Download BIOL2165 - UWI St. Augustine - The University of the West Indies

THE UNIVERSITY OF THE WEST INDIES
ST AUGUSTINE
FACULTY OF SCIENCE AND TECHNOLOGY
DEPARTMENT OF LIFE SCIENCES
COURSE OUTLINE
Course title: Genetics II
Course Code: BIOL2165
Credits: 3
Level: TWO
Semester: ONE
Pre-requisites: BIOL1364 Genetics I or BIOL1061 Cell Biology and Genetics and 6 credits from
among the following courses: BIOL1262 Living Organisms I, BIOL1263 Living Organisms II,
BIOL1362 Biochemistry I or BIOL1261 Diversity of Organisms.
Anti-requisite: BIOL2162 Advanced Genetics.
Course Description: Genetics II is a core course for the Biology programme in the Department
of Life Sciences. The major topics of the course are cytogenetics (including epigenetics and
developmental genetics), prokaryotic/ viral genetics, and molecular genetics (including genomics).
Cytogenetics explores chromosomal macromutations (chromosomal deletions, duplications,
inversions and translocations) and their associated cytogenetic effects on plants and animals.
Epigenetics and developmental genetics is a new area of study that explains the environmental
influence on chromatin dynamics, DNA methylation, development and ultimately on inheritance.
An introductory treatment of developmental genetics is also given to understand master control
genes (homeotic genes) that regulate a cascade of genes that control development. Prokaryotic/
viral genetics provides insights into prokaryotic/ viral reproduction, recombination; genetic
complementation, mapping; and genetic regulation. Molecular genetics provides the fundamental
basis for the understanding of Molecular Biology and as such deals with DNA replication,
transcription, translation and controls. Genomics provides an insight into where genetics is
evolving (including an introduction to applications).
Assumed Knowledge: Students should be skilled in the basic principles of genetics including the
nuclear genome; the cell cycle; Mendelian genetics and extensions; and gene mapping. In addition,
students should have mastered the basic concepts of Biochemistry including the structure and
function of biomolecules.
Course organization
The course is divided into three sections: cytogenetics (40%), prokaryotic/ viral genetics (20%),
and molecular genetics (40%).
Cytogenetics will be taught in the first 5 weeks in the following order:
Chromosomal macromutations (their detection-both cytological and genetic, and the significance
of each type of macromutation (benefits, associated conditions and diseases, evolutionary
significance) – deletions, duplications (including multigene families and homeotic genes),
inversions, translocations, autopolyploids, allopolyploids, aneuploids; epigenetics; and homeobox
genes.
Prokaryotic genetics will be taught in weeks 6 and 7 in the following order:
Importance of prokaryotic genetics, comparison of prokaryotic and eukaryotic genomes,
recombination in prokaryotes (transformation, transduction and conjugation), conjugation
mapping, recombination and complementation tests (their uses and limitations), and transposition;
viral genetics- bacteriophage genetics (mating, recombination, genetic mapping).
Molecular genetics focusses mainly on the eukaryotic genome and will be taught from week8 to week-12 in the following order:
DNA replication, transcription, translation, their associated processes, end products and their
regulation; the genetic code; and genomics (including the evolution of today’s concept of a gene
and a gene locus).
Purpose of the course
Genetics II (BIOL 2XXX) aims to build on the foundation of basic principles in Genetics through
the delivery of advanced topics spanning three major topics: Cytogenetics, Prokaryotic Genetics
and Molecular Genetics. This course will serve as a core requirement for the fulfillment of the
Biology major in the Department of Life Sciences, University of the West Indies. Furthermore,
this course serves as the feeder course to Microbiology, Microbial Biotechnology, Molecular
Biology, Plant Biotechnology, Animal Biotechnology, and Crop Improvement as well as several
M. Phil. and Ph.D. programmes offered in these aforementioned areas in the Department of Life
Sciences. Careers which demand an advanced knowledge of Genetics include Plant Breeders,
Conservation Geneticists, Biotechnologists and Genetic Engineers as well as teachers of Biology
at the secondary and tertiary school levels.
Lecturer information
Dr. Winston Elibox, Room 312, 3rd Floor Natural Science Building, Tel: 6622002 Ext. 83108; Email: [email protected]
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Office hours: Monday – Friday: 12:00 p.m. – 4:00 p.m.
