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208SYLL09.doc

  1. 1. COURSE OUTLINE Course Number: Course Title: BIO208 GENETICS Credits: 4 Hours: 3 lecture/3 laboratory Required texts: iGenetics: A Molecular Approach, 2nd ed. Peter J. Russell Benjamin Cummings Publishers Course Coordinator: L. Blinderman Office: MS 110 Phone: 570-3833 blinderl@mccc.edu www.mccc.edu/~blinderl Catalogue Description: A survey course examining gene activity at the molecular and organismal levels. Principles of transmission, molecular, and population genetics are covered with emphases placed on advances in genetic technology and applications. The laboratory exercises address topics in heredity, chromosome structure, recombinant DNA, bioinformatics, and other molecular biology techniques. Three hours of lecture and one three hour laboratory per week. Prerequisites: Successful completion of BIO 102 (C grade or higher) or consent of instructor
  2. 2. 2 Grading Lecture: The lecture grade is based on examination grades, in-class activities, and homework assignments. The instructor must be informed within 12 hours of a missed exam. Makeup exams, given only for a valid and documented absence, are discouraged, and consist of essay questions. Laboratory: The laboratory grade is based on pre-labs, the laboratory notebook, attendance, and participation. The instructor will evaluate student performance throughout the semester. More than one unexcused absence will result in a lower lab grade. There are no makeup laboratories. Lab exams 15% Lab notebook (includes pre-labs and lab homework) 20% Lecture exams 55% Lecture homework , worksheets, presentation 10% Classroom conduct The college welcomes students into an environment that creates a sense of community pride and respect. Attendance It is a student’s responsibility to attend all of his/her classes. If a class meeting is missed, the student is responsible for content covered, announcements made in his/her absence, and for acquiring any materials distributed in class. More than 3 missed lectures may result in a lower grade for the course. The laboratory component of the course is critical to satisfying the course objectives. A student who misses more than two unexcused laboratory sessions will fail the course. A passing grade must be
  3. 3. 3 obtained in the laboratory in order to pass the course. Tardiness It is expected that students will be on time for all classes. Students late for an exam may be denied the opportunity to take the exam. A student who enters the laboratory late may not be able to participate in the lab. Behavior Students are expected to follow ordinary rules of courtesy during class sessions. The instructor has the right to eject a disruptive student from the class at any time. Cell phones and other devices are to be turned off prior to the start of class so that they are not used during class time. Accommodations Any student in this class who has special needs because of a disability is entitled to receive accommodations. Eligible students at Mercer County Community College are assured services under the Americans with Disabilities Act and Section 504 of the Rehabilitation Act of 1973. If you believe you are eligible for services, please contact Arlene Stinson, the Director of Academic Support Services. Ms. Stinson’s office is LB221, and she can be reached at (609) 570-3525. Academic Integrity Statement: Cheating of any kind is not tolerated. Cheating includes copying papers or website information, presenting another person's work as one's own in any way, looking at a student's paper during a test or quiz, looking at notes during an exam or quiz, obtaining information about an exam, quiz, or any other information that other students do not have and the instructor does not intend them to have, or talking during an exam or quiz. Write your own papers using your own words. All violations of academic integrity will be reported to the Academic Integrity Committee. For additional information: Refer to the MCCC Student Handbook. Schedule of Lecture Topics WEEK TOPIC CHAPTERS I Introduction and DNA Structure 1, 2 II Transcription and Translation 5 III Gene Expression 6 IV (continued) EXAM 1 V Mendelian Genetics and Extensions of Mendel 11, 13, 4 VI Chromosomal Basis of Inheritance and Gene 12
