Genetics Syllabus

Biology Dept.

DePauw University
Instructor: Fornari

BIO 320

Genetics

Lecture-MWF 1:30-2:35pm Olin 123
Lab-Th 10:00-11:50am Olin 205
Instructor: Chet Fornari
Olin 232, x4781; e-mail: cfornari

Click here for all registration info

Course Objectives
Topics with Chapter References
and Problem Sets
Words to the Wise
Study Groups
BIO 320 Computer Lab
Links to Genetics Site

Text: Griffiths et. al., W.H. Freeman
Prerequisites: BIO 215

In his book, Awareness, Anthony DeMello says: "Can one be fully human without experiencing tragedy? The only tragedy there is in the world is ignorance; all evil comes from that. The only tragedy there is in the world is unwakefulness and unawareness."

"Some biological disciplines relate to everything that concerns living organisms. This is certainly true for Genetics. The genetic program is the underlying factor of everything organisms do. It plays a decisive role in laying down the structure of an organism, its development, its functions, or activities."

p.123 of This is Biology by Ernst Mayr in a section of the book where he is trying to assign priorities to all the various sub-disciplines of biology.

"I'm trying to free your mind; I can only show you the door. You have to walk through it." Morpheus speaking to Neo in the movie, Matrix.

Course Objectives:
To achieve a basic understanding of four major areas:

I. Molecular Genetics, or the structure, function and regulation of genes in both procaryotes and eucaryotes, as conceptualized in the so-called "Central Dogma" of molecular biology: DNA>DNA>RNA>PROTEIN. Watson, J.D., and Crick, F.H.C. (1953). Genetical implications of the structure of deoxyribonucleic acid. Nature 171:964-969

II. Mendelian/transmission Genetics, or the principles and mechanisms of the inheritance of traits and genes in individuals from one generation to the next. Mendel, Gregor. "Versuche über Pflanzen-Hybriden." Verhandlungen des Naturforschenden Vereines, Abhandlungen, Brünn 4, pp. 3-47 (1866).

III. Genetic Engineering and Recombinant DNA Technology, or the stunningly powerful technology that emerged from a sound theoretical understanding of bacterial genetics and basic cell functions such as DNA replication.

IV. Population and Quantitative Genetics, or the genetic "structure" of populations and how genes change in time, a concept which naturally leads to a consideration of heritability, evolution and other explanations for genetic variation, adaptation, and diversity. Darwin, C. and Wallace, A. (1859). On the tendency of species to form varieties; and on the perpetuation of varieties and species by means of natural selection. J. Linn. Soc. Lond. (Zool.)3:45-62
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Darwin, C. (1860). On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. New York: Appleton

We will attempt to examine these areas of genetics from the perspective of the experimental and historical geneticist so that we can see the relationship between procedures and methods and the development of ideas, hypotheses, concepts and theories, i.e. the processes and products of science. A primary focus of the course is to show how molecular genetics serves to explain many areas of genetics (including Mendelian genetics) and so provides a firmer conceptual basis for all of genetics.
These activities are of course predicated upon the application of a scientific method, a way of thinking and solving problems which includes observation, induction, hypothesis and model building, dedcuction, experimental design, and data interpretation. Biological problems are often approached with the assumption that the structure, function, organization, and evolution of macromolecules is responsible for, or "causes" observable phenotypes of morphology and behavior. This theme will be vigorously pursued and examined in this course, and so forms one of its main concepts.
In order to better acquaint you with these essential concepts, I will assign problem sets on a regular basis (see later section for a fuller discussion of these problem sets). Very unfortunately because of time constraints it is often not possible to trace both the historical development and the full experiments behind some interesting concept or principle; in these cases we will examine and interpret only the data/results of these combined processes and emphasize the main concepts.

V. Other COURSE OBJECTIVES: 1.) to acquire a sharpened "feel" for the Scientific Method in general (the process of doing science), and in particular for how new knowledge is gained in Genetics through hypothesis-building (creation of models) and the testing of these hypotheses/models by experimentation to yield data for critical analyses (the products of science).
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2.) to increase your understanding of all biological phenomena and associated concepts; biology is best (only) understood within a genetic/evolutionary framework.
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3.) to gain a clearer vision of the important concepts and principles in biology so that you can see beneath the large mass of descriptive information and uncover the truly beautiful "picture" lurking within an amazing diversity of form and function.
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4.) to gain a better understanding of yourself, your own life (you are more unique than you imagine), the lives of all creatures, and your role in the complex interactions of the biosphere; to develop a deeper appreciation and respect for all living organisms.

