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South Texas College, Math and Sciences Division

Biology Department BIOL 2416 Genetics Syllabus Fall 2012 Instructor: Office Location: Phone: Email: Course Name: Course Number: Dr. Javier Gonzalez-Ramos J 3-1114 956-872-2038 Genetics BIOL 2416 Section P01

Prerequisite: BIOL 1408, and CHEM 1411 and 1412 with minimum grade of C. Office Hours: M and W 11-01:00 PM. Other times may be scheduled by appointment Class Schedule: Course
Genetics Genetics

Section and Meeting Day

BIOL 2416.P01 BIOL 2416.P01 T R

Place and Meeting Time

10:00 AM-12:50 PM PCNJ 3-504 LAB 10:00 AM-12:50 PM PCNJ 1-412 LEC

Text: Griffiths et al. 2012. Introduction to Genetic Analysis, 10th ed., W.H. Freeman and Company. New York. Blackboard should be checked regularly for up dates and availability of course materials (lab protocols, reading assignments, reviews, etc.). Catalog Course Description: This is a study of the principles of molecular and classical genetics and the function and transmission of hereditary material. It includes population genetics and genetic engineering. Departmental Course Requirements, Evaluation Methods, and Grading Criteria: Total points 600
Lecture Exams Laboratory Notebook Laboratory Reports Lab Portfolio (Best 4) Oral Presentation 4 x 100 points each 1 x 100 points each 6 x 17 points each 1 x 25 points 1 x 25 points 400 points (67%) 100 points (17%) 100 points (17%) 25 points (4.2%) 25 points (4.2%) A 90% (540-600) B = 80% (480-539) C = 70% (420-479) D = 60% (360-419) F 60% ( 360)

Grading: There are no + or grades given at STC, so the final calculated grades will be recorded as <60 = F; 60 - 69 = D; 70 79 = C; 80 89 = B; 90 100 = A. 1


DATE Week 1 Aug 27 Sept 1 st 1 Day Aug. 27 Week 2 Sept 3 Sept 8 Sept 3rd - Labor Day (no class) Week 3 Sept 10 - Sept 15 Sept 12th - Census Day Week 4 Sept 17 Sept 22 Sept 21 (PD - no classes) Week 5 Sept 24 Sept 29 Week 6 Oct 1 Oct 6 Week 7 Oct 8 Oct 13 Week 8 Oct 15 Oct 20 Week 9 Oct 22 Oct 27 Week 10 Oct 29 Nov 3 Week 11 Nov 5 Nov 10

Lecture Reading Assignments*

Chapter 1. The genetic approach to biology Chapter 2. Single-gene inheritance (Intragenic interaction) Chapter 3. Independent assortment of genes (Interallelic interaction) Chapter 4. Mapping chromosomes by recombination (Linkage) Exam 1 (Chapters 1-3) Chapter 6. Gene interaction (Epistasis) Chapter 5. The genetics of bacteria and their viruses Chapter 7. DNA: structure and replication Exam 2 (Chapters 4-6) Chapter 8. RNA: transcription and processing Chapter 9. Proteins and their synthesis Chapter 14. Genomes and genomics Chapter 10. Gene isolation and manipulation Exam 3 (Chapters 7-9) Chapter 15. The dynamic genome (Transposons) Chapter 16. Mutation, repair, and recombination Chapter 11. Regulation of gene expression in bacteria and their viruses (Sel. pp.) Chapter 12. Regulation of gene expression in eukaryotes (Sel. pp.) Chapter 17. Large-scale chromosomal changes (Sel. pp.) Chapter 13. The genetic control of development (Sel. pp.) Chapter 18. Population genetics (Sel. pp.)

Lab Investigations Reading Assignments*

Lab Safety. The Scientific Method and the Writing of a Scientific Report Lab 1: Measurements and the Normal Distribution Probability Concepts: the 2 test Lab 2: Sampling error in populations Lab 1 Report is due Lab 3: Transmission genetics. Segregation of kernel traits in ears of corn ( 2 test) Lab 2 Report is due. Lab 4: Transmission genetics. Monohybrid and dihybrid corn crosses. Planting crosses Lab 3 Report is due. Lab 4: Continuation. Data Collection and test Lab 5: Linkage analysis. Sordaria fimicola Lab 4 Report is due Lab 6: Agarose Gel Electrophoresis with small molecules (dyes) Lab 7: Overnight bacteria culture Lab 6 Report is due Lab 12: Genome sequence detection in soybean and/or Phage: Soybean planting Lab 8: Isolation of plasmid DNA (miniprep) Lab 9: Banana DNA Extraction Lab 8 and 9. Continuation. (DNA yield determination by electrophoresis) Lab 10: Plasmid and Phage Restriction Mapping Lab 10: RFLP analysis by electrophoresis Lab 11: Transformation, and Expression of the -galactosidase and/or GFP proteins in bacteria Lab 12: Extraction of genomic DNA from soybean Labs 7-9 Report due

Nov 16th

Week 12 Nov 12 17 - Deadline to Withdraw

Week 13 Nov 19 24 Nov 22 25th Thanksgiving (no classes) Week 14 Nov 26 Dec 1 Week 15 Dec 3 Dec 8 Week 16 Dec 10 Dec 15

Chapter 19. The inheritance of complex traits (Sel. pp.)