Communication Policy: I prefer communication via e-mail using your UWI email account.
Letter to the students
Dear Students,
I wish you a warm welcome to BIOL2XXX- Genetics II. I am excited that you have decided to
pursue this course which will build on the concepts that you have learned in Genetics I (BIOL1364)
and specifically provide you with a sound knowledge in advanced topics in genetics such as
chromosomal macromutations; epigenetics and developmental genetics, prokaryotic/ viral
genetics and molecular genetics. Chromosomal aberrations such as deletions, duplications,
inversions and translocations can have profound effects on plants and animals including several
genetic diseases of humans. All the multiple gene families that are responsible for things like
immunity, expression of haemoglobin, and body architecture are a result of duplications.
Furthermore most of our important cash crops are derived by duplication of identical or nonidentical genomes (polyploids). We can use translocation heterozygotes to control insect pests.
This course will further show you that although twins have the same genetic make-up, because of
their life history, they are epigenetically different. The area of developmental genetics will show
you how a simple egg can become an adult of its species based on pre-programmed processes
encoded by master control genes (homeotic genes). You will see why prokaryotes are able to
recombine and form new strains that can pose potential threats to us and our food sources. Finally,
you will gain sound knowledge on how DNA is maintained from generation to generation, how it
is replicated, how and when it is transcribed and how the transcribed mRNA is eventually
translated to form the polypeptides/ proteins that carry out the functions of a body.
The course is very modern and gives a brief introduction to all the modern tools of genetics that
are currently being used in the fields of biotechnology, molecular biology, crop improvement,
conservation and medicine. Hence this course serves as a foundation course for many of your
advanced courses as well as many of your future M. Phil. and Ph.D. programmes. The course is
myelearning supported and several resources including the course handbook and other suggested
readings can be accessed at your convenience. Several thought provoking questions will be posted
in the discussion forum of myelearning as we go through the course content and you are
encouraged to participate. Please check your timetables and pay particular attention to lecture
times, quizzes, incourse examinations and tutorials. I wish you a fruitful semester and I look
forward to working with all of you.
Sincerely,
Dr. Winston Elibox
Lecturer
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Course Content
Topic 1: Cytogenetics
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Regulation of gene expression at the chromosomal level
Specialized forms of chromosomes
Chromosomal mutations, changes in chromosome structure: The origins, inheritance,
evolutionary significance and diagnosis of chromosomal deletions, duplications (including
multiple gene families), inversions and translocations
Chromosomal mutations, changes in chromosome number: The origins, inheritance,
evolutionary significance and diagnosis of euploidy (autopolyploid and allopolyploid), and
aneuploidy
Epigenetics (heritable changes in gene function without a change in DNA sequence in
chromosomes): DNA methylation results in different phenotypes in genetically identical
organisms; types of epigenetic imprinting; role of epigenetic markers in the remodeling of
chromatin; inheritance of epigenetic imprints; role of epigenetics in establishing and
maintaining cell identity; epigenetic switching
Homeobox genes (master control genes): Importance of homeobox genes in developmental
processes in multicellular organisms; identifying homeobox genes; phylogenetic
distribution of homeotic genes; regulation of homeotic gene complexes
Topic 2: Prokaryotic/ viral genetics
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Prokaryotic genome structure and organization
Genetic recombination in prokaryotes: conjugation, transduction and transformation
Mechanism of each type of genetic recombination
Creating genetic maps for bacterial chromosomes using conjugation
Transposition (Transposons – mobile segments that cannot exist independent of a
replicon): structure of the three types of transposons- insertion sequence elements,
composite and non-composite; mechanism of transposition; significance of transposons in
multiple drug resistance in bacteria
Gene fine structure analysis: recombination and complementation testing in bacteria;
recombination and complementation spot test in bacteriophages; Benzer’s deletion
mapping technique in bacteriophages
Topic 3: Molecular genetics
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Molecular organization of the eukaryotic genome
Genomics- evolution of the modern concept of a gene
DNA replication in viruses, prokaryotes and eukaryotes
DNA transcription in prokaryotes and eukaryotes
Post transcriptional modifications and mRNA processing
Regulation of gene expression in prokaryotes (negative, positive and attenuation)
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Regulation of gene expression in viruses (bacteriophages )
Regulation of genes in eukaryotes (facultative and condensed chromatin, position effects,
methylation), transcriptional control, post-transcriptional control, translational control and
post-translational control.
