Module

in
Genetics
Table of Contents

Chapter 1 - Introduction to Genetics

1.1 What is Genetics?

1.2 History of Genetics

1.3 Branches of Genetics

Chapter 2 - DNA, RNA and Chromosome

2.1 The DNA

2.2 The RNA

2.3 The Chromosome

2.4 Types of Chromosome

Chapter 3 – Reproductive System

3.1 The Reproductive System

3.2 Human Fertilization

Chapter 4 – Cell Cycle

4.1 Mitosis

4.2 Stages of Mitosis

4.3 Meiosis

Chapter 5 – Fundamentals of Genetics

5.1 Punnett square

5.2 Pedigree

5.3 Law of Inheritance

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Chapter 6 – Matters of Sex
6.1 Sexual Development

6.2 Traits Inherited on the Sex Chromosomes

6.3 Sex-Limited and Sex-Influenced Traits

6.4 X Inactivation

6.5 Genomic Imprinting

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Chapter 1 – Introduction to Genetics

1.1 What is Genetics?

Genetics is the study of genes, genetic variation, and heredity in living

organisms. It is a field of biology that studies how traits are passed from
parents to their offspring. Genetics is a field of science includes the study of
inheritance and genetic variations by investigating the DNA, genes,
genome, chromosome and other components of it. The passing of traits
from parents to offspring is known as heredity, therefore, genetics is the
study of heredity.
The word genetics stems from the ancient
Greek γενετικός genetikos meaning "genitive"/"generative", which in turn
derives from γένεσις genesis meaning "origin".
In a broader sense, we can say, that the study of genes, genome and
chromosome and related inheritance traits is called genetics.

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1.2 History of Genetics
History of Genetics:
Mendel was the pioneer in experimenting and establishing the base of
genetics and hence Gregor Johann Mendel is called the father of genetics.
During the period of 1856 to 1865, he experimented on pea plant and
discovered the phenomenon of “inheritance of traits”. What is called a trait
are now called a gene, that can be inherited from one generation to another
generation.
In 1866, he published his research paper describing the law of
inheritance and independent assortment.

Some of the milestone discoveries in the genetics are enlisted below,

1842: Wilhelm von Nageli, a Swiss botanist, observed the plant cell.
1866: Mendel’s research work published under the title of “experiments on
plant hybridization.”
1869: Friedrich Miescher discovered the nucleic acid.
1888: Waldeyer identified the chromosome present in the cell.
1889: Richard Altmann purified DNA from the protein.
1905: William Bateson coined the term “genetics”.
1908: discovery of Hardy-Weinberg’s law.
1910: Morgan T, explained that the genes are located on the
chromosomes. Also, experimented on Drosophila Melanogaster and
determined the nature of sex-linked traits.
1923: Griffith F, experimented on bacteria and postulated that the DNA is
genetic material.
1953: Watson and Crick identified the structure of DNA.

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1.3 Branches of Genetics

Molecular genetics:
Molecular genetics is an interdisciplinary sub-branch of genetics deals
with the study of the structure and function of DNA as well as genes (at
a molecular level) using techniques such as Polymerase chain reaction
and DNA sequencing.
Using the molecular genetics techniques one can screen pathogenic
mutation, detect SNPs (single nucleotide polymorphism), minor deletion
or duplication at DNA level, changes in the gene expression and identify
mutant DNA sequence.
Using the state of the art techniques such as DNA sequencing we can
also identify some of the novel mutations.

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Polymerase chain reaction, gene cloning, DNA sequencing and DNA
quantification are some of the techniques used in it.
Any of the molecular genetic experiment divided into the 4 sub-steps:
1. Separation of molecule
2. Purification of molecules
3. Processing of molecule
4. Detection of molecule
Separation is a process of extracting molecules like DNA or mRNA from
other cell debris.
We have covered so many articles on DNA extraction. Some of the DNA
extraction methods are enlisted here:
1. Phenol chloroform DNA extraction method
2. Proteinase K DNA extraction method
After that DNA is purified using the ready to use-kit or using alcohol.
Once the purified – good quantity DNA is obtained, it is further
processing for the downstream applications.
PCR:
The polymerase chain reaction is a process in which we can amplify
millions of copies of a DNA segment of our interest in vitro.
The process is temperature-dependent, divided into three steps,
Denaturation: the double-stranded DNA denatured into single-stranded
one.
Annealing: the Sequence-specific DNA primer binds/anneal to its
complementary sequence on single-stranded DNA.
Extention: the taq DNA polymerase amplifies the DNA using the 3′ end
of the primer.
DNA cloning: DNA cloning is a traditional method for the synthesis of
DNA. Using a cloning vector our sequence of interest can be ynthesised
by the bacterial transformation. The method is time-consuming and not
so accurate. synthesised by the bacterial transformation. The method is
time-consuming and not so accurate.
DNA sequencing: The method of
reading the sequence of DNA using a
computational tool is called a DNA
sequencing. In this method, we can
actually analyse any variation or new
mutation in our sequence of interest
using the fluoro-labelled dNTPs.