Lab 11. Continuation Lab 12. Soybean and/or Phage gene sequence amplified by PCR Lab 10 Report due Oral Presentation: Review of an Important Lab 12. Continuation. Electrophoresis of genetics topic soybean and/or Phage amplified genes by Lab Portfolio, and Lab Notebook due PCR

Final Exam (Comprehensive) Dec. 10-15

* Assignment-SYN. TASK 1 a piece of work assigned to or demanded of a person 2 any piece of work 3 an undertaking involving labor or difficulty (Websters New World College Dictionary, 4th ed.)

Lab Work: Labs follow the scientific method logic. Labs are done by teams of 4 1 students where setting hypotheses and collecting data is very important. Lab reports are individually reported and turned in by the due date. To qualify for the lab portfolio all lab reports must be turned in by the due date. The titles and topics for oral presentations must be turned in for approval the week of November 12-16. Teams of 5 students can participate in oral presentations on a previously selected and approved genetics topic. Students are encouraged to study in groups, however each student is responsible for turning in their own assignments. Exams: No makeup exams are given. Please remember that the syllabus is a tentative schedule and sometimes exams may fall on a different day than originally scheduled. The exams will cover material from class as well as reading assignments. Attendance is imperative to receiving all pertinent information as to change of scheduling. If a student leaves the room during an exam, the exam is considered to be finished. Attendance. Regular attendance is strongly recommended. This is the single most important predictive factor for success; those students who regularly come to class succeed at a much higher rate than those with irregular attendance. Also, tests are given over material discussed in class. History has shown that for every class that is missed, the test grade goes down by about 10%. However, we all have lives outside STC so sometimes things come up. If you know you will not be in class, please let me know. You will be responsible for completing any activities done that day and for getting class notes from a classmate. Cell Phones and Pagers: These should be turned off before entering the classroom. Do NOT set on vibrate; do NOT leave the room to answer your phone; do NOT make phone calls during class or lab. Repeat offenders will be docked 10 points on their next test. Exceptions will be made in an emergency; please see me before class if you absolutely must be available by phone. Questions and Discussions: Everyone learns better when there is mutual respect. Each person is encouraged to ask questions on the content or related subjects. There are no stupid questions. The same is true for lecture and lab discussions. Every student deserves to express his or her own opinions without interference. Program Learning Outcomes Biology 1. All laboratory science courses include use of the scientific method, data analysis, and biological research. All students have laboratory experience. 2. All courses involve research and evaluation of the scientific literature and students are able to communicate and analyze these findings. 3. The student will be a literate student of science and be able to discriminate between the biological disciplines.

4. The student will be able to participate in civic activities that are concerned with health, wellness of the community and environment, and to improve knowledge and evaluate the basic biological concepts. 5. The student will be able to participate and/or lead in civic activities &/or critical issue affecting the community and environment. Course Learning Outcomes 1. To understand the connections between the fundamental principles that underlines classical and molecular genetics. 2. Distinguish between mitosis and meiosis and explain the fundamental role of meiosis during segregation and independent assortment. 3. To understand and apply the laws of probability and the Chi-square test to determine outcomes of specific genetic crosses. 4. To explain the chromosomal basis of sex determination and apply that understanding to predict the sex of individuals with normal and abnormal complements of sex chromosomes. 5. To describe and understand the mechanisms that control genetic recombination of linked and independent genes. 6. To describe and explain multiple alleles, multiple loci, multiple effects of a single, sexinfluenced characteristics, incomplete dominance and co-dominance predicting their modes of inheritance. 7. To analyze and use pedigrees to display and understand the pattern and predictions of single gene Mendelian inheritance. 8. To describe and understand the structure and function of DNA and RNA, their "subunits" and how they differ. 9. To describe how DNA is duplicated, how DNA is transcribed into RNA and how RNA is translated into proteins. 10. To understand the Genetic Code and how to translate a nucleic acid sequence into an amino acid sequence. 11. To describe and analyze quantitative traits using quantitative genetic analysis, as well as population genetic variation using the Hardy-Weinberg equilibrium analysis. 12. To define and make connections between the basic methods used in gene isolation and generation of recombinant DNA molecules; interpret the results of restriction enzyme analyses and polymerase chain reaction assays; relate these techniques to specific current applications of transgenic technology and functional genomics. Core Course Objectives: 1. Examine the fundamental principles that underline classical and molecular genetics. 2. Describe the structure of prokaryotic and eukaryotic genes, and relate aspects of gene structure to gene expression and protein synthesis. 3. Investigate mechanisms of gene expression and regulation. 4. Describe the basic mechanisms of genetic engineering, and the uses and impacts of this technology. 5. Examine the impact of genetic variation on evolution of populations and species.