The nature of the genetic code, degeneracy of the genetic code
DNA translation: structure and function of the ribosomes, role of tRNA, steps in DNA
translation
Post translational modifications
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Course Goals
At the end of this course, students should have:
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Acquired knowledge of chromosomal macromutations; their importance, detection;
associated disorders and evolutionary significance; and possible applications in medicine
and agriculture.
Acquired knowledge in epigenetics and developmental genetics; their importance in
differentiation, dedifferentiation, development and maintenance of cell types in various
tissues and organs.
Acquired knowledge of prokaryotic/ viral genetics, the importance of studying their
genetics; and their use in the production of high density genetic maps.
Acquired knowledge of the various steps that result in a gene in the DNA of a chromosome
being replicated, transcribed and translated into a polypeptide (protein) and the degeneracy
of the genetic code; genomics and the evolution of the concept of a gene and locus and the
methods of gene regulation.
General objectives
The course aims at providing students with the knowledge, comprehension and application of
advanced genetic principles in the areas of cytogenetics, prokaryotic/ viral genetics and molecular
genetics through lectures, discussions, assignments and tutorials. More specifically, the course will
deal with the organization, structure, function and regulation of the genetic material of prokaryotes
and eukaryotes at the molecular and gross levels. An introduction to the concept of the gene and
methodologies that have led to the advancement of knowledge on gene control will also be
presented. To assess learning, three incourse exams during weeks 5, 8 and 12; three quizzes (weeks
2, 6 and 10) based on three assignments; and one worksheet will be given and graded. The course
is myelearning supported and your manual contains specific course objectives as well as lecture
and assignment outlines and more. Students’ answers to the course questions posted on
myelearning will also be used to assess learning.
Learning outcomes:
At the end of this course, students will be able to:
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Topic 1: Cytogenetics
Introduction to Chromosomes & Chromatin
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Define cytogenetics, state the chromosome theory of inheritance and explain how it led to
the evolution of cytogenetics.
Describe chromosome structure at the macro and ultra-levels and define the unineme
model.
Describe the procedure by which karyotyping is performed and state its importance in
determining basic chromosome number, size, shape, chromosomal macromutations,
ploidy levels.
Differentiate between heterochromatin and euchromatin in a chromosome.
Define and distinguish between the different types of heterochromatin: facultative,
constitutive & condensed.
Describe the staining methods used to visualize the forms of chromatin making up
chromosomes (Feulgen staining, G-banding, FISH, Q-banding, R-banding).
Discuss the role of chromatin in regulating gene expression at the chromosomal level with
a clear definition of the phenomenon of position effects.
Define and describe polytene chromosomes & lampbrush chromosomes as two examples
of specialized forms of chromosomes.
Explain the significance of polytene and lampbrush chromosomes and their role in tissue
specific amplification of gene expression.
Changes in chromosomal structure
Chromosomal Macromutations: Deletions
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Define deletions.
Describe and distinguish between the different types of chromosomal deletions with the
aid of appropriate diagrams.
Describe the cytological and genetic methods used to detect chromosomal deletions.
Explain the consequences of deletions and describe the inheritance of deletions using
specific examples.
Explain the evolutionary significance of chromosomal deletions.
Chromosomal Macromutations: Duplications
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Define duplications.
Describe and distinguish between the different types of chromosomal duplications with the
aid of appropriate diagrams.
Describe the cytological and genetic methods used to detect chromosomal duplications.
Explain the consequences of duplications and describe the inheritance of duplications using
specific examples.
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v.
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Explain the evolutionary significance of chromosomal duplications using specific
examples.
Define multigene family (a form of chromosomal duplication) and briefly describe specific
examples of these (immune system super-family, collagen gene family, cytochrome P450
gene family).
Describe how multigene families arise and evolve to generate functional diversity,
environmental flexibility & developmental flexibility using the immune system super
family as an example.
Define the term, pseudogene, as it relates to gene families and explain how they arise.
Chromosomal Macromutations: Inversions
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Define inversions.
Describe and distinguish between paracentric and pericentric inversions with the aid of
appropriate diagrams.
