CELL STRUCTURE

AND
FUNCTION (CSF-0211)
Class of 2022
January 22 - February 24, 2018

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Introduction

Welcome to the Cell Structure and Function (CSF) module! It is a five weeks
module. This module will introduce you to the basic functioning of the ‘generic’ cell,
how a single cell (zygote) divides, grows and differentiates into a complete human
being. You will learn the structure and functions of the molecules that make up a cell
and how dysfunctions in these molecules can lead to disease. This part of the module
also highlights the role of molecular biology in medicine, both in diagnostics and
therapeutics. The sessions taught during this module will incorporate the general
embryological, physiological, biochemical, anatomical, pharmacological and pathological
aspects of the topic. The research methodology, communication skills and ethics will be
taught as a part of the longitudinal theme. The basic concepts of community medicine
will also be addressed in relation to the themes of the module.

You will be learning most topics in relation to clinical vignettes/cases. These are
used to create an awareness of the clinical relevance of a topic and emphasize why it is
important for you as medical students to know the Basic Sciences. Although all topics
are studied with reference to a particular disease you must extrapolate the basic
concepts you learn to other diseases as well. The learning objectives for each session
are given in this guide to help you direct your learning efforts appropriately and
recognize the knowledge/skill you should have acquired at the end of your learning
session.

When you look at the time table for this module you will notice that the
mode of instruction is going to be multi-pronged with small group discussions (SGDs),
large group discussions/large group interactive sessions (LGDs/LGISs) and practical
sessions. You will be assigned tasks and given time for preparation either in self-directed
learning (SDL) sessions or at home. The group allocations and venues for SGDs will be
posted on your notice boards. Please make it a habit to check these well in time – “I
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didn’t see the notice” should not be an excuse for coming late or unprepared to an SGD.
Many SGDs are preceded by an overview on that topic or followed by large group wrap-
up sessions. The wrap-up sessions are held to reinforce key concepts and allow you to
clarify any point that may still be unclear to you after your SGD. Do not be afraid to ask
questions in class.

Assessments

You will be assessed through formative as well as summative assessments. Make sure
that you attend these sessions. These will help you prepare for the end of module
exams. Summative assessment will be done at the end of the module and will comprise
of MCQs and SAQs. Skills will be assessed in Block IPE.

Integrated Practical Examination (IPE)

IPE is the assessment of your skills. It pertains to identification of gross structures on

cadavers/models/ specimens, history taking, performing simple lab procedures,
demonstration of clinical methods, identifications of specimens/ tissue sections,
interpretation of lab reports and counseling. Each IPE station consists of a case scenario
and a couple of tasks that you are required to perform. Some stations are observed
where an examiner observes you performing the task. Some would be interactive and
some would be just performance in isolation. While preparing for IPEs you must identify
the skill part of your text within the themes of the curriculum and practice them. While
attempting the IPEs, read the case carefully before performing the task as the two are
interrelated.

If you want to succeed you will have to take responsibility for yourselves, set your
priorities and spend your time wisely. Good luck!!

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 CSF Themes

It is mainly divided into 7 themes. Each theme is taught in relation to clinical

cases/vignettes. These are used to create an awareness of the clinical relevance of a
topic. Theme 6 and 7 will be taught longitudinally throughout the module. The themes
are as follows:

1- Basic Cellular Organization in health and disease

2- The Central Dogma of Molecular Biology
3- Molecular Basis of Disease
4- Molecular Biology in Therapeutics
5- Molecular Biology in Diagnostics
6- Physical Development - Cell Growth and Differentiation
7- Longitudinal theme

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1. Basic Cellular organization in health and disease
 Correlate the structure of various components of the cell membrane with their
functions
 Describe the chemical nature of macromolecules (lipids, proteins, carbohydrates
and nucleic acids)
 Discuss the properties of enzymes and the conditions that affect enzymatic
reactions
 Differentiate among the major types of enzyme inhibition with reference to
enzyme kinetics
 Explain the importance of enzymes in diagnostics and therapeutics
 Correlate the structure of cell organelles with their function
 Describe the role of glycocalyx as “Receptors”. Illustrate the mechanism of
 Intracellular Signaling with examples ( including Ion Channel-Linked Receptors; G
Protein-Linked Hormone Receptors; Enzyme-Linked Hormone Receptors;
Intracellular Hormone Receptors; Second Messenger Mechanisms including
Adenylyl Cyclase-cAMP Second Messenger System; Membrane Phospholipid
Second Messenger System and Cell Calcium-Calmodulin Second Messenger
System)
 Differentiate between the mechanisms by which various substances are
transported across the cell membrane.
 Discuss transport of drugs across body membranes and explain the importance of
these mechanisms in various clinical abnormalities
2. The Central Dogma of Molecular Biology
 Explain the process of DNA replication

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 Describe the major steps in transcription of RNA. Correlate the post
transcriptional modifications of mRNA to their function
 Differentiate among the major classes of RNA on the basis of structure and
function
 Describe the major steps of protein synthesis and correlate the action of various
antibiotics
 Explain various mechanisms for the regulation of gene expression
 Correlate the structure and function of cell modifications with clinical
abnormalities
3. Molecular Basis of Disease
 Correlate different types of mutations with their effect on DNA sequence and
cellular function
 Explain how DNA damage leads to mutations if unrepaired and how defects in
DNA repair lead to cancer prone genetic disorders (e.g. XP and HNPCC)
 Identify the chromosomal aberrations leading to birth defects
 Explain the effects of environmental factors on cell function
 Differentiate between heterozygotes and homozygotes; recessive and dominant
alleles; mutations and polymorphisms; genotype and phenotype
 Draw a 3-generation pedigree using standard pedigree symbols
 Analyze pedigrees to determine their mode of inheritance (autosomal recessive,
autosomal dominant, X-linked recessive, X-linked dominant, Y-linked and
mitochondrial)
 Demonstrate the basic skills of genetic counseling in an accurate, non-directive,
sensitive manner without coercion or personal prejudice

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4. Molecular Biology in Diagnostics
 Explain the theory of polymerase chain reaction (PCR) and give examples of its
use in clinical practice
 Describe various assays used in genetic testing
 Explain the application if molecular biology in assessing fetal health
 Discuss the use of DNA microarrays in gene expression analysis and mutation
screening
 Describe the use of DNA as a tool in forensics
5. Molecular Biology in Therapeutics
 Describe the different types of gene therapies and identify associated risks and
challenges
 Explain the role of short interfering RNAs (siRNAs) in fighting diseases
 Describe the use of cloning techniques for the production of therapeutic agents
(recombinant DNA technology)
 Explain the potential of stem cell therapy in curing disease
 Identify the ethical issues in cloning and stem cell research. State the Islamic
Shariah guidelines in this context
 Debate the pros and cons of ‘personalized medicine’
6. Physical development – Cell Growth and Differentiation

 Explain cell cycle and cell division

 Describe the processes of gametogenesis, fertilization & implantation
 Correlate the process of gastrulation and neurulation and their aberrations with
associated congenital defects
 Correlate the mechanism of folding with its consequences
 Enumerate the subdivisions of germ layers and their derivatives
 Describe the embryonic changes in the organogenetic period

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 Explain the regulation of gene expression with relation to embryological
development
 Correlate the effect of gross chromosomal aberrations (structural and numerical)
to human development
 Explain the basis and applications of diagnostic techniques employed for assessing
fetal health
7. Longitudinal Theme

 Understand the basic concepts to research Methodology/Steps of research

 Demonstrate the 7 Cs of Communication, non-verbal communication, barriers of
communication
 Demonstrate the active & passive listening, barriers to effective listening,
neighbor’s model of listening at 2 levels
 Explain the basic concepts of Epidemiology
 Describe the epidemiology of Infectious Diseases
 Explain the health Indicators
 Identify the indicators of Morbidity & Mortality

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Glossary-Embryology
 All descriptions of the adult are based on the assumption that the body is erect,
with the upper limbs by the sides and the palms directed anteriorly
 This is the anatomical position.
 The terms anterior or ventral and posterior or dorsal are used to describe the
front or back of the body or limbs and the relations of structures within the body
to one another.
 When describing embryos, the terms dorsal and ventral are used
 Superior and inferior are used to indicate the relative levels of different
structures
 For embryos, the terms cranial or rostral and caudal are used to denote
relationships to the head and caudal eminence (tail), respectively
 Distances from the source or attachment of a structure are designated as
proximal or distal.
 In the lower limb, for example, the knee is proximal to the ankle and the ankle is
distal to the knee. The median plane is an imaginary vertical plane of section that
passes longitudinally through the body.
 Median sections divide the body into right and left halves
 The terms lateral and medial refer to structures that are, respectively, farther
from or nearer to the median plane of the body
 A sagittal plane is any vertical plane passing through the body that is parallel to
the median plane
 A transverse (axbial) plane refers to any plane that is at right angles to both the
median and coronal planes

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  A frontal (coronal) plane is any vertical plane that intersects the median plane at
a right angle and divides the body into anterior or ventral and posterior or dorsal
parts.

