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Lecture notes: Principles of Genetics.

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 1
I INTRODUCTION

Genetics is the scientific study of inherited variation. Human

genetics is the scientific study of inherited human variation. This field has
been energized in recent years by the Human Genome Project. Scientists
expect that the project will lead to the development of new drugs targeted
to specific genetic disorders. Increasingly, modern genetics involves
genetic engineering; a technique used to manipulate genes and has
produced many advances in medicine.

II PRINCIPLES OF GENETICS

• The site where genes work is the cell.

• Each cell’s function within an organism is determined by the genetic
information encoded in DNA.
• In eukaryotes (organisms whose cells contain a nucleus), DNA
resides within membrane-bound structures in the cell (nucleus,
mitochondria, and chloroplasts in plants).
• In prokaryotes (one-celled organisms that lack internal membrane-
bound structures), DNA floats freely within the cell body.
• DNA is packaged into structures called chromosomes within a cell.
• Every chromosome in a cell contains many genes, and each gene is
located at a particular site, or locus, on the chromosome.
• Chromosomes usually occur in matched pairs called homologues.
• The number of homologous chromosomes in the human body contain
23 pairs of chromosomes.
 2
Animal Cell

• An animal cell typically contains several types of membrane-

bound organs, or organelles.
• The nucleus directs activities of the cell and carries genetic
information from generation to generation.
• The mitochondria generate energy for the cell.
• Proteins are manufactured by ribosomes, which are bound to
the rough endoplasmic reticulum or float free in the
cytoplasm.
• The Golgi apparatus modifies, packages, and distributes
proteins.
• Lysosomes store enzymes for digesting food.
• The entire cell is wrapped in a lipid membrane that selectively
permits materials to pass in and out of the cytoplasm.
 3
A. Cell Division and Reproduction

• Organisms use two types of cell division to ensure that DNA is

passed down from cell to cell during reproduction.
• Simple one-celled organisms reproduce by a process called mitosis.
During mitosis a cell doubles its DNA before dividing into two cells
and distributing the DNA evenly to each resulting cell.
• Organisms that reproduce sexually produce special cells called
gametes, or egg and sperm.
• During sexual reproduction, an egg and sperm unite to form a zygote,
in which the full number of chromosomes is restored.

The Human Life Cycle

• Humans use two types of cell division to ensure that DNA is passed
down from cell to cell during reproduction.
• During mitosis a cell doubles its DNA before dividing into two cells.
• In meiosis, the chromosomes in a gamete cell are reduced by half.
 4
A1 Mitosis

Mitosis

Interphase Prophase Metaphase Anaphase Telophase Cytokinesis

• Mitosis occurs in five stages:

1. Interphase: the start of mitosis, the DNA of each chromosome
replicates. Each chromosome then reorganizes into paired
structures called sister chromatids, with each member of the pair
containing a full copy of the DNA sequence.
2. Prophase: the sister chromatids condense, thickening until they
appear joined at a single site, known as the centromere.
3. Metaphase: the sister chromatids line up in the middle of the cell.
4. Anaphase: the chromatid pairs split apart at the centromere, and
each half of the pair then moves toward opposite poles of the cells.
5. Telophase: the final stage of mitosis, a nuclear membrane forms
around the chromosomes at each pole of the cell.
• Mitosis ends with the formation of two new cells, each with a
matching full set of chromosomes.
• The cytoplasm divides; the cell membrane pinches inward
ultimately producing two daughter cells (Cytokinesis).
 5
A2 Meiosis
Meiosis

Interphase I Prophase I Metaphase I Anaphase I Telophase I Prophase II Metaphase II Anaphase II Telophase II

• Meiosis comprises two successive nuclear divisions.

• First division of meiosis:
1. Prophase I: Each chromosome duplicates and remains closely
associated. These are called sister chromatids.
2. Metaphase I: Homologous chromosomes align at the equatorial plate.
3. Anaphase I: Homologous pairs separate with sister chromatids
remaining together.
4. Telophase I: Two daughter cells are formed with each daughter
containing only one chromosome of the homologous pair.
• Second division of meiosis:
1. Prophase II: DNA does not replicate.
2. Metaphase II: Chromosomes align at the equatorial plate.
3. Anaphase II: Centromeres divide and sister chromatids migrate
separately to each pole.
4. Telophase II: Cell division is complete. Four haploid (n) daughter cells
are obtained.

