Rdmiguel Genetics

Republic of the Philippines
DAVAO DEL SUR STATE COLLEGE

Sulop Extension Campus
Sulop, Davao del Sur
GENETICS
A Course Pack Prepared by
Richie D. Miguel, Lic. Agr.
Faculty, Agriculture Department

Institute of Agriculture and Related Sciences
Miguel, R.D. (2020). Genetics for Flexible Learning. | 1

Course Pack Structure
Module I: The Science of Heredity and Variation

Lesson 1. Definition and Basic Concepts of genetics
Lesson 2. The Beginnings of Genetics
Students Learning Outcomes
At the end of the module, students will be able to:

1. Understand, discuss and explain the principles and concepts involved in the
study of heredity and variation.
2. Know the history of genetics
Module II. Mendel’s Laws and The Chromosomal Basis of Heredity

Lesson 1. Mendel’s Laws
Lesson 2. Mitosis and Meiosis
Lesson 3. Probability and Statistics
Lesson 4. Sex Determination, Sex Linkage, And Pedigree Analysis
Lesson 5. Linkage and Mapping in Eukaryotes, Prokaryotes and Bacterial Viruses
Lesson 6. Cytogenetics
Students Learning Outcomes

1. Describe the basic concept of Mendel’s Laws

2. Describe the principles of the chromosomal basis of heredity
Module III. The Chemical Basis of Heredity
Lesson 1. The Chemical Nature of the Gene and DNA Replication
Lesson 2. Gene Expression: Transcription and Translation
Lesson 3. Control of Gene Expression
Lesson 4. DNA Mutation, Repair and Recombination
Lesson 5. Genomics, Biotechnology and Recombinant DNA
Lesson 6. Non-Mendelian Inheritance
Students learning Outcomes

1. Understand the concepts of the chemical basis of heredity
2. Describe the central dogma
3. Describe the forces that affects gene expression
4. Discuss non-mendelian concept of inheritance
Module IV. Quantitative, Population and Evolutionary Genetics

Lesson 1. Quantitative Genetics
Lesson 2. Population and Evolutionary Genetics
Students learning Outcomes

1. Define and describe important population and quantitative genetic concepts
and its applications

Table of Contents
Module I. The Science of heredity and Variation 1

Lesson 1. Definition and Basic Concepts 2
Lesson 2. The Beginnings of Genetics 6
Module II. Mendel’s laws and the Chromosomal Basis of Heredity 10

Lesson 1. Mendel’s Laws 11
Lesson 2. Mitosis and Meiosis 24
Lesson 3. Probability and Statistics 33
Lesson 4. Sex Determination, Sex linkage and Pedigree Analysis 43
Lesson 5. Linkage and Mapping in Eukaryotes, prokaryotes and Bacterial Viruses 54
Lesson 6. Cytogenetics 65
Module III. The Chemical Basis of Heredity 72

Lesson 1. The Chemical nature of the Genes and DNA Replication 73
Lesson 2. Gene Expression: Transcription and Translation 92
Lesson 3. Control of Gene Expression 103
Lesson 4. DNA Mutation, Repair and Recombination 110
Lesson 5. Genomics, Biotechnology and Recombinant DNA 118
Lesson 6. Non-Mendelian Inheritance 133
Module IV. Quantitative, Population and Evolutionary Genetics 140

Lesson 1. Quantitative Genetics 141
Lesson 2. Population and Evolutionary Genetics 148

Module 1
Principles and Practices of Plant Breeding
Module Overview
Plant breeding aims to improve crops in

terms of yield, tolerance to environmental condition,
resistance to pest and diseases and for aesthetic
purposes. Plant breeding requires knowledge in
production and genetics. In this module principles
and practices of plant breeding will be introduced.
Unit I discuss the definition of terms related to plant
breeding, its nature and importance. We will also look
back into the history and development of plant
breeding. The issues involve in the development of
improve crop varieties will also be discussed. Unit II
explores the patterns of evolution of cultivated
species and the concept of centers of origin and
diversity. In Unit III, we will discover the mode of
reproduction of crop species, pollination control and
plant breeding methods for specific characters. The
last part of this module (Unit IV) explores variety
testing and release, seed production and distribution
of commercial varieties in the Philippines.
Objectives
At the end of this module, students are expected to:
 Understand the nature and importance of plant breeding
 Understand and describe the patterns of evolution of cultivated crop species and
the concepts of centers of origin and diversity.
 Understand and demonstrate the mode of reproduction and breeding methods of
self- and cross-pollinated crop species
 Discuss the methods of varietal testing, release, production and distribution of
commercial crop varieties in the Philippines.
Lessons in this Module

Unit I. Introduction to Plant Breeding
Unit II. Patterns of Evolution of Cultivated Species and the Concept of Centers of Origin and
Diversity
Unit III. Mode of Reproduction of Crop Species, Pollination Control and Plant Breeding Methods
for Specific Characters
Unit IV. Variety Testing and Release, Seed Production and Distribution of Commercial
Varieties in the Philippines

Module 1
Unit I. Introduction to Plant Breeding
Time Frame: 5 Hours Lesson 1
Learning Objectives Definition, Nature and Importance

 Define the important terms
of Plant Breeding
related to plant breeding.
Introduction
 Describe the nature of plant
breeding. Crop improvement is realized through plant
 Describe the importance of breeding. Plant breeding is important for the
plant breeding. sustainability of crop production in relation to
Key Concepts adaption to the changing climatic condition, pest
insurgence as well as exponential increase in
❖ Genetic terminologies population. This lesson discusses the definition of
❖ Basic concepts
terms related to plant breeding. We will discover the
❖ Importance of genetics
❖ Role of genetics nature of plant breeding for the improvement of
❖ Scope of genetics cultivated crop species. We will also discuss the
importance of plant breeding.
ActivityActivity
1 The Basics of Genetics
1
Let us test your memory with common Analysis
genetic terminologies. You probably 1. How many of the terms you
encountered them in your biology class. answered correctly? Which
term(s) did you have difficulties
Procedure:
in defining?
1. Give your own definition for each 2. Having defined the common
common genetic terms you see on terms in genetics, how important
the box below. is genetics to your daily life?
2. Once you are finished, compare it 3. What is the role of genetics in
to the definition you found on the your pursuit of a career in
internet, in a dictionary or in a agriculture?
book.
Define the following terms:

12. DNA 1. Biotechnology 6. Transmission genetics
13. Gene 2. Variation 7. Molecular Genetics
14. Cell 3. Mutation 8. Population genetics
15. Chromosome 4. Inheritance 9. Alleles
16. Nucleus 5. Heredity 10. Genotype
11.Biotechnology

Basic Concepts of Genetics
____________________________________________________________________________________
• Cells are of two basic types: eukaryotic

and prokaryotic
• A gene is the fundamental unit of heredity
• Genes come in multiple forms called
alleles
• Genes encode phenotypes
• Genetic information is carried in DNA and
RNA
• Genes are located on chromosomes
• Chromosomes separate through the
processes of mitosis and meiosis
• Genetic information is transferred from
DNA to RNA to protein
• Mutations are permanent, heritable
Figure 1.1.1. Representation of
changes in genetic information
the three dimensional structure
• Some traits are affected by multiple of DNA
factors
• Evolution is genetic change
Genetics is the study Heredity deals with Agricultural genetics is
and manipulation of the transmission of the application of
heredity and the genetic material genetic principles to
variation in living from parent(s) to improve plants and
organisms. offspring animals for food and
fiber.
Importance of Genetics
____________________________________________________________________________________
• Humans possess genes that influence our lives (height, weight, hair color, skin
pigmentation, susceptibility to diseases and disorders, intelligence and
personality)
• Agriculture is dependent on genetics to greatly increase crop yields and provide
many desirable traits, such as disease and pest resistance, special nutritional
qualities, and characteristics that facilitate harvest.
• Used widely in pharmaceutical industry to efficiently produce drugs
• The biotechnology industry employs molecular genetic techniques to develop
and mass-produce substances of commercial value.
• Plays an important role in medicine (identification and treatment of diseases)
Important breakthrough in agriculture using genetics

GMO - a plant or animal that has been genetically modified through the
addition of a small amount of genetic material from other organisms
through molecular techniques. Examples of GM Crops include Bt Corn, Bt
potatoes, RR Soybeans

Role of Genetics
____________________________________________________________________________________
In Biology:
• Genetics provides one of biology’s unifying
principles: All organisms use nucleic acids for their
genetic material and all encode their genetic
information in the same way.
• Genetics provide support in the study of many other
biological disciplines.
• Developmental biology relies heavily on genetics:
tissues and organs form through the regulated
expression of genes
• Fields as taxonomy, ecology, and animal behavior Figure 1.1.2. Traditional rice
plant (left) and modern, high-
are making increasing use of genetic methods.
yielding rice plant (right).
• The study of almost any field of biology or medicine Genetic plays an important role
is incomplete without a thorough understanding of in crop improvement.
genes and genetic methods.
In Agriculture:
• Genetics is the principal scientific basis for the improvements of plants and
animals used for food and fiber.
• The science of genetics enables plant and animal breeders to predict, to
varying extents, the outcome of genetic manipulation of plants and
animals.
The Three Major Areas of Genetics

____________________________________________________________________________________
▪ Transmission genetics, also known as • Mendels Principles
classical genetics, encompasses the • Mitosis and Meiosis
basic principles of genetics and how • Sex Determination
traits are passed from one generation • Sex linkage
• Chromosomal Mapping
to the next.
• Cytogenetics
▪ Molecular genetics concerns the • Chemistry and Structure of DNA

chemical nature of the gene itself: how • Chemistry of DNA
genetic information is encoded, • Transcription
replicated, and expressed. It includes • Translation
• DNA Cloning and Genomics
the cellular processes of replication, • Control of Gene Expression
transcription, and translation. • DNA Mutation and Repair
• Extrachromosomal Inheritance
▪ Evolutionary/Population genetics
explores the genetic composition of • Quantitative Genetics
groups of individual members of the • Hardy-Weinberg Equilibrium
same species (populations) and how • Assumptions of equilibrium
that composition changes over time • Evolution
• Speciation
and space.

Activity
Application
1
Understanding and Synthesizing the Concept

1. Describe some of the ways in which your own genetic makeup affects
you as a person. Be as specific as you can.
2. GMO crops such as Bt and glyphosate tolerant corn are now preferred
to grow by farmers in reducing pesticide use. What role did genetics
play in the development of these GMO crops?
3. Find a journal article that covers some aspect of genetics. Briefly
summarize the article. Does this article focus on transmission,
molecular, or population genetics?

Module 1
The Science of Heredity and Variation

Time Frame: 2.5 Hours Lesson 2
Learning Objectives The Beginnings of Genetics

At the end of this lesson, you
are expected to: Introduction
 Understand the history of
genetics.
This lesson explores the history of genetics. We
 Be acquainted with will begin with the prehistoric evidences that human
important dates and understood and applied the principles of heredity. We
names of individuals who will then look at the earliest written records that the
made great contribution early civilization genetic manipulation through
to genetics. pollination and selection of crops having the best
traits. We will then go further when modern genetics
Key Concepts
began to rise from seventeenth century until today.
Furthermore, scientists and their contribution to
❖ Prehistoric Evidences genetics will be highlighted. Finally, our last topic for
❖ Early written records this lesson focuses on the latest genetic development
❖ Historical development in and its future.
modern genetics
ActivityActivity
1
1 The Modern Maize and Its Ancestor
It was believed that maize Analysis

ascended from teosinte (Zea mays
1. Compare the characteristics
ssp. mexicana), a lowland wild
of maize and teosinte. List
grass growing in Central America.
down the similarities and
Procedure differences among its
characteristics.
1. Observe the characteristics of
2. What do you think the
maize such growth habit,
processes involve in the
leaves, plant height, ear and
evolution of teosinte to
kernels. Record your
modern maize? Did it evolved
observations.
naturally or did humans
2. Search the internet and write
interfere with its evolution?
down the characteristics of
teosinte the same as what you
have recorded for maize.

Prehistoric Evidences
____________________________________________________________________________________
• 10,000 and 12,000 years ago. The first
evidence that humans understood and applied
the principles of heredity is found in the
domestication of plants and animals by
selection and cultivation of wild plants and
animals that had desirable traits
• 10,000 years ago. The world’s first
agriculture is thought to have developed in the
Middle East.
o Selective breeding produced woollier
and more manageable goats and sheep
and seeds of cereal plants that were
larger and easier to harvest
• 4,000 years ago. Sophisticated genetic Figure 1.2.1. Assyrian bas-relief
sculpture showing artificial pollination
techniques were already in use in the Middle
of date palms at the time of King
East Assurnasirpalli II, who reigned from
o Assyrians and Babylonians developed 883–859 B.C. (Metropolitan Museum
several hundred varieties of date palms of Art, gift of John D. Rockefeller Jr.,
that differed in fruit size, color, taste, and 1932.)
time of ripening. Concept
• 2,800 years ago. Assyrians use artificial
Humans first applied genetics
fertilization to control crosses between date
to the domestication of plants
palms and animals between
• Other crops and domesticated animals were approximately 10,000 and
developed by cultures in Asia, Africa, and the 12,000 years ago. This
domestication led to the
Americas
development of agriculture
and fixed human settlements.
Early Written Records

____________________________________________________________________________________
• Hindu, 2000 years ago - attribute many
traits to the father. Differences between
siblings can be accounted for by effects
from the mother.
• The Talmud – presented accurate
understanding of the inheritance of
hemophilia.
• The ancient Greeks - developed the
concept of pangenesis and the concept of
the inheritance of acquired
characteristics.
• Ancient Romans developed practical
measures for the breeding of plants and
animals.
Historical Developments in Modern Genetics
____________________________________________________________________________________
• In the seventeenth century, biologists proposed the idea
of preformationism, which suggested that a miniature
adult is present inside the egg or the sperm and that a
person inherits all of his or her traits from one parent.
• Gregor Mendel discovered the principles of heredity by
studying the offspring of crosses between varieties of
peas and analyzing the pattern of transmission of traits
in subsequent generations.
• Robert Hooke (1653–1703) discovered cells in 1665.
• Nehemiah Grew (1641–1712) reported that plants
reproduce sexually by using pollen from the male sex
cells
• Joseph Gottleib Kölreuter (1733–1806), early plant
breeder who carried out numerous crosses and studied
pollen under the microscope
• Robert Brown (1773–1858) described the cell nucleus
in 1833.
• Matthis Jacob Schleiden (1804–1881) and Theodor
Schwann (1810–1882) proposed the concept of the cell
theory in 1839
• Charles Darwin (1809–1882), Laid the theory of
evolution through natural selection and published his
ideas in On the Origin of Species in 1856. Figure 1.2.3. Gregor Mendel, the father of
• Nehemiah Grew (1641–1712) reported that plants modern genetics. Mendel first discovered
reproduce sexually by using pollen from the male sex the principles of heredity by crossing
cells. different varieties of pea plants and
analyzing the pattern of transmission of
• Joseph Gottleib Kölreuter (1733–1806) carried out
traits in subsequent generations.
numerous crosses and studied pollen under the (Hulton/Archive by Getty Images.)
microscope.
• Walter Flemming (1843–1905) observed the division
of chromosomes in 1879 and published a superb In 1992, first commercial GM crop,
description of mitosis. FlavrSavr tomato was the first
• August Weismann (1834–1914) Proposed the germ- commercially approved and
plasm theory, which holds that the cells in the grown genetically modified (GM)
reproductive organs carry a complete set of genetic crop for human consumption.
information that is passed to the gametes.
• Walter Sutton (1877–1916) proposed in 1902 that
In 1995, the first complete DNA
genes are located on chromosomes.
• Thomas Hunt Morgan (1866–1945) discovered the sequence of a free-living
first genetic mutant of fruit flies in 1910 and used fruit organism - the bacterium
flies to unravel many details of transmission genetics. Haemophilus influenzae — was
• Ronald A. Fisher (1890–1962), John B. S. Haldane determined, and the first
(1892–1964), and Sewall Wright (1889–1988) laid the complete sequence of a
foundation for population genetics in the 1930s. eukaryotic organism (yeast) was
• James Watson (b. 1928) and Francis Crick (b. 1916) reported a year later.
described the three-dimensional structure of DNA in
1953, ushering in the era of molecular genetics.
In 1995, Bt corn, engineered to
• Walter Gilbert (b. 1932) and Frederick Sanger (b.
1918) developed methods for sequencing DNA in 1977. resist the European corn borer
• Kary Mullis (b. 1944) and others developed the was produced by the Pioneer
polymerase chain reaction, a technique for quickly Hibred company.
amplifying tiny amounts of DNA, in 1986
In 1996, RR (Roundup ready)
soybean, a was introduced by
Monsanto.

Activity
Application
1
Understanding and Getting Acquainted with people and events

1. When and where did agriculture first arise? What role did genetics play in
the development of the first domesticated plants and animals?
2. Illustrate the concept of pangenesis in contrast with the germ-plasm
theory.
3. How did developments in botany in the seventeenth and eighteenth
centuries contribute to the rise of modern genetics?
4. How did developments in cytology in the nineteenth century contribute
to the rise of modern genetics?
5. Who first discovered the basic principles that laid the foundation for our
modern understanding of heredity?
6. List some advances in genetics that have occurred in the twentieth
century.
References
Pierce, B. (2017). Genetics: A Conceptual Approach, 6th edition. WH Freeman, New
York.
Tamarin, R. (2001). Principles of Genetics, 7th edition. The McGraw-Hill, New York.
Acquaah, J. (2012). Principles of Plant Genetics and Breeding, 2nd edition. Wiley-
Blackwell, United Kingdom

Module 2
Mendel’s Laws and the Chromosomal Basis of Heredity
Module Overview
Earth is teeming with diversity of species

of plants animals and microorganisms. Despite
the assortments of species, all organisms have an
important feature in common – all use the same
genetic system. Genes can be transmitted from
one generation to another. This Module explores
the principles of heredity which put forward by
Gregor Mendel. Throughout this module, number
of concepts are linked: the laws of segregation,
dominance and independent assortment
including statistics and probabilities and the
extensions and modifications to Mendel’s Laws.
This module also explores the reproduction of
cells and the transmission of genes to the new cell
through mitosis and meiosis.
Objectives
 Understand Mendel’s laws – segregation and independent assortment.
 Understand the process of cell reproduction through mitosis and meiosis.
 Understand probability theory and statistical tests of hypotheses.
 Understand the influencing forces that determine sex and inheritance
patterns and the determination of inheritance patterns using pedigree
analysis.
 Understand the mechanism of inheritance of genes located on the same
chromosome and the methods of mapping gene in eukaryotes, prokaryotes
and bacterial viruses.
 Understand the mechanism of variation in chromosome structure and
number.

Lesson 1. Mendel’s Laws
Lesson 2: Mitosis and Meiosis
Lesson 3. Probability and Statistics
Lesson 4. Sex Determination, Sex Linkage, and Pedigree Analysis
Lesson 5. Linkage and Mapping in Eukaryotes, Prokaryotes and Bacterial Viruses
Lesson 6. Cytogenetics

Module 2

Lesson 1
Time Frame: 5 Hours
Learning Objectives Mendel’s Laws

 Understand that genes are
discrete units which control Introduction
an organism 's appearance;
Mendel discovered the principles of inheritance
 Understand Mendel’s laws of
by performing experiments on pea plants through
inheritance: segregation and
crossing. The result of his experiment lead him to
independent assortment;
conclude that crossing two different purebred varieties
 Understand that dominance is
together will express only one feature and when the
a function of allellic
offspring are self-fertilized, the resulting progeny will
interaction while epistasis is a
express the two different traits. From this discovery he
function of non-allellic gene
concluded that: organisms have discrete factors that
interaction; and
determine its features,; organisms possess two versions
 Describe how genes generally
of each factor; each gamete contains only one version of
regulate enzyme activity.
each factor; parents contribute equally to the inheritance
Key Concepts of offspring as a result of the fusion between randomly
❖ Mendel: The Father of selected egg and sperm; for each factor, one version is
Genetics dominant over another and will be completely expressed
❖ Important Genetic Terms if present. With his conclusions, principles of segregation,
❖ Law of Segregation principles of independent assortment and concept of
❖ Law of Dominance dominance were established. There are modifications on
❖ Law of Independent Mendel’s principles firstly because the law of independent
Assortment assortment does not hold true for genes located on the
❖ Genotypic Interaction
same chromosome. Finally, not all genes show a complete
❖ Epistasis
❖ Biochemical Genetics dominance hierarchy – some genes show co-dominance
or incomplete dominance.
Activity
Activity 2.1
1 Terms to Remember
This activity will enable you to be familiarized with the common terms used in this
lesson. Define the following terms:
Gene Heterozygote Genotype

Allele Homozygote Trait
Locus Phenotype Characteristic
Analysis
1. What is the relationship among the terms allele, locus, gene, and
genotype?
2. What are the differences between gene and allele
3. How do you differentiate phenotype from phenotype?
4.

Mendel: The Father of Genetics
____________________________________________________________________________________
• Gregor Mendel, an Austrian monk first
discovered the principles of heredity by
Mendel’s Success
conducting experiments on pea plants. Mendel’s approach to the study
• He conducted breeding experiments from 1856 of heredity was effective for
to 1863 and presented his results publicly at several reasons:
meetings of the Brno Natural Science Society in
1865.  His choice of experimental
• Mendel’s paper from these lectures was subject the pea plant Pisum
published in 1866. sativum offered clear
• He died at the age of 61 on January 6, 1884, advantages for genetic
unrecognized for his contribution to genetics. investigation.
• The significance of Mendel’s discovery was  Much of Mendel’s success
unappreciated until 1900, when three can be attributed to the
botanists—Hugo de Vries, Erich von Tschermak, seven characteristics that he
and Carl Correns - began independently chose for study.
conducting similar experiments with plants and  He adopted an experimental
arrived at conclusions similar to those of Mendel. approach.
Figure 2.1.1. Mendel used pea plant (Pisum sativum) for his experiment on heredity. He
examined seven characteristics namely: seed color, seed shape, seed coat color, pod color, pod
shape, flower position and stem length. (Photo from Wally Eberhart/Visuals Unlimited)
Important Genetic Terms

• Gene - A genetic factor (region of DNA) that helps determine a characteristic
• Allele - One of two or more alternate forms of a gene
• Locus - Specific place on a chromosome occupied by an allele
• Genotype - Set of alleles that an individual possesses
• Heterozygote - An individual possessing two different alleles at a locus
• Homozygote - An individual possessing two of the same alleles at a locus
• Phenotype - The appearance or manifestation of a character
• Character or characteristic - An attribute or feature

Mendel’s Law of Inheritance
____________________________________________________________________________________
The Principles of Segregation
Principles of Segregation states that individuals Mendel proposed the Law of
possess two alleles and a parent passes only one Segregation after observing
allele to his/her offspring. One allele is given by the that pea plants with two
female parent and the other is given by the male different traits produced
parent. The two factors may or may not contain the offspring that all expressed the
same information. dominant trait, but the
following generation expressed
• If the two alleles are identical, the individual is
the dominant and recessive
called homozygous for the trait. If the two
traits in a 3:1 ratio.
alleles are different, the individual is called
heterozygous.
• The presence of an allele does not promise that
Testing for the Law of
the trait will be expressed in the individual that
Segregation
possesses it.
• In heterozygous individuals, the only allele that Monohybrid cross – a cross
is expressed is the dominant. The recessive between parents that differed
allele is present, but its expression is hidden. in a single characteristic.
• The genotype of an individual is made up of the Mendel’s first experiment was
many alleles it possesses. An individual’s the crossing of homozygous
physical appearance, or phenotype, is round seed and homozygous
determined by its alleles as well as by its wrinkled seed followed by his
environment. second experiment where he
allowed the F1 seeds to self-
fertilize.

Fig. 2.1.2. Mendel’s monohybrid cross experiments. Conclusion: The traits of the parent plants do not
Result of Monohybrid Cross
blend. Although F1 plants display the phenotype of one parent, both traits are passed to F2 progeny in
a 3:1
1. ratio.
Each(Pierce,
plantB. must
(2017).possess
Genetics: Atwo
Conceptual Approach.6th ed)
genetic factors coding for a
character. Although the F1 plants
display the phenotype of only one
parent, they must inherit genetic
factors from both parents because
they transmit both phenotypes to
the F2 generation (Fig 4b).
2. The two alleles in each plant
separate when gametes are
formed, and one allele goes into
each gamete (Fig 4a).
3. Only the trait encoded by round
allele (R) was observed in the F1—
all the F1 progeny had round
seeds. Those traits that appeared
unchanged in the F1 heterozygous
offspring Mendel called dominant,
and those traits that disappeared
in the F1 heterozygous offspring
he called recessive (Fig 4d).
4. The two alleles of an individual
plant separate with equal
probability into the gametes (Fig
4c).
The Concept of Dominance
The concept of dominance states that,
when two different alleles are present
in a genotype, only the trait of the
dominant allele is observed in the
phenotype
• Dominant alleles are expressed
exclusively in a heterozygote,
while recessive traits are
expressed only if the organism is
homozygous for the recessive
allele.
• A single allele may be dominant
over one allele, but recessive to
another.
• Not all traits are controlled by
simple dominance as a form of Figure 2.1.3. Result of Mendel’s monohybrid cross.
inheritance; more complex forms It revealed the principle of segregation and the
concept of dominance. . (Pierce, B. (2017).
of inheritance have been found to
Genetics: A Conceptual Approach.6th ed)
exist

Dominance is Not Universal
Mendelian concept
• In the heterozygous condition, only one allele
(dominant) is expressed
Incomplete dominance
• Heterozygote has phenotype intermediate to
homozygous phenotypes
• Incomplete dominance example can be found in skin
color of eggplant (Fig. 5)
Codominance
• the heterozygote’s phenotype includes the phenotypes
of both homozygotes
• Example of codominance is the ABO blood series, in m
which a heterozygous IA/IB individual will express both
antigens, resulting in blood type AB.
Multiple Alleles Figure 2.1.4. Fruit color

inheritance in eggplant.
• Not all genes have only two forms (alleles), many have (Pierce, B. (2017). Genetics: A
multiple alleles Conceptual Approach.6th ed)
• No matter how many alleles for the gene exist in the
multiple allelic series, however, a diploid individual
will have only two alleles, one on each homologous
chromosome.