Describe the cytological and genetic methods used to detect chromosomal inversions.
Explain and illustrate the meiotic consequences of crossovers within inversion loops for
pericentric and paracentric inversion heterozygotes.
Describe and explain the phenotypic effects associated with chromosomal inversions using
specific examples.
Define the term apparent crossover suppression as it relates to chromosomal inversions
and explain how it differs from actual crossover suppression associated with other
chromosomal macromutations such as deletions.
Explain the evolutionary significance of chromosomal inversions using specific examples.
Chromosomal Macromutations: Translocations
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Define translocations.
Describe and illustrate the different types of chromosomal translocations.
Describe the cytological and genetic indicators used to detect chromosomal translocations.
Describe and distinguish between alternate, adjacent-1 & adjacent-2 segregation patterns
observed in meiosis for translocation heterozygotes.
Explain and illustrate the meiotic consequences of translocations in heterozygotes.
Describe and explain the phenotypic effects associated with chromosomal translocations
using specific examples (Robertsonian translocation; Down syndrome, familial Down
syndrome).
Explain the application of translocation heterozygotes in pest control.
Explain the evolutionary significance of chromosomal translocations using specific
examples.
Changes in chromosome number
Polyploidy
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i.
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Define and distinguish between the basic chromosome number (x), the haploid number (n)
and the total chromosome number.
Define the term polyploidy.
Define and distinguish between the two main forms of ploidy: euploidy & aneuploidy.
Define and distinguish between autopolyploidy and allopolyploidy as forms of euploidy.
Explain how non-disjunction in mitosis and meiosis can lead to the formation of
autopolyploids.
Explain how autopolyploidy can be induced artificially.
Describe the inheritance of autopolyploidy and explain the sterility observed in triploids.
Describe the polyploidy series in Musa spp. (autopolyploids).
Explain and illustrate how interspecific hybridization followed by duplication and
diplodization can lead to the formation of fertile allopolyploids.
Discuss the role of allopolyploidy in evolution using specific examples.
Define and distinguish between the two forms of aneuploidy: hypoploidy & hyperploidy
Heritable changes in cellular expression that occur without a change in the DNA sequence
Epigenetics & Chromatin Dynamics
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Define the terms epigenetics and imprinting.
Describe the process of DNA methylation and explain its epigenetic effect on chromatin
remodeling and gene expression.
Identify methylation, phosphorylation & acetylation as epigenetic markers and describe the
mechanism by which these epigenetic patterns are established on histone proteins in the
remodeling of chromatin.
Explain how epigenetic imprints are inherited.
Explain the role of epigenetics in establishing and maintaining cell identity.
Define the term epigenetic switching and differentiate between this process in plants and
animals.
Explain the significance of epigenetics in the development of cancer in humans.
Master control genes that regulate a cascade of other genes and control development in
multicellular organisms
Homeotic genes- master control genes
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Define homeotic genes as being gene families that share a common DNA sequence
element (homeobox) in multicellular organisms
Explain the function of homeotic genes- master control genes (switch genes) that specify
developmental patterns (regulation) by turning different processes of cellular
differentiation on or off.
Discuss how homeotic genes begin regulation from the very early stages of embryogenesis.
Discuss the mechanism of function of homeotic genes in Drosophila melanogaster.
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Discuss the origin and phylogenetic distribution of homeotic genes.
Describe how homeotic genes are identified.
Discuss how mutations in homeotic gene families such as the Hox gene can affect rib and
limb development in humans.
Topic 2: Prokaryotic/ viral genetics
Genetic Recombination in Bacteria - Conjugation
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Describe the main distinguishing features between eukaryotic and prokaryotic genomes
with particular regard to structure, organization, inheritance/transmission &
recombination.
Define the term conjugation as it relates to bacterial recombination and state the
requirements for successful genetic transfer via bacterial conjugation.
Describe the U-tube experiment that provided evidence for conjugation as a mechanism of
gene transfer between bacterial cells, eventually leading to genetic recombination.
Describe the functions of the F-factor and its role in bacterial conjugation.
Define and distinguish between donor (F+-strain) and recipient cells (F--strain).
Define the terms plasmid and episome and explain how they are different from each other.
Compare and contrast bacterial conjugation involving F+, Hfr & Lfr strains giving detailed
descriptions of the mechanism of transfer from donor to recipient.