Meiosis ensures that reproduction will produce a zygote that has

received one set of chromosomes (n) from each parent to form a full
set of chromosomes known as the diploid number (2n).
 6
B. Human Chromosomes

• Humans have 23 pairs of chromosomes. Twenty two pairs, the

autosomes, are the same in either sex and are numbered from 1-
22. The 23rd chromosome pair is called the sex chromosome, this
chromosome pair consists of two X chromosomes in women, and
men have one X + one Y chromosomes.

C. DNA Structure

• The structure of DNA encodes all the information every cell needs.
• DNA molecules form chains of building blocks called nucleotides.
• Each nucleotide consists of a sugar molecule called deoxyribose
that bonds to a phosphate molecule and to a base.
• DNA uses four bases in its structure: Adenine (A), Cytosine (C),
Guanine (G), and Thymine (T).
• The pairing of bases in the DNA double helix is highly specific (A
always joins with T, and G always links to C). These base
combinations, known as complementary base pairing.
• Genes line up in a row along the length of a DNA molecule.
 7
• In humans a single gene can vary in length from 100 to over
1,000,000 bases.
• Genes make up less than 2% of the length of a DNA molecule. The
rest of the DNA molecule is made up of long, highly repetitive
nucleotide sequences "junk” DNA".

The DNA double helix

Nucleotide

D. DNA Replication (duplication)

• During replication of DNA, the DNA double helix unwinds and

bonds joining the base pairs break, separating the DNA molecule
into two separate strands.
• Each strand of DNA directs the synthesis of another complementary
strand.
• The unpaired bases of each DNA strand attach to bases floating
within the cell.
• The complementary bases then link to each other, forming a new
DNA double-helix molecule. Thus the original DNA molecule
replicates into two DNA molecules that are exact duplicates.
 8
DNA Replication (duplication)

E. The Genetic Code

• A gene is a segment of DNA.

• The biochemical instructions found within most genes, known as the
genetic code, specify the chemical structure of a particular protein.
• A gene consists of a promoter (regulate the initiation of
transcription), the codons for a protein (protein-encoding sequence)
and a stop codon (terminate the transcription).
• Many of the genes are duplicates.
• The DNA structure of a gene determines the arrangement of amino
acids in a protein.

The Gene
 9
F. Protein Synthesis

• Proteins are composed of long chains of amino acids.

• The process of utilizing the genetic code to create proteins, known as
protein synthesis, has two steps: transcription and translation.

F1. Transcription

• Transcription transfers the genetic code from a molecule of DNA to

an intermediary molecule called ribonucleic acid (RNA).
• The two compounds have three critical differences:

1) The structure of RNA incorporates the sugar ribose rather than

deoxyribose in DNA.
2) RNA uses the base Uracil (U) instead of Thymine (T).
3) RNA usually exists as a single strand, unlike the double-helix
structure that normally characterizes DNA.

• Transcription involves the production of a messenger RNA (mRNA).

• The process begins when the two strands of a DNA molecule
separate, a task directed by the enzyme RNA polymerase.
• After the double helix splits apart, one of the strands serves as a
template, for the formation of a complementary mRNA molecule.
• Free-floating individual bases within the cell bind to the bases on the
DNA template to form a strand of mRNA.
• In eukaryotes, the mRNA strand consists of coding regions called
exons (link together to form an mRNA strand) separated by regions
called introns (do not contribute to protein synthesis).
 10
F2. Translation

