BIOLOGY 2030 / BIOL 2035 CLASS OUTLINE [Introductory Genetics and Lab]

Autumn 2008

Joseph M. Papenfuss, PhD and Kevin N. Sorensen, PhD

CATALOG COURSE DESCRIPTION

This course introduces transmission, population and quantitative genetics incorporating both molecular and classical aspects of genetic studies.

The laboratory component allows for student application of the above principles with an emphasis on investigative learning and collaboration.

Prerequisites: MATH 1040 or higher and any BIOL core class (ie BIOL 1610, BIOL 1010, etc) or instructor permission

Co-requisites: Both the lecture BIOL 2030 and the lab BIOL 2035 must be taken concurrently.

COURSE JUSTIFICATION

The Introductory Genetics lecture course (BIOL 2030) and laboratory (BIOL 2035) are part of the biology majors lower division core. These courses are taught at every institution except Utah Valley State College. At Weber State University and Utah State University, the courses are ZOOL 3300 and BIOL 3200, respectively. Our students receive credit for the Utah State University lecture course and for the lab course BIOL 4100. The University of Utah has only the lecture course BIOL 2030. Some of the institutions have not yet changed the course designations and numbers. In order for Snow College students to transfer as juniors on track in their majors programs to these institutions, genetics should be offered. The laboratory component of this course (BIOL 2035) is to give additional learning opportunities to our students so that they should be well-prepared to transfer to the four-year institutions. "Labs for learning" is a hallmark of Snow College.

COURSE OBJECTIVES

The course objectives are to understand basic gene function in prokaryotes and eukaryotes, fission and mitosis, recombination in viruses and bacteria and in eukaryotes (meiosis and molecular techniques), mechanisms of inheritance and gene expression in both individuals and populations. Homework will emphasize story problems and applications often requiring simple statistical analyses to augment comprehension of key genetics concepts. Labs will complement learning by providing preserved and living specimens, slides, and hands-on demonstration materials and experiments for study. Students should gain increased understanding and problem-solving skills that will be beneficial in their continuing studies. Also, students should have a basic foundation upon which to evaluate critical issues surrounding “genetic engineering” and the Human Genome Project.

Outcomes

Students will understand basic gene function in prokaryotes and eukaryotes, cell division processes of fission and mitosis, recombination in viruses and bacteria and in eukaryotes (meiosis and molecular techniques), and how these relate to mechanisms of inheritance and gene expression in both individuals and populations.

Students will begin to understand how mathematical models and simple statistics are used in applying the scientific method to basic concepts in genetics.

Students will be introduced to current computer programs for genetic manipulation and genome analysis as well as some laboratory instrumentation including microscopes, computers, thermocyclers, microcentrifuges, laminar flow hoods, safety cabinets, etc., and to aseptic technique and other laboratory procedures for manipulating genetic material.

Students will have a basic understanding from which to evaluate critical issues surrounding "genetic engineering" and the Human Genome Project.

COURSE CONTENTS (BIOL 2030)

nature of the hereditary material

DNA structure

DNA replication in prokaryotes; contrast eukaryote replication

prokaryote / eukaryote genes

RNA transcription

repressible lac operon and inducible trp operon regulation

post-transcriptional processing

genetic code

translation or protein synthesis

post-translational processing

colinearity of genes and polypeptides

mutations -- point, frameshift, small deletions and duplications, insertion

deletion mapping

enzymes and cell metabolism

DNA and RNA manipulations: restriction digests, Southern blot, Northern blot, PCR primer analysis, plasmid preparation, transformation, isolation and purification, etc.