EMBRYONIC TERMINOLOGY

 Oocyte (L. ovum, egg). The female germ or sex cells are produced in the ovaries.
When mature, the oocytes are called secondary oocytes or mature oocytes.
 Sperm (Gr. sperma, seed). The sperm, or spermatozoon, refers to the male germ
cell produced in the testes (testicles).
 Zygote This cell results from the union of an oocyte and a sperm during
fertilization. A zygote or embryo is the beginning of a new human being.

Gestational Age

 Difficult to determine exactly when fertilization (conception) occurs because the

process cannot be observed in vivo (within the living body).The age of the embryo
or fetus is calculated from the presumed first day of the last normal menstrual
period.
 This is the gestational age, which is approximately 2 weeks longer than the
fertilization age because the oocyte is not fertilized until approximately 2 weeks
after the preceding menstruation

Cleavage

 A series of mitotic cell divisions of the zygote that result in the formation of early
embryonic cells, blastomeres.
 The size of the cleaving zygote remains unchanged because at each succeeding
cleavage division, the blastomeres become smaller

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Morula (L. morus, mulberry)

 Solid mass of 12 to approximately 32 blastomeres formed by cleavage of a zygote.

 Blastomeres change their shape and tightly align themselves against each other to
form a compact ball of cells[compaction]

Blastocyst (Gr. blastos, germ + kystis, bladder)

 After 2 to 3 days, the morula enters the uterus from the uterine tube (fallopian
tube).
 Soon a fluid-filled cavity, the blastocystic cavity, develops inside it
 This change converts the morula into a blastocyst

Implantation

 The process during which the blastocyst attaches to the endometrium, the
mucous membrane or lining of uterus, and subsequently embeds in it

Gastrula (Gr. gaster, stomach)

 During gastrulation (transformation of a blastocyst into a gastrula), a three-

layered or trilaminar embryonic disc forms (third week).
 The three germ layers of the gastrula (ectoderm, mesoderm, and endoderm)
subsequently differentiate into the tissues and organs of the embryo

Neurula (Gr. neuron, nerve)

 It is the early embryo during the third and fourth weeks when the neural tube is
developing
 It is the first appearance of the nervous system and the next stage after the
gastrula

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Embryo (Gr. embryon)

 The term refers to the developing human during its early stages of development.
 The embryonic period extends to the end of the eighth week (56 days), by which
time the beginnings of all major structures are present

Conceptus (L. conceptio, derivatives of zygote)

 It means the embryo and its adnexa (L., appendages or adjunct parts) or
associated membranes (i.e., the products of conception). The term includes all
structures that develop from the zygote, both embryonic and extraembryonic.
 Hence, it includes the embryo as well as the embryonic part of the placenta and
its associated membranes: amnion, chorionic (gestational) sac, and umbilical
vesicle or yolk sac

Primordium (L. primus, first + ordior, to begin)

 The term refers to the beginning or first discernible indication of an organ or

structure. The terms anlage and rudiment have similar meanings.

Fetus (L., unborn offspring)

 After the embryonic period (8 weeks) and until birth, the developing human is
called a fetus.
 During the fetal period (ninth week to birth), differentiation and growth of the
tissues and organs formed during the embryonic period occur
 Changes occurring during the embryonic period are very important because they
make it possible for the tissues and organs to function.
 The rate of body growth is remarkable, especially during the third and fourth
months and weight gain is phenomenal during the terminal months.

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Abortion (L. aboriri, to miscarry)

 It is a premature stoppage of development and expulsion of a conceptus from the

uterus or expulsion of an embryo or fetus before it is viable-capable of living
outside the uterus.
 An abortus is the products of an abortion (i.e., the embryo/fetus and its
membranes

Types of abortion

 Threatened abortion (bleeding with the possibility of abortion) is a complication

in approximately 25% of clinically apparent pregnancies.
 Despite every effort to prevent an abortion, approximately half of these concepti
ultimately abort.
 A spontaneous abortion is one that occurs naturally and is most common during
the third week after fertilization. Approximately 15% of recognized pregnancies
end in spontaneous abortion, usually during the first 12 weeks
 A habitual abortion is the spontaneous expulsion of a dead or nonviable embryo
or fetus in three or more consecutive pregnancies.
 An induced abortion is a birth that is medically induced before 20 weeks (i.e.,
before the fetus is viable).
 This type of abortion refers to the expulsion of an embryo or fetus induced
intentionally by drugs or mechanical means
 A complete abortion is one in which all the products of conception are expelled
from the uterus.
 A missed abortion is the retention of a conceptus in the uterus after death of the
embryo or fetus.

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  A miscarriage is the spontaneous abortion of a fetus and its membranes before
the middle of the second trimester

Trimester

 It is a period of three calendar months during a pregnancy.

 Obstetricians commonly divide the 9-month period of gestation into three
trimesters.
 The most critical stages of development occur during the first trimester (13
weeks) when embryonic and early fetal development is occurring.

Postnatal Period

 It is the period occurring after birth.

Infancy

 It refers to the earliest period of extra uterine life-roughly the first year after
birth.
 An infant aged 1 month or younger is called a newborn or neonate

Childhood

 The period from approximately 13 months until puberty

Puberty

 Occurs usually between the ages of 12 and 15 years in girls and 13 and 16 years in
boys
 Secondary sexual characteristics develop and the capability of sexual
reproduction is attained.

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  Pubertal development follows a consistent pattern and is defined by the
appearance of secondary sexual characteristics (e.g., pubic hair development,
breasts in females, and growth of external genitalia in males
 It ends in females with the first menstrual period or menarche, the beginning of
the menstrual cycles or periods.
 It ends in males when mature sperms are produced

Adolescence

 The period from approximately 11 to 19 years of age, this is characterized by

rapid physical and sexual maturation.
 It extends from the earliest signs of sexual maturity-puberty-until the attainment
of adult physical, mental, and emotional maturity.
 The ability to reproduce is achieved during adolescence.
 The general growth rate decelerates as this period terminates, but growth of
some structures accelerates (e.g., female breasts and male genitalia).

Adulthood (L. adultus, grown up)

 Attainment of full growth and maturity

 It’s generally reached between the ages of 18 and 21 years.
 Ossification and growth are virtually completed during early adulthood (21 to 25
years).
 Thereafter, developmental changes occur very slowly

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 RECOMMENDED BOOKS

 Textbook of Human Physiology

(Guyton and Hall)
 Biochemistry – Lippincott’s Illustrated Reviews
(Champe, Harvey and Ferrier)
 Marks’ Essentials of Medical Biochemistry – A Clinical Approach (Lieberman,
Marks and Smith)
 Harper’s Illustrated Biochemistry
(Murray, Bender, Botham, Kennelly, Rodwell and Weil)
 Emery’s Elements of Medical Genetics 13th Edition
(Turnpenny and Ellard)
 The Developing Human: Clinically Oriented Embryology
(Moore and Persaud)
 Park Text Book of Community Medicine

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 Time Table
The time table for each week will be
available in the Dropbox and your notice
boards

Student distribution and location for small

group discussions will also be posted on
these notice boards

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 ICONS

This icon indicated the beginning of a new vignette/case.

This icon identifies the learning objectives associated with

each vignette.

This icon represents definitions of some medical terminology

given in the vignettes that may currently be unfamiliar.

This icon is for the questions that are given with each vignette.
You will not find the answers to these questions in
your text books. These will (hopefully) help you to think and
reason critically.

Recommended reading

This icon indicates skill sessions

This icon is for the self-assessment exercises given in the guide

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 Note!