• Translation takes place in ribosomes. The information coded in the

four bases found in mRNA is translated into the instructions
encoded by the 20 amino acids used in the formation of proteins.
• In eukaryotes, mRNA travels out of the nucleus into the cytoplasm
to attach to a ribosome.
• Another form of RNA called transfer RNA (tRNA) is found in the
cytoplasm of the cell. There are many different types of tRNA, and
each type binds with one of the 20 amino acids used in protein
formation.
• One end of a tRNA binds with a specific amino acid. The other end
carries three bases, known as an anticodon.
• The anticodon of the tRNA undergoes complementary base pairing
with a series of three bases on the mRNA, known as the codon.
• The mRNA codon codes for the type of amino acid carried by the
tRNA.
• A second tRNA bonds with the next codon on the mRNA. The
resident tRNA transfers its amino acid to the amino acid of the
incoming tRNA and then leaves the ribosome.
• This process continues repeatedly until the formation of a
polypeptide chain (a chain of amino acids).
• The process ends when the entire sequence of mRNA has been
translated.
• The polypeptide chain falls away from the ribosome as a newly
formed protein, ready to go to work in the cell.
 11

Conversion Of Genetic Information

The Central Dogma (Information Flow in the Cell)

 12
G. Mutations

• Any alteration in the structure of a gene results in a mutation.

• The altered genes continue to replicate in their changed form unless
another mutation occurs.
• Most mutations harm an organism and the implications can be
significant. For example, the amino acid sequence distinguishing
normal hemoglobin from the altered form of hemoglobin responsible
for sickle-cell anemia differs by only a single amino acid.
• In a Substitution (point mutation), a single nucleotide replaces
another nucleotide.
• Deletion or Insertion even a single base from a normal sequence
during transcription can disrupt translation by shifting the “reading
frame” of every subsequent codon.
• For example, in frameshift mutation an mRNA strand may include
two codons in the following sequence: AUG UGA. The addition of a
Cytosine base at the beginning of this sequence shifts the “spelling” of
these codons so that they read: CAU GUG. This may result in an
incorrect amino acid sequence during translation, or the protein may be
truncated. This type of alteration could result in the production of a
protein with no real function or one with a harmful effect.
• In transposition mutation, parts of DNA (containing one or more
genes) move from one chromosome to another (jumping genes or
transposons) which change the type of amino acids in protein.
• Mutations can occur spontaneously, or can be caused by exposure to
physical or chemical agents in the environment called mutagens.
 13
• Common mutagens include ultraviolet rays and various chemicals,
such as nitrous acid and high-energy radiation (such as X rays) which
cause damage and disrupting the function of many genes.
• The cell has highly effective self-repair mechanisms that can correct
the harmful changes made by mutations.

Types of Mutations
• In Substitution (point mutation),
a single nucleotide replaces
another nucleotide.
• Deletion (subtracting) or
Insertion (Adding) of a single
base from a normal sequence can
disrupt translation by shifting the
“reading frame” of every
subsequent codon.

H Gene Regulation

• Different cells within an organism share the same set of chromosomes.

• In each cell some genes are active while others are not.
• Each cell produces different proteins according to its needs so that it
does not waste energy by producing proteins that will not be used.
• A variety of mechanisms regulate gene activity in cells. One method
involves turning on or off gene transcription, sometimes by blocking
the action of RNA polymerase (an enzyme that initiates transcription).
 14
• Gene regulation may also involve mechanisms that slow or speed the
rate of transcription, using specialized regulatory proteins that bind to
DNA. A region of DNA known as an operon controls this gene
regulation process.
• Gene regulation in eukaryotes is more complex than in prokaryotes.

III. MENDELIAN INHERITANCE

• Gregor Mendel was the first scientist to observe that characteristics

were inherited as separate units (genes), each of which was inherited
independently of the others.
• Mendel suggested that each parent has pairs genes but contributes only
one of each pair to offspring.
• Mendel recognized that a gene can exist in different forms (alleles),
and he concluded that when an organism has two different alleles, one
of the two may be dominant (represented by a CAPITAL letter) and
the other is said to be recessive (represented by a small letter).
• Mendel also demonstrated that the patterns of inheritance observed in
his experiments with single traits also apply to cases involving more
complex gene combinations.

