THE UNIVERSITY OF THE WEST INDIES ST AUGUSTINE FACULTY OF SCIENCE AND TECHNOLOGY DEPARTMENT OF LIFE SCIENCES COURSE OUTLINE

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1 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.

2 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 week- 8 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, 3 rd Floor Natural Science Building, Tel: Ext ; E- mail: Winston.Elibox@sta.uwi.edu 2

3 Office hours: Monday Friday: 12:00 p.m. 4:00 p.m. Communication Policy: I prefer communication via using your UWI 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 3

4 Course Content Topic 1: Cytogenetics 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 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 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) 4

5 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 Course Goals At the end of this course, students should have: 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: 5

6 Topic 1: Cytogenetics Introduction to Chromosomes & Chromatin i. Define cytogenetics, state the chromosome theory of inheritance and explain how it led to the evolution of cytogenetics. ii. Describe chromosome structure at the macro and ultra-levels and define the unineme model. iii. Describe the procedure by which karyotyping is performed and state its importance in determining basic chromosome number, size, shape, chromosomal macromutations, ploidy levels. iv. Differentiate between heterochromatin and euchromatin in a chromosome. v. Define and distinguish between the different types of heterochromatin: facultative, constitutive & condensed. vi. Describe the staining methods used to visualize the forms of chromatin making up chromosomes (Feulgen staining, G-banding, FISH, Q-banding, R-banding). vii. Discuss the role of chromatin in regulating gene expression at the chromosomal level with a clear definition of the phenomenon of position effects. viii. Define and describe polytene chromosomes & lampbrush chromosomes as two examples of specialized forms of chromosomes. ix. 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 i. Define deletions. ii. Describe and distinguish between the different types of chromosomal deletions with the aid of appropriate diagrams. iii. Describe the cytological and genetic methods used to detect chromosomal deletions. iv. Explain the consequences of deletions and describe the inheritance of deletions using specific examples. v. Explain the evolutionary significance of chromosomal deletions. Chromosomal Macromutations: Duplications i. Define duplications. ii. Describe and distinguish between the different types of chromosomal duplications with the aid of appropriate diagrams. iii. Describe the cytological and genetic methods used to detect chromosomal duplications. iv. Explain the consequences of duplications and describe the inheritance of duplications using specific examples. 6

7 v. Explain the evolutionary significance of chromosomal duplications using specific examples. vi. 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). vii. Describe how multigene families arise and evolve to generate functional diversity, environmental flexibility & developmental flexibility using the immune system super family as an example. viii. Define the term, pseudogene, as it relates to gene families and explain how they arise. Chromosomal Macromutations: Inversions i. Define inversions. ii. Describe and distinguish between paracentric and pericentric inversions with the aid of appropriate diagrams. iii. Describe the cytological and genetic methods used to detect chromosomal inversions. iv. Explain and illustrate the meiotic consequences of crossovers within inversion loops for pericentric and paracentric inversion heterozygotes. v. Describe and explain the phenotypic effects associated with chromosomal inversions using specific examples. vi. 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. vii. Explain the evolutionary significance of chromosomal inversions using specific examples. Chromosomal Macromutations: Translocations i. Define translocations. ii. Describe and illustrate the different types of chromosomal translocations. iii. Describe the cytological and genetic indicators used to detect chromosomal translocations. iv. Describe and distinguish between alternate, adjacent-1 & adjacent-2 segregation patterns observed in meiosis for translocation heterozygotes. v. Explain and illustrate the meiotic consequences of translocations in heterozygotes. vi. Describe and explain the phenotypic effects associated with chromosomal translocations using specific examples (Robertsonian translocation; Down syndrome, familial Down syndrome). vii. Explain the application of translocation heterozygotes in pest control. viii. Explain the evolutionary significance of chromosomal translocations using specific examples. Changes in chromosome number Polyploidy 7