Although all topics are being studied

with reference to a particular disease
you must extrapolate the basic
concepts you learn to other diseases as
well

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 Theme 1

Basic Cellular organization

In health and disease

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 Vignette 1:

A 55yrs old man presents with increasing fatigue, 15 pound weight loss,
and microcytic anemia. Colonoscopy identifies a mass in the ascending colon and biopsy
specimens reveal well-differentiated colorectal cancer (CRC). The mass was surgically
removed. The patient was started on a combination of 5-flourouracil, leucovorin and
oxaliplatin as adjuvant therapy. One week after receiving the first cycle of therapy, he
experiences significant toxicity in the form of bone marrow suppression, diarrhea and
altered mental status.

Session: Cell Cycle

You should be able to know:

 What is cell cycle

 Describe the stages of cell cycle
 Explain the checkpoints to regulate cell cycle
 Relationship of cell cycle with cell division

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 Vignette 2

A recently married lady with previously regular menstrual periods

consulted her family physician after she had missed her menstrual period.
She was feeling nauseous early morning and had vomited after breakfast
on a few occasions

Theme 6: Physical Development - Cell Growth and Differentiation

Embryology Session 1: Male Reproductive System

The student should be able to describe:

 Developmental periods – abortion

 Descriptive terms in embryology
 Basic anatomy of components of male reproductive system
 Location of testis
 Location and names of intratesticular and extratesticular ducts
 Cells seen in seminiferous tubules and in interstitial tissues of testis
 Origin of primordial germ cells and their migration
 Phases of spermatogenesis and changes seen in each phase
 Changes occurring during spermiogenesis

 What normal condition would you suspect in this case and how
would you confirm this?
 What are the various proposed explanations for early morning
sickness in such
cases?

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Theme 6: Physical Development - Cell Growth and Differentiation

Embryology Session 2: : Female reproductive System, Oogenesis,

Menstrual Cycle

The student should be able to describe

 Components of female reproductive system
 Basic anatomic features of ovaries, uterine tubes, uterus and cervix
 Histologic features of endometrium
 Origin and fate of oogonia
 Formation and growth of ovarian follicles- distinguishing features of different
ovarian follicles
 Correlate gametogenesis with various aberrations
 Phases of menstrual cycle
 Histological changes seen in uterine endometrium during menstrual cycle
 Correlation between ovarian and menstrual cycle
 Factors involved in process of ovulation
 Ovulation and its consequences
 Composition, function and fate of corpus luteum

Theme 6: Physical Development - Cell Growth and Differentiation

Embryology Session 3

The student should be able to describe

 Capacitation and acrosome reaction in sperm
 Viability and transport of gametes
 The fate of the female gamete if it is not fertilized
 The process of fertilization, its phases/stages and its correlation with possible
outcomes

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 The hormonal basis of the pregnancy test
 Conversion of zygote into blastocyst
 Changes in endometrium prior to implantation- decidua reaction
 The normal and abnormal sites of implantation of blastocyst with their
outcome
 Formation of bilaminar germ disc
 The normal and abnormal sites of implantation of blastocyst with their
outcome
 Functions of syncytiotrophoblsts
 Changes in endometrium and blastocyst in 2nd week

Identify components of conceptus during 2nd week of development?

What normal condition would you suspect in this case and how would you
confirm this?
What are the various proposed explanations for early morning sickness in such
cases?

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TEST YOURSELF!

VOCABULARY – Cell division

a. Meiosis 1. X and Y
Chromosomes that do not differ
b. gametes 2.
between the sexes
One of the two identical halves of a
c. Karyotype 3.
replicated chromosome
Microtubule organizing centers at the
d. Mitosis 4.
spindle poles
e. Interphase 5. Cells in the testes that undergo meiosis
f. Syncytium 6. Division of the cytoplasm
Haploid germ cells that unite at
g. Synapsis 7.
fertilization
An animal cell containing more than one
h. Sex chromosomes 8.
nucleus
i. Cytokinesis 9. Pairing of homologous chromosomes
One diploid cell gives rise to two diploid
j. Anaphase 10.
cells
The array of chromosomes in a given
k. Chromatid 11.
cell
The part of the cell cycle during which
l. Autosomes 12.
the chromosomes are not visible
One diploid cell gives rise to four
m. Centromere 13.
haploid cells
Cell produced by meiosis that does not
n. Centrosomes 14.
become a gamete
The time during mitosis when sister
o. Polar body 15.
chromatids separate
p. Spermatocytes 16. Connection between sister chromatid

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 Vignette 3

Introduction: A 2 year old boy.

Presenting complaint: Chronic productive cough not responding to

antibiotics.

Medical history: Abdominal distention, failure to pass stool, and vomiting (emesis) as
an infant. He continues to have bulky, foul-smelling stools.

Family history: Several relatives with chronic lung and “stomach” problems, and some
died at a young age.

Examination: Ill appearing, slender male in moderate distress. No fever. No diarrhea.

Desquamating skin lesions present on his legs. The lung exam reveals poor air
movement in the base of lungs bilateral and a coarse rattling sound (crepitating)
throughout both lung fields.

Investigations: Positive chloride sweat test.

Diagnosis: Cystic fibrosis (CF).

Genetic analysis: DNA analysis reveals the presence of the deltaF508 mutation in the
CFTR gene (deletion of phenylalanine at position 508 of the CFTR protein).

Emesis = vomiting

Crepitation = a coarse rattling sound like that of grating the ends of a fractured
bone

Session: Structure and functions of the cell membrane

You should be able to

 Correlate the structure of various components of the cell membrane

(lipids, proteins and carbohydrates) with their functions

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 Textbook of Human Physiology (Guyton and Hall)

Session: Amino Acids/Protein structure

You should be able to

 Classify amino acids on the basis of their side chains.

 Differentiate between essential and non-essential amino acids
 Describe the nature of the peptide bond
 Describe the four levels of protein structure (primary, secondary, tertiary and
quaternary) and the types of chemical bonding involved
 Appreciate the structure- function correlation of proteins with reference to
disease.
 State the energy content of 1 gm of protein

Recommended Reading:

Lippincott’s Illustrated Reviews - Biochemistry

Session: The chemical nature of lipids

At the end of this session you should be able to

 Define lipids
 Classify lipids in the basis of structure
 Enlist functions of lipids and dietary fats
 State the energy content of 1 gm of fat
 Differentiate between
- Saturated and unsaturated fatty acids
- Cis and trans fatty acids
- Omega 3 and omega 6 fatty acids
- Essential and non-essential fatty acids
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 Lippincott’s Illustrated Reviews - Biochemistry 5/6th Edition

Harper’s Illustrated Biochemistry- 29th Edition

CF is one of the most common, severe genetic disease found in Caucasian

populations. It has an incidence of 1 in 2500 and carrier frequency of 1 in 25.

Given that the median life expectancy of a CF patient is the mid-30s, can you think of
why CF would have such a high incidence in these populations?

Vignette 4

Introduction: A 3 week premature baby boy born to a diabetic mother by

cesarean section.

Presenting complaints: Bluish discoloration of the skin and mucus membranes

(cyanosis) with apnea.
Examination: Unusual breathing movement -- drawing back of chest muscles with
breathing. APGAR score less than 5
Investigations: lecithin/sphingomyelin ratio of amniotic fluid at 34th week of gestation
= 1.2
Laboratory investigations: Blood gas analysis of baby indicates low oxygen and excess
acid in the body fluids. Blood culture negative for infection.
Diagnosis: Acute respiratory distress syndrome (ARDS)/ Infant respiratory distress
syndrome (IRDS)
Apnea: brief stop in breathing

APGAR score: quick method to assess the health of a newborn, 1-5 minutes after

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birth. Based on Breathing effort, Heart rate, Muscle tone, Reflexes, Skin color. Scores 3
and below = immediate lifesaving measures required, 4 to 6 =some measures to aid
breathing may be required, 7 to 10 = normal.

Session: Structure, function and distribution of complex lipids

For this session you should focus on the

 classification of complex lipids on the basis of their chemical structure

 distribution and functions of complex lipids
 basis of various clinical disorders (ARDS, Niemann-Pick disease, lysosomal storage
diseases) associated with abnormalities in the degradation of complex lipids
IMPORTANT: You do not need to learn the synthesis of these lipids

Lippincott’s Illustrated Reviews - Biochemistry

Complex Lipid Metabolism, 6th Edition – Chapter 17

Is the amniotic fluid LS ratio a routine test carried out in all pregnant women or
is there a reason why the LS ratio was investigated in this case of this pregnant mother?