A. Mendel’s Laws:

1. Law of segregation: states that alleles brought together in the F1

generation can be segregated in the F2 generation.
2. Law of Independent Assortment: states that most of the characters
of parents can appear in any combination in their offspring.
 15
• Mendel’s Laws

B. Exceptions to Mendel’s Rules

• The genetic principles that Mendel first discovered in plants apply to

humans as well, but sometimes genes do not easily conform to the so-
called Mendelian patterns of inheritance.

B1. Incomplete Dominance

• In cases of incomplete dominance, the inheritance of a dominant and a

recessive allele results in production of intermediate characteristics.
For example, four-o’clock paint plants may have red, white, or pink
flowers. Plants with red flowers have two copies of the dominant allele
R for red flower color (RR). Plants with white flowers have two copies
 16
of the recessive allele r for white flower color (rr). Pink flowers result
in plants with one copy of each allele (Rr).

B2. Quantitative Inheritance

• Traits such as skin color differ from the ones Mendel studied because
they are determined by more than one pair of genes.
• In this form of inheritance, known as quantitative inheritance, each
pair of genes has only a slight effect on the trait, while the cumulative
effect of all the genes determines the physical characteristics of the
trait.
• At least four pairs of genes control human skin color.

B3. Multiple Alleles

• Certain traits are controlled by multiple alleles that have complex rules
of dominance.
• In humans, for example, the gene for blood type has three alleles: IA,
IB, and I, with three alternatives for each member of a gene pair, there
are six possible combinations of these genes (IAIA, IBIB, ii, IAi, IBi,
IAIB).
• Although there are six possible combinations, humans have only four
major blood types: A, B, AB, and O. This results because both IA and
IB dominate over i, but not over each other, so a person with a gene
combination of IAIA or IAi has blood type A.
• The gene combinations IBIB and IBi both produce blood type B.
• IAIB results in a blood type AB, and ii results in blood type O.
 17
B4. Gene Linkage

• Today scientists understand that independent assortment occurs when

the genes affecting the phenotypes are found on different
chromosomes.
• When genes occur on the same chromosome, they are inherited as a
single unit. Genes inherited in this way are said to be linked.

B5. Sex-Linked Traits

• Most chromosome pairs consist of identical (homologous) partners.

• In humans, there is one pair of chromosomes in which the partners
noticeably differ from each other. These are called the sex
chromosomes because they determine the differences between males
and females.
• In human females, the sex chromosomes consist of two X
chromosomes, while males have an X chromosome and a shorter Y
chromosome with many fewer genes.
• A male’s X chromosome may contain a recessive allele associated with
a genetic disorder, such as hemophilia and red-green color blindness in
humans.
• Males do not have a normal second copy of the gene on the Y
chromosome to mask the effects of the recessive gene, and disease
typically results in the above cases.
 18
IV. GENES AND DISEASES

• The bases for hereditary diseases are the changes in genes which are
passed on from one generation to the next via the germ line cells.
• About 5% of all newborn babies have inherited disorders which are
the 5th most frequent cause of death.
• Most deaths result from inherited heart disorders followed by
anomalies of the central nervous system as well as urogenital
anomalies and gastrointestinal anomalies (digestive organs).

A. Genetic characteristics of inherited diseases

A1. Chromosome aberrations:

• Changes in the chromosomes themselves are either expressed by a

change in the number of chromosomes (numerical, +) or by changes
in the chromosomal structure (structural e.g. translocation: transfer of
chromosome segments to make a non-homologous chromosome).
• Advanced age in the mother is one risk factor for numerical
chromosome aberrations.

Types of Mutations and Structural Chromosome aberrations

 19
A2. Monogenic diseases:

• In monogenic diseases, only a single gene is altered (mutant) with the

consequence that the pattern for a specific protein is imperfect, which
in turn leads to the development (manifestation) of a disease.
• Monogenic diseases are often rare and cause severe illnesses. Sickle
cell disease is an example of this.
• At present, over 6,000 genes are known whose mutations lead to
various monogenic disorders. Currently, a molecular genetics analysis
can be made on 1,000 of these diseases.