8 i. Define and distinguish between the basic chromosome number (x), the haploid number (n) and the total chromosome number. ii. Define the term polyploidy. iii. Define and distinguish between the two main forms of ploidy: euploidy & aneuploidy. iv. Define and distinguish between autopolyploidy and allopolyploidy as forms of euploidy. v. Explain how non-disjunction in mitosis and meiosis can lead to the formation of autopolyploids. vi. Explain how autopolyploidy can be induced artificially. vii. Describe the inheritance of autopolyploidy and explain the sterility observed in triploids. viii. Describe the polyploidy series in Musa spp. (autopolyploids). ix. Explain and illustrate how interspecific hybridization followed by duplication and diplodization can lead to the formation of fertile allopolyploids. x. Discuss the role of allopolyploidy in evolution using specific examples. xi. 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 i. Define the terms epigenetics and imprinting. ii. Describe the process of DNA methylation and explain its epigenetic effect on chromatin remodeling and gene expression. iii. 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. iv. Explain how epigenetic imprints are inherited. v. Explain the role of epigenetics in establishing and maintaining cell identity. vi. Define the term epigenetic switching and differentiate between this process in plants and animals. vii. 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 i. Define homeotic genes as being gene families that share a common DNA sequence element (homeobox) in multicellular organisms ii. 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. iii. Discuss how homeotic genes begin regulation from the very early stages of embryogenesis. iv. Discuss the mechanism of function of homeotic genes in Drosophila melanogaster. 8

9 v. Discuss the origin and phylogenetic distribution of homeotic genes. vi. Describe how homeotic genes are identified. vii. 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 i. Describe the main distinguishing features between eukaryotic and prokaryotic genomes with particular regard to structure, organization, inheritance/transmission & recombination. ii. Define the term conjugation as it relates to bacterial recombination and state the requirements for successful genetic transfer via bacterial conjugation. iii. Describe the U-tube experiment that provided evidence for conjugation as a mechanism of gene transfer between bacterial cells, eventually leading to genetic recombination. iv. Describe the functions of the F-factor and its role in bacterial conjugation. v. Define and distinguish between donor (F + -strain) and recipient cells (F - -strain). vi. Define the terms plasmid and episome and explain how they are different from each other. vii. Compare and contrast bacterial conjugation involving F +, Hfr & Lfr strains giving detailed descriptions of the mechanism of transfer from donor to recipient. viii. Define the term F -factor and explain how it is formed. ix. Define the term F-mediated sexduction and explain how it leads to the formation of merozygotes. x. 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. xi. Describe the three conjugation mapping methods- interrupted mating, gradient of transfer and recombination mapping- used in constructing genetic maps of the bacterial chromosome. xii. Critically assess the three mapping techniques in relation to each other highlighting any advantages or disadvantages that might be associated. xiii. Perform problem-based solving in case studies involving conjugation mapping. Genetic Recombination in Bacteria Transduction (mediated through a bacteriophage) i. Define the term bacteriophage and distinguish between virulent and temperate phages. ii. Compare and contrast the lytic and lysogenic infection cycles of λ-phage with the aid of appropriate diagrams. iii. Define and distinguish between the terms prophage & lysogen. 9

10 iv. Describe in detail the production of generalized & specialized transducing particles. v. 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. vi. Distinguish between Hft-lysate and Lft-lysate. Genetic Recombination in Bacteria - Transformation i. Define the term transformation as it relates to genetic recombination in bacteria. ii. Explain in detail the mechanism of bacterial transformation, highlighting the steps and the essential requirements for the process to occur. iii. Describe Griffith s experiment which demonstrated genetic recombination via transformation in Pneumococci bacteria. iv. Define the term competency and describe how competency can be artificially induced in bacteria. v. Discuss the factors that affect transformation efficiency. Transposition in prokaryotes (ability of genes to change position in the bacterial chromosome) i. Define the term transposition as the mobilization of genetic elements from one location in the genome to another. ii. Describe and illustrate the structure of the three types of transposons: insertion sequence elements, composite and non-composite transposons and distinguish between them. iii. Explain the function of transposase enzyme in the mobilization of insertion sequence elements. iv. Describe the mechanism of transposition of insertion sequence elements and explain how target site sequences become duplicated. v. Discuss the role and significance of transposons in multiple drug resistance. Gene Fine Structure Analysis in prokaryotes i. Define complementation and distinguish it from recombination. ii. Explain the difference the between recombination testing and complementation testing especially with respect to their uses. iii. Describe in detail how recombination testing and complementation (cis-trans) testing are carried out. iv. Discuss the merits and limitations of complementation tests. v. Construct complementation maps based on cis-trans test data. vi. Define and distinguish between the terms cistron, muton & recon. 10