Can you think of factors that would affect the incidence of IRDS in a population?

Vignette 5

Introduction: 18 year old exchange student from Nigeria.

Presenting complaint: Bloating, abdominal cramps and intermittent

diarrhea ever since arriving in Pakistan 3 months earlier.

These symptoms appear about an hour after consuming breakfast & disappear when
dairy products are removed from her diet.

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Laboratory investigation: Hydrogen breath test positive

Diagnosis: Secondary lactose intolerance

Advice: She was advised to avoid dairy products and to take a tablet containing lactase
in case she did eat any product containing milk.

Session: Chemical nature of carbohydrates

At the end of this session you should be able to
 Define and classify carbohydrates
 Differentiate between isomers, epimers and enantiomers of
carbohydrates
 Explain the biological importance of monosaccharides, disaccharides and
polysaccharides
 Explain glycosides and glycosidic bonds
 State the energy content of 1 gm of carbohydrate

Harper’s Illustrated Biochemistry

Lippincott’s Illustrated Reviews - Biochemistry

What possible significance does the student’s race have in this scenario? Can you think
of reasons why distribution of diseases would show racial or ethnic differences? Which
do you think came first during human evolution, lactose tolerance or lactose
intolerance?
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Session: Cell signaling

 Describe the role of glycocalyx as “Receptors”.

 Illustrate the mechanism of Intracellular Signaling with examples including
- Ion Channel-Linked Receptors;
- G Protein-Linked Hormone Receptors;
- Enzyme-Linked Hormone Receptors;
- Intracellular Hormone Receptors;
- Second Messenger Mechanisms including cAMP Second Messenger
System; Membrane Phospholipid Second Messenger System and Cell
Calcium-Calmodulin Second Messenger System

Textbook of Human Physiology (Guyton and Hall)

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 Vignette 6

Presenting complaint: A 50 year old man complains of severe retrosternal

pain radiating to his left arm and jaw.
Medical History: Severe chest pain on exertion that is relieved by sitting down. He is
hypertensive and is on ACE inhibitors for the last two years
Examination: Anguished, dyspneic male, with hand clutched to chest. He is nauseated
and has vomited a few times.
Family History: His father died of a Myocardial Infarction and his younger brother is also
taking ACE inhibitors.
Investigations: EKG, CK-MB, LDH, Troponin I & T
Emergency treatment: Injection streptokinase
Diagnosis: Myocardial Infarction (MI)
Dyspnea = Shortness of breath; retrosternum= Behind the sternum (the
breastbone);

Myocardial Infarction = heart attack

Session: Chemical properties of enzymes

By the end of this session you should be able to explain

 Enzyme nomenclature
 Properties of enzymes
 Mechanism of enzyme action
 Factors that affect reaction velocity of enzymatic reactions

Lippincott’s Illustrated Reviews - Biochemistry

32
Session: Chemical properties of isoenzymes and the clinical applications of enzymes

By the end of this session you should be able to explain

 Recognize the importance of enzymes/isoenzymes (including LDH, CK,

ALT, AST, AP) in clinical diagnostics

Lippincott’s Illustrated Reviews - Biochemistry

Session: Enzyme Kinetics/Regulation of Enzyme Activity

At the end of this session you should be able to describe

 Enzyme kinetics based on the Michaelis-Menten equation

 Significance of Km and Vmax of a reaction
 Different types of enzyme inhibitors and their effect on enzyme kinetics
 Various mechanisms for the regulation of enzymatic reactions

Lippincott’s Illustrated Reviews – Biochemistry

33
 The following experimental data were collected during a study of the catalytic
activity of an intestinal peptidase with the substrate glycylglycine

Glycylglycine +H2O  2 Glycine

[S](mM) Product formed (umol/min)

1.5 0.21

2.0 0.24

3.0 0.28

4.0 0.33

8.0 0.40

16.0 0.45

Use graphical analysis to determine the Km and Vmax for this enzyme preparation.

34
 Vignette 7

Introduction: A young female 25 yrs of age gave birth to a baby boy in a

local hospital.

Presenting complaint: She complained to her gynecologist the next morning that her
tummy was still protruding, and that she was worried about this.

On examination: Her uterus was bulky.

She was told by the doctor that in a few weeks her uterus will regress back to normal
size.

Vignette 8

Introduction: A 16 year old boy with a history of inability to exercise due to

muscle weakness. There have also been episodes of hemianopia and mild
hemiparesis that lasted several days

Presenting complaint: headache, seizures and loss of vision

Family history: Maternal aunt suffered from a similar condition

Lab Investigations: Accumulation of lactic acid (lactic acidosis).

Other Investigations: Muscle mitochondria were isolated and respiratory complex one
was reduced. A point mutation in the mitochondrial DNA was identified

Diagnosis: Mitochondrial myopathy, encephalopathy, lactic acidosis and stroke-like

episodes (MELAS)

hemianopia: loss of vision in either the whole left or the whole right half of the
field of vision. hemiparesis: weakness on one side of the body

35
Session: Structure and function of cell organelles

The above cases are related to the functioning of only two of the major cell
organelles. However you must be able to describe

 the structure and function of all organelles found in the human cell (including
Mitochondria; Golgi apparatus; Lysosomes; Ribosomes; Peroxisomes;
Endoplasmic reticulum)

Textbook of Human Physiology (Guyton and Hall)

Vignette 9

Introduction: An unresponsive 25-year old woman, brought to the ER.

Presenting complaint: Her family members revealed that she had taken
three doses of “weight loss” pills. She developed headache, fever, chest pain, profuse
sweating and weakness soon afterwards and then lost consciousness.

On Examination: Temperature 105.5oF, pulse 151 beats per minute, blood pressure
40/10. She was dead within 15 minutes. After death, rigor mortis set in after 10 minutes
and her temperature rose to 115oF after another 10 min.

Among her personal effects a plastic bottle containing the weight loss pills were found,
which on analysis proved to contain 2,4,dinitrophenol.

Rigor mortis (Latin : rigor, stiffness + mortis, death.) Muscular stiffness following
death. In humans it commences after about 3 hours, reaches maximum stiffness
after 12 hours, and gradually dissipates until approximately 72 hours (3 days) after
death.

36
Session: Electron transport chain/Oxidative phosphorylation

You should be able to

 explain the location and function of the components of the electron

transport chain (ETC)
 describe the fate of NADH and FADH2 in the ETC
 describe the role of the proton gradient in ATP synthesis in the
mitochondria
 explain the role of uncoupling proteins in dissipating the proton gradient and
correlate with the given case
 Identify inhibitory agents along with their sites of inhibition in the ETC

Lippincott’s Illustrated Reviews - Biochemistry

Why did rigor mortis set in so soon after death in the above case?

How do synthetic uncouplers cause weight loss?

Vignette 10

A 25 years old man presented to OPD for cough, fever, chest pain and
difficulty in breathing. He has a past history of recurrent respiratory tract
infections. He is married since three years and has been investigated for
infertility which revealed immotile sperms.

Systemic examination showed dextrocardia.

He was diagnosed as Kartagener syndrome.

37
Dextrocardia= A congenital condition in which the heart is pointed toward the right side
of the chest instead of normally pointing to the left.

Vignette 11

Introduction: A 47-year-old male presented to the Oral Medicine Clinic.

Presenting complaint: 3-month history of oral ulceration with considerable discomfort

and significantly affected normal oral function.

Examination: Blood-filled blisters and ulcers over the inner aspect of lower lip and
cheek.

Diagnosis: Pemhigus vulgaris.

Session: Cytoskeleton and cell junctions

You should be able to describe

 Location, formation and structure of microtubules, microfilaments and

intermediate filaments
 Role of microtubules in maintenance of cell shape and complex cell movements
 Role of microfilaments in cellular contractile systems and as mechanical stiffeners
 Role of intermediate filaments in mechanical stress
 How the cytoskeleton links together parts of the cell
 Correlate the structure and function of cell surface modifications with clinical
abnormalities
 Structure and functions of extra cellular matrix
 Role of extracellular matrix in cell adhesion
 Location, structure and functions of cell junctions: Tight junctions, adhering
junctions, desmosomes, gap junctions, hemidesmosomes

38
 1. Human Physiology- From Cells to System by Lauralee Sheerwood
2. Junqueira's Basic Histology

What is the difference between flagella and cilia? What is the role of cilia and
mucus in your airway passage?