ABO Blood Group - Classic Example of Multiple Alleles in Human
• ABO blood groups are important in blood transfusions, and result from a series of three alleles
(IA, IB and i) that combine to produce four phenotypes (A, B, AB and O).
• Both IA and IB are dominant to i, while IA and IB are codominant to each other. The resulting
phenotypes are (Table 13.1):
o People with genotype i/i are blood type O.
o People with genotype IA/IA or IA/i are blood type A.
o People with genotype IB/IB or IB/i are blood type B.
o People with genotype IA/IB are blood type AB.
• ABO inheritance follows Mendelian principles. For example, a type O individual’s genotype is
i/i. Possible genotypes of the parents could be:
o i/i and i/i (both blood type O).
o IA/i and i/i (one type A, the other type O).
o IA/i and IA/i (both type A).
o IB/i and i/i (one type B, the other type O).
o IB/i and IB/i (both type B).
o IA/i and IB/i (one type A, the other type B).
• Blood typing may be used in cases of disputed parentage. Blood typing does not prove the
identity of a parent. It can, however, eliminate individuals who are not biological parents of a
particular child. Example:
o A child with blood type AB (IA/IB) could not have a parent with type O (i/i).
o Blood type data are not considered adequate legal proof for parenthood in most states,
and DNA fingerprinting is generally used.

Principles of Independent Assortment
Mendel’s principles of independent
Mendel experimented with
assortment states that genes do not plants that differed in the form
influence each other with regard to the and color of their peas: he
sorting of alleles into gametes; every crossed true-breeding
(homozygous) plants that had
possible combination of alleles for every seeds that were round and
gene is equally likely to occur. yellow with plants that
produced seeds that were
wrinkled and green. F1 plants
all had round, yellow seeds,
which demonstrated that
round was dominant to
wrinkled and yellow was
dominant to green. When these
F1 plants were self-fertilized,
they produced an F2
generation that had all four
possible combinations of the
two seed characteristics:
round, yellow seeds; round,
green seeds; wrinkled, yellow
seeds; and wrinkled, green
seeds at a ratio closed to 9:3:3:1
Testing for the Law of

Independent Assortment
Dihybrid cross: a cross
between two true-breeding
parents that express different
traits for two characteristics.
Figure 2.1.5. Mendel’s Dihybrid Cross

Experiment. Pierce, B. (2017). Genetics:
A Conceptual Approach.6th ed

Dihybrid and Trihybrid Testcross
Figure 2.1.6. A branch diagram can be used for determining Figure 2.1.6. A branch diagram can be used for determining the phenotypes and expected
the phenotypes and expected proportions of offspring from a proportions of offspring from a trihybrid cross (RrYyCc x RrYyCc). Pierce, B. (2017). Genetics:
dihybrid testcross (RrYy x rryy). Pierce, B. (2017). Genetics: A A Conceptual Approach.6th ed
Conceptual Approach.6th ed

Genotypic Interaction
____________________________________________________________________________________
Phenotypes result from complex interactions of Two types of interactions
molecules under genetic control. Genetic analysis occur:
can often detect the patterns of these reactions. 1. Different genes control the
For example: same general trait,
collectively producing a
• In the dihybrid cross A/a B/b X A/a B/b, nine
phenotype.
genotypes will result.
2. One gene masks the
• If each allelic pair controls a distinct trait and
expression of others
exhibits complete dominance, a 9:3:3:1
(epistasis) and alters the
phenotypic ratio results.
• Deviation from this ratio indicates that
phenotype.
interaction of two or more genes is involved in
producing the phenotype.
Gene Interactions That Produce New Phenotypes

• Nonallelic genes that affect the same characteristic may interact to give novel
phenotypes, and often modified phenotypic ratios.
Example:
Four distinct comb phenotypes in chickens, resulting from all possible combinations of a
dominant and recessive allele at each of two gene loci.
1. Rose comb (R/-p/p)
2. Walnut comb (R/-P/-)
3. Pea comb (r/r P/-)
4. Single comb (r/r p/p)
Figure 2.1.8. Independent assortment in the determination of

Fig. 2.1.7. Four distinct comb
comb type in chicken.
phenotypes in chicken

Epistasis
____________________________________________________________________________________
In epistasis, one gene masks the expression of

Epistasis is interaction
another, but no new phenotype is produced.
between genes that affect
Several possibilities for interaction exist, all phenotype
producing modifications in the 9:3:3:1 dihybrid ratio:
 Epistasis may be caused by recessive  A gene that masks
alleles, so that a/a masks the effect of B another is epistatic.
(recessive epistasis).  A gene that gets masked
 Epistasis may be caused by a dominant is hypostatic.
allele, so that A masks the effect of B.
 Epistasis may occur in both directions
between genes, requiring both A and B to
produce a particular phenotype (duplicate
recessive epistasis).
Recessive Epistasis
Example: Coat color determination in
labrador retriever dogs
• Gene B/- makes black pigment, while b/b
makes brown.
• Another gene, E/- allows expression of
the B gene, while e/e does not.
• Genotypes and their corresponding
phenotypes:
1. B/-E/- is black
2. b/bE/- is brown (chocolate)
3. -/-e/e produces yellow with nose and Figure 2.1.9. Color determination in
lips either dark (B/-e/e) or pale Labrador retriever dogs with recessive
(b/be/e) epistasis
Dominant Epistasis
Example: Summer squash fruit have 3 common colors, white, yellow, and green.
• Yellow is recessive to white but dominant to green.
• Gene pairs are W/w and Y/y.
1. W/- are white no matter the genotype of the other locus.
2. w/w are yellow in Y/- and green in y/y.
• white molecule is converted to a green intermediate and then to a yellow end
product.
1. Dominant Y required to convert green intermediate to yellow.
2. Dominant W inhibits white-to-green conversion, resulting in white fruit.

Figure 2.1.10. Color
determination in
summer squash
showing white is
dominant to yellow and
yellow is dominant to
green
Duplicate Recessive Epistasis

Duplicate recessive epistasis (complementary gene action) involves two loci that each
produce an identical phenotype, showing a 9;7 ratio.
Example: Flower color determination in sweet peas
• Purple is dominant for flower color, and when a true-breeding purple plant is crossed
with a true-breeding white one, the F2 shows a typical 3;1 ratio.
• White strains usually breed true, but occasionally the cross of two different white strains
(p/pC/C´P/Pc/c) will produce an F1 that is entirely purple (P/pC/c).
• The F2 of this cross will be 9⁄16 purple (P/-C/-), and 7⁄16 white (3⁄16 P/-c/c+3⁄16
p/pC/-+1⁄16 p/pc/c).
• All of the white F2 plants will breed true, as will 1⁄9 of the purple F2 plants (P/PC/C).
• Two genes appear to be involved. The C/c alleles determine whether the flower can have
color, and the P/p alleles determine whether purple is produced.
Figure 2.1.11. Flower color

determination in sweet peas
with duplicate recessive
epistasis

Biochemical Genetics
____________________________________________________________________________________
Inborn Errors of Metabolism
Several human conditions, that occur in individuals who are homozygous for
recessive alleles.
Examples of conditions with enzyme defect (see Fig. 13)
• Albinism
• Alkaptonuria
• Tyrosinosis
• Genetic goitrous cretinism
• Phenylketonuria (PKU)
Figure 2.1.12 In humans, errors in melanin synthesis produce different physical conditions and diseases,
depending on which part of the tyrosine (an amino acid) metabolic pathway is disrupted. The broken
arrows indicate that there is more than one step in the pathways; the conditions listed occur only in
homozygous recessives. Tamarin, R. H. (2001). Principles of Genetics (7th ed). New York. The McGraw−Hill
Companies

One-Gene-One-Enzyme Hypothesis
• A theory in the early 1940s that each gene controls the synthesis or activity
of a single enzyme.
• The concept was proposed by American geneticist George Wells Beadle and
American biochemist Edward L. Tatum, who conducted their studies in the
mold Neurospora crassa (See Fig. 15)
Figure 2.1.13 Pathway of niacin synthesis in Neurospora. Each arrow represents an enzyme-
mediated step. Each question mark represents a presumed but (at the time Beadle and Tatum
were working) unknown compound.
Tamarin, R. H. (2001). Principles of Genetics (7th ed). New York. The McGraw−Hill Companies
Activity
Application
1 Test Your Understanding
1. What is the law of segregation? Why is it important?

2. What is the law of dominance? How does dominance differ from incomplete dominance?
3. Mendel crossed tall pea plants with dwarf ones.The F1 plants were all tall. When these F1
plants were selfed to produce the F2 generation, he got a 3:1 tall-to- dwarf ratio in the
offspring. Predict the genotypes and phenotypes and relative proportions of the F3
generation produced when the F2 generation was selfed.
4. In the human ABO blood system, the alleles IA and IB are dominant to i. What possible
phenotypic ratios do you expect from a mating between a type A individual and a type B
individual?
5. What is the principle of independent assortment? How is it related to the principle of
segregation?
6. A particular variety of corn has a gene for kernel color and a gene for height with the
following phenotypes:
A. CC, Cc: purple kernels
B. TT: tall stem
C. cc: white kernels
D. Tt: medium height stem
E. tt: dwarf stem
Give the proportions of genotypes and phenotypes produced if a dihybrid plant is
selfed.
7. What are the differences between dominance and epistasis?
8. What is albinism? Describe the error in metabolism of melanin.

Module 2

Learning Objectives Mitosis and Meiosis

 Describe the
morphology of the Introduction
chromosome
 Understand the Life cycle in most organisms begin with the
processes involved in fertilized egg. Division takes place multiple times to
mitosis and meiosis produce an adult organisms. The adult create a gamete
 Analyze the relationship that combine with another and life cycle start over again.
between Mendel 's laws Life cycle in plants and animals go through the process of
and meiosis mitosis and meiosis. Mitosis and meiosis are sequences of
events that take place in appropriating genetic
Key Concepts information during cell reproduction through an active
interaction of DNA synthesis, movement of chromosomes
❖ Chromosomes and cell division. These processes are responsible for the
❖ Cell Cycle transmission of genetic information from the mother cells
❖ Mitosis to the daughter cell and are the basis of similarities and
❖ Meiosis differences between parents and offspring.
❖ Life Cycles
❖ Chromosomal Theory
of Heredity
Activity
Activity 2.2
1 The Cell and Life Cycle
Procedure:
1. Illustrate the life cycle of plants and animals. Label each stages of the cycle.
2. Draw plant and animal cells. Label each organelles and other structures.
3. Draw the cell cycle. Label each stages of the cycle.
Analysis
1. Compare the differences between plant and animal life cycles

2. Describe the similarities and differences between plant and animal
cells.
3. Describe the stages in cell cycle?

The Cell
____________________________________________________________________________________
Basic Cell Types
Prokaryotic cell found in
unicellular organisms with a
relatively simple cell structure
Eukaryotic cell has a
compartmentalized cell
structure divided by intracellular
membranes.
Figure 2.2.1. A cell of a prokaryote
Figure 2.2.2. Eukaryotic Cell: Animal (left) and plant (right) cell.
Table 2.2.1. Differences between prokaryotic and eukaryotic cells
Prokaryotic Cells Eukaryotic Cells

Taxonomic Groups Bacteria All Plants, fungi, animals, protists
Size Usually less than 5 µm in greatest Usually greater than 5 m in smallest
dimension dimension
Nucleus No true nucleus, no nuclear Nuclear membrane
membrane
Genetic Material One circular molecule of DNA, little Linear DNA molecules complexed with
protein histones
Mitosis and Absent Present
Meiosis

Chromosomes
____________________________________________________________________________________
• Chromosomes were discovered by C.
von Nägeli in 1842 after staining
techniques were developed that
made them visible.
• The term chromosome, which W.
Waldeyer coined in 1888, means
“colored body.”
• Each chromosome in one set has a
corresponding chromosome in the
other set, together constituting a
homologous pair
• The nucleoprotein material of the
chromosomes is referred to as
chromatin.
• When diffuse, chromatin is referred
to as euchromatin; when condensed
and readily visible, as
Figure 2.2.3. The structure of eukaryotic
heterochromatin.
chromosome. (Pierce, B. (2017). Genetics: A
Conceptual Approach.6th ed)
Chromosome Structure
Three Essential Elements of a Functional Chromosome
 Centromere - the attachment point for spindle microtubules, which are the
filaments responsible for moving chromosomes during cell division.
➢ Kinetochore - is the proteinaceous structure on the surface of the
centromere to which microtubules of the spindle attach
 Telomeres - the natural ends, the tips, of a linear chromosome they serve to
stabilize the chromosome ends.
 Origins of replication - the sites where DNA synthesis begins; they are not
easily observed by microscopy
Four Major Types of Chromosomes

• Metacentric- centromere is in
the middle of the chromosome
• Submetacentric – centromere is
located near the middle of the
chromosome
• Acrocentric centromere is at the
very near the end of the
chromosome.
• Telocentric – centromere is at
the end of the chromosome
•
Figure 2.2.4. Four major types of chromosome:
metacentric, submetacentric, acrocentric, telocentric

Chromosome Characteristics
• Homomorphic chromosome pairs are
pairs that are made up of identical partners Chromosomes of Diploid cells
• Heteromorphic chromosome pair are sex occur in pair where one
chromosomes, which in some species are of member of each pair came
unequal size. from each parent
Table 2.2.2. Chromosome number of selected species Haploid cells, which include
Number of the reproductive cells, have
Species Chromosomes only one copy of each
(2n) chromosome.
Human being (Homo sapiens) 46
Garden pea (Pisum sativum) 14
Karyotype is the total
Fruit fly (Drosophila melanogaster) 8
chromosomal complement of a
Corn (Zea Mays) 20
cell
Rice (Oryza Sativa) 24
Soybean (Glycine max) 40
Arabidopsis thaliana 10
Sorghum (Sorghum bicolor) 20
Cricket (Gryllus domesticus) 22
Indian fern (Ophioglossum 1,260
reticulatum)
Cell Cycle and Mitosis

____________________________________________________________________________________
Cell Cycle
• The cell cycle is the stages through which it passes from one division to the next.
• This process is critical to genetics because, through the cell cycle, the genetic instructions
for all characteristics are passed from parent to daughter cells.
• A new cycle begins after a cell has divided and produced two new cells.
• A new cell metabolizes, grows, and develops.
• At the end of its cycle, the cell divides to produce two cells, which can then undergo
additional cell cycles.
Figure 2.2.5. The cell cycle. (Pierce, B. (2017). Genetics: A Conceptual Approach.6th ed)
Two Major Phases of Cell Cycle
Interphase Stages of Mitosis

Interphase is the extended period of growth and 1. Prophase - is the first phase of mitosis,
development between cell divisions. the process that separates the
duplicated genetic material carried in
Interphase is divided into three phases: the nucleus of a parent cell into two
identical daughter cells. During
 G1 (Gap 1) period where the cell grows, prophase, the complex of DNA and
and proteins necessary for cell division proteins contained in the nucleus,
are synthesized; this phase typically lasts known as chromatin, condenses.
2. Prometaphase begins when the
several hours.
nuclear membrane dissolves. Proteins
 S phase (for DNA synthesis), in which each attach to the centromeres creating the
chromosome duplicates. kinetochores. Microtubules attach at
o Before S phase, each chromosome is the kinetochores and the
composed of one chromatid; following chromosomes begin moving.
S phase, each chromosome is 3. Metaphase. Spindle fibers align the
chromosomes along the middle of the
composed of two chromatids cell nucleus. This line is referred to as
 G2 (gap 2). In this phase, several the metaphase plate. This organization
additional biochemical events necessary helps to ensure that in the next phase,
for cell division take place when the chromosomes are separated,
each new nucleus will receive one copy
Mitosis Phase of each chromosome.
4. Anaphase. The paired chromosomes
 Mitosis phase is the part of the cell cycle in separate at the kinetochores and move
which the copies of the cell’s to opposite sides of the cell. Motion
chromosomes (sister chromatids) are results from a combination of
separated and the cell undergoes division. kinetochore movement along the
 A critical process in Mitosis is the spindle microtubules and through the
separation of sister chromatids to provide physical interaction of polar
microtubules.
a complete set of genetic information for
5. Telophase. Chromatids arrive at
each of the resulting cells. opposite poles of cell, and new
 Mitosis phase is divided into six stages: membranes form around the daughter
o the five stages of mitosis (prophase, nuclei. The chromosomes disperse and
prometaphase, metaphase, anaphase are no longer visible under the light
and telophase) microscope. The spindle fibers
o cytokinesis disperse, and cytokinesis or the
partitioning of the cell may also begin
during this stage.
6. Cytokinesis. In animal cells,
cytokinesis results when a fiber ring
• Interphase is the period between cell
composed of a protein called actin
divisions, in which the cell grows, around the center of the cell contracts
develops, and prepares for cell division. pinching the cell into two daughter
cells, each with one nucleus. In plant
• Mitosis phase is the period of active cell cells, the rigid wall requires that a cell
division. plate be synthesized between the two
daughter cells.

Figure 2.2.6. Interphase, stages of mitosis and cytokinesis
Meiosis
____________________________________________________________________________________
• Meiosis is a type of cell division that
reduces a diploid cell to a haploid cell. Meiosis II differs from mitosis in
• It is a two-division process that produces that chromosome number has
already been halved in meiosis I,
four cells from each original parent cell.
and the cell does not begin with the
The two divisions are known as meiosis I same number of chromosomes as it
and meiosis II. does in mitosis.
• Like mitosis, meiosis is preceded by an
interphase stage that includes G1, S, and
G2 phases
Two Phases of Meiosis

• Meiosis I - the reduction division
• the number of chromosomes per cell is
reduced by half
• Meiosis II – the equational division the
events in this phase are similar to those of
mitosis.
Figure 2.2.7. The two phases of

meiosis: meiosis I and Meiosis II
How is meiosis different from mitosis?
 Mitosis consists of a single nuclear division and is usually accompanied by a single
cell division. Meiosis, on the other hand, consists of two divisions.
 After mitosis, chromosome number in newly formed cells is the same as that in the
original cell, whereas meiosis causes chromosome number in the newly formed cells
to be reduced by half.
 Finally, mitosis produces genetically identical cells, whereas meiosis produces
genetically variable cells.
The Stages of Meiosis
Figure 2.2.7. The two phases of meiosis: meiosis I and Meiosis II

Substages of Prophase I
1. Leptotene - chromosomes contract and become visible.
2. Zygotene - chromosomes continue to condense; homologous chromosomes begin to
pair up and begin synapsis, a very close pairing association. Each homologous pair of
synapsed chromosomes consists of four chromatids called a bivalent or tetrad.
3. Pachytene - chromosomes become shorter and thicker, and a three-part
synaptonemal complex develops between homologous chromosomes.
• homologous chromosomes exchange genetic information called crossing over.
• crossing over produce genetic variation by the random distribution of maternal
and paternal chromosomes.
4. Diplotene - The centromeres of the paired chromosomes move apart. The two
homologs remain attached at each chiasma (plural, chiasmata), which is the result of
crossing over.
5. Diakinesis - chromosome condensation continues, and the chiasmata move toward
the ends of the chromosomes as the strands slip apart; so the homologs remained
paired only at the tips. Near the end of prophase I, the nuclear membrane breaks
down and the spindle forms.
Consequences of Meiosis
 First, meiosis comprises two divisions; so each original cell produces four cells (there
are exceptions to this generalization, as, for example, in many female animals)
 Second, chromosome number is reduced by half; so cells produced by meiosis are
haploid.
 Third, cells produced by meiosis are genetically different from one another and from
the parental cell.
Meiosis in the Life Cycle of Plants and Animals
Figure 2.2.8. Plants

alternate from
diploid and haploid
life stages. (Pierce,
B. (2017). Genetics:
A Conceptual
Approach. 6th ed)

Figure 2.2.9. Gamete formation in humans. (Pierce, B. (2017). Genetics: A Conceptual Approach. 6th
ed)
Relationship of Meiosis and the Chromosomal Basis of Heredity

____________________________________________________________________________________
 Meiosis serves as the cellular basis of genetic crosses in most eukaryotic organisms.
 It is the basis for the rules of inheritance

Activity
Application
1 Comprehension and Synthesis
1. Describe the differences between prokaryotic and eukaryotic cells.

2. Name the essential elements of a functional chromosome and describe their
functions
3. Describe the stages in the cell cycle
4. Describe each stages of meiosis I and meiosis II.
5. Discuss the life cycle of plants and animals. What are the differences and
similarities in their life cycle?

Module 2

Learning Objectives
 Understand the rules of
Probability and Statistics
probability and their genetic
applications.
 Understand hypothesis Introduction
testing and the use of chi
square in in genetics. One of Mendel’s objectives in conducting his
Key Concepts experiments on pea plants was to establish a way of
❖ Chromosomes predicting the outcome of crosses with different
❖ Cell Cycle phenotypes between plants. In order to predict the
❖ Mitosis outcomes of the crosses he made, he applied simple
❖ Meiosis mathematics in his experiment by turning numbers into
❖ Life Cycles ratios and inferring the mechanism of inheritance from
❖ Chromosomal Theory of them. In this lesson, we'll first learn a simple, shorthand
Heredity method using the Punnett square to predict the result of a
genetic cross results and then learn how to use probability
to predict cross outcomes.
Activity
Activity 2.3
1
Predicting the Outcome Using the

Procedure:
Punnett Square
Using the Punnett square,
predict the outcome of the
following crosses: Analysis
1. XX x Xy 1. Which of the crosses results in offspring with
2. Tt x Tt 1:1 ratio?
2. Which of the crosses bears offspring that are
3. AB x ab all heterozygotes?
3. Which of the crosses results in 25%
homozygous dominant, 50% heterozygous
and 25% homozygous recessive offspring?

Predicting the Outcomes of Genetic Crosses
___________________________________________________________________________________
The Punnett square is a short-hand
method of predicting the genotypic and
phenotypic ratios of progeny from a
genetic cross.
• When traits are expressed by an

organism, they result from two copies
of a gene: one from the mother and
one from the father.
• Genes can appear in one of two forms:
dominant or recessive. The
recessive form will be masked if a
dominant form is present.
• Since each parent may have a
different combination of the genes,
three possible conditions may occur:
.1. AA is called homozygous
dominant. Both genes are the
same and dominant. The
dominant trait is expressed.
.2. Aa is called heterozygous. The
organism has a dominant gene
and a recessive gene. The
dominant trait usually masks the
recessive, so the dominant trait is
expressed.
.3. aa is called homozygous
recessive. Both genes are the
same and recessive. The
recessive trait is expressed.
• When offspring are produced, parents
can pass on either of their genes.
Figure 2.3.1. Mendel’s experiment on a cross

between tall and dwarf pea plant varieties.
Punnett square can be used to predict
genotypic or phenotypic ratios.
A Punnett square is constructed by drawing a grid, putting the gametes produced by one
parent along the upper edge and the gametes produced by the other parent down the left
side (Figure 2.3.1b). Each cell (a block within the Punnett square) contains an allele from
each of the corresponding gametes, generating the genotype of the progeny produced by
fusion of those gametes. In the upper left-hand cell of the Punnett square in Figure 2.3.1b,
a gamete containing T from the tall plant unites with a gamete containing t from the short
plant, giving the genotype of the progeny (Tt). It is useful to write the phenotype
expressed by each genotype; here the progeny will be tall, because the tall allele is
dominant over the short allele.