Define the term F’-factor and explain how it is formed.
Define the term F-mediated sexduction and explain how it leads to the formation of
merozygotes.
Differentiate between F+, Hfr, Lfr & F’ strains with respect to the nature of the F-factor,
the ability to convert recipients to donors, fate of transferred DNA, recombination
frequency & probability of recombination for any given bacterial gene.
Describe the three conjugation mapping methods- interrupted mating, gradient of transfer
and recombination mapping- used in constructing genetic maps of the bacterial
chromosome.
Critically assess the three mapping techniques in relation to each other highlighting any
advantages or disadvantages that might be associated.
Perform problem-based solving in case studies involving conjugation mapping.
Genetic Recombination in Bacteria – Transduction (mediated through a bacteriophage)
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Define the term bacteriophage and distinguish between virulent and temperate phages.
Compare and contrast the lytic and lysogenic infection cycles of λ-phage with the aid of
appropriate diagrams.
Define and distinguish between the terms prophage & lysogen.
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Describe in detail the production of generalized & specialized transducing particles.
Compare and contrast generalized and specialized modes of transduction especially with
respect to the type of phage life cycle employed, range of transducing capability, efficiency
of transduction, probability of transduction for a given gene & fate of transferred DNA.
Distinguish between Hft-lysate and Lft-lysate.
Genetic Recombination in Bacteria - Transformation
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Define the term transformation as it relates to genetic recombination in bacteria.
Explain in detail the mechanism of bacterial transformation, highlighting the steps and the
essential requirements for the process to occur.
Describe Griffith’s experiment which demonstrated genetic recombination via
transformation in Pneumococci bacteria.
Define the term competency and describe how competency can be artificially induced in
bacteria.
Discuss the factors that affect transformation efficiency.
Transposition in prokaryotes (ability of genes to change position in the bacterial
chromosome)
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Define the term transposition as the mobilization of genetic elements from one location in
the genome to another.
Describe and illustrate the structure of the three types of transposons: insertion sequence
elements, composite and non-composite transposons and distinguish between them.
Explain the function of transposase enzyme in the mobilization of insertion sequence
elements.
Describe the mechanism of transposition of insertion sequence elements and explain how
target site sequences become duplicated.
Discuss the role and significance of transposons in multiple drug resistance.
Gene Fine Structure Analysis in prokaryotes
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Define complementation and distinguish it from recombination.
Explain the difference the between recombination testing and complementation testing
especially with respect to their uses.
Describe in detail how recombination testing and complementation (cis-trans) testing are
carried out.
Discuss the merits and limitations of complementation tests.
Construct complementation maps based on cis-trans test data.
Define and distinguish between the terms cistron, muton & recon.
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Gene Fine Structure Analysis in viruses
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Describe the inheritance of plaque morphology in bacteriophages.
Describe the complementation spot test to determine whether mutations are in the same or
different cistrons.
Describe the role of complementation and recombination in the mapping of the rII-locus
in bacteriophage T4.
Describe Benzer’s deletion mapping technique and discuss its significance in gene fine
structure analysis.
Topic 3: Molecular genetics
Molecular genetics- molecular organization of the eukaryotic genome
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Outline the experiments that clearly showed that DNA is the genetic material.
Discuss the components that make up the non-repetitive, moderately repetitive and highly
repetitive sequences of the genome and the role of each of the three types of sequences.
Define the terms intron and exon and discuss the functions of each.
Critically discuss the evolutionary origin of introns: (introns first, introns early, introns
late).
Discuss the theories on the evolution of genes in light of the understanding of the variation
of gene structure in organisms.
Genomics
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Define the term genomics and discuss the importance of genomic analysis.
Describe and differentiate between functional and comparative genomics.
Demonstrate knowledge of gene estimates for the human genome and discuss why previous
estimates have been continually lowered.
Discuss the organization and complexity of the human genome.
Describe and discuss the functions and origins of non-genic sequences in the human
genome: (STR’s, LINES, SINES, microsatellites, minisatellites & VNTR’s).
Outline the evolution of concept of a gene and gene locus from the Mendelian concept to
the modern concept using genomics.
Describe the role of STR’s and microsatellites in DNA fingerprinting.