11 Gene Fine Structure Analysis in viruses i. Describe the inheritance of plaque morphology in bacteriophages. ii. Describe the complementation spot test to determine whether mutations are in the same or different cistrons. iii. Describe the role of complementation and recombination in the mapping of the rii-locus in bacteriophage T4. iv. 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 i. Outline the experiments that clearly showed that DNA is the genetic material. ii. 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. iii. Define the terms intron and exon and discuss the functions of each. iv. Critically discuss the evolutionary origin of introns: (introns first, introns early, introns late). v. Discuss the theories on the evolution of genes in light of the understanding of the variation of gene structure in organisms. Genomics i. Define the term genomics and discuss the importance of genomic analysis. ii. Describe and differentiate between functional and comparative genomics. iii. Demonstrate knowledge of gene estimates for the human genome and discuss why previous estimates have been continually lowered. iv. Discuss the organization and complexity of the human genome. v. Describe and discuss the functions and origins of non-genic sequences in the human genome: (STR s, LINES, SINES, microsatellites, minisatellites & VNTR s). vi. Outline the evolution of concept of a gene and gene locus from the Mendelian concept to the modern concept using genomics. vii. Describe the role of STR s and microsatellites in DNA fingerprinting. Genotypic function of DNA - DNA structure and models of replication i. Describe the structure of DNA including its double helical nature consisting of complementary antiparallel strands (opposite polarity) and its major components. ii. Define nucleotides as the building blocks of DNA molecules and state the constituents of a nucleotide monomer unit. iii. Differentiate between the terms nucleotide and nucleoside. 11

12 iv. Describe in detail the Messelson & Stahl experiment which demonstrated the semiconservative model of DNA replication. v. Describe and explain the experimental evidence to support a bi-directional mode of DNA replication. vi. Describe and distinguish between theta-mode (moving fork) and sigma-mode (rolling circle) replication. vii. Identify the enzymes involved in DNA replication as DNA polymerases and state the necessary requirements for successful DNA replication. viii. Explain what is meant by semi-discontinuous replication of DNA and describe the evidence that revealed this characteristic feature of DNA replication. ix. Define the terms leading strand, lagging strand & Okazaki fragment as they relate to semidiscontinuous DNA replication. x. Explain what is meant by the growing point paradox of DNA replication and how it has been resolved. xi. Define the term replisome as a multi-enzyme complex responsible for the replication of DNA. xii. Illustrate the structure of a typical prokaryotic replisome by means of a clearly labeled diagram and describe the functions of the constituent enzymes. xiii. Differentiate between the replication apparatus of prokaryotes and eukaryotes. xiv. Describe in detail the steps involved in DNA replication (initiation, elongation & termination) and how they are facilitated by the replisome. xv. 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 i. Define the term transcription as it relates to the Central dogma of biology. ii. Identify the enzyme involved in DNA transcription as RNA polymerase and describe its characteristic features including the essential requirements for its function. iii. Explain in detail the steps involved in the process of transcription (initiation, elongation & termination). iv. Compare and contrast the process of transcription in prokaryotes and eukaryotes. v. Draw and annotate the typical structure of prokaryotic and eukaryotic genes identifying the major differences between the two. vi. 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. vii. Describe and illustrate the steps involved in intron-splicing pathways that lead to the production of mature mrna in eukaryotes. viii. Describe the post-transcriptional modifications involved in the production of mature eukaryotic mrna that affect mrna stability: 3 -polyadenylation & 5 -capping. 12