Probability
• Another method for determining the
outcome of a genetic cross is to use the rules
of probability, as Mendel did with his
crosses.
• Probability expresses the likelihood of a
particular event occurring. It is the number
of times that a particular event occurs,
divided by the number of all possible
outcomes.
Types of Probabilities
• The probability (P) that an event will occur is the number of favorable cases (a) divided by the
total number of possible cases (n):
P = a/n
The probability can be determined either by observation (empirical) or by the nature of the event
(theoretical).
Example:
We observe that about one child in ten thousand is born with phenylketonuria. Therefore, the
probability that the next child born will have phenylketonuria is 1/10,000.
The odds based on the geometry of an event are, for example, like the familiar toss of dice. A die
(singular of dice) has six faces. When that die is tossed, there is no reason one face should land up
more often than any other. Thus, the probability of any one of the faces being up (e.g., a four) is
one-sixth:
P = a/n = 1/6
Similarly, the probability of drawing the seven of clubs from a deck of cards is
P = 1/52
The probability of drawing a spade from a deck of cards is

P = 13/52 = 1/4
The probability (assuming a 1:1 sex ratio, though the actual ratio is about 1.06 males per female
born in the United States) of having a daughter in any given pregnancy is
P = 1/2
And the probability that an offspring from a self-fertilized dihybrid will show the dominant
phenotype is
P = 9/16
From the probability formula, we can say that an event with certainty has a probability of one, and
an event that is an impossibility has a probability of zero. If an event has the probability of P, all
the other alternatives combined will have a probability of Q = 1 - P; thus P + Q = 1. That is, the
probability of the completely dominant phenotype in the F2 of a selfed dihybrid is 9/16. The
probability of any other phenotype is 7/16, and when the two are added together, they equal
16/16, or 1.

Rules of Probability
1. Product Rule (Multiplication). When
the occurrence of one event is
independent of the occurrence of other
events, the product rule is used: The
probability that two independent events
will both occur is the product of their
separate probabilities. This is known as
the and rule.
For example, the probability of throwing

a die two times and getting a four and
then a six, in that order, is
P =1/6 x 1/6 = 1/36
2. Sum Rule (Addition). When events are

mutually exclusive, the sum rule is used:
The probability that one of several
mutually exclusive events will occur is the
sum of the probabilities of the individual
events. This is also known as the either-or
rule.
For example, what is the probability,

when we throw a die, of its showing either
a four or a six? According to the sum rule,
P = 1/6 + 1/6 + 2/6 = 1/3
3. Binomial Theorem. The binomial

theorem is used for unordered events:
Figure 2.3.2. The product rule and sum
The probability that some arrangement
rule can be used to predict the probability
will occur in which the final order is not of an event.
specified is defined by the binomial
theorem.
Uses of Rules
What is the probability when tossing two pennies simultaneously of getting a head and a
tail?
There are several ways to calculate the probability. The problem can be solved using the
three rules.
By using combination of rule 1 and 2, For each coin, the probability of getting a head (H) or a
tail (T) is
for H: P = 1/2
for T: Q = 1/2

Tossing the coins one at a time, it is possible to get a head and a tail in two ways:
first head, then tail (HT) or first tail, then head (TH)
Within a sequence (HT or TH), the probabilities apply to independent events. Thus, the
probability for any one of the two sequences involves the product rule (rule 2):
1/2 x 1/2 = 1/4 for HT or TH
The two sequences (HT or TH) are mutually exclusive. Thus, the probability of getting either
of the two sequences involves the sum rule (rule 1):
1/4 + 1/4 = 1/2

Thus, for unordered events, we can obtain the probability by combining rules 1 and 2. The
binomial theorem (rule 3) provides the shorthand method. To use rule 3, we must state the
theorem as follows: If the probability of an event (X) is p and an alternative (Y) is q, then the
probability in n trials that event X will occur s times and Y will occur t times is
𝑛! 𝑠 𝑡
𝑃= 𝑝 𝑞
𝑠! 𝑡!
In this equation, s + t = n, and p + q = 1. The symbol !, as in n!, is called factorial, as in “n
factorial,” and is the product of all integers from n down to one.
For example, 7! = 7 x 6 x 5 x 4 x 3 x 2 x 1. Zero factorial equals one, as does anything to the

power of zero (0! = n0 = 1).
Now, what is the probability of tossing two coins at once and getting one head and one tail?
In this case,
n = 2, s and t = 1, and p and q = 1/2. Thus,

2! 2𝑥1 1 1 1
𝑃= (1/2)1 (1/2)1 = 𝑥 𝑥 = 2( ) = 1/2
1! 1! (1)(1) 2 2 4
Genetic related problems:

What is the probability that a family with 7 children will have five girls and 2 boys?
We assume that the probability of either a son or a daughter equals 1/2. Thus, using a
Punnett square
X X Probability:
X XX XX ½ girl (p)
Y XY XY ½ boy (q)
Since the order is not specified, we use rule 3:

Since the order is not specified, we use rule 3:
7! 7𝑥6𝑥5𝑥4𝑥3𝑥2𝑥1 1 1 1 1 1 1 1 5040 1 21
𝑃= (1/2)5 (1/2)2 = 𝑥 𝑥 𝑥 𝑥 𝑥 𝑥 𝑥 = ( )=
5! 2! (5𝑥4𝑥3𝑥2𝑥1)(2𝑥1) 2 2 2 2 2 2 2 240 128 128
What would happen if we asked for a specific family order, in which four girls were born,
then two boys, and then one girl? This would entail rule 2; for a sequence of six independent
events:
P = 1/2 x 1/2 x 1/2 x 1/2 x 1/2 x 1/2 x1/2= 1/128
Using binomial expansion in rule 3. The formula for rule 3 is the formula for the terms of
the binomial expansion. That is, if (p + q)n is expanded (multiplied out), the formula
(n!/s!t!)psqt gives the probability for any one of these terms, given that p + q = 1 and that s + t
= n. Since there are (n = 1) terms in the binomial, the formula gives the probability for the
term numbered (t + 1).The binomial for this situation is (p + q)7 because there are seven
children in the family (n = 7). The expansion is:
(p + q)7 = p7 + 7p6q + 21p5q2 + 35p4q3 + 35p3q4 + 21p2q5 + 7pq6 + q7
p7 = the first term having the probability of 7 daughters

7p6q = the second term having the probability of 6 daughters and 1 son
21p5q2 = the third term having the probability of 5 daughters and 2 sons
35p4q3 = the fourth term having the probability of 4 daughters and 3 sons
35p3q4 = the fifth term having the probability of 3 daughters and 4 sons
21p2q5 = the sixth term having the probability of 2 daughters and 5 sons
7pq6 = the seventh term having the probability of 1 daughter and 6 sons
q7 = the eighth term having the probability of sons
Going back to our problem. What is the probability that a family with 7 children will have five
girls and 2 boys? We are looking for a probability of 5 girls and 2 boys, for these we will use
the third term 21p5q2, hence,
21p5q2 = 21(1/2)5(1/2)2 = 21(1/32)(1/4) = 21/128
Another method is using the Pascal’s Triangle to obtain the coefficient. Pascal’s triangle is a
triangular array made up of coefficients in the binomial expansion. It is calculated by starting
any row with a 1, proceeding by adding two adjacent terms from the row above, and then
ending with a 1.

We will use the same problem we already solved using the shorthand method and binomial
expansion method
1 1
1 2 1
1 3 3 1
1 4 6 4 1
1 5 10 10 5 1
1 6 15 20 15 6 1
1 7 21 35 35 21 7 1
These numbers give us the combinations for any psqt term. That is, in our previous example, n
= 7; so we use the (n + 1), or row eight of Pascal’s triangle. (The second number in any row of
the triangle gives the power of the expansion, or n. Here, 7 is the second number in the row.)
We were interested in the case of 5 daughters and 2 sons in a family of seven children, or p5q2,
where p is the probability of having a girl (1/2) and q is the probability of having a boy (1/2).
Hence, we are interested in the third term of the eight row of Pascal’s triangle, which will tell
us the number of ways of getting a family with 5 daughters and 2 sons That number is 7.Thus,
using Pascal’s triangle, we see that the solution to the problem is
21(1/2)5(1/2)2 = 7(1/32)(1/4) = 21/128
If we observe the result using shorthand, binomial expansion and Pascal’s Triangle, in solving
rule 3 probability problem, we obtain the same result.
Statistics
Hypothesis Testing.
Statistics is a branch of probability theory that helps Determining whether to
the experimental geneticist in three ways: support or reject a hypothesis
experimental design, summarizing data and by comparing the data to the
hypothesis testing. predictions of the hypothesis.
For example, Sampling distribution: the

In one of Mendel’s experiments, F1 heterozygous pea frequencies with which various
plants, all tall, were self-fertilized. In the next possible events could occur in a
particular experiment
generation (F2), he recorded 787 tall offspring and
277 dwarf offspring for a ratio of 2.84:1. Mendel saw
this as a 3:1 ratio, which supported his proposed
Was the ratio of 787:277 really
rule of inheritance.
indicative of a 3:1 ratio?

The Goodness-of-Fit Chi-Square Test
To use the goodness-of-fit chi-square test, we
first determine the expected results. The chi-
square test must always be applied to numbers
of progeny, not to proportions or percentages.
Let’s consider a locus for coat color in domestic

cats, for which black color (B) is dominant over
gray (b). If we crossed two heterozygous black
cats (Bb x Bb), we would expect a 3:1 ratio of
black and gray kittens. A series of such crosses
yields a total of 50 kittens—30 black and 20
gray. These numbers are our observed values.
We can obtain the expected numbers by
multiplying the expected proportions by the
total number of observed progeny. In this case,
the expected number of black kittens is ¾ x 50
= 37.5 and the expected number of gray kittens
is ¼ x 50 = 12.5. The chi-square (x2) value is
calculated by using the following formula:
(𝑂𝑏𝑠𝑒𝑟𝑣𝑒𝑑 − 𝐸𝑥𝑝𝑒𝑐𝑡𝑒𝑑)2
𝑋2 = ∑
𝐸𝑥𝑝𝑒𝑐𝑡𝑒𝑑
Where ∑ means the sum of all the squared

differences between observed and expected
divided by the expected values.
To calculate the chi-square value for our black

and gray kittens, we would first subtract the
number of expected black kittens from the
number of observed black kittens
30 - 37.5 = -7.5
and square this value:
-7.52 = 56.25. Figure 2.3.3. Calculation of goodness-of-fit Chi

Square test
We then divide this result by the expected
number of black kittens,
56.25/37.5 = 1.5
We repeat the calculations on the number of

expected gray kittens:
(20 - 12.5)2/12.5 = 4.5
To obtain the overall chi-square value, we sum

the (observed - expected)2/expected values:
1.5 + 4.5 = 6.0

Determining the probability associated with this calculated chi-square value
• This step requires a comparison between the calculated chi-square value (6.0) with theoretical
values that have the same degrees of freedom in a chi-square table.
• For a goodness-of-fit chi-square test, the degrees of freedom are equal to n - 1, where n is the
number of different expected phenotypes.
• In our example, there are two expected phenotypes (black and gray); so n = 2 and the degree of
freedom equals 2 - 1 = 1.
• Obtain the probability from a chi-square table (Table 3.4).
• The degrees of freedom are given in the left hand column of the table and the probabilities are given
at the top; within the body of the table are chi-square values associated with these probabilities.
• First, find the row for the appropriate degrees of freedom; for our example with 1 degree of
freedom, it is the first row of the table.
• Find where our calculated chi-square value (6.0) lies among the theoretical values in this row. The
theoretical chi-square values increase from left to right and the probabilities decrease from left to
right.
• Our chi-square value of 6.0 falls between the value of 5.024, associated with a probability of .025,
and the value of 6.635, associated with a probability of .01.
• Probability associated with our chi-square value is less than .025 and greater than .01. So, there is
less than a 2.5% probability that the deviation that we observed between the expected and the
observed numbers of black and gray kittens could be due to chance.
• Most scientists use the .05 probability level as their cutoff value: if the probability of chance being
responsible for the deviation is greater than or equal to .05, they accept that chance may be
responsible for the deviation between the observed and the expected values. When the probability
is less than .05, scientists assume that chance is not responsible and a significant difference exists.
• The expression significant difference means that some factor other than chance is responsible for
the observed values being different from the expected values. In regard to the kittens, perhaps one
of the genotypes experienced increased mortality before the progeny were counted or perhaps
other genetic factors skewed the observed ratios.
• In choosing .05 as the cutoff value, scientists have agreed to assume that chance is responsible for
the deviations between observed and expected values unless there is strong evidence to the
contrary. It is important to bear in mind that even if we obtain a probability of, say, .01, there is still
a 1% probability that the deviation between the observed and expected numbers is due to nothing
more than chance.
Table 1.3.1. Critical values of X2 distribution

ApplicationActiv
2.3
ity 1 Testing Probabilities
1. In cats, black coat color is dominant over gray. A female black cat whose
mother is gray mates with a gray male. If this female has a litter of six
kittens, what is the probability that three will be black and three will be
gray?
2. In a family of seven children, what is the probability of obtaining the
following numbers of boys and girls?
a. All boys
b. All children of the same sex
c. Six girls and one boy
d. Four boys and three girls
e. Four girls and three boys
3. In snapdragons, the allele for red flowers is incompletely dominant over the
allele for white flowers, and thus heterozygotes have pink flowers. What
ratios of snapdragon flower colors would you expect to see among progeny
generated from the following crosses?
a. Red x white
b. Red x pink
c. White x pink
d. White x white
e. Pink x pink
f. Red x red
4. In guinea pigs, the allele for black coat color (B) is dominant over the allele
for white coat color (b). At an independently assorting locus, an allele for
rough coat (R) is dominant over an allele for smooth coat (r). A guinea pig
that is homozygous for black color and rough coat is crossed with a guinea
pig that has a white and smooth coat. In a series of matings, the F1 are
crossed with guinea pigs having white, smooth coats. From these matings,
the following phenotypes appear in the offspring: 24 black, rough guinea
pigs; 26 black, smooth guinea pigs; 23 white, rough guinea pigs; and 5
white, smooth guinea pigs.
a. Using a chi-square test, compare the observed numbers of progeny
with those expected from the cross.
b. What conclusions can you draw from the results of the chi-square
test?
c. Suggest an explanation for these results.

Module 2

Learning Objectives
Sex Determination, Sex Linkage and
 Analyze the bases of sex Pedigree Analysis
determination in various
organisms
 Analyze the patterns of Introduction
inheritance of traits that loci
regulate in the sex In the previous lessons we studied the law of
chromosome segregation and independent assortment. These laws,
 use pedigrees to determine after it was discovered by Mendel, became the basis of
succeeding studies with and array of different organisms.
Key Concepts
Exceptions to Mendel’s laws were observed and
❖ Sex Determination
modifications and extension to the law were established.
❖ Sex Linkage
Some of the extensions in Mendel’s laws include sex
❖ Pedigree Analysis
determination and sex linkage. The first part of this lesson
focuses on sex determination. Once we understand the
concepts of sex determination we will explore how genes
differ in males and female through sex linkage. The last
part of this lesson focuses on pedigree analysis where we
study human genetic characteristics and the techniques in
the study of human inheritance.
Activity
Activity 2.4
1 Mechanism of Sex Determination
In humans and other organisms, sex can be determine by the presence or absence of a Y
chromosome, the type of gonads, the sex hormones and the internal and the external genitalia.
Procedure:
1. Draw a picture of a male and female fowl (chicken, turkey, etc.). Alternatively, take a picture
of a male and female fowl. Print the picture and paste it in your activity notebook
2. Identify and label each part of the fowl.
Analysis
• What are the differences in the features of each part of male and
female fowl?
• What factor/s determine the maleness and the femaleness of a
fowl?
• What is the sex-determining system used in fowls.

Sex Determination
___________________________________________________________________________________
Determinants of Organism’s Sex
• Sex Chromosomes. Genetic and hormonal control

• The ploidy of an individual. Hymenoptera (bees, ants, wasps), can determine sex;
males are haploid and females are diploid
• Allelic mechanisms may determine sex by a single allele or multiple alleles not
associated with heteromorphic chromosomes
• Environmental factors. Temperature determines the sex of some geckos, and the sex
of some marine worms and gastropods depends on the substrate on which they land
Sex Chromosomes
Four types of chromosomal sex-determining mechanisms:

• XX-XY: in human beings or fruit flies, the females have a homomorphic pair of
chromosomes (XX) and males are heteromorphic (XY).
• ZZ-ZW: males are homomorphic (ZZ), and females are heteromorphic (ZW).
• X0: the organism has only one sex chromosome, as in some grasshoppers and beetles;
females are usually XX and males X0.
• Compound chromosomal mechanisms: several X and Y chromosomes combine to
determine sex, as in bedbugs and some beetles
XX-XY System
• The XY situation occurs in human beings.
• Females have forty-six chromosomes arranged in twenty three homologous,
homomorphic pairs.
• Males, with the same number of chromosomes, have twenty-two homomorphic pairs
and one heteromorphic pair, the XY pair
Figure 2.4.1.
A human male
karyotype.

• The XY situation occurs in human beings.
• Females have forty-six chromosomes
arranged in twenty three homologous,
homomorphic pairs.
• Males, with the same number of
chromosomes, have twenty-two
homomorphic pairs and one
heteromorphic pair, the XY pair.
• During meiosis, females produce gametes
that contain only the X chromosome
(homogametic), whereas males produce
two kinds of gametes, X- and Y-bearing
(heterogametic).
• In Drosophila, the system is the same, but
the Y chromosome is almost 20% larger
than the X chromosome
Rare instances where individual form extra

sets or lack of chromosomes
• Polyploids (triploids with 3n,
tetraploids with 4n, etc.)
o Klinefelter syndrome. Males with
XXY chromosome is most common
while few have XXXY and XXXXY
chromosomes
o Poly-X Females. Female having
XXX (triplo-X Syndrome) and
much rarer having XXXX and Figure 2.4.2. In XX-XY system, there is
XXXXX chromosomes a chance of equal number of male and
• Aneuploids. Individuals that have female is produced.
more or fewer than the normal
number of chromosome. Usually
come about when a pair of Sex Determination in Plants
chromosomes fails to separate
properly during meiosis, an • Hermaphrodites. Hermaphroditic
occurrence called nondisjunction. flowers have both male and female
o Turner syndrome. Females with parts. The male parts are the anthers
only one X chromosome or X0. and filaments, making up the stamen,
• Existence of polyploid and aneuploid and the female parts are the stigma,
individuals makes it possible to test style, and ovary, making up the pistil.
whether the Y chromosome is male i.e. mango, sunflower, rice
determining. • Monoecious (Greek, one house).
o In humans, the absence of Y Bearing both male and female flowers
chromosome makes an individual on the same plant. i.e. cucurbits, maize
female.
• Dioecious (Greek, two houses). Plants
o In drosophila, the absence of Y
with just male or just female flowers.
chromosome produces male.
i.e. date palm, male papaya

ZZ-ZW System Haploidy
• In this system, the female is • Some insects in the order
heterogametic and the male is Hymenoptera (bees, wasps, and
homogametic. ants) have no sex chromosomes;
• To prevent confusion with the XX-XY instead, sex is based on the number
system, the sex chromosomes in this of chromosome sets found in the
system are labeled Z and W, but the nucleus of each cell.
chromosomes do not resemble Zs and • Males develop from unfertilized
Ws. eggs, and females develop from
• Females in this system are ZW; after fertilized eggs
meiosis, half of the eggs have a Z • The cells of male hymenopterans
chromosome and the other half have a possess only a single set of
W. chromosomes (they are haploid)
• Males are ZZ; all sperm contain a single inherited from the mother.
Z chromosome. • The cells of females possess two
• The ZZ-ZW system is found in birds, sets of chromosomes (they are
moths, some amphibians, and some
diploid), one set inherited from
fishes.
the mother and the other set from
XX-XO System the father.
• In this system, females have two X
chromosomes (XX), and males possess
a single X chromosome (XO). There is
no O chromosome; the letter O signifies
the absence of a sex chromosome.
• The XX-XO system is found on
grasshoppers and crickets.
Compound chromosomal systems

A complex sex determination system.
• For example, Ascaris incurva, a
nematode, has eight X chromosomes
and one Y. The species has twenty six
autosomes.
o Males have thirty-five
chromosomes (26A + 8X + Y)
o Females have forty-two
chromosomes (26A + 16X ).
• During meiosis, the X chromosomes
unite end to end and so behave as one
unit.
Genic Sex-Determining Systems

• Genotypes at one or more loci Figure 2.4.3. Hymenpterans produces
determine the sex of an individual. females that are diploid when eggs are
• In chromosomal sex-determining fertilized. Unfertilized eggs will produce
systems, sex is actually determined by males that are haploid.
individual genes.
• For example, in mammals, a gene
located on the Y chromosome
determines the male phenotype

• For example, in mammals, a gene Environmental factors in determining
located on the Y chromosome sex in many reptiles.
determines the male phenotype
• In both genic sex determination and Although most snakes and lizards have
chromosomal sex determination, sex is sex chromosomes, in many turtles,
controlled by individual genes; the crocodiles, and alligators, temperature
difference is that, with chromosomal during embryonic development
sex determination, the chromosomes determines sexual phenotype.
that carry those genes appear different • In turtles, warm temperatures
in males and females. produce females during certain
Environmental Sex Determination times of the year, whereas cool
❖ Genes have had a role in sex temperatures produce males.
determination, but sex is determined • In alligators, cool temperatures
fully or in part by environmental factors produce females while warm
in a number of organisms temperatures produce males.
Sequential hermaphroditism – sexual
development where each individual animal Sex Determination in Drosophila
can be both male and female, although not at
the same time. • The fruit fly Drosophila
melanogaster, has eight
Example of environmental sex chromosomes: three pairs of
determination
autosomes and one pair of sex
Common Slipper Limpet (Crepidula chromosomes
fornicata) • Normally, females have two X
chromosomes and males have an X
• Each limpet begins life as a swimming chromosome and a Y chromosome.
larva. The first larva to settle on a solid, • The presence of the Y chromosome
unoccupied substrate develops into a does not determine maleness in
female limpet. It then produces Drosophila; instead, each fly’s sex is
chemicals that attract other larvae, determined by a balance between
which settle on top of it. These larvae genes on the autosomes and genes
develop into males, which then serve on the X chromosome. This type of
as mates for the limpet below. After a sex determination is called the genic
period of time, the males on top balance system.
develop into females and, in turn, • The X chromosome contains genes
attract additional larvae that settle on with female producing effects,
top of the stack, develop into males, whereas the autosomes contain
and serve as mates for the limpets genes with male-producing effects.
under them. • Consequently, a fly’s sex is
• Sex is determined environmentally by determined by the X:A ratio, the
the limpet’s position in the stack. number of X chromosomes divided
by the number of haploid sets of
autosomal chromosomes.
Chromosome complement and sexual phenotypes in Drosophila

The Y Chromosomes The role of sex chromosomes
• The X chromosome contains genetic

• In both human beings and fruit flies, the
information essential for both sexes;
Y chromosome has very few functioning
at least one copy of an X chromosome
genes.
is required for human development.
In human beings two homologous
regions exist, one at either end of the X • The male-determining gene is located
and Y chromosomes, allowing the on the Y chromosome. A single copy of
chromosomes to pair during meiosis. this chromosome, even in the
These regions are termed presence of several X chromosomes,
pseudoautosomal. produces a male phenotype.
• The absence of the Y chromosome
In Drosophila results in a female phenotype.
• The Drosophila Y chromosome is known • Genes affecting fertility are located on
to carry genes for at least six fertility the X and Y chromosomes. A female
factors: usually needs at least two copies of
o two on the short arm (ks-1 and ks-2) the X chromosome to be fertile.
o four on the long arm (kl-1, kl-2, kl-3, • Additional copies of the X
and kl-5). chromosome may upset normal
• The Y chromosome carries two other development in both males and
known genes: females, producing physical and
o bobbed, which is a locus of ribosomal mental problems that increase as the
RNA genes (the nucleolar organizer) number of extra X chromosomes
o Suppressor of Stellate or Su(Ste), a increases.
gene required for RNA splicing.

Sex Linkage
___________________________________________________________________________________
Sex-Linked Characteristics
Sex-linked characteristics are determined
by genes located on the sex chromosomes.
• Genes on the X chromosome determine
X-linked characteristics; those on the Y
chromosome determine Y-linked
characteristics.
• Most sex-linked characteristics are X-
linked. Only a few are Y-linked.
• The pattern of inheritance for sex-
linked characteristics differs from that
exhibited by genes located on
autosomal chromosomes. Males and
females differs in their sex
chromosomes
X Linkage in Drosophila
• T. H. Morgan demonstrated the X-

linked pattern of inheritance in
Drosophila in 1910, when a white-eyed
male appeared in a culture of wild-type
(red-eyed) flies ( See the result of the
crosses in Figure 2.4.4)
• Since females have two X
chromosomes, they can have normal
homozygous and heterozygous allelic
combinations. But males, with only one
copy of the X chromosome, can be
neither homozygous nor heterozygous.
• hemizygous is the presence of X-
linked genes (and other genes
present in only one copy) in males.
• Pseudodominance is a single copy
of a recessive allele determines the
phenotype
Figure 2.4.4. Morgan’s X-linked crosses

for white eyes in fruit flies. (a) Original and
F1 crosses. (b) Reciprocal crosses.