Genotypic function of DNA - DNA structure and models of replication
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Describe the structure of DNA including its double helical nature consisting of
complementary antiparallel strands (opposite polarity) and its major components.
Define nucleotides as the building blocks of DNA molecules and state the constituents of
a nucleotide monomer unit.
Differentiate between the terms nucleotide and nucleoside.
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Describe in detail the Messelson & Stahl experiment which demonstrated the semiconservative model of DNA replication.
Describe and explain the experimental evidence to support a bi-directional mode of DNA
replication.
Describe and distinguish between theta-mode (moving fork) and sigma-mode (rolling
circle) replication.
Identify the enzymes involved in DNA replication as DNA polymerases and state the
necessary requirements for successful DNA replication.
Explain what is meant by semi-discontinuous replication of DNA and describe the
evidence that revealed this characteristic feature of DNA replication.
Define the terms leading strand, lagging strand & Okazaki fragment as they relate to semidiscontinuous DNA replication.
Explain what is meant by the growing point paradox of DNA replication and how it has
been resolved.
Define the term replisome as a multi-enzyme complex responsible for the replication of
DNA.
Illustrate the structure of a typical prokaryotic replisome by means of a clearly labeled
diagram and describe the functions of the constituent enzymes.
Differentiate between the replication apparatus of prokaryotes and eukaryotes.
Describe in detail the steps involved in DNA replication (initiation, elongation &
termination) and how they are facilitated by the replisome.
Compare and contrast prokaryotic and eukaryotic DNA replication with particular
emphasis on differences relating to the linear nature of eukaryotic chromosomes and the
circularity nature of prokaryotic DNA molecules.
Phenotypic Function of DNA - Transcription
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Define the term transcription as it relates to the Central dogma of biology.
Identify the enzyme involved in DNA transcription as RNA polymerase and describe its
characteristic features including the essential requirements for its function.
Explain in detail the steps involved in the process of transcription (initiation, elongation &
termination).
Compare and contrast the process of transcription in prokaryotes and eukaryotes.
Draw and annotate the typical structure of prokaryotic and eukaryotic genes identifying the
major differences between the two.
Explain the consequences of the eukaryotic split-gene structure on the production of mature
mRNA and the need to remove introns from heterogeneous mRNA by splicing.
Describe and illustrate the steps involved in intron-splicing pathways that lead to the
production of mature mRNA in eukaryotes.
Describe the post-transcriptional modifications involved in the production of mature
eukaryotic mRNA that affect mRNA stability: 3’-polyadenylation & 5’-capping.
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Regulation of Prokaryotic Gene Expression – lac Operon (negative control with
superimposed positive control)
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Explain the importance of systems to regulate the expression of genes.
Define the term operon and explain the advantage of gene expression using an operon
system.
Explain what is meant by a negative control system and a positive control system and be
able to differentiate between the two.
Distinguish between the two types of negative control systems: inducible & repressible
and give examples of such systems.
Describe and illustrate the structure of the lac operon.
List and explain the functions of the structural genes of the lac operon along with the
regulatory sequences involved in controlling expression of the genes.
Explain the differences between cis-acting and trans-acting control elements.
Explain in detail how the negative and positive control systems of the lac operon function
to regulate expression of the structural genes.
Regulation of Prokaryotic Gene Expression – trp operon (negative control with
superimposed attenuation)
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Describe and illustrate the structure of the trp operon.
Identify and explain the functions of the structural genes of the trp operon along with the
regulatory sequences involved in controlling expression of the genes.
Explain in detail how the negative control system of the trp operon functions to regulate
expression of the structural genes.
Define the term attenuation and explain in detail how it is employed in the regulation of
the trp operon.
Explain the alternative TRAP mechanism of control of the trp operon in B. subtilis.
Temporal control of genes in bacteriophages
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Describe and discuss how altering the specificity of RNA polymerase by modification of
the sigma factor in the host by the SPO1 phage can result in transcription of the phage
genes in a temporal manner.
Describe and discuss how anti-termination regulates the transcription of genes of the
lambda phage in a temporal manner.
Regulation of genes in eukaryotes: facultative and condensed chromatin, position effects,
methylation
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Discuss how RNA polymerase cannot bind to chromatin in tightly coiled heterochromatic
regions in eukaryotic genomes resulting in non-transcription of genes in that region.