A3. Polygenic diseases:

• It is the interaction of several gene alterations (mutations) which leads

to the development of an illness.
• Polygenic diseases are very common in the population. Environmental
factors (e.g. nutrition, exercise) usually contribute to the manifestation
of these diseases (multifactorial diseases).
• Examples of diseases for which a combination of several genes and
environmental factors are thought to be responsible is Short
sightedness, Diabetes and High blood pressure.

B. Inheritance rules for human genetic diseases

B1. Inheritance process in monogenic diseases

• These inheritance patterns were already observed by Gregor Mendel in

his famous cross-breeding experiments with peas, which form the basis
for today's comprehensive family tree analyses.
 20
Inheritance rules for genetic diseases

• Genes can be represented as more or less strongly influencing factors for

the development of an illness.
• Every illness (X) lies within the control pattern triangle, none lie on an
edge or a corner and predominate factors depends on where the illness is
located inside the triangle.

B1.1. Family Pedigree

• Family pedigrees trace specific genetic characteristics through three

or more generations.
• Pedigrees which illustrate the inheritance of a gene associated with
cystic fibrosis help genetic counselors to identify which individuals in
a family are at risk of either inheriting a genetic disorder or being a
carrier for a disorder.

Family Pedigree
 21
B1.2. Autosomal dominant inheritance process

• A dominant condition is transmitted in unbroken descent from each

generation to the next.
• Only one of the two homologous genes is mutated and although
another normal gene is present (heterozygosity), the illness still appears
(dominant gene effect). If, therefore, one of the parents carries this
gene, there is a 50% probability that it will be transmitted to each
child. Both men and women can be affected by this.
• This inheritance pattern accounts for over 60% of monogenic diseases,
representing by far the most common inheritance process.
• A typical pedigree might looks like this:

• Examples include Tuberous sclerosis and neurofibromatosis.

B1.3. Autosomal recessive inheritance process

• A recessive trait will only manifest itself when both homologous genes
are mutated (homozygosity) in order to produce an illness in the
affected person.
• Both sexes can be affected and individuals, who only receive one
version of the mutated gene, are called carriers (heterozygotes).
 22
• If, both parents are carriers, there is a 25% chance that the child will
receive both mutated genes and so develop the illness.
• If it is a severe condition the homozygotes will not live, thus most
occurrences of the condition will be in matings between two (or
carriers).
• A typical autosomal recessive pedigree might look like this:

• Examples include many metabolic diseases (e.g. cystic fibrosis, and

phenylketonuria).

B1.4. X chromosome inheritance (sex-linked inheritance)

• Women have two X chromosomes. If they have a recessively acting

mutated gene on one X chromosome, they are carriers for the
corresponding illness.
• Men have only one X chromosome, since the other sex chromosome is
a Y chromosome. If they have the mutated gene on the X
chromosome, they will develop the illness as a rule.
• If a woman is a carrier for the illness inherited by the X chromosome,
there is a 50% chance that she will pass on this illness to her son. Her
daughters have a 50% chance of becoming a carrier for this illness.
• A few X-chromosomal genes have a dominant action; in such cases
women can also develop the illness.
 23

B2. Inheritance process in polygenic diseases

• There are always several genes involved in causing polygenic diseases

with different types of interaction possible.
• One or more environmental factors may contribute to the manifestation
of the corresponding illness.
• In general, there is a transition from the healthy state to the
pathological state in polygenic diseases.

V. IDENTIFICATION OF INHERITED DISEASES

A. Conventional genetic tests

A1. Phenotype analysis

• The simplest and the most common type of genetic analysis.

• The analysis involves proteins, the end product of the genes. These
proteins determine the way an individual’s body looks.
• In this type of investigation, a certain body characteristics of the
individual (a phenotype) is examined and compared with members of a
normal population.
• A phenotype analysis is facilitated by conventional clinical and
chemical investigation methods, such as a physical examination to
 24
determine the red-green blindness phenotype, ultrasound or a blood
analysis to determine the blood group.

Red-Green Color Blindness Test

• Individuals with normal color
vision will see the number 57,
while those with red-green
deficiencies will see the number
35.
• Color blindness, an inability to
distinguish between red and
green and sometimes between
blue and yellow, is caused by a
defect in one of the three color-
sensitive cells in the retina.