  4. 4. 4 Linkage VII Chromosome Variations 17 EXAM 2 VIII Bacterial Genetics 18 X (continued) 19 XI Recombinant DNA Technology 8 XII (continued) EXAM 3 XIII DNA mutation, Repair, Transposable Elements 7 XIV Applications of Recombinant DNA Technology 9 XV Population and Evolutionary Genetics 13 EXAM 4 Laboratory Schedule Lab Topic 1 Lab notebook, Bioinformatics (computer lab) 2 Isolation of DNA from animal and plant tissue 3 Human DNA fingerprinting via the polymerase chain reaction (PCR) 4 Electrophoresis, UV spectrophotometry 5 LP#1 6 Mendelian Genetics, Chi Square, Probability, Pedigree analysis 7 Cytogenetics, Karyotyping (computer lab) 8 Restriction enzyme mapping 9 DNA mapping/ electrophoresis (continued) 10 LP #2 11 Translation of mRNA (computer lab) 12 Gene Expression: Transformation of bacteria with pGLO recombinant plasmid 13 Transformation analysis 14 Human evolutionary and population genetics (computer lab) *The Laboratory Schedule may be revised LABORATORY SAFETY Your instructor will call attention to safety precautions. FOOD AND DRINKS ARE NOT ALLOWED IN THE LABORATORY, ever! For working with chemicals: 1. Wear gloves and safety goggles 2. In the event of a spill, notify your instructor immediately 3. Wash your hands with soap and water 4. Wipe down your lab bench with disinfectant before and after use 5. Read labels and follow instructions carefully 6. Never use mouth suction in filling pipettes with chemical reagents. Use a suction bulb. Note the location of: 1. the eye-wash station, fume hood, fire blanket, fire extinguisher, and safety goggles
  5. 5. 5 2. the master shut-off switch for electricity 3. the unobstructed exits Before leaving, make certain that: 1. all equipment is turned off 2. the chair is pushed in 3. all work surfaces and equipment in the chemical or biological laboratory are thoroughly cleaned and left in a neat condition THE COURSE INSTRUCTOR RESERVES THE RIGHT TO CHANGE THE SCHEDULE AND GRADING PROCEDURE AT ANY TIME Course Competencies/Goals 1. Elucidate the structure and packaging of DNA 2. Analyze the architecture of eukaryotic and prokaryotic genes and describe the regulation of gene expression at the molecular level 3. Explore transmission genetics and solve problems in the transmission of traits 4. Investigate chromosomal architecture, sex linkage, karyotypes, and aneuploidy 5. Examine microbial genetics, mechanisms of gene transfer, and use of microbes as model organisms 6. Explore the techniques and goals of genomics, biotechnology, transgenics organisms, and cloning 7. Explore molecular mechanisms of DNA mutation and repair 8. Investigate topics in population and evolutionary genetics 9. Develop skills in pipetting, gene cloning, bacterial transformation, restriction enzyme digestion, DNA fingerprinting via the polymerase chain reaction, bioinformatics, gel electrophoresis, DNA and protein purification, spectrophotometry, centrifugation, and other laboratory techniques Lecture Objectives by Unit UNIT 1 DNA, Transcription, and Gene Expression Students will be able to: 1. Review model organisms used in genetics 2. Distinguish between molecular, transmission, population, and quantitative genetics 3. Compare and contrast prokaryotes and eukaryotes 4. Describe functional properties of DNA including replication, storage of information, mutation, gene expression 5. Analyze the experiments by Griffith that uncovered a transforming factor 6. Evaluate the contributions of Avery et al and Hershey and Chase to the identification of DNA as the genetic material. 7. Discuss the elucidation of the DNA double helix by Franklin, Watson and Crick. 8. Provide a description of the structure of DNA including base complementation, antiparallel strands, sugar/phosphate backbone, nucleotide composition, major and minor grooves 9. Examine Chargaff’s observations of nucleotide composition in DNA 10. Contrast B-, Z-, and A-DNA 11. Review the life cycle of T2 bacteriophage 12. Examine the genetic material of viruses 13. Describe the genome of the bacterial chromosome