Sex-Limited and Sex-Influence Traits
Sex-Limited Traits
Sex-limited traits are traits expressed in only one sex, although the genes are present
in both.
• Breast and ovary formation in women
• Facial hair distribution and sperm production in men.
• Plumage patterns in birds—in many species, the male is brightly colored.
• Horns found only in males of certain sheep species.
• Milk yield in mammals is expressed phenotypically only in females
Sex-Influenced Traits
Sex-influenced, or sex-conditioned, traits appear in both sexes but occur in one sex more than
the other.
• Pattern, or premature, baldness in human beings is an example of a sex-influenced trait.
In women, it is usually expressed as a thinning of hair rather than as balding. Apparently
testosterone, the male hormone, is required for the full expression of the allele.
Pedigree Analysis
______________________________________________________________________________________
Pedigree
• Visual representation of family tree with

history of studied trait
o Proband – person originally studied
• Oldest generation at the top; youngest
generation at the bottom
• Roman numerals used for generations (I
being the oldest)
• Numbered from left to right within a
single generation
Figure 2.4.5. Standard symbols used in

pedigree

Figure 2.4.6. Hemophilia in the royal family of Europe
Autosomal Recessive traits
• Trait seen in roughly equal amounts of

males and females
• Seem to skip generations
o Affected individual can have
unaffected parents
Autosomal Dominant
• Equal frequency of males and females
• No skipping of generations
• All affected individuals have an
affected parent
• (affected individuals tend to be
heterozygous)
• Some traits are lethal in homozygous
Figure 2.4.7. Pedigree of autosomal
form
recessive trait
o Achondroplasia

X-Linked Recessive
• Affected phenotype seen more

commonly in males
• Tend to skip generations
• Affected males do not pass trait to sons
X linked Dominant
• Do not skip generations
• Seen in both males and females
• Females may be more numerous
• Females can get disease from either
parent while males can only get from Figure 2.4.8. Pedigree of autosomal
mother dominant trait
• Affected male will have 100%
daughters affected
Y linked
• Only males are affected
• Affected males will have 100% affected
sons
• Do not skip generations
Twin Studies
Dizygotic
• Non-identical twins; fraternal
• 2 separate eggs fertilized
• 50% average relatedness; same as any
sibling pair
Monozygotic Figure 2.4.9. Pedigree of X-linked recessive

trait
• Identical
• One zygote that splits very early in
embryonic development
Concordance studies
• Monozygotic twins are 100%
genetically identical; dizygotic approx
50%
• Used to evaluate genetic vs
environmental factors
• Genetic influenced traits will show
higher concordance in monozygotic
twins
Figure 2.4.10. Pedigree of X-linked

dominant trait

Concordance of monozygotic and dizygotic
twins for several traits
Figure 2.4.11. Pedigree of Y-linked

dominant trait
Application 2.41
Activity
Comprehension and Synthesis
Comprehension
1. What are the determinants of the sex of an organism?
2. Discuss the four types of chromosomal sex-determining mechanism.
3. Differentiate polyploidy, aneuploidy and haploidy.
4. How do monoecious organisms differ from dioecious organisms?
5. Explain the effects of the environment to the sex determination of reptiles.
6. What makes a Drosophila male and what makes it a female?
7. Define pedigree.
Synthesis
1. A fruit fly has XXXYY sex chromosomes; all the autosomal chromosomes are normal. What
sexual phenotype will this fly have?
2. Color blindness in humans is most commonly due to an X-linked recessive allele. Karen
has normal vision, but her mother is color blind. George is color blind. If Karen and George
marry and have a child together, what is the probability that the child will be color blind?
3. The following pedigree shows the inheritance of a recessive trait. What is the chance that
the couple III-3 and III-4 will have an affected child?

Module 2

Learning Objectives
Linkage and Mapping in Eukaryotes,
At the end of this lesson, you are Prokaryotes and Bacterial Viruses
expected to:
❖ Understand the analytical
methods to identify the Introduction
relative positions of genes
on chromosomes in diploid Linked genes located on the same chromosome do
eukaryotic organisms not strictly follow Mendel’s principle of independent
❖ Define bacteria and assortment, but instead, they tend to be inherited
bacterial viruses and together. The first part of this lesson explores the
understand the methods of comparison of inheritance of two linked genes with the
studying them inheritance of two genes that assort independently. We
❖ Describe life cycles and will then examine how crossing over breaks up linked
sexual processes in bacteria
genes as well as the physical methods of determining the
and bacteriophages
❖ Discuss the sexual
chromosomal locations of genes. Towards the end, we will
processes of bacteria and study bacteria and bacterial viruses and their life cycle
their viruses and sexual processes.
Key Concepts
• Linkage Mapping in
Eukaryotes
• Linkage and Mapping in
Prokaryotes and Bacterial
Viruses
Activity
Activity 2.5
1 Independent Assortment: A Review
1. A dihybrid cross will result in a phenotypic ratio of 9:3:3:1, assuming we follow Mendel’s law of
independent assortment. To test your knowledge, work on the activity below before jumping into
the main lesson.
A cross between a tall (TT) garden pea with round (RR) seeds and a dwarf (tt) garden pea with
wrinkled (rr) will produce progeny with 9:3:3:1 penotypes.
Analysis
1. What are the processes involved in coming up with the 9:3:3:1

phenotypic ratio?
2. In what generation does it show the 9:3:3:1 ratio?

Linkage and Mapping in Eukaryotes
___________________________________________________________________________________
Genetic Principles
• Principle of Segregation
Diploid organisms have two alleles for each
gene. Separate during meiosis – only one
gamete enters each gamete
• Principle of Independent Assortment

Two alleles of a gene separate independently
from alleles at other loci/other genes
Chromosomes
Chromosomes follow independent assortment IF:
• Genes are located of different chromosomes
BUT:
o If genes are on the same chromosome, they
tend to travel together
o Linked genes – close together on the same
chromosome
Crossing Over
• If 2 genes are on the same chromosome, but far
apart, crossing over can allow for
recombination of gametes
• Genes very far apart on the same chromosome

will always be separated by crossing over, and
are not considered to be linked
Figure 2.5.1. Dihybrid cross of sweet
pea. F2 progeny do not appear in
9:3:3:1 ratio expected with
independent assortment
[Pierce, B. (2009). Genetics: A Conceptual
Approach, Third Edition. W.H. Freeman and
Company.]
Figure 2.5.2. Crossing over takes place in meiosis and is responsible for recombination.
[Pierce, B. (2009). Genetics: A Conceptual Approach, Third Edition. W.H. Freeman and Company.]

Notation for Crosses with Linkage
• Horizontal lines indicate actual
chromosome
A B
a b
o *individual heterozygous for 2 different
genes where both dominant alleles are on
one chromosome, and both recessive
alleles are on its homologous
chromosome
• Can be abbreviated by AB/ab
Testcross for linkage
• For determination if two genes are linked
(close together on the same chromosome)
or not
Set-up:
• One individual heterozygous for both
traits x individual homozygous
recessive for both traits
MmDd x mmdd
• If not closely linked, alleles will assort

independently
• MmDd individual can form 4 different
types of gametes Figure 2.5.3. Crossing over between linked
• 50% recombinant offspring/50% genes produces nonrecombinant and
non-recombinant offspring recombinant offspring.
[Pierce, B. (2009). Genetics: A Conceptual Approach,
Third Edition. W.H. Freeman and Company.]
Figure 2.5.4. Crossing over between linked

genes produces nonrecombinant and
recombinant offspring. In this testcross, genes
are linked and there is some crossing over.
[Pierce, B. (2009). Genetics: A Conceptual Approach,

MD/md x md/md Crossing over
• Single cross over produces 50%
• If closely linked, 2 alleles will
nonrecombinant chromosomes (same
always travel together
configuration as parental
o all offspring are non-
chromosome) and 50% recombinant
recombinant (Figure 2.5.5)
chromosomes (new allelic
combination)
Meiosis II
Figure 2.5.6. Crossing over produces half

nonrecombinant gametes and half recombinant
gametes.
[Pierce, B. (2009). Genetics: A Conceptual Approach, Third
Edition. W.H. Freeman and Company.]
Calculation of Recombination Frequency

Figure 2.5.5. Crossing over between 𝑅𝑒𝑐𝑜𝑚𝑏𝑖𝑛𝑎𝑛𝑡 𝐹𝑟𝑒𝑞𝑢𝑒𝑛𝑐𝑦 =
𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑟𝑒𝑐𝑜𝑚𝑏𝑖𝑛𝑎𝑛𝑡 𝑝𝑟𝑜𝑔𝑒𝑛𝑦
𝑥100
𝑡𝑜𝑡𝑎𝑙 𝑛𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑝𝑟𝑜𝑔𝑒𝑛𝑦
completely linked genes only produces
nonrecombinant offspring.
[Pierce, B. (2009). Genetics: A Conceptual Approach, In figure 2.5.4 testcross, progeny exhibit
Third Edition. W.H. Freeman and Company.] new combinations of traits; so the
recombination frequency is:
8+7
𝑥100 = 12%
55 + 53 + 8 + 7

Coupling and Repulsion
For heterozygous individuals
• Cis configuration/coupling
o Both wildtype alleles are on one chromosome; both mutant alleles are on the
homologous chromosome
• Trans configuration/repulsion
o Each chromosome has one wildtype allele and one mutant allele
Figure 2.5.6. The arrangement of linked genes on a chromosome (coupling or repulsion) affects the
results of a testcross. Linked loci in the Australian blowfly, Lucilia cuprina, determine the color of the
thorax and that of the puparium..
Recombination
• Interchromosomal
o Between genes on different chromosomes
o Independent assortment/random segregation during Metaphase/Anaphase I
o Produces 50% recombinant/50% non-recombinant gametes
• Intrachromosomal
o Between genes on same chromosome
o Crossing over during Prophase I
o Usually produces recombinant gametes less than 50%. Unless very far apart on the
same chromosome

Genetic Mapping
• Relative position of different genes based on recombination rates
• Does NOT state actual chromosome, or position (locus)
• Distance measured in map units or centimorgans (cM)
o 1 m.u. (or cM) = 1% recombination
Genetic mapping example
A and B = 5 m.u.
A and C = 15 m.u.
B and C = 10 m.u.
A and D = 8 m.u.
B and D = 13 m.u.
C and D = 23 m.u.
• Any genes with 50% recombination are either on different chromosomes, or very far
apart on the same chromosome (crossing over always separates them)
Physical mapping
• Locates gene to a specific chromosome/region of chromosome
Deletion mapping
• Chromosome deletion studies – how phenotype is affected/what genes may be missing
• Duchenne m.s.
o X linked disease – but where on X?
o Some affected males have small deletions – common deleted area must be where
gene is located
Bacterial and Viral Genetic Systems

____________________________________________________________________________________
_
Bacteria Culturing bacteria
• Petri dishes
• Prototrophic o Growth media in agar
o Wild-type o Isolate individual colonies. Each
o Can grow on minimal media colony originates from a single
o Contains minimal nutrients – bacterium
carbon, nitrogen, phosphorous, • Suspension culture
vitamins, ions o Liquid media
• Auxotrophic o Bacteria dies off when nutrients
o Cannot produce an essential are used up or waste buildup
enzyme or manufacture essential becomes toxic
molecules o Bacteria grow singularly – no
o Will only grow on media that colonies
contains the “missing” substance
o Complete media

Replica plating
• Gives “carbon copies” of petri dish
colonies
• Use sterilized velvet to make a stamp
o Some bacteria from each colony is
transferred to velvet, and then
transferred to new dishes
Bacterial genome
• Most consist of a single, circular Figure 2.5.7. Petri dish culture of bacteria
chromosome Edition. W.H. Freeman and Company.]
o Some have several chromosomes,
and a few have linear chromosomes
• Very little “extra” DNA between genes
• Plasmids
o Small, circular, extra-chromosomal
DNA
o Usually non-essential
o Replicate independent of
chromosomal DNA
o Have their own origin of replication
F factor episome
• Episome. A plasmid that can replicate
independently AND also has the ability
to incorporate into chromosomes
Gene transfer in bacteria Figure 2.5.8. Suspension culture of bacteria

Conjugation Edition. W.H. Freeman and Company.]
• One bacteria directly transfers DNA to

another bacterium
• Cytoplasmic connection forms, and
either entire plasmid or part of the
chromosome is transferred from donor
to recipient
• Crossing over may occur between
homologous regions
o Creates recombinant DNA
o Extra DNA is degraded
• Fertility factor/F factor contains ori and
genes needed for conjugation
F+ and F-
o F+ contains F factor Figure 2.5.9. Replica plating of bacteria
o Forms a sex pilus – extension of cell [Pierce, B. (2009). Genetics: A Conceptual Approach, Third
membrane Edition. W.H. Freeman and Company.]
o Extends and comes in contact with
F- receptor
o F factor separates, and one strand is
transferred into F-
▪ Double stranded DNA is created
and F- becomes F+

Hfr bacteria
o F+ cell that has F factor
incorporated into chromosome
• As F factor enters recipient, some
chromsome enters – amount depends
on time length of contact
• Donor DNA made into double-
stranded Figure 2.5.10. Bacterial gene transfer through
o Crossing over can occur between conjugation
homologous regions Edition. W.H. Freeman and Company.]
o Any DNA not incorporated is
degraded
• Recipient is not usually converted to
F+ since the F factor is nicked in the
middle
F′ bacteria
• F factor excises out of a chromosome
in a Hfr cell Figure 2.5.11. Bacterial gene transfer through
o May remove part of chromosome transformation.
as well [Pierce, B. (2009). Genetics: A Conceptual Approach, Third
• F′ plasmid now contains F factor and
some genes from chromosome
o Enters F- bacteria
o Produces merozygotes – partially
diploid
Transformation
• Bacteria takes up DNA from
surrounding environment
• Recombination may occur Figure 2.5.12. Bacterial gene transfer through
• Uptake of DNA and incorporation into transduction.
chromosome or plasmid [Pierce, B. (2009). Genetics: A Conceptual Approach, Third
o Naturally occurring – dead
bacteria
o Artificially introduced
• Competent – cells able to take up DNA
o CaCl2, heat shock, electrical fields
o Makes membrane more
permeable to DNA
o DNA does not have to have
bacterial origin
• Transformants – bacteria that have
incorporated foreign DNA

E. Coli as model organism
• Many strains are avirulent
• Small and rapid reproduction
• Easy to culture
• Genome is single chromosome - haploid
o Small genome
o 4.5 million bp/4,000 genes
• Wild-type are prototrophic
Figure 2.5.13. The E. coli.


Viral Genetics RNA Viruses
• DNA or RNA (single or double • Positive strand RNA viruses
stranded) as genetic material o Single strand directly codes for
• Can not reproduce on their own viral proteins
• Bacteriophages – viral particles that • Negative strand RNA viruses
infect bacteria o Must make complementary RNA
strand, which then codes for
Bacteriophage proteins
Lytic cycle • Retroviruses
• Virulent phages o Incorporate into host genome
• Viral DNA is injected into host cell ▪ Must make DNA from RNA
where it replicated, transcribed, and ▪ Reverse transcriptase
translated into more phages • Makes cDNA from DNA or
• Host cell bursts open to release viral RNA template
particles o Enters host genome as a provirus
▪ Can be transcribed and
Lysogenic cycle translated
• Temperate phages o Some retroviruses contain
• Phage DNA is incorporated into host oncogenes
genome – prophage ▪ Cause tumors
• Passed onto all progeny cells
• Can be transcribed and translated
• Can exit from host genome to enter
lytic cycle
Transduction
• Generalized
o Any gene is transferred
o During lytic cycle, bacterial DNA
is degraded
▪ Some may enter viral protein
coat instead of viral genetic
material - Transducing
phages Figure 2.5.14. Lytic and lysogenic cycle of
bacteriophage.
▪ Can become incorporated [Pierce, B. (2009). Genetics: A Conceptual Approach, Third
into new host’s genome Edition. W.H. Freeman and Company.]
• Specialized
o Few genes are
transferred/genes near certain
sites of chromosome
o During lysogenic cycle,
prophage enters at specific sites
of host’s genome
o When prophage excises, it may
do so imperfectly and bring
some hot DNA with it
▪ Then introduced to new host Figure 2.5.15. Viral genetic transfer through
transduction.

Activity
Application 2.5
1 Test Your Knowledge
1. In guinea pigs, white coat (b) is recessive to black coat (B) and wavy hair (s) is recessive to
straight hair (S). A breeder crosses a guinea pig that is homozygous for white coat and wavy
hair with a guinea pig that is black with straight hair. The F1 are then crossed with guinea pigs
having white coats and wavy hair in a series of testcrosses. The following progeny are
produced from these testcrosses:
black, straight 40
black, wavy 22
white, straight 25
white, wavy 38
a.Are the genes that determine coat color and hair type assorting independently? Carry
out chi-square tests to test your hypothesis.
b. If the genes are not assorting independently, what is the recombination frequency
between them?
2. Map and show the distance between each loci with the following recombination frequencies:
Loci Recombination frequency (%)

A and D 12
B and D 17
C and D 26
A and F 15

Module 2

Learning Objectives
Cytogenetics
At the end of this lesson, you are
expected to: Introduction
❖ Describe the existence and
impacts of chromosomal The word cytogenetics is the combination of
breakage and reunification
❖ Describe the nature and
the words cytology and genetics. Cytology is the
effects of chromosome study of cells. Cytogenetics is thus defined as the
variations in both human study of cells from the perspective of genetics. In
and non-human species general, it is the study of changes in the gross
structure and number of chromosomes in cells. In
Key Concepts
this lesson, we will explore how these alterations
• Variation in Chromosomal
Structure happen and what their consequences are to the
• Variation in Chromosomal organism.
Number
Activity
Activity 2.5
1 Chromosomal Variation
Procedure
1. Look for plants having color variegation on its leaves, flowers or fruits.
2. Take a photograph, print the photograph and attach it to your activity notebook.
3. Find out what cause/s the color variegation.
Analysis
1. What causes color variegation?
2. In what way does chromosomal variation affect phenotypes?

Variation in Chromosomal
Structure
Chromosomal Rearrangements
➢ Mutations that change the structure of
individual chromosomes.
Four Types of Chromosomal Rearrangement
1. Duplications
o A mutation that doubles part of a
chromosome.
o In individuals heterozygous for a
chromosome duplication, the
duplicated region of the chromosome
loops out when homologous
chromosomes pair in prophase I of
meiosis.
o Duplications often have major effects
on the phenotype, possibly by altering
gene dosage.
Types of Duplications
• Tandem. Repeated segment is right
after the original
• Displaced. Repeated segment is
located elsewhere on chromosome, or Figure 2.6.1. The four types of chromosomal
on a different chromosome rearrangement. [Pierce, B. (2009). Genetics: A
• Reverse. Sequence is inverted from Conceptual Approach, Third Edition. W.H. Freeman and
Company.]
the original sequence
Duplication in Heterozygotes
• During paring of homologous
chromosomes, duplicated region loops
out
• Offspring receive two copies of
involved genes from parent with
duplication, and a third copy of the
other parent
o Partial trisomy for all involved
genes
o Alters gene dosage
Figure 2.6.2. Duplication of chromosome in an

individual. It loops out during pairing at
prophase I. [Pierce, B. (2009). Genetics: A Conceptual
Approach, Third Edition. W.H. Freeman and Company.]

2. Deletions
o Loss of a portion of chromosome
o Large deletions can be seen
cytogenetically; microdeletions by
FISH
o If the deleted region includes the
centromere, entire chromosome will
be lost
o Usually lethal in homozygous form
In Heterozygotes
o Normal chromosome must loop out
during pairing
Figure 2.6.3. Chromosome loops out during
o Partial monosomy for all involved
chromosome pairing in prophase I in a
genes
heterozygous individual for deletion. [Pierce, B.
o Affects gene dosage (2009). Genetics: A Conceptual Approach, Third Edition.
▪ Pseudodominance. Expression W.H. Freeman and Company.]
of mutant/recessive phenotype
due to loss of normal/dominant
copy
▪ Haploinsufficiency. Both copies
of the gene are needed to
manufacture adequate amount of
gene product. One gene doesn’t
produce enough for a normal
phenotype
3. Inversions
o Two breaks in chromosome, then
flipped and reinserted
o Paracentric inversion. Both breaks
occur in one arm
o Pericentric inversion. Breaks on
both arms; centromere is involved.
Can change morphology by altering
centromere position Figure 2.6.4. The chromosomes form an
inversion loop during pairing in prophase I in
Effects of Inversion an individual heterozygous for a paracentric
o Disruption of a gene – no functional inversion. [Pierce, B. (2009). Genetics: A Conceptual
product
o Change in gene position can affect
gene expression
Inversion loops
• Chromosomes have to loop when pairing
Paracentric inversion loops

o If crossing over occurs within loop:
o Creates a dicentric chromosome and
an acentric chromosome
▪ Acentric is lost
▪ Dicentric forms a dicentric bridge,
and breaks
• Nonviable recombinant gametes
Mosaicism
• Nondisjunction in later development can cause “patchiness” – normal cells and abnormal
cells
• Approximately 50% of Turner syndrome can be mosaics
• 45, XO/46, XX
Polyploidy
• Extra sets of chromosomes
o Triploid – 3n; tetraploid – 4n
• Common in plants – more tolerant of extra sets of chromosomes
Autopolyploidy
• Extra set is from same species
o Error in cell division
• Extra chromosome caused pairing problems; especially with odd numbers
o 3n usually sterile; produce small seeds
▪ Bananas; “seedless” watermelon
Allopolyploidy
• Hybridization between two species
o AABBCC x GGHHII
o F1 generation ABCGHI – not homologous
▪ Gametes are inviable, but may be able to reproduce asexually
o Nondisjunction error can lead 2x, which could then reproduce sexually
Figure 2.6.10. In meiosis of an autotriploid,

homologous chromosomes can pair or not pair in three Figure 2.6.11. Allopolyploids usually
ways. [Pierce, B. (2009). Genetics: A Conceptual Approach, Third arise from hybridization between
Edition. W.H. Freeman and Company.] two species followed by chromosome
doubling. [Pierce, B. (2009). Genetics: A
Conceptual Approach, Third Edition. W.H.
Freeman and Company.]

Module 3
The Chemical Basis of Heredity

Learning Objectives The Chemical Nature of the Gene and DNA

❖ Describe the properties of a
Replication
genetic material
❖ examine the structure of Introduction
DNA, the genetic material
❖ investigate the processes of DNA is a complex chemical compound which
DNA replication carries the genetic of all living organisms. The instructions
❖ Discuss the central dogma in the DNA are transmitted by RNA. This lesson explores
of molecular biology the chemistry of gene. In the first part of the lesson, we
will be learning about the properties of genetic materials
Key Concepts
and examine the structure of DNA. The final part focuses
❖ Early DNA Studies on the processes of DNA replication in bacteria and
❖ Nucleotide Structure eukaryotes.
❖ DNA Double Helix
❖ DNA Methylation
Activity
Activity 3.1
1
The Molecular Structure of DNA
The structure of DNA was discovered by Watson and Crick in the 1953. They described
its 3-dimensional structure, the double helix. In this activity you will be familiarizing
with the structure of DNA by building a double helix using recycled materials.
Procedure:
1. Familiarize yourself with the structure of DNA in Figure 3.1.5.

2. Collect recyclable materials that can be used to bulid a 3-D model of the double
helix.
3. Build the double helix replicating each element shown in the figure.
4. Include labels and/or legends for your model.
Analysis
1. What is DNA made up of?

2. What are the differences between the DNA of eukaryotes and
prokaryotes

• Oswald Avery published 1944
o His study is based on Griffith’s
findings.
o Concluded that when DNA is
degraded, no transformation
occurs
o DNA - genetic material.
• Alfred Hershey and Martha

Chase 1952
o Concluded that phage injects
DNA, not protein, into bacteria;
DNA genetic material
• Maurice Wilkins and Rosalind

Franklin early 1950s
o Worked independently on X ray
crystallography
o Diffraction pattern gives
information on molecular
structure (Figure 3.1.4)
➢ James Watson and Francis Crick Figure. 3.1.3. Hershey and Chase demonstrated that
o Published paper detailing DNA DNA carries the genetic information in
structure in 1953 bacteriophages. [Pierce, B. (2009). Genetics: A Conceptual
o Based on published data and Approach, Third Edition. W.H. Freeman and Company.]
unreleased information
o
o 1962 won Nobel prize along
with Maurice Wilkins
RNA as Genetic Material

➢ Heinz Fraenkel Conrat and Bea
Singer 1956
o Demonstrated that RNA can
serve as genetic material in
viruses
o Created hybrid virsuses;
progeny particles were of RNA
type
Figure. 3.1.4. Fraenkal-Conrat and Singer’s

experiment demonstrated that, in the tobacco
mosaic virus, RNA carries the genetic
information. [Pierce, B. (2009). Genetics: A Conceptual

The Structure of DNA
Figure. 3.1.5. The Structure of DNA. It consist of a sugar and phosphate backbone and complementary
pairs of nitrogenous bases. The DNA is a helical structure in a spiral form.