Vignette 12

Introduction: A 6 year old boy brought to the OPD

Presenting complaint: Watery diarrhea and nausea since last two days.

Examination: Moderately dehydrated

Temp: 99oF

Pulse: 100/min

Systemic examination was normal.

Advice: His mother was advised to give him homemade solution of sugar and salt with
lemon added to it.

39
Session: Transport Across the Cell Membrane

By the end of this session you should be able to

 Differentiate between the mechanisms by which various substances are

transported across the cell membrane.

Identify how cells change shape in solutions of different concentrations

What is a concentration gradient? Is it correct to refer to “concentration

gradient of water”?

Can solutions with the same concentration of different solutes have different osmotic
pressures?

Vignette 13

A female infant was brought to a pediatric clinic with a large mass situated
between her anus and sacrum. The mass was surgically removed.
Histopathology report showed the mass to contain derivatives of the basic germ layers
(e.g. teeth etc.) and diagnosed as sacro-coccygeal teratoma.

Theme 6: Physical Development - Cell Growth and Differentiation

 Embryology Session 4
the student should be able to
describe the formation and fate of primitive streak

 describe the formation of the 3 basic germ layers

40
  describe formation, role and fate of notochord

 describe the process of neurulation

 Correlate the process of gastrulation and neurulation with clinical

presentations

 Formation, function and fate of allantois

 Formation, development, fate and derivatives of somites

 Describe development of chorionic villi

 Describe abnormal growth of trophoblasts

Embryology Session 5

The student should be able to

 Describe phases of embryonic development

 Describe folding of embryo in median and horizontal planes

 Correlate the mechanism of folding with its consequences [changes occurring

in the structure of the embryo]

 Enumerate the subdivisions of germ layer and their derivatives

 Describe weekly changes in the embryo during organogenetic period

 Describe estimation of embryonic and gestational age

1. What is the probable embryological origin of the tumor?

2. Why do these tumors contain various types of tissues derived from all three
germ layers?
3. Does an infant’s sex make it him/ her more susceptible to the development of this
tumor?
4. Can it be diagnosed during the antenatal period?

41
Theme 2
The Central Dogma of
Molecular Biology

42
 Vignette 14

A 74 year old man presents to the OPD with complaints of aches and pains in
his legs and back. He has a history of recurrent infections for the last couple
of years. He finds it difficult to get up in the morning and finds no pleasure
in his daily activities. He complains that his appetite is low and he feels weak and
lethargic most of the time. He reveals that his short term memory has become weak and
he often has problems remembering what he did a few hours ago.

The Nobel Prize in Physiology or Medicine 1962. Francis Crick, James Watson
and Maurice Wilkins for their discoveries “concerning the molecular structure
of nucleic acids and its significance for information transfer in living material"

Session: DNA replication

You should be able to

 Explain the process of DNA replication

 Explain how DNA replication is achieved with high fidelity
 Correlate enzymes of DNA replication with their functions
 Explain the role of telomeres in aging and cancer
 Discuss the mechanism of action of fluoroquinolones, etoposide and nucleoside
analogues (in chemotherapy and treatment for AIDS)

43
For understanding DNA replication find answers to the following

1. The site of initiation of replication is not chosen randomly. How does the cell know
where to start replication???
2. For replication to occur, the parental DNA double helix has to be separated into
single strands. What protein is required to make the DNA single stranded during
replication????
3. Normally complementary single DNA strands reform the double helix. Also single
stranded DNA is vulnerable to damage. What proteins are required keep the DNA
single stranded during replication and to protect it from damage??
4. Each eukaryotic chromosome is one linear DNA double helix (Average ~108 base pairs
long). With a replication rate of 2 kb/minute, replicating one human chromosome
would require ~35 days (S phase of eukaryotic cell cycle = 6-8 hrs). How are
eukaryotic DNA molecules replicated in time????
5. The two DNA strands twist around each other to form a helix. As the two strands are
pulled apart it leads to the tightening of the twists in regions upstream of replication
initiation points and the introduction of ‘supercoils’. How are supercoils removed
from the DNA helix????
6. The primary DNA replication enzyme, DNA polymerase, can only add nucleotides to
an existing strand of nucleotides i.e., it cannot start the replication process by itself.
How does replication get started????
7. DNA polymerase can only add nucleotides in one direction, 5’ → 3’ i.e., creation of
both the new strands is in the 5’ → 3’ direction. However, the two DNA strands are
antiparallel to each other --- one runs 5’ → 3’ and the other 3’ → 5’. Both strands
have to be replicated. How is the problem of directionality solved????

8. The solution to problem 6 requires the excision of RNA primers and their
replacement by DNA. Which enzyme is involved in this step and how does it work
????

9. The solutions to problems 7 and 8 leave the newly synthesized DNA with single
strand breaks or ‘nicks’. Which enzyme is involved this sealing these breaks ????
44
10. The mis-incorporation of a single nucleotide during replication could lead to
deleterious or even lethal mutations. How is replication fidelity maintained ????

11. In eukaryotes DNA polymerase cannot fill the gaps at ends of chromosomes after
RNA primer is removed. If this gap is not filled, chromosomes would become shorter
each round of replication! How are the telomeric regions replicated without
shortening of chromosomes???

12. Some viruses (e.g. Retroviruses) have single or double stranded RNA as their
genome. How do they replicate?? What are the characteristics of their
polymerases??

13. DNA replication is said to be “semi conservative”. What is meant by this????

The Nobel Prize in Physiology for Medicine 2009. Elizabeth H. Blackburn,

Carol W. Greider and Jack W. Szostak for the discovery of "how chromosomes
are protected by telomeres and the enzyme telomerase"

Lippincott’s Illustrated Reviews - Biochemistry

45
 The picture below is a depiction of DNA replication as originally proposed by
Watson and Crick. On the basis of what is now known what do you think is
wrong with this picture?

46
 TEST YOURSELF!

Choose the best matching phrase in the right column for each of the
terms in the left column.

Vocabulary – DNA structure and replication

a. Pyrimidine 1. The strand that is synthesized

discontinuously during replication

b. Deoxyribose 2. The sugar within the nucleotide subunits of

DNA

c. Hydrogen bonds 3. A nitrogenous base containing a double ring

d. Complementary bases 4. Noncovalent bonds that hold the two

strands of the double helix together

e. Origin 5. Meselson and Stahl experiment

f. Okazaki fragments 6. Structures at ends of eukaryotic

chromosomes

g. Purine 7. Two nitrogenous bases that can pair via

hydrogen bonds

h. Topoisomerases 8. A nitrogenous base containing a single ring

i. Semiconservative 9. A short sequence of bases where unwinding

replication of the double helix for replication begins

j. Lagging strand 10. Short DNA fragments formed by

discontinuous replication of one of the
strands

k. Telomeres 11. Enzymes involved in controlling DNA

supercoiling

47
48
 Vignette 15

A 3-year-old boy, was referred to the dermatology clinic for evaluation of

severe sun sensitivity and freckling.

On physical examination, he was photophobic and had conjunctivitis and prominent

freckled hyperpigmentation in sun-exposed areas; his development and physical
examination were otherwise normal.

The parents of the child revealed that they were first cousins; no one else in the family
was similarly affected.

The dermatologist explained that the boy had classic features of xeroderma
pigmentosum (XP), that is, "parchment-like pigmented skin".

To confirm the diagnosis, he had a skin biopsy to evaluate DNA repair and ultraviolet
(UV) radiation sensitivity in his skin fibroblasts.

The results of this testing confirmed the diagnosis of XP. Despite appropriate preventive
measures, the boy developed metastatic melanoma at 15 years of age and died 2 years
later.

His parents had two other children; neither was affected with XP.