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Cytogenetics:
Cytogenetics is a sub-branch of genetics including the study of
inheritance through chromosomal analysis using techniques such as
karyotyping, chromosomal staining and chromosomal banding and
FISH.
Structural and numerical chromosomal abnormalities can be screened
using cytogenetic techniques.

Major deletions and duplications (more 10kb) can only be detected

using FISH or DNA microarray techniques.

Disease Abnormality Cytogenetic indication

Down syndrome Numerical Trisomy 21

Klinefelter One extra X chromosome

syndrome Numerical in male (XXY).

Philadelphia Translocation between

syndrome Structural chromosome 9 and 22

monosomy in female,
Turner syndrome Numerical single X chromosome.

Neuroblastoma Structural Chromosome 1p deletion

Some of the structural and numerical anomalies are enlisted in the table
below,

We have already covered a beautiful article on cytogenetics, you can

read it here:
Read our article on Cytogenetics: A Brief Introduction To Cytogenetics.
Human genetics:
The branch of genetics comprises the study of genetic alteration and
its role in the development of the disease especially in humans is called
human genetics.

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Using the cytogenetic, molecular genetics, phylogenetic, population
genetics and clinical genetic methods, any mutation can be
characterised which involved in the development of the disease.
We can study,
 The inheritance pattern of disease.
 The severity of the disease.
 Possibility of inheritance in the consecutive generation
Furthermore, more recently, the genetic techniques are also used in the
screening, prognosis and diagnosis of cancer. So many oncogenes are
now known due to the advancement in genetic.

Preimplantation genetics:
Characterizing or profiling the genetic composition of the embryo
before implantation, the branch of genetics is known as preimplantation
genetics.
Even, the genetic profile of an oocyte or sperm is checked before
fertilization is also covered in the preimplantation genetic study.
The major application of preimplantation genetic is to screen the high-
risk pregnancy.
A couple having the previous history of any genetic disorder can be
suggested for preimplantation genetics.
Selective abortions can be prevented by doing the preimplantation
genetic analysis prior to embryo formation.
Some of the cells from the pre-embryonic stage are taken and grown in
a lab.
That cells can be used for molecular genetic analysis or cytogenetic
analysis, see the figure below,

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Broadly we can say that any of the genetic abnormality or disease can
be identified prior to implantation.
Although the field has some most promising applications, the PIGD still
under pre-clinical trial phase.
Clinical genetics:
This genetic field is involved with the study of disease, finding the root of
the disease, its adverse and related effects and its inheritance pattern.
Plant genetics:
The branch of the genetics deals with the study of genetic variation
and chromosomal abnormalities in plants covered under the plant
genetics.
The mechanism of inheritance was developed from experimenting with
plants. The foundation of genetics laid by experimenting on pea plant by
father of genetics, Mendel.
The state of the art genetic tools like karyotyping, PCR and DNA
sequencing are used in the plant research and GMO studies too.
Genetically modified plant species have tremendous economic value.
Plant genome is modified for creating new variation in native plant
species to increase yields, creating disease resistance, to increase the
nutrition level and to create stress resistance.
BT-cotton and BT- brinjal is the best example of genetically modified
plant species.
Ploidy level in the plant (polyploidy or aneuploidy) can be studied using
standard karyotyping method whereas any alteration in the DNA or any
gene can be studied using the PCR and sequencing method.
Furthermore, species and speciation studies can also be possible using
genetic tools.
Nicotiana benthamiana, Arabidopsis thaliana and Brachypodium
distachyon are some of the model organism used in the plant genetic
studies.
New variation in the plant species can be induced using the gene-editing
method.
One of the traditional gene-editing methods is Agarobacterium mediated
gene transfer.
Mainly the genome of the dicot plants is edited by introducing the gene
in the T-plasmid of Agrobacterium.

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Modern methods like gene gun, particle bombardment and viral vector-
mediated gene transfer are more accurate and advanced methods used
for plant genomic research.
Microbial genetics:
The microbial genetics is an applied branch of genetics includes the
study of the genes, genotypes ad gene expression of microorganism for
various genetic engineering applications.
The study includes bacteria, viruses, archaea, protozoa and some
fungi.
Excluding the RNA viruses, DNA is genetic material in both prokaryotes
as well as in eukaryotes, in addition to this, the hereditary and genotypic
processes in microbes are similar to eukaryotes hence the microbes can
be used as a model organism for studying the genetic traits.
For instance, the operon model has provided information on gene
expression and regulation of different enzymes involved in the
metabolism of biomolecules such as lactose.
Some of the microbes are the proven causative agent for the disease.
By studying those microorganisms infectious diseases can be
prevented.
Furthermore, vaccines and antibiotics against any microbes can be
developed by studying their genetic profile.
New antibiotic resistance species of microorganism can also found using
tools like PCR or DNA sequencing.
Apart from all these, the
microbial genetic study helps in
genetic engineering practices
such as developments of
therapeutic drugs and therapeutic
proteins.
All these studies can be possible
because of the genetic tools used
for the microbial genetic analysis.

Metagenomics:
Meta: Vast or huge, Genomics: a study of genetics or inheritance
The branch of the genetics that deals with the study and identification of
different microorganisms from the environmental sample using modern
genetics techniques is called metagenomic studies.