The Primary Structure of DNA
Nucleotide
• Nucleoside + phosphate
• Nucleoside is made of sugar + base
Nucleotide Structure
• Pentose (5 carbon) sugar
o 1′ to 5′ “′” refers to carbon in
Figure. 3.1.6. A nucleotide contains either a ribose
sugar (not base)
sugar (in RNA) or a deoxyribose sugar (in DNA).
o RNA – ribose [Pierce, B. (2009). Genetics: A Conceptual Approach, Third Edition.
o -OH at 2′ carbon W.H. Freeman and Company.]
o Less stable
o DNA – deoxyribose
o -H at 2′ carbon
• Phosphate group
o Phosphorous and 4 oxygen
o Negatively charged Figure. 3.1.7. A nucleotide
o Attached to 5′ carbon contains a phosphate group.
• Nitrogenous base [Pierce, B. (2009). Genetics: A
Conceptual Approach, Third
o Covalently bonded to 1′ carbon Edition. W.H. Freeman and
o Purine Company.]
▪ Double-ringed; six- and five-
sided rings
▪ Adenine
▪ Guanine
o Pyrimidine
▪ Single-ringed; six-sided ring
▪ Cytosine
▪ Thymine (DNA only)
▪ Uracil (RNA only)
Figure. 3.1.8. A nucleotide contains either a purine or a pyrimidine base. [Pierce,

B. (2009). Genetics: A Conceptual Approach, Third Edition. W.H. Freeman and Company.]

Secondary Structures of DNA
The Double Helix

• 2 antiparallel strands with bases in interior
• Bases held together by hydrogen bonds
o 2 between A and T; 3 between G and C
• Complementary base pairing;
complementary strands
Helices
• B-DNA
o Watson and Crick model
o Shape when plenty of water is present
o Right hand/clockwise turn; approx 10
bases per turn
• A-DNA
o Form when less water is present; no
proof of existence under physiological
conditions
o Shorter and wider than B form
bases per turn
• Z-DNA
o Left hand/counterclockwise turn
o Approx 12 bases per turn Figure. 3.1.11. B-DNA consists of an alpha
o Found in portions with specific base pair helix with approximately 10 bases per turn.
sequences (alternating G and C) Edition. W.H. Freeman and Company.]
o Possible role in transcription regulation.
Figure. 3.1.12. DNA can assume several

different secondary structures. These
structures depend on the base sequence of the
DNA and the conditions under which it is
placed. [Pierce, B. (2009). Genetics: A Conceptual

Genetic implications
• Watson and Crick indicated

structure revealed mode of
replication
o H bonds break and each
strand serves as a template
for new strand due to
complementary base
pairing
• Central dogma
o Replication
▪ DNA from DNA
o Transcription
▪ RNA from DNA
o Translation
▪ Polypeptide/protein from mRNA
Special Structures
Sequences with a single strand of nucleotides
may be complementary and pair – forming Figure. 3.1.12. The three major pathways of
double-stranded regions information transfer within the cell:
• Hairpin replication, transcription, and translation..
o Region of complementary bases form Edition. W.H. Freeman and Company.]
base; loop formed by unpaired bases
in the middle
• Stem
o No loop of hairpin
• Cruciform
o Double-stranded
o Hairpins form on both strands due
to palindrome sequences
• Complex structures can form within a
single strand
Figure. 3.1.13. Both DNA and RNA can form

special secondary structure. Hairpin (top),
stem (bottom) and secondary structure
showing many hairpins (left). [Pierce, B. (2009).
Genetics: A Conceptual Approach, Third Edition. W.H.

DNA methylation
• Addition of methyl groups to certain bases
• Bacteria is frequently methylated
o Restriction endonucleases cleave
unmethylated sequences
• Amount of methylation varies among
organisms
o Yeast – 0%
o Animals – 5%
o Plants – approx 50%
• Methylation in eukaryotic cells is Figure. 3.1.14. Cytosine bases are often
associated with gene expression methylated to form 5-methylcytosine in
o Methylated sequences are low/no eukaryotic DNA. [Pierce, B. (2009). Genetics: A
transcription Conceptual Approach, Third Edition. W.H. Freeman and
Company.]
Bends in DNA
• Series of 4 or more A-T base pairs cause
DNA to bend
o Affects ability of proteins to bind to
DNA’ affects transcription
• SRY gene
o Produces SRY protein
▪ Binds to certain DNA sequences;
bends DNA
– Facilitates binding of
transcription proteins
– Activates genes for male traits Figure. 3.1.15. The DNA helix can bend by the
binding of proteins to the DNA molecule. [Pierce,
B. (2009). Genetics: A Conceptual Approach, Third Edition.
W.H. Freeman and Company.]
DNA Replication
• The duplication of DNA each time the cell divides
The Central Problem of Replication: Errors arise whenever information is copied; the more
times it is copied, the greater the number of errors.
Solution:
1. Genetic information must be accurately copied every time a cell divides
• Replication has to be extremely accurate.
o One error/million bp leads to 6400 mistakes every time a cell divides, which would
be catastrophic.
2. Replication must take place at a high speed.
• Replication also takes place at high speed.
o E. coli replicates its DNA at a rate of 1000 nucleotides/second.
Proposed DNA replication models:

• Conservative replication model

• Dispersive replication model
• Semiconservative replication model
❖ All replications takes place at a semiconservative manner.
Figure. 3.1.16. Three proposed models of replication are conservative replication, dispersive
replication, and semiconservative replication. [Pierce, B. (2009). Genetics: A Conceptual Approach, Third Edition.
Semiconservative Replication
Meselson and Stahl’s experiment:
• Two isotopes of nitrogen:
o 14N common form; 15N rare, heavy
form
o E.coli were grown in 15N media
first, then transferred to 14N media
o Cultured E.coli were subjected to
equilibrium density gradient
centrifugation
Figure. 3.1.16. Meselson and Stahl used

equilibrium density gradient centrifugation to
distinguish between heavy 15N DNA and
lighter 14N DNA. [Pierce, B. (2009). Genetics: A
Conceptual Approach, Third Edition. W.H. Freeman and
Company.]

Figure. 3.1.18. Theta replication is a type of replication common in E. coli and other organisms
possessing circular DNA. [Pierce, B. (2009). Genetics: A Conceptual Approach, Third Edition. W.H. Freeman and
Company.]
Figure. 3.1.19. Rolling-circle replication takes place in some viruses and in the F factor of E. coli.

Secondary Structures of DNA
The Double Helix

• 2 antiparallel strands with bases in interior
• Bases held together by hydrogen bonds
o 2 between A and T; 3 between G and C
• Complementary base pairing;
complementary strands
Helices
• B-DNA
o Watson and Crick model
o Shape when plenty of water is present
bases per turn
• A-DNA
o Form when less water is present; no
proof of existence under physiological
conditions
o Shorter and wider than B form
bases per turn
• Z-DNA
o Left hand/counterclockwise turn
o Approx 12 bases per turn Figure. 3.1.11. B-DNA consists of an alpha
o Found in portions with specific base pair helix with approximately 10 bases per turn.
sequences (alternating G and C) Edition. W.H. Freeman and Company.]
o Possible role in transcription regulation.
Figure. 3.1.12. DNA can assume several

different secondary structures. These
structures depend on the base sequence of the
DNA and the conditions under which it is
placed. [Pierce, B. (2009). Genetics: A Conceptual

Figure. 3.1.20. DNA synthesis takes place in opposite directions on the two DNA template strands.
DNA replication at a single replication fork begins when a double-stranded DNA molecule unwinds to
provide two single-strand templates. [Pierce, B. (2009). Genetics: A Conceptual Approach, Third Edition. W.H.
Bacterial DNA Replication

• Initiation:
o 245 bp in the oriC (single
origin replicon)
o an initiator protein (DnaA
in E.coli)
• Unwinding:
o Initiator protein
o DNA helicase
o Single-strand-binding
proteins (SSBs)
o DNA gyrase
(topoisomerase)
• Elongation:
o Primers: an existing group
of RNA nucleotides with a
3-OH group to which a
new nucleotide can be
added. It is usually 10–12
nucleotides long.
o Primase: RNA polymerase
o carried out by DNA
Figure. 3.1.21. E. coli DNA replication begins when
polymerase III initiator proteins bind to oriC, the origin of replication.
• Removing RNA primer: DNA [Pierce, B. (2009). Genetics: A Conceptual Approach, Third Edition. W.H.
polymerase I
o Connecting nicks after
RNA primers are
removed: DNA ligase
• Termination: when replication fork meets or by termination protein

Components required for replication in bacterial cells
Component Function
Initiator protein Binds to origin and separates strands of DNA to initiate
replication
DNA helicase Unwinds DNA at replication fork
Single-strand-binding Attach to single-stranded DNA and prevent secondary

proteins structures from forming
DNA gyrase Moves ahead of the replication fork, making and resealing
breaks in the double-helical DNA to release the torque that
builds up as a result of unwinding at the replication fork
DNA primase Synthesizes a short RNA primer to provide a 3'-OH group for
the attachment of DNA nucleotides
DNA polymerase III Elongates a new nucleotide strand from the 3'
DNA polymerase I Removes RNA primers and replaces them with DNA
DNA ligase Joins Okazaki fragments by sealing breaks in the sugar–

phosphate backbone of newly synthesized DNA
The fidelity of DNA replication

• Proofreading: DNA polymerase I: 3 → 5 exonuclease activity removes the incorrectly
paired nucleotide
• Mismatch repair: corrects errors after replication is complete
Rules of Replication
1. Replication is always semiconservative.
2. Replication begins at sequences called origins.
3. DNA synthesis is initiated by short segments of RNA called primers.
4. The elongation of DNA strands is always in the 5’→3’ direction.
5. New DNA is synthesized from dNTPs; in the polymerization of DNA, two phosphates are
cleaved from a dNTP and the resulting nucleotide is added to the 3’-OH group of the
growing nucleotide strand.
6. Replication is continuous on the leading strand and discontinuous on the lagging strand.
7. New nucleotide strands are made complementary and antiparallel to their template
strands.
8. Replication takes place at very high rates and is astonishingly accurate, thanks to precise
nucleotide selection, proofreading, and repair mechanisms.

Figure. 3.1.22. DNA helicase unwinds DNA by binding to the lagging-strand template at each
replication fork and moving in the 5’→ 3’ direction. [Pierce, B. (2009). Genetics: A Conceptual Approach, Third
Eukaryotic DNA Replication

• Eukaryotic DNA Replication is similar to bacterial replication but differs in several
aspects
• Autonomously replicating sequences (ARSs) 100–120 bps
• Origin-recognition complex (ORC) binds to ARSs to initiate DNA replication
• The licensing of DNA replication by the replication licensing factor
o MCM: Minichromosome maintenance
• Eukaryotic DNA polymerase
DNA polymerases in eukaryotic cells
5'→ 3' 3' → 5'

DNA Polymerase Exonuclease
Polymerase Activity Activity Cellular Function
a (alpha) Yes No Initiation of nuclear DNA synthesis

and DNA repair; has primase activity
d (delta) Yes Yes Lagging-strand synthesis of nuclear

DNA, DNA repair, and translesion
DNA synthesis

e (epsilon) Yes Yes Leading-strand synthesis
g (gamma) Yes Yes Replication and repair of

mitochondrial DNA
j (zeta) Yes No Translesion DNA synthesis
h (eta) Yes No Translesion DNA synthesis
u (theta) Yes No DNA repair
i (iota) Yes No Translesion DNA synthesis
k (kappa) Yes No Translesion DNA synthesis
l (lambda) Yes No DNA repair
m (mu) Yes No DNA repair
s (sigma) Yes No Nuclear DNA replication (possibly),

DNA repair, and sister-chromatid
cohesion
f (phi) Yes No Translesion DNA synthesis
Rev1 Yes No DNA repair
Note: The three polymerases listed at the top of the table are those that carry out nuclear
DNA replication.
Nucleosome Assembly
• Eukaryotic DNA
complexed to histone
proteins in nucleosomes
• Nucleosomes reassembled
quickly following
replication
• Creation of nucleosomes
requires
o Disruption of original
nucleosomes on the
parental DNA
o Redistribution of
preexisting histones on
the new DNA
o The addition of newly
synthesized histones to
complete the formation
of new nucleosomes
Figure. 3.1.23. Experimental procedure for studying how
nucleosomes dissociate and reassociate in the course of
replication. [Pierce, B. (2009). Genetics: A Conceptual Approach, Third

Location of replication within the nucleus
• DNA polymerase is fixed in location
and template RNA is threaded
through it.
DNA synthesis at the ends of chromosomes
• The ends of linear eukaryotic DNA
molecules are replicated by the
enzyme telomerase.
Figure. 3.1.24. DNA synthesis at the ends

of circular and linear chromosomes must
differ. [Pierce, B. (2009). Genetics: A Conceptual
Approach, Third Edition. W.H. Freeman and
Company.]
Figure. 3.1.25. The enzyme telomerase is

responsible for the replication of
chromosome ends. [Pierce, B. (2009). Genetics: A
Conceptual Approach, Third Edition. W.H. Freeman
and Company.]

Application 3.11
Activity
Test Your Knowledge
1. Describe the chemical nature of the gene.

2. Describe the processes involved in bacterial and eukaryotic DNA
replication.

Module 3

Lesson 2
Time Frame: 5 Hours
Learning Objectives Gene Expression: Transcription and
Translation
❖ Discuss the types of RNA and
their roles in gene
expression Introduction
❖ Describe the process of
transcription, including start Transcription is the synthesis of RNA molecules,
and stop signals, in both with DNA as a template, and it is the first step in the
prokaryotes and eukaryotes transfer of genetic information from genotype to
❖ Discuss posttranscriptional phenotype. The process is complex, and requires a
changes in eukaryotic number of protein components. Translation is the
messenger RNAs, including process of protein synthesis by ribosomes in the
an analysis of intron removal cytoplasm or endoplasmic reticulum. The genetic
❖ Discuss the mechanism of information in DNA is used as a basis to create messenger
protein biosynthesis, in RNA (mRNA) by transcription. Single stranded mRNA
which organisms, using the then acts as a template during translation.
information in DNA, string
together amino acids to form
proteins
❖ Discuss the genetic code
Activity
Activity 3.2
1 The Central Dogma
Key Concepts
1. In 1957,
EarlyFrancis
DNA Studies
Crick stated that "DNA makes RNA, and RNA makes protein." In this
2. Nucleotide Structure
3. activity
DNAyou willHelix
Double learn how genes are expressed.
4. DNA Methylation
Procedure:
5.
1. Illustrate the steps in central dogma.
Analysis
1. Describe the steps in the central dogma.

2. What is the importance of central dogma in the study of
genetics?

RNA Structure
• Nucleotides
o Ribose sugar – OH at 2′ C
▪ Unstable; short-lived molecule
• Nitrogenous bases
o Adenine
o Guanine
o Cytosine
o Uracil
• Nucleotide polymer held together by
phosphodiester bonds
• Usually single-stranded due to short regions
of complementary sequences, can base pair to
form stems, hairpins, etc.
Primary structure
• Nucleotide sequence
Secondary structure
• Formed by complementary regions
• Has greater variety than helix of DNA
• Various shapes have different functions
Figure 3.2.2. The structure of RNA. [Pierce, B.

(2009). Genetics: A Conceptual Approach, Third Edition.
Figure 3.2.1. Primary and secondary structure of

RNA. [Pierce, B. (2009). Genetics: A Conceptual Approach,
Differences between DNA and RNA
Characteristic DNA RNA

Composed of nucleotides Yes Yes
Type of Sugar Deoxyribose Ribose
Presence of 2’-OH group No Yes
Bases A, G, C, T A, G, C, U
Nucleotides joined by phosphodiester bonds Yes Yes
Double or single stranded Usually double Usually single
Secondary structure Double helix Many types
Stability Quite stable Easily degraded

Classes of RNA
•
• Ribosomal RNA (rRNA)
o Joins with protein subunits to form ribosomes
▪ Site of polypeptide synthesis
• Messenger RNA (mRNA)
o Codes for a polypeptide
▪ Amino acid sequence
o Pre-messenger/primary transcript
▪ In eukaryotic cells only
• Needs to be modified before exiting the nucleus
▪ Prokaryotic mRNA can start to be translated before transcription is
complete
• Transfer RNA (tRNA)
o Brings specific amino acid to the ribosome for incorporation into the growing
polypeptide
• Small nuclear RNA (snRNA)
o Joins with small nuclear proteins to form snRNPs – small nuclear ribonuclear
proteins
▪ Assist with post-transcriptional modifications of primary transcript
• Splices out introns
• Small nucleolar RNA (snoRNA)
o Aids in the processing of rRNA
• MicroRNA (miRNA) and small interfering RNA (siRNA)
o In eukaryotic cells
o RNAi – RNA interference
o Initiates degradation or inhibition of mRNA molecules
• Piwi-interacting RNA (piRNA)
o Found in mammalian testes
o Regulation of sperm development
Location and function of different classes of RNA molecules

Class of RNA Cell Type Location of function Function
in eukaryotic cell*
Ribosomal RNA (rRNA) Bacterial and Cytoplasm Structural and
eukaryotic functional
components of the
ribosome
Messenger RNA (mRNA Bacterial and Nucleus and Cytoplasm Carries genetic code for
eukaryotic protein
Transfer RNA (tRNA) Bacterial and Cytoplasm Helps incorporate
eukaryotic amino acids into
polypeptide chain
Small nuclear RNA Eukaryotic Nucleus Processing of pre-
(snRNA) mRNA
Small nucleolar RNA Eukaryotic Nucleus Processing and
(snoRNA) assembly
of rRNA
Small cytoplasmic RNA Eukaryotic Cytoplasm Variable
(scRNA)
All eukaryotic RNAs are transcribed in the nucleus.

Transcription: Synthesizing RNA from DNA
• During DNA replication, the entire
DNA molecule is copied
• In transcription, only a small
section of DNA is used for the
synthesis of RNA
o Usually one gene at a time,
or several genes (in
prokaryotes)
• Only one of the two strands of
DNA gets transcribed into RNA
o Transcribed/template Figure 3.2.3. RNA molecules are synthesized that
strand are complementary and antiparallel to one of the
o Nontemplate strand = two nucleotide strands of DNA, the template strand..
coding strand Edition. W.H. Freeman and Company.]
▪ “coding” strand
gives RNA
sequence (replace T with U)
• In DNA, one strand may be the template strand for one gene, while another strand may
be the template strand for another gene.
• Transcription occurs in the 5′→3′ direction of the RNA molecule
o Complementary and antiparallel to the DNA strand
Transcription Unit
• Promotor
o Upstream from coding
region
o Specific DNA sequence
o Serves as attachment site
for transcription
molecules
o Sequence is NOT
transcribed into RNA
• RNA coding region
• Terminator
o Downstream from coding Figure 3.2.4. A transcription unit includes a
region promoter, an RNA-coding region, and a terminator
o Is transcribed into RNA; [Pierce, B. (2009). Genetics: A Conceptual Approach, Third Edition.
sequence is later
removed
o Specific sequence to halt
transcription
RNA polymerase
• Does NOT require a primer
• Prokaryotic RNA polymerase
o Single type of polymerase
used for all transcription Figure 3.2.5. In bacterial RNA polymerase, the core
o Composed of 5 enzyme consists of four subunits: two copies of alpha (α), a
polypeptide subunits – single copy of beta (β), and single copy of beta prime (β’).
core enzyme [Pierce, B. (2009). Genetics: A Conceptual Approach, Third Edition.
o (σ) sigma factor W.H. Freeman and Company.]

▪ Binds with core enzyme to create holoenzyme
▪ Controls binding to promotor
• Without sigma, polymerase will bind anywhere on DNA
▪ Various sigma factors are present for different promotor types
▪ Releases from core protein after transcript is several nucleotides long
• Eukaryotic RNA polymerase
o Different classes for different types of RNA
o Consists of multiple subunits
▪ Core enzyme with accessory proteins at different stages
Bacterial Transcription
Processes of Bacterial Transcription
1. initiation, in which the transcription apparatus assembles on the promoter and begins
the synthesis of RNA;
2. elongation, in which RNA polymerase moves along the DNA, unwinding it and adding
new nucleotides, one at a time, to the 3’ end of the growing RNA strand; and
3. termination, the recognition of the end of the transcription unit and the separation of
the RNA molecule from the DNA template.
Initiation
• Specific DNA sequence at promoter
• Consensus sequence
o Most common nucleotides in a
particular position
o R = purine
o Y = pyrimidine
o N = any
Bacterial Promoters Figure 3.2.6. Actual and consensus

• Two consensus sequences sequence in bacterial transcription.
[Pierce, B. (2009). Genetics: A Conceptual
• Any change/mutation in promoter region Approach, Third Edition. W.H. Freeman and
alters the rate of transcription Company.]
o Down mutation – reduces rate of
transcription
o Up mutation – increases rate of
transcription
▪ Rare
Holoenzyme
• Binds to promotor consensus sequences
only, but enzyme covers larger area
• Polymerase alters its structure and binds Figure 3.2.7. In bacterial promoters,
more tightly, unwinding DNA consensus sequences are found upstream
o Begins at -10 sequence and of the start site, approximately at
continues downstream positions -10 and -35.. [Pierce, B. (2009).
• Bases on consensus sequence location, Genetics: A Conceptual Approach, Third Edition. W.H.
enzyme’s active site is in position +1 Freeman and Company.]
• First RNA nucleotide is placed

complementary to DNA sequence

Elongation
• After transcript is approximately 12
nucleotides long, polymerase structure
alters so it is no longer bound to
consensus sequences
o Moves downstream
o Sigma factor is usually released
• Polymerase continues to unwind DNA
downstream and rewind upstream
o Transcription bubble
▪ Positive supercoiling
ahead of bubble;
negative supercoiling
behind
• Topoisomerase
enzymes relieve
tension
Termination
Rho-independent
• Contains inverted complementary Figure 3.2.8. Termination by bacterial rho-
sequences that form a hairpin when independent terminators is a multistep process.
transcribed [Pierce, B. (2009). Genetics: A Conceptual Approach, Third
o Slows transciption Edition. W.H. Freeman and Company.]
•
• 2nd repeat sequence is polyA (polyU on
RNA)
o Weak (due to 2 H bonds
between each), and transcript
separates from DNA template
Rho-dependent
• Rho factor protein
o Binds to regions with no
secondary structure
• RNA sequence upstream from
termination doesn’t form secondary
structure
o Rho factor binds to RNA and
moves toward 3′ end
• At a hairpin, transcription slows and
rho factor can “catch up” to DNA/RNA
o Rho has helicase activity
▪ Breaks H bonds and
separates RNA from
DNA Figure 3.2.9. The termination of transcription
in some bacterial genes requires the presence of
the rho protein.. [Pierce, B. (2009). Genetics: A
Company.]

Modifications for eukaryotic transcription
• Nucleosome structure
o DNA associated with histone proteins
▪ Acetylation of histones reduces their positive charge; makes DNA more
accessible
• Initiators
o Promotors
▪ Have varied sequences to attract different polymerase types
• Polymerases have several associated accessory proteins
▪ Directly upstream from gene
o Enhancers
▪ Can be located far away from gene
▪ DNA loops around to bring enhancer (with activator protein) to
promotor region
▪ Some sequences can be repressors/silencers
• Termination
o Different polymerases have different mechanisms for termination
Figure 3.2.9. The termination of transcription in some bacterial genes requires the presence of the
rho protein.. [Pierce, B. (2009). Genetics: A Conceptual Approach, Third Edition. W.H. Freeman and Company.]

The Genetic Code
• Nucleotide sequence must code for
specific amino acids
• Francis Crick – 3 nucleotides code for
one amino acid
o codon
• 64 codons
o 61 code for an amino acid
o “degenerate”
▪ More than one codon
can code for the same
amino acid
The Degeneracy of the Code

• tRNA
o 30-50 tRNA for 20 amino
acids
o Isoaccepting tRNA have
different anticodons but still
carry the same amino acid
• Wobble Figure 3.2.10. The genetic code consists of 64
o 1st nucleotide in anticodon codons and the amino acids specified by these
pairs with the 3rd codon of codons. The codons are written 5’:3’, as they
mRNA appear in the mRNA. AUG is an initiation codon;
o Flexibility in bonding allows UAA, UAG, and UGA are termination codons.
one tRNA to recognize more Edition. W.H. Freeman and Company.]
than one codon
▪
▪ Still codes for same
amino acid
Reading Frame
• Determined by the START/initiation
codon
o AUG – also codes for
methionine
• No overlapping or skipping of bases
• Termination/stop codons
o Also called nonsense codons Figure 3.2.11. Wobble may exist in the pairing of
• Universality a codon on mRNA with an anticodon on tRNA.
o With rare exception, genetic [Pierce, B. (2009). Genetics: A Conceptual Approach, Third
code is read the same by all
organisms
tRNA charging
• Attachment of appropriate amino acid
• Aminoacyl-tRNA synthetase (20 different)
o Recognize specific sequences in certain regions of tRNA, and binds the
appropriate amino acid to 3′ acceptor arm of tRNA
o Forms aminoacyl-tRNA

Figure 3.2.12. An amino acid becomes attached to the appropriate tRNA in a two-step reaction. [Pierce,
Translation
• Occurs at ribosomes
o Attaches to 5′ end of mRNA and
moves toward 3′ end
o Binding determined by Shine-
Dalgarno sequence in
prokaryotic cells/
modifications in eukaryotic
cells
Initiation of Translation
• Ribosome has two subunits – small
(30S) and large (50S)
o Complete ribosome (70S)
• Initiation factors bind to small unit,
prohibiting small unit from binding
with large subunit
o Now free to bind to mRNA
• Aminoacyl-tRNAmet attaches to
initiation/ start codon
• Large ribosomal subunit attaches
Ribosome
• Has three sites for tRNA
o A (aminoacyl) site
o P (peptidyl) site
o E (exit) site
• Initiator tRNAmet enters P site; all Figure 3.2.13. The initiation of translation in
other tRNA first enter the A site bacterial cells requires several initiation factors
o A→P→E and GTP. [Pierce, B. (2009). Genetics: A Conceptual

Elongation
• Next codon is exposed in the A site
o Charged tRNA enters A
• Peptide bond forms between the P site
amino acid and A site amino acid
o Peptidyl transferase
• Translocation
o ribosome moves down mRNA
molecule
o P site tRNA enters E site
o A site tRNA with growing
polypeptide enters P site
o A site now has next codon
exposed; ready for next tRNA
o During next shift, E site tRNA is
released into cytoplasm to be re- Figure 3.2.14. The initiation of translation in
charged with another specific bacterial cells requires several initiation
amino acid factors and GTP. [Pierce, B. (2009). Genetics: A
Company.]
Termination
•
• A STOP codon enters A site
o No appropriate tRNA
• Release factors enter A site
o Ribosome subunits dissociate
o Polypeptide is released from last
tRNA
Post-translation modifications
• Methionine cleaved off; chain possibly
cleaved
• Carbohydrates attached (forms
glycoproteins)
• Folding into proper 3D shape
o Aided by chaperone proteins
Figure 3.2.15. Translation ends when a stop

codon is encountered. [Pierce, B. (2009). Genetics: A
Company.]