applications of laboratory techniques to genetic analysis

chromosome structure and morphology (pro- / eukaryote)

binary fission

mitosis

meiosis

contrast mitosis and meiosis

Mendel’s laws of dominance, segregation, independent assortment

relate meiosis to segregation and independent assortment

introduce probability concepts

Punnett Square, forking or foiling methods for gametic and zygotic ratios

genotypes / phenotypes

Chi squares goodness of fit statistical testing

binomial and Poisson distributions in statistical analyses

penetrance / expressivity

partial or incomplete dominance, multiple alleles, codominance, lethals

quantitative traits introduced

pleiotrophy

epistasis -- distinct patterns

linkage or non-independence of genes

chiasmata and meiotic recombination

linkage groups

two- and three-point mapping

interference

random spore and tetrad analyses

map distance versus physical distance

unequal crossing-over and dosage effects

nondisjunction and aneuploidy

polyploidy

chromosomal aberrations -- inversions, translocations, deletions, duplications

genetic variation

Hardy-Weinberg equilibrium and assumptions:

mutation, selection, migration, genetic drift (bottle-neck, founder effect)

selection-mutation balance

inbreeding and inbreeding coefficient

phenotypic assortative mating

natural selection

heterozygote advantage

cytoplasmic inheritance / maternal effect

artificial selection (plant and animal breeding)

inbred lines, heterosis, estimating genetic and environmental variances

heritability

pesticide / pest resistance

"genetic engineering"

Human Genome and other projects

LAB CONTENTS (BIOL 2035)

1. mitosis (Allium, whitefish)

2. meiosis (Zea, [Lilium, Ascaris])

3. autosomal dihybrid F2 and testcross ratios (Zea)

4. epistatic ratios (Zea)

5. restrict pUC and lambda; mix and ligate

6. bacterial transformation and lac operon expression (E. coli)

7. plasmid extraction

8. PCR and e-gel electrophoresis

9. DNA fingerprinting

10. X-linkage (Drosophila)

11. nondisjunction and aneuploidy, chromosomal mutations (human syndromes)

12. two- and three-point mapping (Drosophila, Zea)

13. tetrad analysis (Sordaria)

14. Hardy-Weinberg equilibrium (Sorghum) ?

REQUIRED TEXTS and / or MATERIALS

David R. Hyde (2009) Introduction to Genetic Principles. McGraw-Hill Higher Education Boston

Joseph M. Papenfuss and Kevin N. Sorensen (2008) Laboratory Manual for BIOL 2035

General Education Outcomes

1. Read effectively, constructively, and critically.

Take-home, open-book, open-notes tests challenge the student's ability to obtain the necessary knowledge in order evaluate genetics problems in the light of synthetic and critical thinking processes.

2. Write clearly, informatively, and persuasively.

Student written responses, both answers and problem-solving approaches, to the take-home tests noted above will be evaluated for clarity and appropriate brevity, and for accuracy.

3. Retrieve, evaluate, interpret, and deliver information through a variety of traditional and electronic media.

Students will complete one major laboratory project which will require the use of traditional and electronic media. Homework and tests often require additional research as well.

7. Apply scientific reasoning to a variety of contexts.

Students will demonstrate scientific reasoning throughout the various topics considered in course content in their responses to tests, homework, projects, discussions, etc.

EVALUATION OF STUDENT PERFORMANCE

Students are more effective in the learning process if they read the material before lecture or lab, and then review notes and materials after class. Depending on individual preparation and quality of effort, usually two hours of study are required for every hour in class to earn an "A" grade.

BIOL 2030

two 150-point lecture tests

one comprehensive departmental final exam worth 150 points

twenty homework assignments worth 100 points total

50 discretionary points for participation in lecture and homework solutions on black/whiteboard

BIOL 2035

eleven 50-point labs including quizzes and/or write-ups

50 discretionary points for preparedness and participation in labs

There will be no make-up for any test or lab without prior arrangement !!! Some labs cannot be made up!!

Students with medical, psychological, learning or other disabilities desiring accommodations, academic adjustments, or auxiliary aids will need to contact the Accessibility Resource Center, room 211 Greenwood Center, phone number (435) 283-7321.  The Americans With Disabilities Act (ADA) Coordinator at the Accessibility Resource Center (ACR) determines eligibility for and authorizes the provision of appropriate services and aids.

An A or 4.0 is earned with 92% of the total points counted. Cheating results in an F for the item in question and with a grade of 0.0 for the course in the event cheating occurs a second time.

The grades are now letter grades and correspond to numerical and percentage grades in the following table.