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Different types of organisms can be studied and identified by studying
the recovered environmental sample without using the cultivation or
culturing method.
The traditional microbiology techniques such as culturing or cultivation
may not help in the identification of all organism present in any
biological/ environmental samples.
A majority of microbial diversity has been missed, contaminated or not
cultured properly that creates a loophole in the study.
Using genetic tools such as DNA sequencing or polymerase chain
reaction, one can identify microbial diversity in any biological sample.
Shotgun sequencing and PCR direct sequencing is commonly used for
the metagenomic analysis.
By extracting DNA from any biological sample, one can identify and
characterise any microorganism present in that sample using the
species-specific and sequence-specific primers and bioinformatic tools.
A powerful tool sequencing can even identify any unknown organism or
new microbe or strains of microorganism.
Population genetics:
An interdisciplinary branch of the genetics includes the study of genetic
difference within and between the population or individual is known as
population genetics.
By doing mathematical calculations, statistical analysis, fieldwork and
genetic analysis one can calculate the genetic frequency, allelic
frequency and other factors with respect to the population.
Epigenetics:
The branch of the genetics deals with the study of alterations in an
organism caused by gene expression rather than alteration caused by a
gene mutation.
In simple words, epigenetics is a study of a switch on and off of gene
expression.
Different genes expressed in different amount in different cells and
create various tissue types.
What we eat, how we sleep, how we exercise and stress has a major
impact on our epigenetic profile.
Some of the epigenetic factors like methylation, ubiquitination,
acetylation and histone modification and activate oncogene and causes
cancer.

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Biochemical genetics:
The branch of the genetics related to studying the chemistry of DNA,
gene, chromosome, RNA and related biomolecules is called as
biochemical genetics.
Physiological genetics:
Physiological genetics deals with the study of physiological
characteristics such as sex differentiation and sex determination, blood
group factor and sickle cell anaemia like physiological conditions.
Quantitative genetics:
It is actually a branch of the population genetics which studies the
continuously varying phenotypes. The correlation between phenotype
and related genotype is the base for quantitative genetics.
Conservation genetics:
Again, conservative genetics is a subfield of population genetics in
which, using the genetic tools and by understanding the dynamics of
genes and its expression profile, endangered species of plants, animals
and other organisms can be conserved.
Behavioural genetics:
The field of genetics study the behavioural phenotypes of an organism
governed by the genetic factors are called behaviour genetics.The
behaviour of an organism is influenced by the interaction between the
environment and genetic composition.Some of the behaviours of ours
are governed by inherited genetic factors. Read our article on
it: Behavioural Genetics: Science behind the behaviour.

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 CHAPTER 2: DNA, RNA and
CHROMOSOMES

2.1 the DNA

DNA
Most organisms contain DNA except
some viruses which contain RNA as their
genetic material. DNA was discovered by
two scientists- Watson and Crick and their
model of the structure of DNA are called
the Watson and Crick model. The structure
of DNA is said to be a double- helical
structure with two strands of DNA that are
wound around each other. Each strand of
DNA is made up of a sequence of
nucleotide monomers. Each nucleotide is
made up of:

 Deoxyribose sugar
 One of the four nitrogen bases
 Phosphate group
The nitrogen bases found in a DNA molecule are Adenine, Thymine,
Cytosine, and Guanine. The nucleotides create a chain via covalent bonds
that are formed between the phosphate of one nucleotide and the sugar of
the adjacent one. The two strands of DNA are held together by hydrogen
bonds between complementary nitrogen bases i.e. Adenine with Thymine
and Cytosine with Guanine.

A DNA molecule is said to be stable enough to be able to replicate itself.

DNA replication involves RNA intermediates. The part of the DNA which
codes for specific proteins during the replication is called as the gene.

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2.2 The RNA

RNA

Image Source: javatpoint

Unlike the DNA, RNA is a single-stranded genetic material. The nucleotide

bases present in RNA are similar to those in DNA except that thymine is
replaced by uracil and pairs with adenine. While DNA is the genetic material
in most organisms, RNA is found in a few viruses. RNA is of three types
depending on their function:

 tRNA or transfer RNA- helps transfer the amino acids from the mRNA to
the ribosomes.
 mRNA or messenger RNA- helps to carry the codes for amino acids
from the DNA to the ribosomes
 rRNA or ribosomal RNA- are found on the ribosomes and help in protein
synthesis.

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2.3 The chromosome

Image Source: pinterest

Now that we know what the units of heredity are, let us understand what
chromosomes are. The DNA that is found in the nucleus of each cell occurs
as a tightly coiled package around proteins called as histones. These thread-
like packaged structures of DNA are called as chromosomes.

Humans have 23 pairs of chromosomes (or 46 chromosomes). 22 pairs

are called autosomes and one pair is called the sex chromosomes. Females
in humans have 2 X(XX) chromosomes whereas males have one X and one
Y (XY) chromosomes. The number of chromosomes varies in different
animal species.

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 Each chromosome is said to be divided into two unequal halves by a
centromere into two arms. The short arm is called as ‘p arm’ and the longer
arm is known as the ‘q arm’.