Application 3.2 1
Activity
Test Your Knowledge
1. What are the processes involved in DNA transcription and translation?

2. What is the end product of gene expression?
References:
References
York.

Module 3

Learning Objectives Control of Gene Expression

❖ Discuss the process in which Gene regulation is the mechanisms and systems
inducible and repressible that control the expression of genes. This lesson begin
operons work with the discussion of the necessities of gene regulation
❖ Describe examine the which include the levels at which gene expression is
control of transcription in controlled and the difference between genes and
eukaryotes and bacteria regulatory elements. We then examine gene regulation in
❖ Discuss the process in which bacterial cells. Further into this lesson, we explore gene
transposable genetic regulation in eukaryotic cells. We will also examine the
elements transpose and how transposable elements control gene expression.
control gene expression in Lastly, we will take a look into ther transcriptional and
eukaryotes and bacteria post transcriptional mechanisms of controlling gene
❖ Discuss other expression in eukaryotes, bacteria and phages.
transcriptional and
posttranscriptional
mechanisms of control of
gene expression in
eukaryotes, bacteria and
phages
Activity
Activity 3.3
1 Creating Giant Mice through Gene
❖ Key Concepts Regulation
❖ Early DNA Studies
❖ In 1982, a group
Nucleotide of molecular geneticists led by Richard Palmiter at the University of
Structure
❖ Washington produced gigantic mice that grew to almost twice the size of normal mice.
DNA Double Helix
❖ DNA Methylation
❖ Procedure:
Read the article on how the giant mice were created.
Analysis
1. Briefly summarize the article.
2. Describe how the transgenic mice with the gene for rat growth hormone
grow so big?

Control of Gene Expression
• Gene expression may be controlled at different levels, including the alteration of gene
structure, transcription, mRNA processing, RNA stability, translation, and
posttranslational modification.
• Much of gene regulation is through the action of regulatory proteins binding to specific
sequences in DNA.
• Prokaryotic organisms regulate gene expression in response to their environment.
• Eukaryotic cells regulate gene expression to maintain homeostasis in the organism.
Regulatory Proteins
• Gene expression is often controlled by regulatory proteins binding to specific DNA

sequences.
• regulatory proteins gain access to the bases of DNA at the major groove
• regulatory proteins possess DNA-binding motifs
• DNA-binding motifs are regions of regulatory proteins which bind to DNA
o Helix-turn-helix motif - consists of two alpha helices connected by a turn.
o Homeodomain motif - consists of three alpha helices; the third helix fits in a major
groove of DNA.
o Zinc finger motif - consists of a loop of amino acids containing a single zinc ion.
Most proteins containing zinc fingers have several repeats of the zinc-finger motif.
Each zinc finger fits into the major groove of DNA and forms hydrogen bonds with
bases in the DNA.
o Leucine zipper motif - consists of a helix of leucine nucleotides and an arm of basic
amino acids. DNA-binding proteins usually have two polypeptides; the leucine
nucleotides of the two polypeptides face one another, whereas the basic amino
acids bind to the DNA.
o Steroid receptor binding motif - has two alpha helices, each with a zinc ion
surrounded by four cysteine residues. The two alpha helices are perpendicular to
one another: one fits into the major groove of the double helix, whereas the other
is parallel to the DNA.

o Helix-loop-helix binding motif - consists of two alpha helices separated by a loop
of amino acids. Two polypeptide chains with this motif join to form a functional
DNA-binding protein. A highly basic set of amino acids in one of the helices binds
to the DNA.
Prokaryotic Regulation of Gene Expression

• Control of transcription initiation can be:
o positive control – increases transcription when activators bind DNA
o negative control – reduces transcription when repressors bind to DNA regulatory
regions called operators
• Prokaryotic cells often respond to their environment by changes in gene expression.

• Genes involved in the same metabolic pathway are organized in operons.
• Some operons are induced when the metabolic pathway is needed.
• Some operons are repressed when the metabolic pathway is no longer needed.
lac Operon
• The lac operon contains genes for the use of lactose as an energy source.
• Regulatory regions of the operon include the CAP binding site, promoter, and the
operator.
• The coding region contains genes for 3 enzymes:
o β-galactosidase, permease, and transacetylase
• The lac operon is negatively regulated by a repressor protein:

o lac repressor binds to the operator to block transcription
o in the presence of lactose, an inducer molecule binds to the repressor protein
o repressor can no longer bind to operator
o transcription proceeds
• In the presence of both glucose and lactose, bacterial cells prefer to use glucose.
• Glucose prevents induction of the lac operon.
o binding of CAP – cAMP complex to the CAP binding site is required for induction of
the lac operon
o high glucose levels cause low cAMP levels
o high glucose > low cAMP > no induction

trp Operon
• The trp operon encodes genes for the biosynthesis of tryptophan.
• The operon is not expressed when the cell contains sufficient amounts of tryptophan.
• The operon is expressed when levels of tryptophan are low.
• The trp operon is negatively regulated by the trp repressor protein
o trp repressor binds to the operator to block transcription
o binding of repressor to the operator requires a corepressor which is tryptophan
o low levels of tryptophan prevent the repressor from binding to the operator
Eukaryotic Regulation of Gene Expression

• Controlling the expression of eukaryotic genes requires transcription factors.
o general transcription factors are required for transcription initiation
▪ required for proper binding of RNA polymerase to the DNA
o specific transcription
factors increase
transcription in
certain cells or in
response to signals
General Transcription Factors

• General transcription
factors bind to the
promoter region of the
gene.
• RNA polymerase II then
binds to the promoter to
begin transcription at the
start site (+1).
• Enhancers are DNA sequences to which specific transcription factors (activators) bind
to increase the rate of transcription.
Coactivators and Mediators

• Coactivators and mediators are also required for the function of transcription factors.
• coactivators and mediators bind to transcription factors and bind to other parts of the
transcription apparatus
Eukaryotic Chromosome Structure

• Eukaryotic DNA is packaged into chromatin.
• Chromatin structure is directly related to the control of gene expression.
• Chromatin structure begins with the organization of the DNA into nucleosomes.
• Nucleosomes may block RNA polymerase II from gaining access to promoters.
Methylation
• Methylation (the addition of –CH3) of DNA or histone proteins is associated with the
control of gene expression.
• Clusters of methylated cytosine nucleotides bind to a protein that prevents activators
from binding to DNA.
• Methylated histone proteins are associated with inactive regions of chromatin.

Posttranscriptional Regulation
• Control of gene expression usually involves the control of transcription initiation.
• But gene expression can be controlled after transcription, with mechanisms such as:
o RNA interference
o alternative splicing
o RNA editing
o mRNA degradation
RNA interference
• involves the use of small RNA molecules
• The enzyme Dicer chops double stranded RNA into small pieces of RNA
• micro-RNAs bind to complementary RNA to prevent translation
• small interfering RNAs degrade particular mRNAs before translation
• Introns are spliced out of pre-mRNAs to produce the mature mRNA that is translated.
Alternative splicing
• Recognizes different splice sites in different tissue types.
• The mature mRNAs in each tissue possess different exons, resulting in different
polypeptide products from the same gene.
RNA editing
• Creates mature mRNA that are not truly encoded by the genome.
• Mature mRNA molecules have various half-lives depending on the gene and the location
(tissue) of expression.

• The amount of polypeptide produced from a particular gene can be influenced by the
half-life of the mRNA molecules.
Protein Degradation
• Proteins are produced and degraded continually in the cell.
• Proteins to be degraded are tagged with ubiquitin.
• Degradation of proteins marked with ubiquitin occurs at the proteasome.
Transposable Elements
• Transposable genetic elements, transposons, or even jumping genes, are regions of the
genome that can move from one place to another.
• In some cases, transposition is conservative: the transposons move without copying
themselves. They are liberated from the donor site by double strand breaks in the DNA.
• In other cases, transposition is replicative: a copy of the transposon is inserted while the
original stays in place.
• This mechanism involves only single strand breaks of the DNA at the donor site.
Bacterial Transposable Elements

IS elements (insertion sequences)
• The first transposable elements discovered in bacteria
• the simplest transposons
• consist of a central region of about 700 to 1,500 base pairs surrounded by an inverted
repeat of about 10 to 30 base pairs, the numbers depending on the specific IS element.
• The central region of the IS element contains a gene or genes for the transposing event
(usually genes for transposase and resolvase enzymes)
• the relatively small IS elements carry no bacterial genes
• cut and paste transposons that reside in in bacterial chromosomes and plasmids
Composite transposons
• bacterial cut-and-paste transposons
• denoted by the symbol Tn.
• are created when two IS elements insert near each other
Mechanism of Transposition
• Transposition may take place through a DNA molecule or through the production of an
RNA molecule that is then reverse transcribed into DNA.
• Transposition may be replicative, in which the transposable element is copied and the
copy moves to a new site, or nonreplicative, in which the transposable element excises
from the old site and moves to a new site.
• Retrotransposons transpose through RNA molecules that undergo reverse transcription
to produce DNA.
• In many transposable elements, transposition is tightly regulated.
Transposable elements in Eukaryotic Cell

• Some transposable elements in eukaryotic cells are similar to those found in bacteria,
ending in short inverted repeats and producing flanking direct repeats at the point of
insertion.

• Others are retrotransposons, similar in structure to retroviruses and transposing
through RNA intermediates.
Genotypic and Phenotypic Effects of Transposition

• If transposition takes place into a gene or its promoter, it can disrupt the expression of
that gene.
• Depending on the orientation of a transposon, it can prevent the expression of genes.
• A transposon can also cause deletions and inversions.
Evolutionary Significance of Transposable Elements

• Transposable elements provide some important function for the cell; the genetic
variation.
• Transposable elements provide evolutionary flexibility by inducing mutations.
• Transposable elements do not benefit the cell but are widespread because they can
replicate and spread.
Application 3.31
Activity
Test Your Knowledge
1. Describe the role of regulatory proteins in the regulation of gene expression.

2. Describe the mechanisms of controlling gene expression in prokaryotic and
eukaryotic organisms.
3. Describe the effects of transposable elements on gene expression.
References
Pierce, B. (2017). Genetics: A Conceptual Approach, 6th edition. WH Freeman, New York.
Acquaah, J. (2012). Principles of Plant Genetics and Breeding, 2nd edition. Wiley-Blackwell,
United Kingdom

Module 3
Learning Objectives Gene Mutation and DNA Repair

❖ Describe the nature of This lesson is about how errors arise in genetic
mutation instructions and how those errors are occasionally
❖ Discuss mutagenesis repaired. It begins with the nature of mutation which
❖ Describe the processes of include its categories, types, effects on phenotype and
DNA repair causes of mutation. We will also explore mutagens and
Key Concepts learn how they alter DNA sequences. The last part of this
• DNA Mutation lesson discusses the different methods in DNA repair.
• DNA Repair
Activity
Activity 3.4
1 The biological impacts of the Fukushima nuclear
accident on the pale grass blue butterfly
A disastrous nuclear accident happened in Japan’s Fukushima Nuclear Power Plant after a
powerful earthquake on March 2011. This result to genetic mutation in pale grass blue butterfly.
In this activity, you will understand how radiation causes mutation in living organisms.
Procedure:
Read the article “The biological impacts of the Fukushima nuclear accident on the pale grass
blue butterfly”.
Analysis
1. Briefly summarize the article.
2. Describe the impacts of nuclear radiation exposure to the genotypic and
phenotypic constitution of the blue grass butterfly

Mutation
• Inheritable change in genetic material
• Cells from cell division; offspring from reproduction
Categories of Mutation
• Somatic mutations
o Mitosis yields genetically identical cells
o can lead to mosaicism
o Tumor – uncontrolled growth
• Germ-line mutations
o Arise in cells destined to become gametes
o Passed to offspring; present in every cell of organism
• Gene mutations
o Affect a single gene
• Chromosomal mutations
o Large-scale changes
o May be observable with a microscope
Figure 3.4.1. Two basic classes of mutations: somatic mutations and germ-line mutations. [Pierce, B. (2009).
Genetics: A Conceptual Approach, Third Edition. W.H. Freeman and Company.]
Types of mutations
• Base substitution/point mutation
o One base is replaced by
another
o Transition
o One purine
replaced by another
purine; one
pyrimidine replace
by another
pyrimidine
o Transversion Figure 3.4.2. A transition is the substitution of a purine for
o Purine replaced by a a purine or a pyrimidine for a pyrimidine; a transversion is
pyrimidine, or vice the substitution of a pyrimidine for a purine or a purine for
versa a pyrimidine. [Pierce, B. (2009). Genetics: A Conceptual Approach, Third
• Insertion or deletion
o One or more nucleotides
o Frameshift mutation
o

o In mRNA genes, affect all amino
acids downstream, unless in
groups of three in normal codon
place
• Expanding trinucleotide repeats
o Certain genes contain tandem
repeats
o Number of repeats can increase
in offspring due to strand
slippage or uneven crossing
over.
Phenotypic effects
• Missense mutation
o Causes incorrect amino acid
to be placed in polypeptide
o Neutral mutation – protein
function is not affected due Figure 3.4.3. Types of mutation. [Pierce, B. (2009).
Genetics: A Conceptual Approach, Third Edition. W.H. Freeman
to amino acids having and Company.]
similar properties
• Nonsense mutation
o Introduces a premature STOP codon
o Results in a truncated polypeptide
• Silent mutation
o Due to codon redundancy, mutation still codes for the same amino acid
• Loss of function
o Functional polypeptide is not made
o Recessive
o Normal gene still makes correct polypeptide
• Gain of function
o Abnormal polypeptide is produced
o dominant
Figure 3.4.4. Base substitutions can cause (a) missense, (b) nonsense, and (c) silent mutations. [Pierce,

Causes of mutations
• Spontaneous
o Natural changes/errors
o Replication errors or
chemical changes
• Induced
o Caused by environmental
agents
▪ Chemical,
radiation
Spontaneous replication errors

• Tautomers
• Wobble
• Strand slippage
• Unequal crossing over
Tautomers
• Various forms of nitrogenous
bases
o Position change of a proton
(hydrogen ion)
• Can exhibit unconventional base
pairing
o Rare form of C can bond with
A; rare form of G can bond
with T
• Originally thought to be major
source of mutation – no
supporting evidence
Wobble
• Flexibility in DNA helix
• Incorporated error
o TA base pair becomes CA
• One new molecule will have
correct TA, other will have
CG
o Since all bases are correctly
paired, no repair
mechanism can fix Figure 3.4.5. Purine and pyrimidine bases exist in
different forms called tautomers. [Pierce, B. (2009).
Genetics: A Conceptual Approach, Third Edition. W.H. Freeman and
Company.]

Figure 3.4.6. Wobble base pairing leads to a replicated error. [Pierce, B. (2009). Genetics: A Conceptual
Strand slippage
• Causes small insertions or
deletions
• One nucleotide loops out
o On new strand – results in
an insertion
o On old strand – results in a
deletion
Strand slippage in trinucleotide

repeats
• Slippage of new strand can result
in expanded number of repeats in
offspring cells
• Cause of anticipation Figure 3.4.7. Insertions and deletions may result
from strand slippage. [Pierce, B. (2009). Genetics: A
Conceptual Approach, Third Edition. W.H. Freeman and Company.]
Unequal crossing over
• Incorrect alignment of
homologous chromosomes
• Crossing over results in an insertion in one molecule and a deletion in the other
molecule
• Can also cause expanded trinucleotide repeats
Spontaneous chemical changes

• Depurination
o Nucleotide loses its purine base; apurinic
o Can’t act as a template
o A is usually the base placed in the new strand
• Deamination
o Removal of an amino group
o Deaminated cytosine becomes uracil
▪ Since U is not present in DNA, usually correctly by repair mechanisms
o Deaminated methylcytosine becomes thymine
▪ Causes CG to AT – not detected by repair mechanisms

Mutagen
• environmental agent with
ability to alter DNA sequence
Chemically Induced Mutagens

• Base analogs
• Alkylating agents
• Deamination
• Oxidative reactions
• Intercalating agents
Base analogs
•
• Have structure similar to normal
nucleotides
• When ionized, exhibit
unconventional base pairing
• Transition or transversion
mutation shown?
Alkylating agents
• Donates alkyl groups to bases
• Incorrectly base pair
Deamination
• Can occur spontaneously or be
induced
• Adenine becomes hypoxanthine
(pairs with C)
•
• Guanine becomes xanthine (pairs
with T)
Oxidative reactions
• Reactive forms of oxygen
• Causes transversions Figure 3.4.8. 5-Bromouracil (a base analog)
• G pairs with A resembles thymine, except that it has a bromine atom
Intercalating agents in place of a methyl group on the 5-carbon atom.
• Insert themselves into DNA – Because of the similarity in their structures, 5-
bromouracil may be incorporated into DNA in place of
distorts molecule thymine. Like thymine, 5-bromouracil normally pairs
• Often causes frameshift mutations with adenine but, when ionized, it may pair with
guanine through wobble. [Pierce, B. (2009). Genetics: A
Radiation Conceptual Approach, Third Edition. W.H. Freeman and Company.]
• Ionizing radiation
o High energy breaks
phosphodiester bonds
o

o Results in double-
stranded breaks
• UV light
o Pyrimidine dimers –
usually thymine
dimers
o Causes TpT to
covalently bond
▪ Replication of
DNA is blocked
and cell dies, or
transcription is blocked
DNA Repair
• Mismatch repair
• Direct repair
• Base excision repair Figure 3.4.9. 5-Pyrimidine dimers result from
• Nucleotide excision repair Ultraviolet light [Pierce, B. (2009). Genetics: A Conceptual
Mismatch Repair
• Corrects replication errors/improper base pairing not fixed by DNA polymerase III
• Recognizes structural distortions
• New strand section is cut out and replaced
o Old strand is methylated – strand distinction
Direct Repair
• Converts altered nucleotide back to original form
• Methylguanine binds with A
o Enzymes remove methyl group to return to normal guanine
• Photolyase
o Found in E. coli and some eukaryotes (not humans)
o Break covalent bonds of dimers
Base Excision Repair

• Repairs abnormal/ modified bases
• Nitrogenous base is first removed
o Apurinic or apyrimidic site
• Followed by removal of rest of nucleotide
• DNA polymerase replaces nucleotide; DNA ligase seals nick by forming phosphodiester
bond
Nucleotide excision repair (NER)

• Removes lesions that distort DNA helix
• Several enzymes/ genes involved
o Recognize distortion
• DNA strand is separated; single-strand binding proteins stabilize
• Large section is removed
• DNA polymerase fills in; DNA ligase seals nicks

Application 3.41
Activity
Test Your Knowledge
1. What is the difference between somatic mutations and germ-line mutations?

2. What is the difference between a missense mutation and a nonsense mutation?
A silent mutation and a neutral mutation?
3. How do alkylating agents, nitrous acid, and hydroxylamine produce mutations?
4. What types of mutations are produced by ionizing and UV radiation?
5. List at least three different types of DNA repair and briefly explain how each is
carried out.
References
York.

Module 3

Learning Objectives Genomics, Biotechnology and

Recombinant DNA
expected to:
❖ Describe the concepts of Introduction

Genomics
❖ Describe the techniques Advance genetic studies and improvement of techniques
used in recombinant in the manipulation of gene brought about benefits but
DNA technology also faced ethical and legal concerns especially in the
❖ Describe applications of areas of reproduction and cloning of organisms. The first
Recombinant DNA part of this lesson explores the field of genetics involved
Technology in the study of the whole genome, genomics. We will
focus on its concepts including its different areas. The
Key Concepts second part focuses on the techniques and application of
• Genomics Recombinant DNA technology. In addition we will
• Biotechnology and discuss ethical and legal issues concerning biotechnology
Recombinant DNA
Activity
Activity 3.5
1 The Inception of GMO
Genetically modified organisms (GMO) are product of manipulating genes through recombinant
DNA technology. In this activity, you will understand the beginnings of genetically modified
organisms.
Procedure
Read the article “From Corgis to Corn: A Brief Look at the Long History of GMO Technology”
here http://sitn.hms.harvard.edu/flash/2015/from-corgis-to-corn-a-brief-look-at-the-long-
history-of-gmo-technology/
Analysis
3. When did the modern modification began?

4. What was the first GMO
5. Cite some controversial issues involving GMO.

Genomics
• Genomics is the field of genetics that attempts to understand the content, organization,
and function of genetic information contained in whole genomes.
• It involves the study of all genes at the DNA, mRNA, and proteome level as well as the
cellular or tissue level.
• First coined in 1986 by Tom Roderick, a geneticist at the Jackson Laboratory in Maine,
during a meeting about the mapping of the human genome.
• Genomics is the study of all genes present in an organism.
• It includes studies of intragenomic phenomena such as heterosis, epistasis, pleiotropy
and other interactions between loci and alleles within the genomes.
History of Genetics
• Genomics is a concept that was first developed by Fred Sanger in early 1970s, who first
sequenced the complete genome of a virus and of a mitochondrion.
• In 1972, Walter Fiers and his research group became the first to sequence a gene. They
sequenced the gene of Bacteriophage MS2.
• In 1995, Hamilton O. Smith and his team became the first to sequence a genome of a free
living organism – that of Haemophilus influenzae.
Difference Between Genetics and Genomics

Genetics Genomics
Genetics is the study of heredity. Genomics is the study of the entirety of an
organism’s genes
“Gene" refers to a specific sequence of DNA “Genome” refers to an organism's entire
on a single chromosome genetic makeup
Genetics involves the study of functions and Genomics addresses all genes and their inter
composition of the single gene relationships
Subfield of Genomics
• Structural Genomics - is concerned with sequencing and understanding the content of
genomes.
• Functional Genomics - attempts to understand the function of information in genomes.
• Comparative Genomics - compares the content and organization of genomes of different
organisms
Structural Genomics
• Structural genomics concerns the organization and sequence of the genome.
• The first steps in characterizing a genome is to prepare its maps:
o Genetic Maps
o Physical Maps
• These maps provide information about the:
o relative locations of genes
o Molecular markers
o chromosome segments
Genetic Maps
• Genetic maps (also called linkage maps) provide a rough approximation of the locations
of genes relative to the locations of other known genes.

• These maps are based on the genetic function of recombination
• Individuals heterozygous at two or more genetic loci are crossed, and the frequency of
recombination between loci is determined by examining the progeny.
• Recombination frequency between two loci is 50%, then the loci are located on different
chromosomes or are far apart on the same chromosome.
• Recombination frequency <50%, the loci are linked.
• For linked genes, the rate of recombination is proportional to the physical distance
between the loci.
• Distances on genetic maps are measured in percent recombination (centimorgans, cM)
or map units.
Limitations in Genetic Maps

• Resolution or detail.
o 3.4 billion base pairs of DNA and has a total genetic distance of about 4000 cM,
an average of 850,000 bp/cM.
o Even if a marker occurred every centimorgan (which is unrealistic), the
resolution in regard to the physical structure of the DNA would still be quite low.
• They do not always accurately correspond to physical distances between genes.
o Based on rates of crossing over, which vary; so the distances on a genetic map
are only approximations of real physical distances along a chromosome.
Physical Maps
• Based on the direct analysis of DNA, and they place genes in relation to distances
measured in number of base pairs, kilobases, or megabases.
• A common type of physical map is one when a pieces of genomic DNA is cloned in
bacteria or yeast.
• Physical maps generally have higher resolution and are more accurate than genetic
maps. Physical maps are often used to order cloned DNA fragments.
Techniques for creating physical maps

1. Restriction mapping, which determines the positions of restriction sites on DNA
2. Sequence-tagged site (STS) mapping, which locates the positions of short unique
sequences of DNA on a chromosome
3. Fluorescent in situ hybridization (FISH), by which markers can be visually mapped to
locations on chromosomes
4. DNA sequencing
Restriction Mapping
• Restriction mapping determines the relative positions of restriction sites on a piece of
DNA.
• When a piece of DNA is cut with a restriction enzyme.
• The fragments are separated by gel electrophoresis.
• The number of restriction sites in the DNA and the distances between them can be
determined by the number and positions of bands on the gel.
Example:
We have sample of a linear 13,000-bp (13-kb) DNA fragment
• 1st sample is cut with the restriction enzyme EcoRI.
• Second sample of the same DNA is cut with BamHI.