Session: DNA damage and repair

You should be able to

 Explain how various types of DNA damage if unrepaired lead to

mutations
 Explain the effect cigarette smoke on DNA
 Describe the mechanisms involved in DNA repair (including mismatch, base
excision, nucleotide excision and recombination repair)
 Recognize how defects in DNA repair systems lead to cancer prone genetic
disorders (XP, HNPCC, breast cancer etc)

49
 Lippincott’s Illustrated Reviews - Biochemistry

Why does DNA contain thymine and not uracil? As thymine requires more
energy to produce, the cell must be deriving some benefit for its production.
(Hint: Think spontaneous deamination of cytosine)

Vignette 16

Introduction: A 28 year old woman presents to the ER

Presenting complaint: Severe nausea, abdominal cramping and copious diarrhea

Examination: vital signs show tachycardia and poor skin turgor indicates dehydration

History: She tells the attending physician that her symptoms started 6 hours after
dinner. She is asked to recall everything she had eaten that day. She reports that she
had eaten a mushroom omelet using mushrooms that she had picked herself earlier
that day while on a hike.

Diagnosis: α-amanitin poisoning associated with ingestion of species Amanita

50
 Management: Aggressive intravenous fluid and electrolyte treatment and active
charcoal to absorb circulation toxins. Increased monitoring of hepato-renal function.
Patient recovers after about 5 days.

Session: Gene transcription

At the end of this session you should be able to

 Identify the major types of cellular RNA and their functions

 Describe the major steps in transcription of an RNA molecule
 Differentiate between prokaryotic and eukaryotic gene transcription
 Correlate the posttranscriptional modifications of eukaryotic mRNA with their
function
 Discuss the mechanism of action of the antibiotics that specifically inhibit
prokaryotic RNA synthesis

Lippincott’s Illustrated Reviews – Biochemistry

51
 Vignette 17

Introduction: A 3 year old girl

Presenting Complaints: Difficulty breathing for a few hours.

H/ O Present Illness: Developed fever and sore throat 6 days back. Fever was high grade
and associated with chills and nausea. For the last 2 days she has experienced difficulty
in swallowing.

Past History: No H/O immunization. No other significant past history.

Social History: Lower socio-economic status. Father: Laborer

Examination:

GPE:- A 3 years old girl looking ill and in severe respiratory distress with :

Pulse = 142/min B.P 50/30

Temp 102 F R/R = 32/min

Local examination reveals swelling of the neck.

Throat Exam: A grayish non-adherent membrane extending through the glottis down to
the larynx.

Diagnosis: Upper respiratory tract infection, Fever (high grade), pseudomembrane on

tonsils, pharynx, or nasal cavity

Management:

1. If severe Respiratory distress; Intubate

2. Give DIPHTHERIA anti-toxin

3. Antibiotics: Preferably Erythromycin orally or I/v for 14 days.

52
Session: Protein synthesis

You should be able to explain

 how nucleotide sequence is translated into the amino acid sequence of

a protein
 initiation, elongation and termination of protein synthesis
 how differences in prokaryotic and eukaryotic protein synthesis have been
exploited to produce various antibiotics

Lippincott’s Illustrated Reviews – Biochemistry

53
Theme 3: Molecular
Basis of Disease

54
Session: Mutations: Genomics as a Probe for Disease Biology

Abstract: Although our understanding of pathology has grown rapidly in

recent decades, the underlying mechanisms of many diseases remain
obscure. Genomic research offers a new opportunity for determining how
diseases occur, by taking advantage of experiments of nature and a
growing array of sophisticated research tools to identify the molecular
abnormalities underlying disease processes.

In this review I examine examples in which genomic research has improved

our understanding of molecular pathobiology and consider its potential for
contributing to the study of common complex diseases.

Wylie Burke, M.D., Ph.D.

N Engl J Med 2003; 349: 969-74.

Although this review article form NEJM is 12 years old now, it is still serves as useful
illustration of the importance of genetic research in helping us understand the
pathological basis of many diseases.

Session: Mutations: genomics as a probe for disease biology

You should also be able to

 Classify different types of mutations (including nonsense, silent,

missense and triplet repeat expansion, transitions and transversions)
according to their effect on DNA sequence and protein structure
 Compare loss-of-function and gain-of-function mutations
 Differentiate between somatic and germ line mutations
 Differentiate between mutations and polymorphisms

Lippincott’s Illustrated Reviews – Biochemistry (for the description of

nonsense, silent, missense and triplet repeat expansion mutations)

55
 You are working in a DNA laboratory and identify a previously
uncharacterized DNA variant (C or T at position 423) in the intron of a gene.
Can you think of ways to determine which one of the two (C or T) is ancestral?

Session: Regulation of Gene Expression in Eukaryotes

By the end of this session you should be able to

Define epigenetics

And explain the regulation of eukaryotic gene expression through:

 trans- and cis- acting molecules

 intracellular and cell surface receptors
 alternative splicing
 mRNA editing
 mRNA stability (in iron metabolism) (we’ll do RNA interference in therapeutics)
 translation of mRNA
 modifications to DNA

Lippincott’s Illustrated Reviews – Biochemistry

56
 TEST YOURSELF!

Choose the best matching phrase in the right column for each of the terms in the left
column.

VOCABULARY – Transcription/Translation

a. Codon 1. Removing base sequences corresponding to

introns from the primary transcript

b. Reading frame 2. UAA, UGA, or UAG

c. Frameshift mutation 3. The strand of DNA that has the same base
sequence as the primary transcript

d. Degeneracy of the 4. A transfer RNA molecules to which the

genetic code appropriate amino acid has been attached

e. Nonsense codon 5. A group of three mRNA bases signifying one

amino acid

f. Initiation codon 6. Most amino acid are not specified by a single

codon

g. Template strand 7. Using the information in the nucleotide sequence

of a strand of DNA to specify the nucleotide
sequence of a strand of RNA

h. Coding strand 8. The grouping of mRNA bases in threes to be read

as codons

i. Intron 9. AUG in a particular context

j. RNA splicing 10. Produces different mature mRNAs from the same

57
 primary transcript

k. Transcription 11. Addition or deletion of a number of base pairs

other than three into the coding sequence

l. Translation 12. A sequence of base pairs within a gene that is not

represented by any bases in the mature mRNA

m. Alternative splicing 13. The strand of DNA having the base sequence
complementary to that of the primary transcript

n. Charged tRNA 14. Using the information encoded in the nucleotide

sequence of an mRNA molecule to specify the
amino-acid sequence of a polypeptide molecule

o. Reverse transcription 15. Copying RNA into DNA

58
Session: Mendelian patterns of inheritance

By the end of this session you should be able to

 Differentiate between heterozygotes and homozygotes; recessive and

dominant alleles; genotype and phenotype
 Draw a pedigree of a family with a genetic disorder on the basis of information
elicited from your patient using standard pedigree symbols
 Analyze pedigrees to determine their mode of inheritance (autosomal
recessive, autosomal dominant, X-linked recessive, X-linked dominant, Y-linked
and mitochondrial)
 Calculate the probability of passing on disease gene(s) to one’s progeny based
on the Mendelian laws of inheritance

59
 DRAWING A PEDIGREE:

If more than one individual in a family is afflicted with a disease, it indicates that the
disease may be inherited. As a doctor, you need to look at the family history to
determine whether the disease is indeed inherited and, if it is, to establish the mode of
inheritance. For a disease trait, you will have to examine existing family members to
determine who is affected and who is not. Once family history is determined, you will
draw up the information in the form of a family tree (pedigree) that uses a particular set
of standardized symbols, given in the table below. This information contained in the
pedigree can then be used to predict recurrence risk in future generations.

60
 TEST YOURSELF!

Identify the Mendelian mode of inheritance in the following pedigrees:

61
62
Theme 4: Molecular
Biology in Therapeutics

63
 Vignette 18

Introduction: A 68 year old hypertensive male

Presenting complaints: Redness in right eye, gradual loss of vision,

trouble in differentiating colors and missing areas of vision.

Family History: Positive hypertension for 20 years

Examination: Hemorrhage in right eye, Loss of central vision

Diagnosis: Age-related macular degeneration (AMD)

Treatment: The doctor tell the patient that although there was no current cure for
AMD, exciting new treatment modalities based on the principle of RNA interference
were now in Phase III clinical trials and may be on the market soon.

On researching the disease further, the man finds out that animal trials using embryonic
stem cell to replace the damaged ones had been very successful and scientists were
predicting that this treatment would become a routine, one-hour procedure generally
available in six or seven years’ time. He was however disturbed by ethical implications of
using embryonic stem cells.