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 2.4 The Types of Chromosome
Types of Chromosomes
Chromosomes are divided into two parts (p and q arms) with a
constriction point called a centromere in the middle.
The centromere can be located in different positions and this
forms the basis for the four different classes of chromosome:

Metacentric – centromere is in middle, meaning p and q arms are of

comparable length (e.g. chromosomes 1, 3, 16, 19, 20)
Submetacentric – centromere off-centre, leading to shorter p arm relative
to q arm (e.g. chromosomes 2, 4 – 12, 17, 18, X)
Acrocentric – centromere severely off-set from centre, leading to much
shorter p arm (e.g. chromosomes 13 – 15, 21, 22, Y)
Telocentric – centromere found at end of chromosome, meaning no p arm
exists (chromosome not found in humans)

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 Chapter 3 – The Reproductive
System
Human reproductive system, organ system by which humans
reproduce and bear live offspring. Provided all organs are present, normally
constructed, and functioning properly, the essential features of
human reproduction are (1) liberation of an ovum, or egg, at a specific time
in the reproductive cycle, (2) internal fertilization of the ovum by
spermatozoa, or sperm cells, (3) transport of the fertilized ovum to
the uterus, or womb, (4) implantation of the blastocyst, the early embryo
developed from the fertilized ovum, in the wall of the uterus, (5) formation
of a placenta and maintenance of the unborn child during the entire period
of gestation, (6) birth of the child and expulsion of the placenta, and (7)
suckling and care of the child, with an eventual return of the maternal
organs to virtually their original state.
For this biological process to be carried out, certain organs and structures
are required in both the male and the female. The source of the ova (the
female germ cells) is the female ovary; that of spermatozoa (the male germ
cells) is the testis. In females, the two ovaries are situated in the pelvic
cavity; in males, the two testes are enveloped in a sac of skin, the scrotum,
lying below and outside the abdomen. Besides producing the germ cells,
or gametes, the ovaries and testes are the source of hormones that cause
full development of secondary sexual characteristics and also the proper
functioning of the reproductive tracts. These tracts comprise the fallopian
tubes, the uterus, the vagina, and associated structures in females and
the penis, the sperm channels (epididymis, ductus deferens, and
ejaculatory ducts), and other related structures and glands in males. The
function of the fallopian tube is to convey an ovum, which is fertilized in the
tube, to the uterus, where gestation (development before birth) takes place.
The function of the male ducts is to convey spermatozoa from the testis, to
store them, and, when ejaculation occurs, to eject them with secretions
from the male glands through the penis.

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 Organs of the female reproductive system.Encyclopædia Britannica, Inc.
Organs of the male reproductive system.Encyclopædia Britannica, Inc.

At copulation, or sexual intercourse, the erect penis is inserted into the vagina, and
spermatozoa contained in the seminal fluid (semen) are ejaculated into the female
genital tract. Spermatozoa then pass from the vagina through the uterus to the fallopian
tube to fertilize the ovum in the outer part of the tube. Females exhibit a periodicity in
the activity of their ovaries and uterus, which starts at puberty and ends at
the menopause. The periodicity is manifested by menstruation at intervals of about 28
days; important changes occur in the ovaries and uterus during each reproductive, or
menstrual, cycle. Periodicity, and subsequently menstruation, is suppressed during
pregnancy and lactation.

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3.2 Human Fertilization

Human fertilization is the union of a human egg and sperm,

usually occurring in the ampulla of the fallopian tube.[1] The result
of this union is the production of a zygote cell, or fertilized egg,
initiating prenatal development. Scientists discovered the
dynamics of human fertilization in the nineteenth century.[2]
The process of fertilization involves a sperm fusing with an ovum.
The most common sequence begins
with ejaculation during copulation, follows with ovulation, and
finishes with fertilization. Various exceptions to this sequence are
possible, including artificial insemination, in vitro fertilization,
external ejaculation without copulation, or copulation shortly after
ovulation.[3][4][5] Upon encountering the secondary oocyte, the
acrosome of the sperm produces enzymes which allow it to
burrow through the outer jelly coat of the egg. The sperm plasma,
then fuses with the egg's plasma membrane, the sperm head
disconnects from its flagellum and the egg travels down the
Fallopian tube to reach the uterus.

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 Chapter 4 Cell Cycle

The cell cycle

Actively dividing eukaryote cells pass through a series of stages known collectively as
the cell cycle: two gap phases (G1 and G2); an S (for synthesis) phase, in which the
genetic material is duplicated; and an M phase, in which mitosis partitions the genetic
material and the cell divides.

 G1 phase. Metabolic changes prepare the cell for division. At a certain point - the
restriction point - the cell is committed to division and moves into the S phase.
 S phase. DNA synthesis replicates the genetic material. Each chromosome now
consists of two sister chromatids.
 G2 phase. Metabolic changes assemble the cytoplasmic materials necessary for
mitosis and cytokinesis.
 M phase. A nuclear division (mitosis) followed by a cell division (cytokinesis).
The period between mitotic divisions - that is, G1, S and G2 - is known as interphase.