A	4.0	92%	C	2.0	72%
A -	3.7	89%	C-	1.7	69%
B +	3.3	85%	D +	1.3	65%
B	3.0	82%	D	1.0	62%
B -	2.7	79%	D -	0.7	59%
C +	2.3	75%	F	0.0	< 59%

A reading schedule follows below.

MONDAY	TUESDAY	Wednesday	THURSDAY	FRIDAY
		8/20	8/21 Chpts 1 Introduction and Chpt 3 Mitosis and Meiosis	8/22 Chpt 3 cont.
8/25 Chpt 2 Mendelian Genetics	8/26 Chpt 2 cont. Last day to pay tuition and fees.	8/27	8/28 Chpt 2 cont.	8/29 Lab 1 Mitosis
9/1 LABOR DAY	9/2 Chpt 5 Modifications to Mendelian Patterns of Inheritance	9/3	9/4 Chpt 5 cont.	9/5 Lab 2 Meiosis
9/8 Chpt 5 cont.	9/9 Chpt 5 cont. and Chpt 4 Sex Linkage and Pedigree Analysis	9/10	9/11 Chpt 4 cont. Last day to add/drop classes without fee or a "W".	9/12 Lab 3 Autosomal Dihybrid F2 and TC Inheritance
9/15 Chpt 4 cont.	9/16 Chpt 6 Linkage and Mapping in Eukaryotes	9/17	9/18 Chpt 6 cont.	9/19 Lab 4 Epistasis
9/22 Chpt 6 cont.	9/23 Chpt 6 cont.	9/24	9/25 Chpt 7 Molecular Basis of Inheritance and Gene Expression	9/26 Lab 5 Two and Three-point Mapping
9/29 Chpt 7 cont.	9/30 Chpt 12 Recombinant DNA Technology	10/1	10/2 Chpt 12 cont.	10/3 Lab 6 Tetrad Analysis
10/6 Chpt 13 Application of Recombinant DNA Technology	10/7 Chpt 13 cont.	10/8	10/9 Chpt 13 cont.	10/10 Lab 9 Restrict pUC18 and l
10/13 Chpt 9 DNA Replication	10/14 Chpt 10 Gene Expression: Transcription	10/15	10/16 Fall Vacation	10/17 Fall Vacation
10/20 Chpt 10 cont.	10/21 Chpt 11 Gene Expression: Translation	10/22	10/23 Chpt 11 cont.	10/24 Lab 9 cont. Ligation and Transformation
10/27 Chpt 15 Genetics of Bacteria and Bacteriophages	10/28 Chpt 15 cont. and Chpt 16 Gene Expression: Control in Bacteria and Phages	10/29	10/30 Chpt 16 cont. Final Day to add or drop classes.	10/31 Lab 9 cont. Plasmid Extraction, Restriction, PCR and DNA gel electrophoresis
11/3 Chpt 14 Genomics and Bioinformatics	11/4 Chpt 17 Gene Expression: Control in Eukaryotes	11/5	11/6 Guest lecturer sometime this week?	11/7 Lab 8 DNAStar Genome Analysis
11/10 Chpt 17 cont.	11/11 Chpt 18 DNA Mutation, Repair, and Transposition	11/12	11/13 Chpt 18 cont.	11/14 Lab 9 cont. VNTR and DNA Fingerprinting
MONDAY	TUESDAY	Wednesday	THURSDAY	FRIDAY
11/17 Chpt 19 Extranuclear Inheritance	11/18 Chpt 19 cont.	11/19	11/20 Chpt 8 Changes in Chromosome Structure and Number	11/21 Lab 10 VNTR and DNA Fingerprinting
11/24 Chpt 8 cont.	11/25 Chpt 23 Population genetics	11/26 Thanks-giving Break	11/27 Thanksgiving Holiday Chpt 26 Genetics and Evolution	11/28 Thanksgiving Break Chpt 24 cont. and finish up on molecular genetics labs
12/1 Chpt 23 cont.	12/2 Chpt 23 cont	12/3	12/4 Chpt 24 Quantitative Genetics	12/5 Chpt 24 cont.
12/8 Chpt 25 Evolutionary Genetics	12/9 Final Exam 12:00 to 2:00 PM moved to Friday	12/10	12/11	12/12