The Nobel Prize in Physiology or Medicine 2006. Fire and Mello "for their
discovery of RNA interference - gene silencing by double-stranded RNA"

Session: Molecular Biology in Therapeutics

You should be able to

 Describe the different types of gene therapies and identify associated

risks and challenges
 Explain the role of short interfering RNAs (siRNAs) in fighting diseases
 Explain the potential of stem cell therapy in curing disease

64
 Lippincott’s Illustrated Reviews – Biochemistry

Handouts will be available from the photocopier for these topics

Which features of AMD do you think make it particularly amenable to treatment

by siRNAs? Would you expect dominant or recessive diseases to be likely to be
treated using RNA interference?

Vignette 19

Introduction: A 14-year-old girl, was referred to the endocrinology

clinic for evaluation of absent secondary sexual characteristics (menses
and breast development).

Family history: No other family members had similar problems.

Examination: Her examination was normal except for short stature, Tanner stage I
sexual development, and broad chest with widely spaced nipples. Although born
small for gestational age, she had been in good health and had normal intellect.

Lab investigations: normal growth hormone (GH) level, an elevated follicle-

stimulating (FSH) level, and an abnormal karyotype (45,X).

Diagnosis: Turner syndrome.

Theme 6: Physical Development - Cell Growth and Differentiation

Embryology Session 6: Assessing Fetal Health/Teratogenesis

At the end of this session you should be able to

 Explain the basics of teratogenesis

 Explain the basis and effect of gross chromosomal aberrations
(structural and numerical) on human development
 Explain the basis of different types of aneuploidies
65
 Recognize the clinical features of the common Trisomies, Turner syndrome and
Kleinfelter’s syndrome.
 Identify various agents and environmental factors as teratogens and relate their
probable mode of action on resulting morphological changes in the fetus
 Explain the basis and applications of diagnostic techniques employed for the
diagnosis of fetal defects
 Differentiate between the type of information derived from cytogenetic versus
molecular testing
 Explain the role of genetic mutations to underline the role of genes in
morphogenesis

The Developing Human-Moore and Persaud

X-chromosome monosomy is the only viable human monosomy. Can you think of
possible reasons?

66
 GENETIC COUNSELING

Any couple that has had a child with a serious abnormality must inevitably reflect on
why this happened and whether any child(ren) they choose to have in future might
be similarly affected. Similarly, individuals with a family history of a serious disorder
are likely to be concerned that they could either develop the disorder or transmit it
to future generations. They are also very concerned about the risk that their normal
children might transmit the condition to their offspring. For all those affected by a
genetic condition that is serious to them, great sensitivity is needed in
communication. Just a few words spoken with genuine caring concern can put
patients at ease and allow a meaningful session to proceed; just a few careless words
that make light of a serious situation can damage communication irrevocably. The
importance of confidence and trust in the relationship between patient and health
professional can never be underestimated.

Realization of the needs of such individuals and couples, together with awareness of
the importance of providing them with accurate and appropriate information, has led
to the widespread introduction of genetic counseling clinics in parallel with the
establishment of clinical genetics as a recognized medical specialty.

An individual who seeks genetic counseling is known as a consultand. During the

genetic counseling process it is widely agreed that the counselor should try to ensure
that the consultand is provided with information that enables him or her to
understand:

1. The medical diagnosis and its implications in terms of prognosis and possible
treatment

2. The mode of inheritance of the disorder and the risk of developing and/or
transmitting it

3. The choices or options available for dealing with the risks.

It is also agreed that genetic counseling should include a strong communicative and
67
supportive element, so that those who seek information are able to reach their own
fully informed decisions without undue pressure or stress
Theme 5: Molecular
Biology in Diagnostics

68
 Vignette 20

A 7 year old boy was brought to his pediatrician. His mother reported that
he was excessively thirsty and had been drinking large quantities of water
and juice over the last couple of months. He had also been wetting the bed on a number
of occasions. Laboratory investigations revealed blood glucose levels of 344 mg/dl and
ketonuria. A diagnosis of diabetes mellitus type I was made. He was started on a
treatment regimen of recombinant human insulin after which he made a made a rapid
recovery.

Vignette 21

A couple is expecting their second child. Sickle cell anemia runs in both of
their families. They want to know whether this child could be affected.
Neither they nor their 10-year-old daughter have shown any symptoms of the disease.
They decide to have DNA tests to determine the status of the fetus, as well as to find
out whether they in fact are carriers of the disease gene.

Vignette 22

A 32-year-old female presents to your clinic with concerns over a recently

detected right breast lump. The patient undergoes an examination which
reveals a fixed and non tender breast mass on right side measuring 3 cm. A biopsy is
performed and reveals an intraductal carcinoma. She is invited to participate in an
experimental study that is being carried out to help direct future treatment protocols
and define new drug targets for breast cancer. The researcher explains to her that DNA
microarrays (DNA chips) will be used to study the differences in the gene expression
profiles of tumor versus normal cells. After considering all the pros and cons she gives
her informed consent and allows her tissue samples to be used.

69
Sessions: DNA cloning and PCR/Molecular biology in diagnostics

You should be able to

 describe the use of recombinant DNA technology for the production of

therapeutic agents
 differentiate between a DNA cloning vector and an expression vector
Explain
 the use in molecular hybridization assays in medical diagnostics
 PCR and its use in clinical practice
 The use of restriction fragment length polymorphisms (RFLPs)/short tandem
repeats (STRs) in diagnostics and forensics

 Interpret the results/gel pictures of molecular assays including ASO gels, PCR-RFLP
gels, microarrays and DNA fingerprints

Nobel Prize for Chemistry 1993 - Dr Kary B. Mullis, for his invention of the
polymerase chain reaction (PCR) method.

70
 A crime scene investigation laboratory carried out DNA profiling
of three suspects held for sexual assault. DNA from the victim
and the three suspects was compared to the DNA obtained
from a vaginal swab taken from the victim after the incident.

1 = Victim’s DNA

2 = suspect 1

3 = suspect 2

4 = suspect 3

5 = Vaginal Swab DNA

Based on the above gel which one of the suspects is the perpetrator of the crime?
Why is it necessary to collect victim’s DNA sample for the analysis?

How many different scenarios can you think of where DNA profiling would prove
to be useful?

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Session: Personalized Medicine

In a time of unprecedented scientific breakthroughs and technological advancements,

personalized health care has the capacity to use the sequence of the four chemical
building blocks that comprise DNA, coupled with tell-tale proteins in the blood, to
enable more accurate medical predictions. These include whether an individual is
developing an illness now or will develop it many years in the future, will respond
positively to treatment, or will suffer a serious reaction to a drug.

Personalized medicine introduces the ability to use molecular markers that signal
disease risk or presence before clinical signs and symptoms appear, and it offers the
opportunity to focus on prevention and early intervention rather than on reaction at
advanced stages of disease. In many areas, the clinical interventions can be life-saving.
For example, women with certain BRCA1 or BRCA2 gene variations have up to an 85
percent lifetime chance of developing breast cancer, compared with a 13 percent
chance among the general female population. These women also have up to a 60
percent chance of developing ovarian cancer, compared with a 1.7 percent chance
among the general female population. The BRCA1 and BRCA2 genetic test can guide
preventive measures, such as increased frequency of mammography, prophylactic
surgery, and chemoprevention.

In addition, the genotyping of drug-metabolizing enzymes has produced improved

dosing of drugs for conditions as wide-ranging as depression and anxiety, coronary and
peripheral artery disease, inflammatory bowel disease, and cancer. This has helped
patients avoid harmful side effects, adverse drug interactions, or ineffective treatment.
Thousands of patients have seen dramatic results since the mapping of the genome
more than a decade ago, yet much remains to be done to realize the promise of
personalized medicine. Over a 100 drugs are now labelled with pharmacogenetic
information.

PERSONALIZED MEDICINE CAN:

• Shift the emphasis in medicine from reaction to prevention

• Direct the selection of optimal therapy and reduce trial-and-error prescribing

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• Help avoid adverse drug reactions

• Increase patient adherence to treatment

• Improve quality of life

• Reveal additional or alternative uses for medicines and drug candidates

• Help control the overall cost of health care

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Taken from: The case for personalized medicine. 4th edition 2014. PMC

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 TEST YOURSELF!