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4.1 Mitosis

Mitosis

Mitosis is a form of eukaryotic cell division that produces two daughter cells with the
same genetic component as the parent cell. Chromosomes replicated during the S
phase are divided in such a way as to ensure that each daughter cell receives a copy of
every chromosome. In actively dividing animal cells, the whole process takes about one
hour.

The replicated chromosomes are attached to a 'mitotic apparatus' that aligns them
and then separates the sister chromatids to produce an even partitioning of the genetic
material. This separation of the genetic material in a mitotic nuclear division
(or karyokinesis) is followed by a separation of the cell cytoplasm in a cellular division
(or cytokinesis) to produce two daughter cells.
In some single-celled organisms mitosis forms the basis of asexual reproduction. In
diploid multicellular organisms sexual reproduction involves the fusion of two haploid
gametes to produce a diploid zygote. Mitotic divisions of the zygote and daughter cells
are then responsible for the subsequent growth and development of the organism. In
the adult organism, mitosis plays a role in cell replacement, wound healing and tumour
formation.

Mitosis, although a continuous process, is conventionally divided into five stages:

prophase, prometaphase, metaphase, anaphase and telophase.

A replication followed by two successive nuclear and cellular divisions (Meiosis I and
Meiosis II). As in mitosis, meiosis is preceded by a process of DNA replication that
converts each chromosome into two sister chromatids.

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Meiosis I
Meiosis I separates the pairs of homologous chromosomes.

In Meiosis I a special cell division reduces the cell from diploid to haploid.

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 Prophase I

The homologous chromosomes pair and exchange DNA to form recombinant chromosomes. Prophase I is

divided into five phases:

 Leptotene: chromosomes start to condense.

 Zygotene: homologous chromosomes become closely associated (synapsis) to form pairs of chromosomes
(bivalents) consisting of four chromatids (tetrads).
 Pachytene: crossing over between pairs of homologous chromosomes to form chiasmata (sing. chiasma).
 Diplotene: homologous chromosomes start to separate but remain attached by chiasmata.
 Diakinesis: homologous chromosomes continue to separate, and chiasmata move to the ends of the
chromosomes.

Prometaphase I

Spindle apparatus formed, and chromosomes attached to spindle fibres by kinetochores.

Metaphase I

Homologous pairs of chromosomes (bivalents) arranged as a double row along the metaphase plate. The

arrangement of the paired chromosomes with respect to the poles of the spindle apparatus is random along the

metaphase plate. (This is a source of genetic variation through random assortment, as the paternal and

maternal chromosomes in a homologous pair are similar but not identical. The number of possible

arrangements is 2n, where n is the number of chromosomes in a haploid set. Human beings have 23 different

chromosomes, so the number of possible combinations is 223, which is over 8 million.)

Anaphase I

The homologous chromosomes in each bivalent are separated and move to the opposite poles of the cell

Telophase I

The chromosomes become diffuse and the nuclear membrane reforms.

Cytokinesis

The final cellular division to form two new cells, followed by Meiosis II. Meiosis I is a reduction division: the

original diploid cell had two copies of each chromosome; the newly formed haploid cells have one copy of each

chromosome.

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Meiosis II
Meiosis II separates each chromosome into two chromatids.

The events of Meiosis II are analogous to those of a mitotic division, although the number of chromosomes

involved has been halved.

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 Meiosis generates genetic diversity through:
 the exchange of genetic material between homologous chromosomes during Meiosis I

 the random alignment of maternal and paternal chromosomes in Meiosis I

 the random alignment of the sister chromatids at Meiosis II

Meiosis in females

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28
 Chapter 5 – Fundamentals of
Genetics
5.1 Punnet Square

Punnett Square
A Punnett square is a graphical representation of the possible genotypes
of an offspring arising from a particular cross or breeding event. Creating a
Punnett square requires knowledge of the genetic composition of the
parents. The various possible combinations of their gametes are
encapsulated in a tabular format. Therefore, each box in the table
represents one fertilization event.
The inherent assumption is that each trait is determined by a
single gene locus and that various traits assort independently from one
another. Though this is true for many useful traits, especially when
choosing characters for plant or animal breeding, there are many
exceptions.
This tool was created in the twentieth century, much after Mendel’s
seminal experiments on genetics. However, they are now commonly used
to explain the results that Mendel obtained, especially when combined with
our current knowledge of DNA, genes and chromosomes.

Functions of Punnett Squares

In large-scale experiments, such as those conducted by Mendel, Punnett
squares can accurately predict the ratios of various observable traits as
well as their underlying genetic composition. For instance, when a true-
breeding tall pea plant is cross fertilized with pollen from a true-breeding
short pea plant, the Punnett square can predict that all the offspring will be
tall, and all of them will be heterozygous with both the allele for shortness
and tallness. It can further predict that if these heterozygous plants are
allowed to self-fertilize, approximately seventy-five percent of the second
generation plants will be tall, and the remaining twenty-five percent will be
short. Among the tall plants, one-third will remain true-breeding while the
remaining two-thirds will be heterozygous. This tool is therefore used by

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plant and animal breeders to choose appropriate specimens in order to
obtain offspring carrying a desired trait.