  6. 6. 6 14. Explain the relationship between chromatin, histone and non-histone proteins, chromosomes, and DNA 15. Analyze the architecture of nucleosomes 16. Explain the role of histone proteins and nucleosomes in DNA modeling and in gene expression (epigenetics) 17. Contrast heterochromatin with euchromatin. 18. Review single copy genes and multiple copy (gene families, gene clusters). 19. Compare repetitive DNA: SINES, LINES, STR, centromeric and telomeric DNA 20. Read Watson and Crick’s Nature paper 21. Relate Alu repeats to transposon activity. 22. Distinguish between amino acids, peptides, polypeptides, and proteins 23. Understand the flow of information in gene expression, DNA  RNA  Protein 24. Compare and contrast the function of 5 types of RNA (including RNAi) 25. Provide a detailed overview of transcription and translation 26. Distinguish between the template and non-template strands of DNA 27. Describe the role of RNA polymerase in the 5’ -> 3’ transcription of template strand of DNA 28. Compare RNA polymerase and DNA polymerase 29. Describe the role of the sigma factor in the initiation of transcription in prokaryotes 30. Distinguish between initiation and elongation of the transcript 31. Contrast upstream and downstream sequences 32. Describe the mechanism of promoters in the initiation of transcription including the prokaryotic promoter consensus sequences (-10 and -35) 33. Explain the mechanism of concurrent transcription and translation in prokaryotic cells 34. Note that bacterial DNA lacks introns (no split genes) and may produce polycistronic mRNA 35. Describe eukaryotic promoters (TATA and CCAAT boxes) and the loop mechanism of enhancer action 36. Outline the general role of transcription factors in the generation of mRNA by RNA pol II and in the formation of the pre-initiation complex 37. List the 3 components required for the initiation of transcription in eukaryotes 38. Describe the mechanism of heterogeneous mRNA processing including 5’ capping and 3' polyadenylation 39. Examine the components of hnRNA (pre-mRNA) including the 5’ and 3’ untranslated regions, introns, and cap, and polyA tail 40. Discuss the concept of split genes and role of the spliceosome 41. Analyze coding and noncoding region mutations in the l globin gene that lead to forms of beta thalassemia (handout) and explain the effect of each mutation on gene transcription or mRNA translation 42. Define alternate splicing 43. Describe the relationship of codons to the encoding of amino acids and describe aspects of the genetic code - degenerate, non-overlapping, ordered, near universal, reading frame. 44. Become proficient in the use of a codon table including the start codon and stop codons. 45. Describe translation of mRNA including initiator codon (AUG), and elongation and termination (in brief) 46. Discuss translation including the reading frame, cloverleaf tRNA, anticodon, wobble, large and small ribosomal subunits UNIT 2 Mendelian and Cytogenetics Students will be able to: 1. Discuss the work of Gregor Mendel (Experiments in Plant Hybridization, 1865)
  7. 7. 7 2. Describe the utility of Pisum sativum in monohybrid and dihybrid genetic crosses 3. Describe the experiments by which Mendel developed the principles of: dominance, unit factors in pairs, random (equal) segregation, independent assortment 4. Terms and concepts: true breeding, 1st and 2nd filial generations, self fertilization, cross fertilization, genotype, phenotype, homozygous, heterozygous, dominant allele, recessive allele, gene, gene locus, reciprocal cross, gamete 5. Complete problems illustrating 1 and 2 factor (monohybrid, dihybrid, test) crosses 6. Calculate phenotypic and genotypic ratios using the Punnett square and the forked line methods (including trihybrid cross) 7. Utilize product and sum rules in calculating probabilities of genetic events 8. Employ binomial theory to determine probabilities of events (lab) 9. Utilize Chi Square analysis to determine goodness of fit of observed to predicted data (lab) 10. Recognize human pedigree symbols. Employ pedigree analysis to determine if a trait is inherited in an autosomal, recessive, dominant, sex-linked fashion. 11. Utilize a pedigree to determine the genotype of particular individuals and probability of passing on a particular allele to offspring 12. Review the concept of one gene: one enzyme and Garrod’s work on inborn errors of metabolism 13. Examine genetic based enzyme deficiencies in humans including PKU, albinism, alkaptonuria, and cystic fibrosis (chapter 4) 14. Examine autosomal dominant alleles for achondroplasia and polydactyly 15. Provide appropriate nomenclature for wild type and mutant alleles in Drosophila 16. Investigate sex linked gene inheritance in humans and discuss the mechanism of criss- cross inheritance. 