• Third sample is cut with both EcoRI and BamHI (double digest).
• The resulting fragments are separated and sized by gel electrophoresis.
• Determine the positions of the EcoRI and BamHI restriction sites on the original
13-kb fragment?
➢ Most restriction mapping is done with several restriction enzymes, used alone and in
various combinations, producing many restriction fragments.
➢ With long pieces of DNA (greater than 30 kb), computer programs are used to determine
the restriction maps.
➢ Restriction mapping may be facilitated by tagging one end of a large DNA fragment with
radioactivity or by identifying the end with the use of a probe.
DNA-Sequencing Methods
• The most detailed physical maps are based on direct DNA sequence information.
• 1975 and 1977 Frederick Sanger and his colleagues created the dideoxy sequencing
method based on the elongation of DNA.
• Allan Maxam andWalter Gilbert developed a second method based on the chemical
degradation of DNA.
How the primers are constructed when we don’t know the sequence of DNA?
• By cloning the target DNA in a vector that contains sequences recognized by a common
primer (called universal sequencing primer sites) on either side of the site where the
target DNA will be inserted.
• The target DNA is then isolated from the vector and will contain universal sequencing
primer sites at each end.
Automated dideoxy method

• The ultimate goal of structural genomics is to determine the ordered nucleotide
sequences of entire genomes of organisms.
• The main obstacle to this task is the immense size of most genomes.
o Bacterial genomes are usually at least several million base pairs long
o Eukaryotic genomes are billions of base pairs long and are distributed among
dozens of chromosomes.
o For technical reasons, it is not possible to begin sequencing at one end of a
chromosome and continue straight through to the other end.
o Only small fragments of DNA—usually from 500 to 700 nucleotides—can be
sequenced at one time.
• The DNA be broken into thousands or millions of smaller fragments that can then be
sequenced.
• Again a problem is there:
o Putting these short sequences back together in the correct order.
• Two approaches are used to resolve this task.
1. Map-based sequencing
2. Whole-genome shotgun sequencing

Map-based approach
• Map-based approach, requires the initial creation of detailed genetic and physical maps
of the genome, which provide known locations of genetic markers at regularly spaced
intervals along each chromosome.
o These markers can later be used to help align the short, sequenced fragments into
their correct order.
• After the genetic and physical maps are available, chromosomes or large pieces of
chromosomes are separated by.
• PFGE -large molecules of DNA or whole chromosomes are separated in a gel by
periodically alternating the orientation of an electrical current.
• Flow cytometry: chromosomes are sorted optically by size.
• Each chromosome (or sometimes the entire genome) is then cut up by partial digestion
with restriction enzymes.
• Thus partial digestion produces a set of large overlapping DNA fragments.
• Which are then cloned by using cosmids, yeast artificial chromosomes (YACs), or
bacterial artificial chromosomes (BACs).
• Clones are screened with specific probe. A set of two or more overlapping DNA
fragments that form a contiguous stretch of DNA is called a contig. This approach was
used in 1993 to create a contig of the human Y chromosome consisting of 196
overlapping YAC clones
• Each clone can be cut with a series of restriction enzymes, and the resulting fragments
are then separated by gel electrophoresis. A computer program is then used to examine
the restriction patterns of all the clones and look for areas of overlap. The overlap is
then used to arrange the clones in order
Whole-genome shotgun sequencing

• Small-insert clones are prepared directly from genomic DNA and sequenced.
• Powerful computer programs then assemble the entire genome by examining overlap
among the small-insert clones.
The Human Genome Project

• The Human Genome Project is an effort to sequence the entire human genome.
• Begun in 1990, a rough draft of the sequence was completed by two competing teams:
o An international consortium of publicly supported investigators
o Private company Celera Genomics, both of which finished a rough draft of the
genome sequence in 2000.
Data Supporting Structural Genomics

• In addition to the DNA sequence of an entire genome, several other types of data are
useful for genomic projects and have been the focus of sequencing efforts including:
o SNPs (Single-Nucleotide Polymorphisms)
o ESTs (Expressed-Sequence Tags)
Single-Nucleotide Polymorphisms
• Are single-base-pair differences in DNA sequence between individual members of a
species, arising through mutation.
• Single-nucleotide polymorphisms are numerous and are present throughout genomes.
• In a comparison of the same chromosome from two different people, a SNP can be found
approximately every 1000 bp.

• Because of their variability and widespread occurrence throughout the genome, SNPs
are valuable as markers in linkage studies.
Expressed-Sequence Tags
• Another type of data identified by sequencing projects consists of databases of
expressed-sequence tags (ESTs).
• In most eukaryotic organisms, only a small percentage of the DNA actually encodes
proteins; in humans, less than 2% of human DNA encodes the amino acids of proteins.
• If only protein-encoding genes are of interest, it is often more efficient to examine RNA
than the entire DNA genomic sequence.
• RNA can be examined by using ESTs—markers associated with DNA sequences that are
expressed as RNA.
• RNA Reverse transciptase cDNA Short stretches of cDNA fragments are then sequenced,
and the sequence obtained (called a tag) provides a marker that identifies the DNA
fragment. Expressed-sequence tags can be used to find active genes in a particular tissue
or at a particular point in development.
Functional Genomics
• attempts to understand the function of information in genomes
Goals of functional genomics

• Identifying all the RNA molecules transcribed from a genome (the transcriptome)
• All the proteins encoded by the genome (the proteome).
• Functional genomics exploits both bioinformatics and laboratory- based experimental
approaches in its search to define the function of DNA sequences.
Several methods for identifying genes and assessing their functions are available including:
• In situhybridization
• DNA footprinting
• Experimental mutagenesis
• Use of transgenic animals and knockouts
Predicting Function from Sequence

• The nucleotide sequence of a gene can be used to predict the amino acid sequence of the
protein that it encodes.
• The protein can then be synthesized or isolated and its properties studied to determine
its function.
• This biochemical approach to understanding gene function is both time consuming and
expensive.
• A major goal of functional genomics has been to develop computational methods that
allow gene function to be identified from DNA sequence alone,
• This will bypassing the laborious process of isolating and characterizing individual
proteins.
Homology searches
• Relies on comparing DNA and protein sequences from the same and different organisms.
• Genes that are evolutionarily related are said to be homologous.

• Homologous genes found in different species that evolved from the same gene in a
common ancestor are called orthologs.
• For example, both mouse and human genomes contain a gene that encodes the alpha
subunit of hemoglobin;
• The mouse and human alpha hemoglobin genes are said to be orthologs, because both
genes evolved from an alpha-hemoglobin gene in a mammalian ancestor common to
mice and humans.
• Homologous genes in the same organism are called paralogs
• By duplication of a single gene in the evolutionary past
• Within the human genome is a gene that encodes the alpha subunit of hemoglobin and
another homologous gene that encodes the beta subunit of hemoglobin.
• These two genes arose because an ancestral gene underwent duplication and the
resulting two genes diverged through evolutionary time, giving rise to the alpha- and
beta-subunit genes; these two genes are paralogs.
• Homologous genes (both orthologs and paralogs) often have the same or related
functions; so, after a function has been assigned to a particular gene, it can provide a
clue to the function of a homologous gene.
Database Search for Orthologous

• Databases containing genes and proteins found in a wide array of organisms are
available for homology searches.
• Powerful computer programs have been developed for scanning these databases to look
for particular sequences.
• A commonly used homology search program is BLAST (Basic Local Alignment Search
Tool).
• Suppose a geneticist sequences a genome and locates a gene that encodes a protein of
unknown function.
• A homology search conducted on databases containing the DNA or protein sequences of
other organisms may identify one or more orthologous sequences.
Database Search for Paralogous

• Computer programs can search a single genome for paralogs.
• Eukaryotic organisms often contain families of genes that have arisen by duplication of a
single gene.
• If a paralog is found and its function has been previously assigned, this function can
provide information about a possible function of the unknown gene.
Other sequence comparisons

• Complex proteins often have specific domains.
• Each domain has its characteristic amino acid arrangement
• For example, certain DNA-binding proteins attach to DNA in the same way
o All these proteins have a common DNA-binding domain
o Many protein domains have been characterized, and their molecular functions
have been determined.
o Newly identified gene can be scanned against a database of known domains.
o If it encodes one or more domains of known function, the function of the domain
can provide important information about a possible function of the new gene.

Phylogenetic Profile:
Another computational method for predicting protein function
• Phylogenetic profiling is a bioinformatics technique in which the joint presence or joint
absence of two traits across large numbers of species is used to infer a meaningful
biological connection, such as involvement of two different proteins in the same
biological pathway
• It was first introduced by Pellegrini and co-workers in 1999
• In this method, the presence- and-absence pattern of a particular protein is examined
across a set of organisms whose genomes have been sequenced.
If two proteins are either both present or both absent in all genomes surveyed, the two proteins
may be functionally related.
The genes (proteins) found and lost together should be involved in a common function
1. being involved in the same biological pathway which is therefore incomplete without all
its members in a given genome
2. being beneficial for the phenotype in a particular environment.
Gene Neighbor Analysis

• Genes that encode functionally related proteins are often closely linked in bacteria.
• For example, if two genes are consistently linked in the genomes of several bacteria,
they might be functionally related.
mRNA Expression:
Two dominant approaches
• RNA sequencing
• DNA Microarrays
Microarrays
Monitors the level of each gene:
➢ Is it turned on or off in a particular biological condition?
➢ Is this on/off state different between two biological conditions?
• Microarray is a rectangular grid of spots printed on a glass microscope slide, where each
spot contains DNA for a different gene
Gene Expression and Microarrays

• The development of microarrays has allowed the expression of thousands of genes to be
monitored simultaneously.
• Microarrays rely on nucleic acid hybridization, in which a known DNA fragment is used
as a probe to find complementary sequences
• The probe is usually fixed to some type of solid support, such as a nylon filter or a glass
slide.
• A solution containing a mixture of DNA or RNA is applied to the solid support; any
nucleic acid that is complementary to the probe will bind to it.
• Nucleic acids in the mixture are labeled with a radioactive or fluorescent tag so that
molecules bound to the probe can be easily detected.
Genome-wide Mutagenesis
• One of the best methods for determining the function of a gene is to examine the
phenotypes of individual organisms that possess a mutation in the gene.

• To conduct a mutagenesis screen, random mutations are induced in a population of
organisms, creating new phenotypes.
• Random inducement of mutations on a genome wide basis and mapping with molecular
markers—are coupled and automated in a mutagenesis screen.
• Mutagenesis screens can be used to search for specific genes encoding a particular
function or trait.
Biotechnology and Recombinant DNA Technology

The use or alteration of cells or biological molecules for specific applications
• Transgenics
o Transgenic
▪ “changed genes”
• Recombinant DNA
o DNA from different species mixed together
• Natural or man-made
• Whole organisms or cells
• Possible because the genetic code is universal
o All life uses the same genetic code (A,T,G,C)
Amplifying DNA
• Need many copies for various DNA tests from a small initial sample
• Two techniques
o Polymerase chain reaction (PCR)
o Recombinant DNA technology
Polymerase chain reaction (PCR)

• Done on molecules
• Based on DNA replication
• Rapidly replicates a selected sequence of DNA in a test tube
• Used to:
o Establish blood relationships
o Identify remains
o Convict or exonerate suspects
o Look at pathogens
o Identify genes
• Very sensitive but easily contaminated
Requirements for PCR

• Know parts of the DNA sequence to be amplified
• 2 DNA Primers
o Short, lab-made single-stranded DNA
o One complementary for each strand in the DNA segment to be amplified
• Lots of nucleotides
• Taq DNA polymerase
o From Thermus aquaticus (lives in hotsprings)
• A thermal cycler

Figure 3.5.1. Polymerase chain reaction process (The McGraw-Hill Companies, Inc.).
Recombinant DNA Technology

Recombinant DNA technology is a set of molecular techniques for locating, cutting, joining,
analyzing, and altering DNA sequences and for inserting the sequences into a cell.
Recombinant DNA
• Works in cells
• Adds genes from one type of organism to the genome of another
• Requires:
o Restriction enzyme
o Vector
o Donor DNA
o Host bacteria
Figure 3.5.2. Restriction enzyme (The McGraw-Hill Companies, Inc.).
Cloning Vectors
• Carries DNA from the cells of one species into cells of another
• Any piece of DNA into which another can be inserted

Types of Vectors
• Which vector used depends on size of the gene to be inserted
• Plasmid
o One type of cloning vector
o Small circle of double-stranded DNA
o Occurs naturally in some bacteria and yeasts
Creating Recombinant DNA
Figure 3.5.3. Process of creating recombinant DNA (The McGraw-Hill Companies, Inc.).

Figure 3.5.4. Process of creating recombinant DNA in producing drugs (The McGraw-Hill
Companies, Inc.).
Selecting Recombinant DNA Molecules

• 3 types of cells
o Cells that lack plasmids
o Cells that contain plasmids that do not contain a foreign gene
o Cells that contain plasmids that have the foreign gene
• Plasmids can contain a gene for an enzyme that catalyzes a reaction that makes a blue
color
o If a foreign gene inserts in the middle of this “blue” gene, the bacteria containing
the plasma will not produce the blue color
• Plasmids can contain a gene for antibiotic resistance
o When the antibiotic is applied to the bacterial cells, only those with the plasmid
will survive
Applications of Recombinant DNA

• Drugs (e.g. insulin)
• Pure, human versions e.g. “humulin”
• Transgenic plants e.g. genetically modified (GM) plants
• Transgenic animals e.g. 3xTg-AD mouse

Figure 3.5.5. The process of creating transgenic plant (The McGraw-Hill Companies, Inc.).

Figure 3.5.6. The process of creating transgenic animal.

Application 3.51
Activity
Test Your Knowledge
6. Describe the impact of genomics in the breakthrough of biotechnology.

7. List one agricultural crop and one animal produced using biotechnology and
explain the process of its development.
References
York.

Module 3

Learning Objectives Non-Mendelian Inheritance

❖ analyze the inheritance
In Mendelian concept, a heterozygote expresses
patterns of maternal effects
only one allele. However, other scientists proved that
❖ analyze the patterns of
dominance is not universal where, in heterozygous
cytoplasmic inheritance
condition, expresses intermediate phenotype, expresses
❖ analyze the patterns of
both phenotypes or expresses a different phenotype. In
imprinting
this lesson, we will explore the modification in Mendelian
Key Concepts
concepts. The beginning of this lesson reviews the
❖ Review of Dominance mendelian concept. It then turns to the effects of lethal
❖ Lethal Alleles and multiple alleles. We will also discuss how gene
❖ Multiple Alleles interacts during crosses. In the later part of this lesson, we
❖ Gene interaction will explore Genetic maternal effects, cytoplasmic
❖ Genetic Maternal Effects inheritance and the effects of environment to phenotypic
❖ Cytoplasmic Inheritance expression.
❖ Environmental Effects
Activity
Activity 3.6
1 Genetic Maternal Effect
Wondering why some of your traits resembles exactly like your mother and not your
father? In this activity you will describe the traits you inherited from your mother.
1. List all the traits you inherited from your mother (example: hair color, height,
etc.)
Analysis
1. Compare the traits you inherited from your mother with your siblings.
2. What are the common traits you and your siblings inherited from your
mother.
3. Explain how these maternal traits are inherited.

Review of Dominance
• Mendelian concept
o In the heterozygous
condition, only one allele
(dominant) is expressed
• Incomplete dominance
o Heterozygote has
phenotype intermediate
to homozygous
phenotypes
Incomplete dominance
• Heterozygote has intermediate
phenotype
• Does NOT have to be phenotype
“right in the middle”
• Lighter shade of red to very light
shade of pink
Figure 5.6.1. The type of dominance exhibited by a
Codominance trait depends on how the phenotype of the
• Heterozygote expresses both heterozygote relates to the phenotypes of the
alleles//both phenotypes homozygotes
• MN locus
o Codes of antigen on red
blood cells
o Does not cause significant immune response like ABO or Rh groups
o LM allele = M antigen; LN allele = N antigen
o LMLN individual has both antigens present
Dominance
• “Dominance” can depend on which level you are looking at
• Cystic Fibrosis – autosomal recessive disorder
o Normal allele produces carrier protein in plasma membrane that allows Cl-
passage in/out of cell
o Mutant allele produces defective protein that prohibits Cl - from exiting cell
o Carriers of Cystic Fibrosis
▪ Physiological level – recessive
• Carriers have enough normal channels for unaffected phenotype
▪ Molecular level – codominant
• Carriers have both normal and mutant channel proteins
Incomplete penetrance
• Genotype does not always produce expected phenotype
• Polydactyly
o Dominant allele
o Individuals with dominant allele can occasionally have normal number of digits,
but have affected children
• Penetrance
o % of individuals with a particular genotype that express expected phenotype
o 42 individuals have polydacylous allele; 38 express polydactyly
o 38/42 = 90% penetrance

Variable Expressivity
• Degree to which trait is expressed
• Polydactyly
o Some extra digits are fully functional; others are just small skin tags
• Penetrance and expressivity are due to other genes and environmental factors
o Mere presence of allele does not guarantee expression, or standard “one size fits
all” expression
Lethal alleles
• Cause death at an early age of
development (usually before or
shortly after birth) so some
genotypes are appear among
progeny
• Recessive – need to be
homozygous to be lethal;
heterozygote will have different
phenotype
• Dominant – lethal in both
homozygotes and heterozygotes
o Only transmissible when
lethal after individual has
passed reproductive age
Multiple alleles
• One gene may have more than 2
possible alleles
o Figure 5.6.2. A 2 : 1 ratio among the progeny of a
o Regardless of possible cross results from the segregation of a lethal allele.
alleles in a population, an
individual can only have a
maximum of 2 different alleles
• ABO blood type
o Codes for antigens of
surface of red blood cells
o 3 possible alleles
▪ IA – puts “A” antigen
▪ IB – puts “B” antigen
▪ i – puts no antigen
▪ i is recessive to
both IA and IB; IA
and IB are co-
dominant
o Served as primitive means
of paternity testing
Figure 5.6.3. ABO Blood types and possible blood
transfusion.

Gene interaction
• More than one gene contributes to
a single phenotype
• Polygenic inheritance
Epistasis
• One gene masks the effects of
another gene
• Can be dominant or recessive
• Albinism
o Lack of pigment melanin
o Very light skin and hair;
pink or very light blue eyes
o Duplicate recessive epistasis
o Since pigment production is
a multi-step process
requiring multiple
enzymes, different genes
can each result is albinism
o P generation aaBB (albino) x
AAbb (albino)
o F1 AaBb (normal
pigmentation)
Figure 5.6.4. Gene interaction in which two loci
o F2 9A_B_:3aaB_:3A_bb:1aabb
determine a single characteristic, fruit color, in
o 9 normal pigmentation:7
the pepper Capsicum annuum.
albino
Complementation test
• Test to determine whether two different mutations are at the same locus or different
loci
• Cross homozygous individuals with different mutations
• D. melanogaster
o both apricot (a) eye color and white (b) eye color is recessive to normal wild-type
red
• If same locus, all F1 will have a mutant phenotype
• If different loci, F1 will have wild-type phenotype
Interaction between sex and heredity

• Sex-influenced traits
o Autosomal Mendelian inheritance, but expressed differently in sexes
o Beards on goats
▪ Dominant trait in males
• Expression requires only one allele
▪ Recessive trait in females
• Must be homozygous to have a beard
o Human male pattern baldness
o NOT x-linked
o Dominant in male; recessive in females
o Affected males can be homozygous or heterozygous
o Affected females must be homozygous
o Usually results in “thinning” – variable expressivity

o Difference due to presence of male sex hormones
o Males castrated prior to puberty do not exhibit pattern baldness, even with
genotype
Sex-limited traits
• Autosomal inheritance
• Trait is only expressed in one sex; zero penetrance in other sex
• Domestic chickens
o H = hen plumage; h = cock plumage
o Male hh = cock feather tail
o Female hh = hen feather
▪ Cock plumage never expressed in females
Cytoplasmic inheritance
• Inheritance of DNA in cytoplasm
(mitochondria or chloroplasts)
• Inherited from mother only
o Sperm contributes nucleus,
but no cytoplasm
• Characteristics exhibit extensive
phenotypic variation
o Each cell can contain
hundreds of mitochondria,
and may not have same
genetic information
o Homoplasmy – all the same
o Heteroplasmy – different
genetic information
▪ Ratio of “normal” to
“mutant”
Figure 5.6.5. Cytoplasmically inherited

characteristics frequently exhibit extensive
phenotypic variation because cells and
individual offspring contain various proportions
of cytoplasmic genes.

Genetic maternal effect
• Genotype inherited from both
parents, but phenotype is
determined by MOTHER’S
genotype
• Limnaea peregra
o Dextral coiling (to the
right) is dominant over
sinistral (to the left)
coiling
o Phenotype determined by
mother’s genotype (not
her phenotype)
Genomic Imprinting
• Differential expression of gene
depending of whether it was
inherited from mother or father
• Due to different methylation
patterns of DNA
• Microdeletion of 15p
o Deleted from father –
Prader-Willi syndrome
o Deleted from mother – Figure 5.6.6. Shell coiling in snails is a trait that
Angelman syndrome exhibits genetic maternal effect.
Anticipation
• Genetic trait becomes either more strongly expressed or expressed at an earlier age as it
is passed from generation to generation
• Due to an unstable region of DNA that tends to increase in size in next generation
Environmental Effects
• Himalayan allele in rabbits
o Produces dark fur – nose,
feet, ears
o Develops at temperatures
less than 20°C
o Enzyme is inactivated at
temperatures over 30°C
Phenocopy
• Environmental factors produce a
phenotype that mimics the
phenotype of another genotype
• PKU – phenylketonuria Figure 5.6.7. The expression of a temperature-
o Autosomal recessive sensitive allele, himalayan, is shown in rabbits
o Phenylalanine can not be reared at different temperatures.
broken down; build-up
causes brain damage
o Affected child put on restricted diet - prevents retardation
▪ Can go off diet after nervous system is fully formed (early 20s)

o Affected woman when pregnant must be diet restricted
▪ If not, excess phenylalanine can cross placenta and give child PKU
phenotype, even if genotypically unaffected
Inheritance of Continuous Characteristics

• Discontinuous – few, distinct phenotypes
• Continuous – wide range of phenotypes
o Often form bell-shaped curve when plotted
▪ Height, skin color
o Usually due to multiple genes contributing to a single trait
▪ Polygenic inheritance
Pleiotropy
• One gene affects multiple characteristics
• PKU
o Mental retardation, light skin and eye color
Application 3.61
Activity
Test Your Knowledge
1. The type of plumage found in mallard ducks is determined by three alleles at a

single locus: MR, which codes for restricted plumage; M, which codes for
mallard plumage; and md, which codes for dusky plumage. The restricted
phenotype is dominant over mallard and dusky; mallard is dominant over
dusky (MR > M > md). Give the expected phenotypes and proportions of
offspring produced by the following crosses:
(a) MRM x mdmd

(b) MRmd x Mmd
(c) MRmd x MRM
(d) MRM x Mmd
References:
York.

Module 4
Quantitative, Population and Evolutionary Genetics
Module Overview
The inheritance of complex

characteristics whose phenotypes differ
continuously is the subject of quantitative
genetics. On the other hand, the genetic makeup
of groups of individual is studied by population
genetics and how this composition changes over
time. These module introduces you to the study
of quantitative, population genetics. The first
part of the module focuses on quantitative
inheritance including quantitative
characteristics, statistical methods for analyzing
quantitative characteristics and heritability. The
later part of the module explores population
genetics which include topics on genetic
variation, the Hardy-Weinberg law, non-random
mating and changes in allelic frequencies.
Objectives
• Understand the patterns of inheritance of phenotypic traits controlled by many loci.
• Investigate the way that geneticists and statisticians describe and analyze normal
distributions of phenotypes.
• Define and measure heritability, the unit of inheritance of variation in traits controlled
by many loci.

Lesson 1. Quantitative Genetics
Lesson 2: Population and Evolutionary Genetics

Module 4

Lesson 1
Time Frame: 5 Hours
Learning Objectives Quantitative Genetics
❖ Understand the patterns of
inheritance of phenotypic Introduction
traits controlled by many
As humans we compare our characteristics with
loci.
our parents, some say they inherited their height from
❖ Define and measure
their father and their intelligence from their mother. In a
heritability, the unit of
family we resemble closely to each other as siblings than
inheritance of variation in
to our distant relatives such as our cousins. In the
previous lesson, we qualify our traits using Mendel’s
loci.
principles, however, our traits are complex and one way
Key Concepts to analyze these traits is through the use of quantitative
genetics. This lesson explains quantitative characteristics,
❖ Quantitative statistical methods for analyzing quantitative
characteristics characteristics and heritability.
❖ Statistical methods for
analyzing quantitative
characteristics
❖ Heritability
Activity
Activity 4.1 Qualitative and Quantitative Characteristics
1
Qualitative characteristics deals with the inheritance of traits of kind while quantitative
characteristics deals with the traits of degree. In this activity you will be able to
distinguish qualitative characteristics from quantitative characteristics.
Procedure
1. Observe a group of plants of the same species in your area.
2. List down at least 5 qualitative traits from the species you observed.
3. List down at least 5 quantitative traits from the species you observed.
Analysis
1. Differentiate the qualitative and quantitative traits you observed.