Types of Punnett Squares

Two types of Punnett squares are commonly used. The first is relevant
when a single trait determined by one genetic locus is being observed. This
is called a monohybrid cross and examples include some of Mendel’s
original experiments, where he chose true-breeders for a single trait and
crossed them with members carrying a different allele. For a monohybrid
cross, these are 2X2 squares with four boxes, each representing one
fertilization event between the parent gametes.
The second type is used to predict the outcome of breeding experiments
where two traits are being followed and the Punnett square is larger, with
sixteen boxes. The 4X4 square is necessary since each of the parents can
produce four types of gametes, based on the distribution of the alleles of
the two genes.
When more than two traits are being observed, a Punnett square
becomes unwieldy and other tools are used to predict the outcomes of
such crosses.

Seed Color in Common Pea Plant Pisum sativum

Mendel created true-breeding homozygous plants for both the alleles –

yellow and green color seeds. When he cross pollinated these
homozygotes, he found that all the offspring had yellow seeds. When he
allowed these yellow offspring to undergo self pollination, he was surprised
to find that nearly twenty-five percent of the second generation of pea
plants contained green seeds. He concluded that the yellow allele was
dominant over the green one. In order to better understand this
phenomenon, he crossed some of the first generation plants with yellow
seeds with a true-breeding green plant. This would later be known as a test
cross.
In every Punnett square, an allele is represented by the first letter of the
dominant phenotype. In this case, the dominant yellow color allele is
denoted by the capital letter ‘Y’ and the recessive allele by the small letter
‘y’.

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 Each allele is allowed to segregate
independently into a gamete and the
gametes are represented just outside
the 2X2 table.
Each of the boxes shows one
possible genotype for the offspring. In
this test cross, half the offspring have
yellow seeds and are genotypically
heterozygous. The other half are
homozygous and have green seeds.

Tail And Hair Color in Cats

When a homozygous short-tailed, white haired cat is mated with a long-tailed
brown haired cat, all the offspring appear to inherit one trait from each parent.
They all have short tails and brown hair, showing that brown color is dominant
over white and the allele for a short tail is dominant over the one for a long tail.
When members of this first generation mate with each other, a large majority of
their offspring will have short tails and brown hair. Additionally, there is a three-in-
sixteen probability that the parental combinations will reappear: short tail with
white hair or long tail with brown hair. Finally, there is a one-in-sixteen probability
that a new combination could appear – long-tailed and white colored.
If an animal breeder was looking for a long-tailed, white-haired specimen, he
would know that it would only appear in the second generation.

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5.2 Pedigree

Pedigree analysis describes the process of interpretation of

information displayed as a family tree. The family tree or pedigree is
constructed using a standardized set of symbols and will include
information about the disease status of each individual. If only a single
individual is affected within the family then the pedigree cannot in itself
provide proof for a particular mode of inheritance and cannot
distinguish inherited from noninherited conditions. When more than
one individual is affected then the pattern may provide important clues
or even proof of the mode of inheritance. There are four main patterns
of inheritance that may be seen in a pedigree.

Pedigree showing affected individuals and carriers.

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5.3 Law of Inheritance

Laws of Inheritance
Gregor Johann Mendel was a scientist who is recognized as the Father
and Founder of genetics. Mendel conducted many experiments on the pea
plant (Pisum sativum) between 1856 and 1863. He studied the results of the
experiments and deducted many observations. Thus, laws of inheritance or
Mendel’s laws of inheritance came into existence. Before learning about
Mendel’s laws of inheritance, it is important to understand what the
experiments performed by Mendel were.

Mendel’s Experiments on Pea Plant

Mendel after carefully study selected the pea plant for many reasons:

 The pea plants were easy to grow and maintain

 It has many clearly distinct and contrasting characters.
 The pea plant is an annual plant and so many generations of
the plant can be studied in a short period of time.
 Peas are naturally self-pollinating but can also be cross-pollinated.

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Mendel made a list of contrasting characters which he studied:

Image Source: bioninja

Mendel structured his experiments in a way that he would observe one pair
of contrasting characters at one time. He began his experiments using
purebred lines for contrasting characters.

He cross-pollinated two pure lines for contrasting characters and the

resultant offsprings were called F1 generation (also called the first filial
generation). The F1 generations were then self-pollinated which gave rise to
the F2 generation of second filial generation.

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Results of Mendel’s Experiments
Let us look at the results of Mendel’s experiments on crossing a pure tall pea
plant with a pure short pea plant.

 In the F1 generation, Mendel observed that all plants were tall. there
were no dwarf plants.
 In the F2 generation, Mendel observed that 3 of the offsprings were tall
whereas 1 was dwarf.
 Similar results were found when Mendel studied other characters.
 Mendel observed that in the F1 generation, the characters of only one
parent appeared whereas, in the F2 generation, the characters of the
other parent also appeared.
 The characters that appear in the F1 generation are called dominant
traits and those that appear for the first time in the F2 generation are
called recessive traits.

Conclusions

 The genes that are passed from the parents to the offsprings exist in pairs. These
pairs are called alleles.

 When the two alleles are the same, they are called homozygous. When both the
alleles are different, they are called as heterozygous.

