 2019. An Introduction to Enzyme Kinetics. News-Medical,

viewed 25 August 2021, [Link]
sciences/[Link].

Factors Affecting Enzyme Activity: 6 Factors ([Link])

retrieved August 28, 2021

"Enzymes: Figure 3 (Opens in a new window)," by OpenStax College,

Biology, CC BY 3.0._)

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