Discuss how facultative heterochromatin is regulated to provide environmental flexibility.
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Discuss how transcription of genes in the euchromatin can be affected by their proximity
to the heterochromatic regions.
Discuss how methylation of genes prevents their transcription and this methylation can be
heritable (epigenetics).
Phenotypic Function of DNA - Translation
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Define the term translation as it relates to the Central dogma of biology.
Describe the basic structure of prokaryotic and eukaryotic ribosomes and outline their role
in the process of translation.
Describe the function of tRNA molecules in the process of translation.
Define the terms codon & anti-codon.
Define the Shine-Dalgarno consensus sequence and explain its importance in the initiation
of translation of prokaryotic mRNA.
Explain in detail the steps involved in the process of translation (initiation, elongation &
termination).
Discuss how post translation modifications such as clipping, targeting proteins to
organelles, protein folding, glycosylation and phosphorylation are important for
functionality of the translated protein.
The genetic code
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Describe the nature of the genetic code and explain what is meant by the following features:
triplet code, non-overlapping code, commaless/gapless code, degenerate code & universal
code.
Describe the experiments that provided evidence to demonstrate the triplet nature of the
genetic code.
Explain how Crick’s Wobble hypothesis and iso-accepting species of tRNA enable the cell
system to cope with the degeneracy of the genetic code.
Assignments/ quizzes/ worksheet
a.
Multigene families
By the end of this exercise students should be able to:
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iv.
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Define multigene families
Outline different types of multigene families
Define multigene superfamily with examples
Explain the origin of multigene families
Describe how members of multigene families tend to retain more structural similarity than
would be expected over evolutionary time
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Describe the evolutionary significance of multigene families.
Epigenetics
By the end of this exercise students should be able to:
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ii.
iii.
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Explain why identical twins become epigenetically different as they age, based on their life
histories
Explain the role of epigenetic changes in the induction of cancers in humans
Show how a human’s diet epigenetic imprint can be inherited in his/ her progenies.
Bacterial transformation
By the end of this exercise students should be able to:
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ii.
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iv.
v.
d.
Describe the process of introducing a GFP-plasmid into Xanthomonas axonopodis pv.
dieffenbachiae using electroporation
Relate the process to the normal process of bacterial transformation.
Explain the role of the GFP fluorescence as a selectable marker
Outline the advantages of GFP fluorescence over selection on specific growth media
supplemented with antibiotics
State the factors which influence transformation efficiency.
Worksheet on conjugation mapping in bacteria
By the end of this worksheet students should be able to:
i.
ii.
Calculate genetic distances between bacterial genes
Construct genetic maps of bacterial chromosomes based on case studies using the methods
of interrupted mating, gradient of transfer and recombination mapping.
Course assessment
 In-course
Incourse examinations will include multiple choice questions, structural and short answer type
questions. These exams will assess knowledge, comprehension, application and analysis of course
content.
The quizzes for the assignments will allow students the opportunity to read, comprehend, interpret,
analyze and summarize reports written in the scientific manner and as well reinforce and extend
what is learned during class time.
The worksheet on conjugation will allow students to calculate genetic distances and construct
genetic maps based on the three methods (interrupted mating, gradient of transfer and
recombination mapping). (See the course calendar for the assessment schedule).
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Assessment
In-course Examination #1
In-course Examination #2
In-course Examination #3
Class quiz #1
Class quiz #2
Class quiz #3
Worksheet
Final Examination
Total
Weighting
10%
10%
10%
5%
5%
5%
5%
50%
100%
The final examination comprises multiple choice questions, short answer questions with four to
five parts, structured questions and essay type questions. These questions are meant to test
students’ ability to recall, comprehend, apply and analyze course content in a critical and logical
manner. Students are required to answer ALL questions.
 Overall assessment
Incourse
50%
Final Theory Exam (2 hours)
50%
Evaluation
Two student representatives will be elected from the class. Student feedback will be obtained
officially from the staff-student liaison meetings held twice per semester. However, students are
encouraged to give their feedback on the course via myelearning at any time. Comments will be
assessed critically by the instructor, course coordinator and first examiner and weaknesses will be
addressed to improve on the course in the future.