13 Regulation of Prokaryotic Gene Expression lac Operon (negative control with superimposed positive control) i. Explain the importance of systems to regulate the expression of genes. ii. Define the term operon and explain the advantage of gene expression using an operon system. iii. Explain what is meant by a negative control system and a positive control system and be able to differentiate between the two. iv. Distinguish between the two types of negative control systems: inducible & repressible and give examples of such systems. v. Describe and illustrate the structure of the lac operon. vi. 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. vii. Explain the differences between cis-acting and trans-acting control elements. viii. 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) i. Describe and illustrate the structure of the trp operon. ii. 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. iii. Explain in detail how the negative control system of the trp operon functions to regulate expression of the structural genes. iv. Define the term attenuation and explain in detail how it is employed in the regulation of the trp operon. v. Explain the alternative TRAP mechanism of control of the trp operon in B. subtilis. Temporal control of genes in bacteriophages i. 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. ii. 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 i. 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. ii. Discuss how facultative heterochromatin is regulated to provide environmental flexibility. 13

14 iii. iv. 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 i. Define the term translation as it relates to the Central dogma of biology. ii. Describe the basic structure of prokaryotic and eukaryotic ribosomes and outline their role in the process of translation. iii. Describe the function of trna molecules in the process of translation. iv. Define the terms codon & anti-codon. v. Define the Shine-Dalgarno consensus sequence and explain its importance in the initiation of translation of prokaryotic mrna. vi. Explain in detail the steps involved in the process of translation (initiation, elongation & termination). vii. 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 i. 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. ii. Describe the experiments that provided evidence to demonstrate the triplet nature of the genetic code. iii. 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: i. Define multigene families ii. Outline different types of multigene families iii. Define multigene superfamily with examples iv. Explain the origin of multigene families v. Describe how members of multigene families tend to retain more structural similarity than would be expected over evolutionary time 14

15 vi. Describe the evolutionary significance of multigene families. b. Epigenetics By the end of this exercise students should be able to: i. Explain why identical twins become epigenetically different as they age, based on their life histories ii. Explain the role of epigenetic changes in the induction of cancers in humans iii. Show how a human s diet epigenetic imprint can be inherited in his/ her progenies. c. Bacterial transformation By the end of this exercise students should be able to: i. Describe the process of introducing a GFP-plasmid into Xanthomonas axonopodis pv. dieffenbachiae using electroporation ii. Relate the process to the normal process of bacterial transformation. iii. Explain the role of the GFP fluorescence as a selectable marker iv. Outline the advantages of GFP fluorescence over selection on specific growth media supplemented with antibiotics v. State the factors which influence transformation efficiency. d. Worksheet on conjugation mapping in bacteria By the end of this worksheet students should be able to: i. Calculate genetic distances between bacterial genes ii. 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). 15

16 Assessment Weighting In-course Examination #1 10% In-course Examination #2 10% In-course Examination #3 10% Class quiz #1 5% Class quiz #2 5% Class quiz #3 5% Worksheet 5% Final Examination 50% Total 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 3 rd Edition McGraw Hill Higher Education ISBN: Snustad, D. Peter & Simmons, Michael J. Principles of Genetics 5 th Edition John Wiley & Sons Inc ISBN: Genetics: A Conceptual Approach (Benjamin A. Pierce) 16

17 4. Principles of Genetics 7 th Edition (Robert H. Tamarin) 5. Genes VIII (Benjamin Lewin) 6. Molecular Cell Biology (Lodish et al.) 7. Molecular Biology of The Cell (Alberts et al.) Course Calendar Course Delivery: Topics covered Week Lecture Subjects 1 Course Overview Cytogenetics Introduction to Cytogenetics: Chromosome primary & secondary structure chromosome ultra-structure- Chromatin/ Distribute paper on Evolution of 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 6 Prokaryotic genetics 7 In-course Examination #1 Genetic Transfer in Bacteria: Conjugation Conjugation Mapping Genetic transfer in bacteria: transduction and transformation/ Quiz #2: Epigenetics** Prokaryotic genetics: transposition Gene Fine Structure Analysis in Bacteria: Recombination Testing & Complementation Testing/ Distribute worksheet on conjugation mapping** Gene Fine Structure Analysis - bacteriophages: Deletion Mapping 17

18 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) 11 Phenotypic function of DNA: Post-transcriptional Processing of Eukaryotic mrna/ Quiz #3: Bacterial transformation** Regulation of Prokaryotic Gene Expression: negative control- lac Operon 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 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. 18

19 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. 19