 Dominant characters are described using capital letters and recessive using small
letters. For example, the dominant genes for tallness in a pea plant are written as TT
and recessive genes as tt. The heterozygous genes are written as Tt where the plant
appears tall has the recessive gene which might express itself in the future
generations.

 The appearance of the plant is known as the phenotype whereas the genetic
makeup of the plant is called the genotype. So, a plant with Tt genes appears tall
phenotypically but has a recessive gene.

 During gametogenesis, when the chromosomes become half in the gametes, there
is a 50% chance of either of the alleles to fuse with that of the other parent to form a
zygote.

Based on these observations, Mendel proposed three laws.

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 3 Laws of Inheritance
Mendel proposed three laws:

 Law of Dominance
 The Law of Segregation
 Law of independent assortment

Law of Dominance

Image Source: gladewaterbiology

This law states that in a

heterozygous condition, the allele
whose characters are expressed over
the other allele is called the dominant
allele and the characters of this
dominant allele are called dominant
characters. The characters that appear
in the F1 generation are called as
dominant characters. The recessive
characters appear in the F2 generation.

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Law of Segregation

Image source:
wikipedia

This law states that when two traits come together in one hybrid pair, the
two characters do not mix with each other and are independent of each
other. Each gamete receives one of the two alleles during meiosis of the
chromosome.

Mendel’s law of segregations supports the phenotypic ratio of 3:1 i.e. the
homozygous dominant and heterozygous offsprings show dominant traits
while the homozygous recessive shows the recessive trait.

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Law of Independent Assortment

Image Source: biology-forums

This means that at the time of gamete formation, the two genes segregate
independently of each other as well as of other traits. Law of independent
assortment emphasizes that there are separate genes for separate traits and
characters and they influence and sort themselves independently of the other
genes.

This law also says that at the time of gamete and zygote formation, the
genes are independently passed on from the parents to the offspring.

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 Chapter 6 – Matter of Sex

6.1 Sexual Development

Sexual Development
5th week - All embryos develop two unspecialized gonads.Either testes or
ovaries.
Each such ''indifferent'' gonad forms near two sets of ducts that present
two developmental options.

6th week - The choice to follow a male or female developmental pathway

occurs. Depending upon the sex chromosome constitution and actions of
genes.
Male - if a gene on the Y chromosome called SRY (sex-determining region
of the Y) is activated.
Female – if there's absence of SRY activation.

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 Human males & females have equal number of chromosomes.
Males- have x and y chromosomes.
Females- have two x chromosomes.
Heterogametic sex - w/ 2 different sex chromosomes
Homogametic sex – w/ 2 same sex chromosomes.

Sex chromosomes
X chromosome
- Contains 1,500 genes
- Larger than the Y chromosome
- Acts as a homolog to Y in males
Y chromosome
- Contains 231 genes
– Many DNA segments are palindromes and may destabilize DNA

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Anatomy of the Y chromosome
● Y chromosome has SRY (sex-determining
region of the Y)
SRY - the master regulator of maleness
- turns on genes for production of male
hormones
Y chromosome
● human Y chromosome is particularly
exposed to high mutation rates due to highly
oxidative environment of the testis.

The phenotype forms

● SRY gene encodes a very important type of protein called transcription
factor.
- it stimulates male development by sending signals to the indifferent
gonads.
Sustentacular cells in the testis secrete anti-Mullerian hormone, which
destroys potential female structures.
Interstitial cells in the testis secrete testosterone, which stimulates the
development of male structures.
Some testosterone is also converted to dihydrotestosterone (DHT), which
directs development of the urethra, prostate gland, penis, and scrotum.

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Genetic abnormalities can intervine in different points.
For example:
In Androgen Insensitivity Androgen
Insensitivity Syndrome (OMIM 300068)
(OMIM 300068), caused by mutation in
X chromosome, the absence of
receptors for androgen, stops cells in
early reproductive structures from
receiving the signal to develop as male.
The person looks female but is XY.
Genetic abnormalities can intervine in
different points.

Hermaphroditism - a term for an

individual with both male and female
sexual structures.

Intersex- refers to individuals whose internal structures are inconsistent

with external structures.
Pseudohermaphroditism - presence of both types of structures but at
different stages of life.

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Is Homosexuality inherited?
- a person's phenotype and genotype are consistent, and physical
attraction genotype are consistent, and physical attraction is toward
members of the same sex.
Sex ratio
In Mendel's law of segregation, populations should have approximately
equal numbers of male and female new-borns.
Sex ratio- proportion of males to females in a human population.
Primary sex ratio – At conception
Secondary sex ratio – At birth
Tertiary sex ratio – At maturity Sex ratios can change markedly with age.

6.2 Traits Inherited on the Sex Chromosomes

Y-linked – genes carried on Y chromosome.
In females:
2 copies of X-linked = recessive allele
1 copy of X-linked = dominant allele
In males:
single copy of X-linked = dominant (expression of trait or illness
because there's no copy of gene on the 2nd X chromosome.)

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SEX DETERMINATION DETERMINATION IN HUMANS
An oocyte has a single X chromosome.
A sperm cell has either an X or Y
chromosome. If a Y-bearing sperm cell
with a functional SRY gene fertilizes an
oocyte, the zygote is a male (XY). If an
X-bearing sperm fertilizes an oocyte, the
zygote is a female (XX).
Human male is considered hemizygous
for Xlinked trait because he has only one
set of Xlinked genes.
A male inherits his Y chromosome from his father and X chromosome
from his mother. A female inherits one X chromosome from each parent.