17. Provide examples of X-linked genetic conditions 18. Complete problems illustrating sex-linked inheritance and explain why X-linked recessive traits are more often observed in males. 19. Describe limitations in using humans as genetic subjects 20. Solve problems illustrating incomplete dominance, codominance (MN blood group), and multiple alleles, (human ABO blood group system, C alleles for color in animals) 21. Examine the effect of recessive lethal alleles on expected phenotypic ratios 22. Examine gene interactions, epistasis, and effects on 9:3:3:1 ratio of a dihybrid cross. Complete series of problems 23. Define penetrance, expressivity, pleiotropy, multifactorial traits 24. Examine the effects of the environment on gene expression and phenotype (age on onset, sex, temperature and chemicals) 25. Describe the chromosomal theory of inheritance 26. Distinguish between autosomes and sex chromosomes 27. Compare sex determination systems for various animals 28. Examine sex determination in Drosophila, - females, males, and intersex flies. 29. Investigate sex determination in humans and role of tfm, TDF and the SRY. Explain the existence of XY females and XX males. 30. Analyze X chromosome inactivation using the following concepts: Barr body, dosage compensation, XIC, XIST gene (calico cat example of female mosaic). 31. Relate the number of Barr bodies to number of X chromosomes in a cell 32. Describe the cell-culturing technique of karyotyping. Review a karyotype to observe metacentric, submetacentric, acrocentric, telocentric chromosomes and p and q arms. 33. Define: euploidy, polyploidy, monoploidy, and aneuploidy, deletion, inversion, translocation, duplication 34. Explain why autosomal monosomy is lethal in humans excepting the partial monosomy, 46,5p- (Cri du Chat syndrome)
  8. 8. 8 35. Examine the relationship between gene duplication and the evolution of multigene families 36. Describe a position effect that may result from a chromosomal abnormality 37. Analyze the human aneuploid conditions 47, 21+, and 45, XO, 47 13+ and euploid conditions 46, XX and 46, XY 38. Explain how a Robertsonian translocation can result in familial Down Syndrome 39. Compare amniocentesis and CVS 40. Perform karyotype analysis of chromosomal aberrations (lab) 41. Describe the translocation that leads to the Philadelphia chromosome and CML cancer (lab) 42. Spot generalities concerning the numbers of spontaneously aborted fetus versus live births of aneuploid individuals (handout) UNIT 3 Bacterial Genetics and Recombinant DNA Students will be able to: 1. To compare genomes of mitochondria, H. influenzae, E. coli 2. To describe the E. coli chromosome, size of genome, and nucleoid region 3. To distinguish between a bacterial cell, colony, and lawn 4. To define binary fission 5. To compare bacterial lawns and colonies, solid and liquid cultures 6. To describe stages of bacterial growth-lag, log, stationary, death phases 7. To define: prototroph, auxotroph, minimal and complete media 8. To determine bacterial titer OMIT 9. To contrast nutritional, conditional, and resistance mutations in bacteria 10. To discuss the use of nutritional mutants (auxotrophs) in the study of bacterial conjugation 11. To describe parasexual mating (conjugation) between F+ and F- bacteria 12. To explain the F factor, what it encodes, and the mechanism of transfer from F+ to F- 13. Describe Hfr strains and interrupted mating technique in constructing the E. coli minute map, predict gene order and plasmid integration orientation based on time for gene transfer 14. To explain why recipient cells of an Hfr mating remain F-. 15. To define homologous recombination in a recipient, exconjugant 16. To examine the E. coli minute map and genomic map 17. To discuss the experiments of Lederberg in the discovery of transduction including the use of the U-tube and Salmonella/P22 virus system 18. To describe the mechanism of bacteriophage infection 19. To analyze the mechanism of bacterial recombination via faulty head stuffing in transduction 20. To contrast lysogenic and lytic infection, virulent and temperate phages 21. To contrast generalized and specialized transduction OMIT 22. To analyze the use of virally mediated gene therapy and to provide the example of ADA deficiency 23. To discuss problems in gene therapy 24. To explain the mechanism of transformation and view aspects of plasmids including ori, ampr, plasmid size, extrachromosomal maintained, and the multiple cloning sites for the insertion of foreign genes 25. To examine the pGLO plasmid, ori, ampr ,the GFP gene, and the portion of the arabinose promoter that allows for the regulation of gene expression of GFP by arabinose sugar 26. To transform competent E. coli with a GFP-containing plasmid (lab) 27. To calculate transformation efficiency (colonies/ug DNA) from given data (lab)