A2. Chromosome analysis (cytogenetic investigations)

• Cytogeneticists study chromosomes microscopically.

• This includes microscope examinations to investigate chromosome
alterations in terms of number and in terms of structure.
• There is no detailed investigation of individual genes in such cases,
however, there is a new technique which uses a combination of
cytogenetic and molecular genetics methods (molecular cytogenetics),
in which a fluorescence-labelled DNA sequences are often used as
diagnostic “probes”, e.g. “FISH” (Fluorescence in situ hybridization)
• Examples of chromosome aberrations:
- Klinefelter’s syndrome: 47, XXY.
- Edward's Syndrome (Trisomy 18): 47, XY +18.
- Down’s syndrome (mongolism): 47, XY, +21; or 47, XX, +21.
 25
Chromosome Abnormalities (changes in ploidy)

A3. Karyotype:

• A karyotype is a photographic image that shows the sum of all the

chromosome information in an individual cell.
• Images are rearranged so that the chromosomes are lined up in
pairs, typically beginning with the autosomes (Chromosomes 1-22
and ending with the sex chromosomes - normally XX or XY).
• A complete karyotype helps doctors determine if a person has
extra chromosomes or missing chromosomes, or chromosomes that
have attached to one another in unusual ways.
 26
Karyotype

Normal Human Male Karyotype: 46, XY Normal Human Female Karyotype: 46, XX

Chromosome set for trisomy 21 (male) Klinefelter’s syndrome: 47, XXY.

Cytogenetic Molecular cytogenetics

Edward's Syndrome (Trisomy 18): 47, XY Fluorescence in situ hybridization (“FISH”)
+18. of an interphase cell nucleus showing
Edward's Syndrome using a DNA probe
specific for chromosome 18.
 27
B. Molecular genetics testing (DNA and genome analysis)

• This provides evidence of a gene mutation responsible for producing

the illness. Here it is determined whether the sequence of the DNA
bases (nucleotide sequence) has changed within the affected gene.
• This is done as confirmation of preliminary clinical diagnoses,
evidence of carriers or in predictive (including prenatal) investigations.
• Molecular genetics tests rely on revealing short segments of DNA
sequence information and make use of the complementary nature of
the strands of DNA in order to do this.
• There is different techniques available for revealing specific DNA
double-stranded molecules which are all variations of the same basic
principle:
- In DNA sequencing the units of a specific sequence are read off one
after the other;
- In the polymerase chain reaction (PCR) one or several identical
starting sequences are used to generate so many copies that they can
be seen with the naked eye;
- In the Southern blot procedure a mixture of sequences is sorted
electrophoretically according to size before a specific sequence is
made visible in an autoradiograph using, a radioactively labelled
probe.
• With these techniques any deviation of a gene from the “normal state”
can be revealed, whether it is a deletion, an insertion or an exchange of
individual units (point mutation).
 28
• The term direct genetic test is used if the alteration which is found is
the direct cause of an illness.
• In the indirect genetic test (also known as coupling or segregation
analysis), use is made of the fact that scattered all over the human
genome there are sequence segments in which the two homologous
chromosomes can be different.
• These differences in the sequence are in no way pathological; they are
called polymorphisms and are passed on from generation to
generation.
• Polymorphisms can lie inside or outside the genes, but they always
occupy the same chromosomal position (locus).
• If it has been shown that a polymorphism lies close to a gene
responsible for a disease then it can be used as a disease marker.
• Nevertheless, in view of the growing impact of genetics in medicine
(“genetization”), it must be assumed that, in the future, genetic
parameters will replace many conventional diagnostic investigative
procedures as standard practice because of their objectivity.
 29
Molecular Genetics Testing

• Nucleic acid electrophoresis is a method used to separate DNA

fragments to allow their visualization and/or identification.
• DNA sequencing is used to read off the units of a specific sequence
one after the other.
 30

Polymerase Chain Reaction (PCR)

Southern Blotting: Gel Transfer

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