Choose the best matching phrase in the right column for each of the terms in the left
column.

VOCABULARY – Biotechnology

a. Oligonucleotide 1. A DNA molecules used for transporting

replicating, and purifying a DNA
fragment
b. Vector 2. A collection of the DNA fragments of a
given species, inserted into a vector
c. Sticky ends 3. DNA copied from RNA by reverse
transcriptase
d. Recombinant DNA 4. biometric identification obtained by
examining a person's unique sequence
of DNA base pairs
e. Reverse translation 5. Efficient and rapid technique for
amplifying the number of copies of a
DNA fragment
f. Genomic library 6. Computational method for determining
the possible sequences of base pairs
associated with a particular region of a
polypeptide
g. cDNA 7. Contains genetic material from two
different organisms
h. PCR 8. Short single-stranded sequences found
at the ends of many restriction
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 fragments
i. Hybridization 9. A short DNA fragment that can be
synthesized by a machine
j. DNA fingerprint 10. Stable binding of single-stranded DNA
molecules to each other

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 GLOSSARY - GENETICS
Alleles alternative forms of a single
gene.
Alleles-specific oligonucleotides (ASOs)
Short oligonucleotides that hybridize
with alleles distinguished by a single
base difference
Alternative splicing production of
different mature mRNAs from the same
primary transcript by joining different
combinations of exons
Aminoacyl (A) site site on a ribosome
to which a charged tRNA first binds
Anaphase the stage of mitosis in which
the connection of sister chromatids is
severed, allowing the chromatids to be
pulled to opposite spindle poles
Aneuploid an individual whose
chromosome number is nt an exact
multiple of the haploid number for the
species
Anticodons groups of three
nucleotides on transfer RNA (tRNA)
molecules that recognize codons on the
mRNA by complementary base pairing
and wobble
Barr bodies inactive X chromosomes
observable at interphase as darkly
stained heterochromatin masses
Basal transcription apparatus
complex protein machine that interacts
with complexes of transcription factors
and cis-control elements to mediate the
synthesis of an RNA transcript is spliced
and edited to produce a messenger RNA
(mRNA).
cDNA complementary DNA with a base
sequence that is complementary to that
of the mRNA template and contain no
introns.
Chromatid one of two copies of a
chromosome that exist immediately
after DNA replication.
Chromatin the generic term for any
complex of DNA and protein found in a
cell’s nucleus.
Codominant expression of
heterozygous genotype resulting in
hybrid offspring that resemble both
parents equally for a particular trait
Deamination the removal of an
amino (-NH2) group from normal DNA
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DNA polymorphisms two or more
alleles at a locus detected with any
method that directly distinguishes
differences in DNA sequence. The
sequence variations of a DNA
polymorphism can occur at any position
on a chromosome and may, or may not,
have an effect on phenotype.
DNA probe a purified fragment of
DNA labeled with a radioactive isotope
or fluorescent dye and used to identify
complementary sequence by means of
hybridization.
Domain a discrete region of a protein
with its own function. The combination
of domains in a single protein
determines its overall function
Dominant allele an allele whose
phenotype is expressed in a
heterozygote. See recessive allele.
Exons sequence that are found both in
a gene’s DNA and in the corresponding
mature messenger RNA (mRNA). See
introns.
Frameshift mutations insertions or
deletions of base pairs that alter the
grouping of nucleotides into codons.
Gain-of-function alleles (or mutations)
rare mutations that enhance a gene’s
function or confer a new activity on the
gene’s product
Gene basic unit of biological
information; specific segment of DNA in
a discrete region of a chromosome that
serves as a unit of function by encoding
a particular RNA or protein.
Genome the sum total of genetic
information in a particular cell or
organism
Genotype The specific allelic or genetic
constitution of an organism
Germ cells specialized cells that
incorporate into the reproductive
organs, where they ultimately undergo
meiosis, thereby producing haploid
gametes that transmit genes to the next
generation
Hairpin loops structure formed when a
single strand of DNA or RNA can mentary
base pairing between different regions
in the same molecules
Heterochromatin highly condensed
chromosomal regions within which
genes are usually transcriptionally
inactive
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Heterozygote individual with two
different alleles for a given gene or locus
Homozygote individual with identical
alleles for a given gene or locus
Hybridization the propensity of
complementary single strands of nucleic
acid ---either DNA or RNA___to form
stable double helices. A powerful tool,
hybridization can be used to identify
sequences that are closely related to a
DNA probe
Introns the DNA base sequences of a
gene that are spliced out of the primary
transcript and are therefore not found in
the mature mRNA. See exons.
Karyotype the visual description of the
complete set of chromosomes in one
cell of an organism; usually presented as
a photomicrograph with the
chromosomes arranged in a standard
format showing the number, size, and
shape of each chromosome type.
Lagging strand during replication, DNA
strand whose polarity is opposite to that
of the leading strand. The lagging strand
must be synthesized discontinuously as
small Okazaki fragments that are
ultimately joined into a continuous
strand.
Leading strand during replication, DNA
strand synthesized continuously 5’ to 3’
toward the unwinding Y-shaped
replication fork. Compare with lagging
strand
Loss-of-function mutation (or allele)
DNA mutation that reduces or abolishes
the activity of a gene; most (but not all)
loss-of-function alleles are recessive
Micro-RNA (mRNA) an RNA molecule
21-24 bases in length that is encoded in
the genome of an organism and used by
a cell to modulate gene expression
through the process of RNA interference
Nonsense codons the three stop
codons that terminate translation.
Nucleosome rudimentary DNA
packaging unit; composed of DNA
wrapped around a histone protein core
Oligonucleotide a short single-
stranded DNA molecule (containing less
than 50 bases); can be synthesizer.
Oligonucleotides are used as DNA
probes and as primers for DNA
sequencing or PCR
Pedigree an orderly diagram of a
family’s relevant genetic features,
extending through as many generations
as possible
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Peptide bond a covalent bond that
joins amino acids during protein
synthesis
Phenotype an observable characteristic
Point mutation a mutation of one base
pair
Polygenic trait trait controlled by
multiple genes.
Recessive allele an allele whose
phenotype is not expressed in a
heterozygote. See dominant allele.
Restriction enzymes proteins made by
bacteria that recognize specific, short
nucleotide sequences and cut DNA at
those sites
Restriction fragment length
polymorphism (RELP) variation
between individuals in DNA fragment
size cut by specific restriction enzymes;
polymorphic sequences that result in
RELPs are used as markers on both
physical maps and genetic linkage maps
Reverse transcription the process by
which reverse transciptase synthesizes
DNA strands complementary to an RNA
template. The product of reverse
transcription is a cDNA molecules
RNA splicing a process that deletes
introns and joins together adjacent
exons to form a mature mRNA consisting
of only exons
Sequencing determining the order of
nucleotides (base sequences) in a DNA
or RNA molecule or the order of amino
acids in protein
Silent mutations mutations without
effects on phenotype; usually denotes
point mutations that change one of the
three bases in a codon but that do not
change the identity of the specified
amino acid because of the degeneracy of
the genetic code
Single nucleotide polymorphism (SNP)
a single nucleotide locus with two
naturally existing alleles defined by a
single base pair substitution. SNP loci are
useful as DNA-based markers for formal
genetic analysis
Telomeres specialized terminal
structure on eukaryotic chromosomes
that ensure the maintenance and
accurate replication of the two ends of
each linear chromosomes
Template a strand of DNA or RNA that
is used as a model by DNA or RNA
polymerase or by reverse transcriptase
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for the creation of a new
complementary strand of DNA or RNA

Totipotent description of cell state

during early embryonic development in
which the cells have not yet
differentiated and retain the ability to
produce every type of cell found in the
developing embryo and adult animal

Transition a type of substitution

mutation that occurs when one purine
(A or G) replaces the other purine, or
one pyrimidine. Contrast with
transversions.

Transversions a type of substitution

mutation that occurs when a purine (A
or G) replaces a pyrimidine replaces a
purin

Vocabulary exercises and Glossary taken from

Genetics – From Gene to Genomes – 3rd Edition
– Hartwell, Hood, Goldberg, Reynolds,Silver,
Veres. The MacGraw- Hill Companies

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