Teaching Strategies
The course consists of 33 lectures, THREE assignments (for quizzes), ONE worksheet and THREE
tutorials. The course is myelearning supported and your manual contains specific course
objectives as well as lecture outlines, past exam papers and model answers.
Recommended Texts
1. Brooker, Robert J. Genetics: Analysis & Principles 3rd Edition McGraw Hill Higher Education
2008. ISBN: 9780071287647
2. Snustad, D. Peter & Simmons, Michael J. Principles of Genetics 5th Edition John Wiley &
Sons Inc. 2009. ISBN: 9780470388259
3. Genetics: A Conceptual Approach (Benjamin A. Pierce)
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Principles of Genetics 7th Edition (Robert H. Tamarin)
Genes VIII (Benjamin Lewin)
Molecular Cell Biology (Lodish et al.)
Molecular Biology of The Cell (Alberts et al.)
4.
5.
6.
7.
Course Calendar
Course Delivery: Topics covered
Week
Lecture Subjects
1
Course Overview
Introduction to Cytogenetics: Chromosome primary & secondary structure
chromosome ultra-structure- Chromatin/ Distribute paper on Evolution of
Cytogenetics Multigene Families **
Chromosomal Macromutations: Deletions
2
Chromosomal Macromutations: Duplications-1
Chromosomal Macromutations: Duplications-2/ Quiz #1- Evolution of
multigene families**
Chromosomal Macromutations: Inversions
3
Chromosomal Macromutations: Translocations-1
Chromosomal Macromutations: Translocations-2
Ploidy: Autopolyploidy
4
Ploidy: Allopolyploidy; Aneuploidy
Epigenetics & Chromatin Dynamics-1/ Distribute paper on Epigenetics**
Epigenetics & Chromatin Dynamics-2
5
Homeobox genes
In-course Examination #1
Genetic Transfer in Bacteria: Conjugation
6
Prokaryotic
genetics
Conjugation Mapping
Genetic transfer in bacteria: transduction and transformation/ Quiz #2:
Epigenetics**
Prokaryotic genetics: transposition
7
Gene Fine Structure Analysis in Bacteria: Recombination Testing &
Complementation Testing/ Distribute worksheet on conjugation mapping**
Gene Fine Structure Analysis - bacteriophages: Deletion Mapping
17
In-course Examination # 2
8
Molecular genetics- organization of the eukaryotic genome
Molecular
genetics
Molecular genetics- organization of the eukaryotic genome continues/
Distribute paper on bacterial transformation**
Genomics/ Collect worksheet on conjugation mapping**
9
DNA Structure & Models of Replication
DNA Structure & models of replication continues
DNA Structure & models of replication continues
10
Phenotypic function of DNA: Transcription (Prokaryotes)
Phenotypic function of DNA: Post-transcriptional Processing of Eukaryotic
mRNA/ Quiz #3: Bacterial transformation**
Regulation of Prokaryotic Gene Expression: negative control- lac Operon
11
Regulation of Prokaryotic Gene Expression: negative control with
superimposed attenuation- trp Operon; positive control
Temporal control of genes in bacteriophages
Control in eukaryotes- facultative and condensed heterochromatin, position
effects, methylation
12
Translation and post translational regulation
In-course Examination #3
Tutorial
13
Tutorial
Tutorial
Additional information
Attendance
Attendance in the incourse exams and the quizzes is mandatory. Any student who misses an
incourse exam or a quiz is advised to consult immediately in person or by email with the course
instructor regarding their make-up options. Absence must be accompanied by a written excuse or
medical submitted to the Main office, Life Sciences within 7 days of the missed session. Any
student who was inexcusably absent or who does not write an incourse exam, a quiz or the
worksheet will receive 0% for that exercise.
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How to study for this course
You are encouraged to work together in small cohesive groups as much as possible to go through
the course content. As we go through the various topics, students should attempt to answer all the
sample questions placed on myelearning and discuss the answers amongst themselves. All
comments, questions and concerns provided on a particular topic will be addressed during class
time, via myelearning or FaceBook (account to be created). Your departmental course textbook
on myelearning contains all the topics to be taught and the textbook content is aligned similarly
as the lectures; please read the textbook. Use the responses and comments for your incourse
examinations, quizzes and worksheet as a guide to answering the questions properly. There are
several pass paper questions in the library and you are encouraged to attempt these questions.
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