6. Describe the relationship between genotype and phenotype; recognize different patterns of phenotypic variation. 7. Apply the laws of probability and the Chi-square test to determine outcomes of specific genetic crosses. 8. Summarize the basis of autosomal inheritance, sex-linked inheritance, and cytoplasmic inheritance; give specific examples of different types of inherited diseases and describe their genetic basis. 9. Describe overall chromosome structure, how genes are arranged on chromosomes, how chromosomes are partitioned into cells during mitosis and meiosis, and the effects of aneuploidy. 10. Explain the different stages in the cell cycle, and the behavior of the chromosomes at each stage; describe the mechanisms that govern genetic recombination and regulation of the cell cycle. 11. Summarize the history of gene mapping, and the key experiments and techniques involve, relate this to current molecular mechanisms for gene mapping. 12. Compare and contrast genome arrangement and function in prokaryotic and eukaryotic cells; describe mechanisms of genetic variation and genome mapping in bacterial cells. 13. Explain the interactions that occur between the alleles of one gene, between genes and proteins, and illustrate these concepts with specific examples 14. Describe the chemical and physical structure of DNA molecules; compare and contrast this with RNA molecules 15. Detail the steps and enzymes involved in accurate replication of DNA 16. Explain the mechanism of transcription in prokaryotic and eukaryotic cells; describe the role of promoters, terminators, enhancers, silencers, introns, exons, and catalytic RNA 17. Summarize mechanism of regulation of gene transcription, and give specific examples of regulated systems in prokaryotic and eukaryotic cells 18. Relate chromosome structure and chromatin remodeling to different levels of gene expression 19. Define the basic methods used in gene isolation and generation of recombinant DNA molecules; interpret the results of restriction enzyme analyses and polymerase chain reaction assays; relate these techniques to specific current applications of DNA technology and functional genomics 20. Explain the role of mutations in genetic variation, and describe the actions of specific mutagenic agents, the types of mutations generated, and repair systems in cells 21. Detail the mechanisms by which large-scale changes in chromosome number can occur, and give examples of the results of these processes in living cells 22. Relate genetic variation to differences in natural populations; describe the processes that cause changes in genetic variation at the population level 23. Transmission genetics analysis 24. Relationship between DNA and phenotype 25. Genome structure and engineering 26. Mutation and large-scale chromosomal changes 27. Gene function and regulation

28. The effect of genetic variation on evolution of populations Exemplary Educational Objectives 1. To understand and apply method and appropriate technology to the study of natural sciences. 2. To recognize scientific and quantitative methods and differences between these approaches and other methods of inquiry and to communicate findings, analyses, and interpretation both oral and in writing. 3. To identify and recognize the differences among competing scientific theories. 4. To demonstrate knowledge of the major issues and problems facing modern science, including issues that touch upon ethics, values, and public policies. 5. To demonstrate knowledge of the interdependence of science and technology and their Influence on, and contribution to, modern culture. Departmental Course Intellectual Competencies Reading: Students will read, analyze and interpret the chapters in the text and lab manual covered in class as well as assigned journal articles and master both general methods of analyzing printed materials and specific methods for analyzing the subject matter of individual disciplines. Writing: Students will produce clear, correct and coherent prose adapted to purpose, occasion and audience. Students will discover a topic and develop and organize it and phrase it effectively for their audience through practice and reflection. Computer Literacy: Students will use computer-based technology in communicating, solving problems, and acquiring information. Students should have an understanding of the limits, problems, and possibilities associated with the use of technology, and should have the tools necessary to evaluate and learn new technologies as they become available. Speaking: Students will use clear, coherent, and persuasive language when speaking, using language appropriate to purpose, occasion, and audience. Students will acquire pose and develop control of the language through experience in making presentations to small groups, to large groups, and through the media. Listening: Students will analyze and interpret various forms of spoken communication. Critical Thinking: Students will embrace methods for applying both qualitative and quantitative skills analytically and creatively to subject matter in order to evaluate arguments and to construct alternatives strategies. Students will do problem solving as one of the applications of critical thinking, used to address an identified task. Departmental Course Perspectives: Recognize the importance of maintaining health and wellness.

Develop personal values for ethical behavior. Integrate knowledge and understand the interrelationships of the scholarly disciplines. Developmental Studies Policy: The Colleges Developmental Education Plan requires students who have not met the college-level placement standard on an approved assessment instrument in reading, writing and/or mathematics to enroll in Developmental Studies courses including College Success. Failure to attend these required classes may result in the students withdrawal from ALL college courses Statement if Equal Opportunity: No person shall be excluded from participation in, denied the benefits of, or be subject to discrimination under any program or activity sponsored or conducted by South Texas College on the basis of race, color, national origin, religion, sex, age, veteran status or disability. Alternative Format Statement: This document is available in an alternative format upon request by calling (956) 8722023.

ADA Students with Disabilities Statement: Reasonable accommodations may be made that allow disabled students to be successful at STC. Accommodations may be provided for those students who submit the appropriate documentation by an outside/independent professional evaluator or agency. Contact an STCC ADA/DSS Counselor in the Annex (Pecan) or call (956) 688-2006. Students may volunteer to inform the Instructor about their disability and associated classroom limitations, if applicable