2. Describe the relationship of qualitative characteristics to Mendel’s
principles.

Quantitative Genetics
Qualitative, or Discontinuous
• Characteristics possess only a few distinct
phenotypes. These characteristics are the types
studied by Mendel
Quantitative Characteristics
• Characteristics that vary continuously along a scale
of measurement with many overlapping phenotypes.
• Quantitative characteristics might include height,
weight, and blood pressure in humans, growth rate
in mice, seed weight in plants, and milk production in
cattle.
Factors that Influence Quantitative Characteristics
• Polygenic Traits
o They are influenced by genes at many loci. If many loci take part, many
genotypes are possible, each producing a slightly different phenotype.
• Environment. Quantitative characteristics often arise when environmental factors
affect the phenotype, because environmental differences result in a single genotype
producing a range of phenotypes.
Types of Quantitative Characteristics

• Meristic characteristics
o Measured in whole numbers.
o An example is litter size: a female mouse may have 4, 5, or 6 pups but not 4.13
pups.
o A meristic characteristic has a limited number of distinct phenotypes, but the
underlying determination of the characteristic may still be quantitative.
• Threshold characteristic
o Although threshold characteristics exhibit only two phenotypes, they are
considered quantitative because they, too, are determined by multiple genetic
and environmental factors.
Polygenic Inheritance
Example:
Wheat Berry Color

True-breeding plants with white vs. red berries were crossed to create an F1of intermediate
color, then the F1 plants were crossed to produce the range of colors.

The curve is called a normal distribution, with the
largest number of individuals in the intermediate
range, with fewer at each extreme.
When individual plants from the F2 are selected

and mated, the phenotype of the resulting
offspring also produces a range of phenotypes and
a similarly shaped curve:
There is a range of phenotypes, but most of the
offspring are similar in color to the parents.
Determining the Number of Genes—the 1/4n
Rule
The number of genes may be calculated if
• the proportion of F2 individuals expressing

either of the two most extreme (i.e.
parental) phenotypes can be determined
according to the following formula:
1/4n=proportion of offspring either red or white
Where n = number of loci that are either red or white = 3
1/43 = 1/(4x4x4) = 1/64
Determining the Number of Genes—the (2n + 1) Rule

If n = the number of gene pairs, then (2n + 1) will determine the total number of categories of
phenotypes.
In our example, there were 7 phenotype classes:
(2n+1) = 7
2n/2 =(7-1)/2
n= 6/2=3
Significance of Polygenic Control

• Most traits in animal breeding and agriculture are under polygenic control:
• Height, weight, stature, muscle composition, milk and egg production, speed, etc.
Biometry
• Biometry is the quantitative study of biology and utilizes statistical inference to
analyze traits exhibiting continuous variation.
❖ While the observations of an experiment are hoped to represent the population at large,
there may be random influences affecting samples that adds to variation in the study
population. Statistical analysis allows researchers to predict the sources of variation and
the relative influence of each source.

Purposes of Statistical Analysis
1. Data can be analyzed mathematically and reduced to a summary description.
2. Data from a small but representative and random sample can be used to infer information
about groups larger than the study population (statistical inference).
3. Two or more sets of experimental data can be compared to determine if they represent
different populations of measurements.
Statistical Terms
Mean
• The distribution of two sets of phenotypic measurements cluster around a central value.
• The mean is the arithmetic average of the set of measurements, the sum of all of the
individuals divided by the number of individuals.
• The mean is arithmetically calculated as
Mean = Xi/n
Where Xi is the sum of all the individual values
and n is the number of individual values
Example:
Observed values for eight samples
{2,2,4,4,5,6,6,8}
Xi = 38
38/8 = 4.75 Therefore, the mean for this sample is 4.75
Median
• If the data are arranged from smallest to largest value, the median value is the central
number.
Example: {2,2,4,4,5,6,6,7,8} So the median value for this data set is 5.
Range
• Range is the distance between the smallest value in a set and the largest value in a set.
Example: {2,2,4,4,5,6,6,7,8} The range for this set is 2 to 8.
Frequency Distribution
• Median and range give information about the frequency distribution, or shape of the
curve.
• The values of two different data sets may have the same mean, but be distributed around
that mean differently.
Variance
• Variance is a value that describes the degree to which the values in a data set diverge from
the mean.
• The variance within the data set is used to make inferences or estimate the variation in
the population as a whole.
Calculate Variance (s2)

s2 = (Xi-mean)2 /n – 1

Phenotypic Variance
• Represents the phenotypic differences among individual members of a group.
• can be attributed to several factors:
o Some of the differences in phenotype may be due to differences in genotypes
among individual members of the population.
o Some of the differences in phenotype may be due to environmental
differences.
Components of Phenotypic Variance

1. Genotypic variance (VG)
2. Environmental variance (VE)
3. Genetic–environmental interaction variance (VGE)
The total phenotypic variance can be distributed into three components:

VP=VG + VE + VGE
Components of Genotypic Variance

1. Additive genetic variance (VA)
2. Dominance genetic variance (VD)
3. Genic interaction variance (VI)
The total genotypic variance can be equated to:

VG = VA + VD + VI
Standard Deviation
• Because variance is a squared value (s2) its unit of measurement is also squared (inches,
feet, kg, etc.)
• To express variation in the original units, simply take the square root of the variance, or
standard deviation.
s =  s2
Standard Error of the Mean

• To estimate how much the means of other similar samples from the same population
might vary, we calculate the standard error of the mean.
• The SE is a measure of variation of sample means in repetitions of an experiment, or more
simply, a measure of accuracy of the sample mean.
• SE is the standard deviation, divided by the square root of the number of individuals.
SE = s/n
• Because SE is divided by the square root of n, the value will always be smaller than the
standard deviation.
Expression of Statistical Values

• Typically, data are expressed as means +/- SE.
• So, if you have two different experimental treatments which produce two different means,
they would be expressed like this:
Group A= 16.676 +/- 3.3
Group B= 12.2 +/- 2.1
Expressions of Statistical Data

• Statistical analysis is all about defining the sources of variation.

• Ultimately, we want to be able to assign proportions of the variation to their different
sources, to sort out that variation due to our treatment or design.
Heritability
• Heritability is an estimate of how much variability in a population is due to genetic factors,
separate from environmental factors.
• In genetics, statistics are all about determining the relative impacts of heredity vs.
environment on phenotypic variation.
• Experiments test the source or origin of variation.
• One way to assess genetic influence is to use inbred or genetically similar groups of
animals or plants, and rear them under a range of environmental conditions.
• Variation between different strains reared under similar conditions can be assigned to
genetic differences.
• Variation among members of the same strain reared under different conditions can be
assigned to non-genetic influences, called “environmental” effects.
Types of Heritability
• Broad-sense heritability is the proportion of the phenotypic variance that is due to genetic
variance.
o can be estimated by eliminating the environmental variance component
o H2 is an analysis of variance among individuals of a known genetic relationship.
o H2 measures the degree to which phenotypic variance (VP) is due to genetic
factors with the following limitations
o For a single population
o Under the limits of environmental variation during the study
o The heritability index does not determine the proportion of the total phenotype
due to genetic factors.
o The heritability index does estimate the proportion of observed variation in the
phenotype due to genetic factors in comparison to environmental factors.
o A heritability index close to 1.0 indicates that environmental conditions had little
impact on phenotypic variation in the population observed.
o A heritability index close to 0 indicates that environmental conditions were
almost solely responsible for the phenotypic variation observed in the sample
population.
o (Most of the time, values close to either extreme are not observed because most
of the time, both environment and genetics have effects.)
o
o represents the proportion of phenotypic variance that is due to genetic variance
and is calculated by dividing the genetic variance by the phenotypic variance:
Broad-sense heritability = H2= VG/VP
• Narrow-sense heritability is the proportion of the phenotypic variance due to additive

genetic variance.
o Can be estimated by comparing the phenotypes of parents and offspring or by
comparing phenotypes of individuals with different degrees of relatedness, such
as identical twins and non-identical twins.
o is equal to the additive genetic variance divided by the phenotypic variance:
Narrow-sense heritability = (h2) = VA/VP

Application4.1
Application 3.6
Test Your Knowledge
1. The following table lists yearly amounts of milk produced by 10 two-year-old

Jersey cows. Calculate the mean, variance, and standard deviation of milk
production for this sample of 10 cows.
Annual milk production
(hundreds of pounds)
60
74
58
61
56
55
54
57
65
42
2. Phenotypic variation is analyzed for milk production in a herd of dairy cattle

and the following variance components are obtained.
Additive genetic variance (VA) = .5
Dominance genetic variance (VD) = .2
Genic interaction variance (VI) = .3
Environmental variance (VE) = .3
Genetic-environmental interaction variance (VGE) = .0
(a) What is the narrow-sense heritability of milk production?

(b) What is the broad-sense heritability of milk production?
References
United Kingdom

Module 4

Lesson 2
Time Frame: 10 Hours
Learning Objectives Population and Evolutionary Genetics
❖ Understand the patterns of
inheritance of phenotypic Introduction
loci.
As humans we compare our characteristics with
❖ Define and measure
our parents, some say they inherited their height from
heritability, the unit of their father and their intelligence from their mother. In a
inheritance of variation in family we resemble closely to each other as siblings than
traits controlled by many to our distant relatives such as our cousins. In the
loci. previous lesson, we qualify our traits using Mendel’s
principles, however, our traits are complex and one way
Key Concepts to analyze these traits is through the use of quantitative
genetics. This lesson explains quantitative characteristics,
❖ Quantitative statistical methods for analyzing quantitative
characteristics
characteristics and heritability.
❖ Statistical methods for
analyzing quantitative
characteristics
❖ Heritability
Activity
Activity 4.2 Qualitative and Quantitative Characteristics
1
Qualitative characteristics deals with the inheritance of traits of kind while quantitative
characteristics deals with the traits of degree. In this activity you will be able to
distinguish qualitative characteristics from quantitative characteristics.
Procedure
4. Observe a group of plants of the same species in your area.
5. List down at least 5 qualitative traits from the species you observed.
6. List down at least 5 quantitative traits from the species you observed.
Analysis
3. Differentiate the qualitative and quantitative traits you observed.
4. Describe the relationship of qualitative characteristics to Mendel’s
principles.

Population Genetics
• Population genetics is concerned with the genetic composition of a population and how
it changes with time.
• The gene pool of a population can be described by the frequencies of genotypes and
alleles in the population.
Gene – a discrete unit of hereditary information consisting of a specific nucleotide sequence in

DNA.
Alleles – alternative forms of a gene.
Genotype – the genetic makeup of an individual.

Phenotype – the physical traits of an organism
Genetic Variation
• Refers to diversity in gene frequencies or the differences between individuals or to
differences between populations.
Calculation of Genotypic Frequencies

To calculate a genotypic frequency, we simply add up the number of individuals possessing the
genotype and divide by the total number of individuals in the sample (N). For a locus with three
genotypes AA, Aa, and aa, the frequency (f) of each genotype is:
𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝐴𝐴 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠
𝑓(𝐴𝐴) =
𝑁
𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝐴𝑎 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠
𝑓(𝐴𝑎) =
𝑁
𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑎𝑎 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠
𝑓(𝑎𝑎) =
𝑁
The sum of all genotypic frequencies always equal to 1.
Calculation of Allelic Frequency from Genotypic Frequency
1
𝑝 = 𝑓(𝐴) = 𝑓(𝐴𝐴) + 𝑓(𝐴𝑎)
2
1
𝑞 = 𝑓(𝑎) = 𝑓(𝑎𝑎) + 𝑓(𝐴𝑎)
2
Loci with multiple alleles
We can calculate the frequencies of multiple alleles from the genotypic frequencies by extending
the above equation. Once again, we add the frequency of the homozygote to half the frequency
of each heterozygous genotype that possesses the allele:
1 1
𝑝 = 𝑓(𝐴1 ) = 𝑓(𝐴1 𝐴1 ) + 𝑓(𝐴1 𝐴2 ) + 𝑓(𝐴1 𝐴3 )
2 2
1 1
𝑞 = 𝑓(𝐴2 ) = 𝑓(𝐴2 𝐴2 ) + 𝑓(𝐴1 𝐴2 ) + 𝑓(𝐴2 𝐴3 )
2 2

1 1
𝑟 = 𝑓(𝐴3 ) = 𝑓(𝐴3 𝐴3 ) + 𝑓(𝐴1 𝐴3 ) + 𝑓(𝐴2 𝐴3 )
2 2
Example:
A study on blood types in a population found the following genotypic distribution among the
people sampled:
Phenotype Genotype Number

MM LMLM 1100
MN LMLN 1495
NN L NL N 500
Total 3095
Calculate the genotypic and allelic frequencies.
Solution:
The genotypic frequencies for the population are calculated with the following formula:
𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝐿𝑀 𝐿𝑀 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠 1100
𝑓(𝐿𝑀 𝐿𝑀 ) = = = 0.355
𝑁 3095
𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝐿𝑀 𝐿𝑁 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠 1495
𝑓(𝐿𝑀 𝐿𝑁 ) = = = 0.483
𝑁 3095
𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝐿𝑁 𝐿𝑁 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠 500
𝑓(𝐿𝑁 𝐿𝑁 ) = = = 0.162
𝑁 3095
To calculate the allelic frequencies from genotypic frequencies, we add the frequency of the
homozygote for that genotype to half the frequency of each heterozygote that contains that
allele:
1 1
𝑝 = 𝑓(𝐿𝑀 ) = 𝑓(𝐿𝑀 𝐿𝑀 ) + 𝑓(𝐿𝑀 𝐿𝑁 ) = 0.355 + (0.483) = 0.5965
2 2
1 1
𝑞 = 𝑓(𝐿𝑁 ) = 𝑓(𝐿𝑁 𝐿𝑁 ) + 𝑓(𝐿𝑀 𝐿𝑁 ) = 0.162 + (0.483) = 0.4035
2 2
Hardy-Weinberg Law
• Hardy Weinberg principle States that ; (p+q )² = p² + 2pq + q² =1

• Under the certain condition, allelic frequencies remains constant from generation to
generation. If any one condition is not made, genetic equilibrium will be disturbed and
the population may evolved.
Hardy-Weinberg expectations for loci with multiple alleles

According to the Hardy-Weinberg law, the frequencies of the genotypes at equilibrium depend
on the frequencies of the alleles. If the frequencies of alleles A1, A2, and A3 are p, q, and r,
respectively, then the equilibrium genotypic frequencies will be the square of the allelic
frequencies (p + q + r)2 = p2 + 2pq + q2 + 2pr + 2qr + r2, where:

p2 = f(A1A1)
2pq = f(A1A2)
q2 = f(A2A2)
2pr = f(A1A3)
2qr = f(A2A3)
r2 = f(A3A3)
Testing for Hardy-Weinberg Proportions
Example:
Genotypes of leopard frogs from a population were determined for a locus that encodes the
enzyme malate dehydrogenase. The following numbers of genotypes were observed:
Genotype Number
M1M1 20
M1M2 45
M2M2 42
M1M3 4
M2M3 8
M3M3 6
Total 125
a) Calculate the genotypic and allelic frequencies for this population.

b) What would be the expected numbers of genotypes if the population were in Hardy-
Weinberg equilibrium?
Solution:
The genotypic frequencies for the population are calculated with the following formula:
𝑁𝑢𝑚𝑏𝑒𝑟 𝑜𝑓 𝑀1 𝑀1 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙𝑠 20
𝑓(𝑀1 𝑀1 ) = = = 0.16
𝑁 125
𝑓(𝑀1 𝑀2 ) = = = 0.36
𝑁 125
𝑓(𝑀2 𝑀2 ) = = = 0.336
𝑁 125
𝑓(𝑀1 𝑀3 ) = = = 0.032
𝑁 125
𝑓(𝑀2 𝑀3 ) = = = 0.064
𝑁 125

𝑓(𝑀3 𝑀3 ) = = = 0.048
𝑁 125
To calculate multiple allelic frequencies from genotypic frequencies, we add the frequency of
the homozygote for that genotype to half the frequency of each heterozygote that contains that
allele:
1 1
𝑝 = 𝑓(𝑀1 ) = 𝑓(𝑀1 𝑀1 ) + 𝑓(𝑀1 𝑀2 ) + 𝑓(𝑀1 𝑀3 )
2 2
1 1
𝑝 = 𝑓(𝑀1 ) = 0.16 + (0.36) + (0.032) = 0.356
2 2
1 1
𝑞 = 𝑓(𝑀2 ) = 𝑓(𝑀2 𝑀2 ) + 𝑓(𝑀1 𝑀2 ) + 𝑓(𝑀2 𝑀3 )
2 2
1 1
𝑞 = 𝑓(𝑀2 ) = 0.336 + (0.36) + (0.064) = 0.548
2 2
1 1
𝑟 = 𝑓(𝑀3 ) = 𝑓(𝑀3 𝑀3 ) + 𝑓(𝑀1 𝑀3 ) + 𝑓(𝑀2 𝑀3 )
2 2
1 1
𝑟 = 𝑓(𝑀3 ) = 0.048 + (0.032) + (0.064) = 0.096
2 2
The frequencies of the genotypes expected under Hardy-Weinberg equilibrium are then
calculated by using p2, 2pq, q2, 2pr, 2qr and r2:
p2 = f(M1M1) =(0.356)2 =0.127
2pq = f(M1M2) =2(0.356)(0.548) =0.390
q2 = f(M2M2) =(0.548)2 =0.300
2pr = f(M1M3) =2(0.356)(0.096) =0.068
2qr = f(M2M3) =2(0.548)(0.096) =0.105
r2 = f(M3M3) =(0.096)2 =0.009
Multiplying each of these expected genotypic frequencies by the total number of observed
individuals in the sample (125), we obtain the numbers expected for each genotype:
Genotype Genotypic frequency x N Expected number of

genotypes in a population
M1M1 =0.127 x 125 =15.875
M1M2 =0.390 x 125 =48.75
M2M2 =0.300 x 125 =37.50
M1M3 =0.068 x 125 =8.50
M2M3 =0.105 x 125 =13.25
M3M3 =0.009 x 125 =1.125
Total =125

Five evolutionary forces that can significantly alter the allele frequencies of a population
1. Mutation
2. Migration
3. Genetic drift
4. Nonrandom mating
5. Selection
Mutation
• Mutations are the changes in the genetic sequence or alteration in the genetic material
(the genome) of a cell of a living organism and they are one of the main cause of
diversity among organisms.
• Errors in DNA replication
• The ultimate source of new variation
Migration
• Migration or gene flow occurs when individuals move from one population to another
and interbreed with the latter.
• Migration can either increase or decrease the frequency of a gene depending on whether
the migrants contain higher or lower frequency of the gene involve than the recipients.
• When there is migration, two factors are important to the recipient population; a) the
difference in gene frequencies between two populations; and b) the proportion of
migrant genes that are incorporated each generation
Two types of Migration

1. Immigration. Movement of individuals from one population to another –:
2. Emigration. movement into a population
Genetic Drift
• A phenomenon which occurs while there is a change in gene frequency or allele
frequency in a population.
o Change in allele frequencies due to chance or randomness.
Two types of Genetic Drift:

1. Bottleneck Effect
• A sudden decrease in population size due to natural forces
2. Founder Effect
• When a small number of individuals from a source population establish a new
population genetic variation can be lost.
• The loss of genetic variation due to such an extreme bottleneck
Non-Random Mating
• Assortative mating – mating with individuals that are similar or dissimilar for a given
trait.
o If the phenotype is under genetic control:
▪ Positive assortative mating increases homozygosity and decreases
heterozygosity for the genes affecting the trait
▪ Negative assortative mating increases heterozygosity and decreases
homozygosity for the genes affecting the trait.
• Inbreeding – mating with a close relative.

o Biparental: two different individuals are involved
o Extreme inbreeding
▪ Intragametophytic selfing: mating between gametes produced from the
same haploid individual
• 100% homozygosity in one generation
• Example: some ferns and mosses
The effects of inbreeding on genotype and allele frequencies

• Fewer heterozygotes and more homozygotes
• No change in allele frequency
Evolutionary Consequences of Inbreeding

• In large, random mating populations, most individuals will not suffer from deleterious
effects of recessive deleterious alleles.
• Under inbreeding, increased homozygosity for these recessive deleterious alleles results
in reduced fitness.
Selection
• Artificial selection – Breeder selects for desired characteristics
• Natural selection – Environment selects for adapted characteristics.
Three Types of Natural Selection

1. Stabilizing Selection
o Tends to eliminate the phenotypic extremes.
o The phenotypes close to the mean are preserved by the populations that are
environmentally well adapted.
2. Directional Selection
o The type of selection where one of the extremes in the phenotypic range
becomes most fit and thus preserved.
o Natural directional selection happens when there are changes in the
environment of a well-adapted population.
o With this change, the mutation which were previously disadvantage may
become adapted, thus replacing the existing phenotypes.
3. Disruptive Selection
o Is one where both extremes of the phenotypic range are selected for, thus
preserving differences in the gene pool of a population.
o Natural disruptive selection can occur when several ecological niches become
available to a population.
o Phenotypic extremes may become isolated from one another by occupying
different ecological niches so that the gene flow due to interbreeding ceases.
o Sub – specification can follow and eventually lead to the formation of new
species.

Application4.2
Application 3.6
Test Your Knowledge
1. Compare and contrast the effects of mutation, migration, genetic drift, and
natural selection on genetic variation within populations and on genetic
divergence between populations.
2. The following genotypes were observed in a population:
Genotype Number
BB 50
Bb 55
bb 60
(a) Calculate the observed genotypic and allelic frequencies for this
population.
(b) Calculate the numbers of genotypes expected if this population were in
Hardy-Weinberg equilibrium.
(c) Using a chi-square test, determine whether the population is in Hardy-
Weinberg equilibrium.
References
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Republic of the Philippines

DAVAO DEL SUR STATE COLLEGE

A Course Pack Prepared by

Richie D. Miguel, Lic. Agr.

Faculty, Agriculture Department

Miguel, R.D. (2020). Genetics for Flexible Learning. | 1

Module I: The Science of Heredity and Variation

Students Learning Outcomes

At the end of the module, students will be able to:

Module II. Mendel’s Laws and The Chromosomal Basis of Heredity

Students Learning Outcomes

1. Describe the basic concept of Mendel’s Laws

Students learning Outcomes

Module IV. Quantitative, Population and Evolutionary Genetics

Students learning Outcomes

Miguel, R.D. (2020). Genetics for Flexible Learning. | 2

Module I. The Science of heredity and Variation 1

Module II. Mendel’s laws and the Chromosomal Basis of Heredity 10

Module III. The Chemical Basis of Heredity 72

Module IV. Quantitative, Population and Evolutionary Genetics 140

Miguel, R.D. (2020). Genetics for Flexible Learning. | 3

Principles and Practices of Plant Breeding

Plant breeding aims to improve crops in

Lessons in this Module

Miguel, R.D. (2020). Genetics for Flexible Learning. | 4

Unit I. Introduction to Plant Breeding

Time Frame: 5 Hours Lesson 1

Learning Objectives Definition, Nature and Importance

Define the following terms:

Miguel, R.D. (2020). Genetics for Flexible Learning. | 5

• Cells are of two basic types: eukaryotic

Important breakthrough in agriculture using genetics

Miguel, R.D. (2020). Genetics for Flexible Learning. | 6

The Three Major Areas of Genetics

▪ Molecular genetics concerns the • Chemistry and Structure of DNA

Miguel, R.D. (2020). Genetics for Flexible Learning. | 7

Understanding and Synthesizing the Concept

Miguel, R.D. (2020). Genetics for Flexible Learning. | 8

The Science of Heredity and Variation

Learning Objectives The Beginnings of Genetics

It was believed that maize Analysis

Miguel, R.D. (2020). Genetics for Flexible Learning. | 9

Early Written Records

Miguel, R.D. (2020). Genetics for Flexible Learning. | 11

Understanding and Getting Acquainted with people and events

Miguel, R.D. (2020). Genetics for Flexible Learning. | 12

Mendel’s Laws and the Chromosomal Basis of Heredity

Earth is teeming with diversity of species

Lessons in this Module

Miguel, R.D. (2020). Genetics for Flexible Learning. | 13

Mendel’s Laws and the Chromosomal Basis of Heredity

Learning Objectives Mendel’s Laws

Gene Heterozygote Genotype

Miguel, R.D. (2020). Genetics for Flexible Learning. | 14

Important Genetic Terms

Miguel, R.D. (2020). Genetics for Flexible Learning. | 15

Miguel, R.D. (2020). Genetics for Flexible Learning. | 16

Miguel, R.D. (2020). Genetics for Flexible Learning. | 17

Multiple Alleles Figure 2.1.4. Fruit color

Miguel, R.D. (2020). Genetics for Flexible Learning. | 18

Miguel, R.D. (2020). Genetics for Flexible Learning. | 19

Testing for the Law of

Figure 2.1.5. Mendel’s Dihybrid Cross