  9. 9. 9 28. To contrast constitutively expressed housekeeping genes and genes that are regulated 29. To describe an operon and the usefulness to prokaryotic cells 30. To define the term: polycistronic 31. To understand the regulation of the lac operon by lactose (inducer), repressor, promoter, RNA polymerase, and the structural genes Z,Y,A, beta galactosidase enzyme, operator. 32. To describe the use of lac operon mutants to elucidate control of operon expression in both the presence and the absence of lactose 33. To distinguish between cis and trans acting elements in the lac operon 34. To view examples of the use of GFP as a reporter gene 35. To review the steps of gene cloning using a plasmid and bacterium. Including isolation of DNA from the jellyfish, isolation of the GFP gene using restriction enzymes, ligating the GFP gene into a plasmid, transformation of E. coli with plasmid. 36. To examine the notion of cell “competency” for transformation 37. To understand that conjugation, transformation, and transduction are rare events UNIT 4 Mutation, Applications of DNA Technology, and Population Genetics Students will be able to: 1. Describe various DNA mutations, mechanisms, and effect on cellular function 2. Distinguish between somatic, gametic, random, spontaneous, base substitution, point, frameshift mutations 3. Examine mechanisms of proofreading and mismatch repair 4. View the effects of mutation in Drosophila and in humans 5. Detail the process involved in the creation of transgenic bacteria and provide an example of a human drug produced by recombinant bacteria 6. Examine the advantages of cloning genes for human proteins into bacteria 7. Delve into the process of genetically modified plants and their use in agriculture. Provide pros and cons of GM foods. 8. Examine patent law as it applies to genetically engineered organisms 9. Determine how to regulate tissue specific gene expression so that human proteins are expressed in sheep or goat milk. 10. Examine a variety of transgenic animals currently available for various uses including xenotransplantation, agriculture, models for human disease 11. Compare and contrast 3 types of cloning: gene, reproductive, and therapeutic 12. Review the steps involved in somatic cell nuclear transfer (SCNT) and describe the reason for each step 13. Discuss physiological problems often observed in cloned animals 14. Review the steps involved in the generation of embryonic stem cell lines 15. Discuss the ethical aspects of embryonic stem cell research 16. Define the terms: pluripotent, totipotent, and multipotent stem cell, blastocyst, inner cell mass, differentiation 17. Review the goals of the Human Genome Project 18. Read an autoradiogram of a DNA sequencing gel 19. Define: Genome, Transcriptome 20. Discuss the field of pharmacogenomics (handout), goals, problems, benefits, drug metabolism differences 21. Explore the use of association studies pharmacogenomics 22. Discuss some of the benefits of pharmacogenomics 23. Describe single nucleotide polymorphisms and their potential usefulness in medicine
  10. 10. 10 24. Relate SNPs to the diagnosis of genetic predispositions and to the cause of some genetic diseases 25. Review the differences people exhibit in drug absorption, metabolism, target receptors, side effects, transport, and excretion. 26. Examine Hardy Weinberg assumptions and affects of inbreeding, mating, assortive mating, selection, population size and migration 27. Compute genotypic and allelic frequencies in a student population and analyze with respect to Hardy Weinberg principles (lab) 28. Describe the use of Y chromosome markers (SNPs) in determining ancestry (film, handout) 29. Clone and express GFP gene in bacteria (lab) 30. Analyze and compare transition and transversion rate in mtDNA of H. sapiens, Neanderthal, and other primates (lab) .

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