X-Linked Recessive
Inheritance
An X-linked trait passes from
an unaffected heterozygous
mother to an affected son.
X-Linked Dominant
Inheritance
A female who inherits a dominant X-linked allele has the associated traits
or illness, but a male who inherits the allele is usually more severely
affected because he has only on copy of X-linked allele.

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Incontinentia Pigmenti (IP)
A newborn girl with IP has yellow, pus-filled
vesicles on her limbs that come and go
over the 1st few weeks. Then the lesions
become warty to brown splotches that may
remain for life, although they remain for life.
Males with this condition are so severely
affected that they do not survive to be born.

Congenital Generalized Hypertrichosis

- produces many extra hair follicles, and
hence denser and more abundant in upper
body hair. - Hair growth is milder and
patchier in females because of hormonal
differences and the presence of a second
X chromosome.

Solving a problem: X-linked Inheritance

(using Mendel's Law of Segregation)
Consider a Kallmann syndrome (OMIM 308700), which causes very poor or
absent sense of smell and small testes or ovaries. It is X-linked recessive.
Tanisha does not have Kallmann syndrome, but her brother Jamal and her
maternal cousin Malcolm have it. Tanisha's and Malcolm's parents are
unaffected, as is Tanisha's husband Sam. Tanisha and Sam wish to know
the risk that a son would inherit the condition. Sam has no affected
relatives.
Steps to follow:
1) Look at the inheritance pattern
2) Draw a pedigree
3) List genotypes & phenotypes and their probabilities
4) Assign genotypes and phenotypes

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5) Use Punnett square to determine ratios
6) Repeat for next generation

6.3 Sex-Limited and Sex-Influenced Traits

Sex-limited traits
A sex-limited trait affects a structure or function of the body that is
present in only males or only females.
Sex-influenced trait
In a sex-influenced trait, sex-influenced trait, an allele is dominant in one
sex but recessive in the other.
Pattern baldness is a sex-influenced trait. Male pattern baldness is related
to your genes and male sex hormones. It usually follows a pattern of
receding hairline and hair thinning on the crown, and is caused by
hormones and genetic predisposition.
6.4 X Inactivation
X inactivation- is a process by which one of the two copies of the X
chromosome present in female is inactivated. The inactive X chromosome
is silenced by its being packaged in such a way that it has a
transcriptionally inactive structure is called heterochromatin.
Equaling out the sexes
Females have two alleles for X
chromosome genes but males
have only one but males have
only one
In mammals, X inactivation
balances this inequality and one X
chromosome is randomly
inactivated in each cell.
The inactivated X chromosome is
called a Barr body.

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X inactivation occurs early in prenatal development. A gene called XIST
controls the inactivation. It encodes an RNA that binds to a specific site on
the (inactive) X chromosome and inactivates it.
Effect on the phenotype
A carrier of an X-linked trait that expresses the phenotype is called a
manifesting heterozygote.
A female who is heterozygous for an X-linked recessive gene can
expressed the associated condition if the normal allele is inactivated in the
tissues that the illness affects.

Hunter Syndrome (mucopolysaccharidosis II)

- cells that make the enzyme readily send it to
neighboring cellz essentially correcting the
defect in cells that can't make the enzyme.
Affected boys are deaf, mentally retarded,
have dwarfism and abnormal facial features,
heart damage, and enlarged liver and spleen.

Fabry Disease (alpha-galactosidase A deficiency)

- cells that make the enzyme readily send it to
neighboring cellz essentially correcting the
defect in cells that can't make the enzyme.
Affecteentally retarded, have dwarfism and
abnormal facial features, heart damage, and
enlarged liver and spleen.

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6.5 Genomic Imprinting
The phenotype of an individual differs depending on the gene’s parental
origin.
Genomic Imprinting - a molecule covers a gene or several linked genes
and prevents them from being accessed to synthesize protein.
The silencing the contribution from one parent
Importance of Genomic Imprinting
Imprints are erased during meiosis - Then reinstituted according to the
sex of the individual It takes two opposite sex parents to produce a healthy
embryo
- Male genome controls placenta development
- Female genome controls embryo development
Genomic imprinting can explain incomplete penetrance, in which an
individual is known to have inherited a genotype associated with a
particular phenotype, but has no signs of the traits. The predicted
genotype is present, but the associated phenotype is not expressed.
Imprinting may be an important concern in assisted reproductive
technologies that manipulate gametes to treat infertility.
For example:
Angelman syndrome (OMIM 105830)
and Becwith Wiedemann syndrome
(OMIM 130650) are more prevalent
among the offspring of people who used
in vitro fertilization and intracytoplasmic
sperm injection to become pregnant.

Imprinting Disorders in Humans

Increased severity depends on whether it is inherited from the father or
mother or may depend on uniparental disomy. It means ''two bodies from
one parent'', and refers to an offspring who inherits both copies of a gene
from one parent and none from the other.

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