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Specific topics, with Chapter references:

Please Note: At the beginning of each lecture, I will indicate on the board the exact topics for discussion and the text pages (as outlined directly below) referring to those topics. Keep close track of these topics and assigned text readings for organizing your daily study efforts.

PART I - The Molecular Structure and Function of Genes and Genomes

Ch.2	The Structure of Genes and Genomes (# lectures) p. 18-21 Deducing the Nature of Genes (Genetics in Process 1-2) p. 24-30: DNA structure p. 30-33: introduction to gene structure p. 33-39: fundamental genome structure in a variety of organism types p. 39-48: chromosome structure in eukaryotes Problems: 3, 4, 6-9, 12-14, 16-18, 20-26 Extra Problems: (see network-site handout)
Ch.3	Gene Function (# lectures) p. 52-54: RNA structure p. 54-59: Transcription p. 59-61: RNA processing p. 61-64: Review of protein structure p. 64-68: Translation and the Genetic Code p. 68-72: Review of protein function and Biochemical pathways p. 74-80: Genetic diseases and protein malfunction Problems: 1-4, 6-9, 11-13, 15-17 Extra Problems: (see network-site handout)

PART II - The Inheritance, Recombination, and Interaction of Genes

Ch.4	The Inheritance of Genes (5 lectures) p. 86-91: Biophysics and Biochemistry of DNA Replication p. 91-96: Cell Division and Mitosis, or asexual cell division p. 96-101: Cell Division and Meiosis, or sexual cell division p. 101-110: The Inheritance Patterns of Genes, or Mendelian (Transmission) Genetics p. 111-118: Human Pedigrees and Inheritance Patterns for genetic diseases Problems: 1-4, 5-9, 10-13, 15, 16, 19-21, 23, 25, 28 Extra Problems: (see network-site handout)
Ch.5	The Recombination of Genes (2 lectures) p. 130-137: generating genetic variation by Independent Assortment p. 137-139: generating genetic variation by Crossing Over p. 140-147: generating Linkage Maps by analyzing cross-over frequencies p. 147-150: Chi-square tests Problems: 1-5, 7, 8, 12-15, 17, 18, 20, 23-27, 28, 29 Extra Problems: (see network-site handout)
Ch.6	The Interaction of Genes (3 lectures) p. 166-170: relationship of genotype to phenotype: complementation test p. 170-174: relationship of genotype to phenotype: variation in dominance patterns p. 174-178: relationship of genotype to phenotype: altered dihybrid ratios p. 178-182: examples of gene interactions to produce variation in coat color p. 182-183: penetrance and expressivity Problems: 1-10; 12-15; 17-21; 24--26; 27-32

PART III - Mutations

Ch.7	Gene Mutations (2 lectures) p. 198-202: defining gene mutations and the molecular basis for such mutations p. 209-210: The Luria-Delbruck fluctuation test p. 221-228: from a molecular analysis to understanding the roles of mutations in biochemical, cellular, and developmental pathways Problems: 1-3; 7, 8, 16, 23
Ch.8	Chromosome Mutations p. : p. : Problems:

PART IV - The Genetics of Bacteria & Phages, and Genetic Engineering

Ch.9

The Genetics of Bacteria and Phages (# lectures)
p. 272-274: 3 Gene transfer modes in bacteria; some basic microbiology.
p. 274-277: the biology of F-plasmids, and the conjugation process.
p. 277-280: the genetics of conjugation; recombination and mapping
p. 282: F’ factors (f-prime factors)
p. 282-283: transformation
p. 283-285: phage infection of bacteria; lysis and lysogeny
p. 286-289: lysogeny, integration, generalized & specialized transduction
p. 290-291: Review of Gene Transfer in Bacteria
Problems: 1-4; 6, 8-10; 14-16; 22

Ch.10

Recombinant DNA Technology (# lectures)
p. 300-306: What is Recombinant DNA? Defining the general strategies and tactics of cloning DNA; Restriction enzyme technology
p. 307-312: Cloning a Specific Gene; vector choice and "library" type

p. 312-316: Screening Gene Libraries by using Probes
p. 316-318: Screening Gene Libraries by Functional Complementation
p. 318-320: Positional Cloning vs. Classical Cloning
p. 320-323: Southerns, Northerns, Westerns
p. 323-326: DNA Sequencing and Polymerase Chain Reaction
p. 327-331: Restriction Enzyme site mapping
Problems: 1-6; 9, 10, 17, 19, 20, 22

Ch.11

Applications of Recombinant DNA Technology (# lectures)
p. 342-346: RFLP's and Reverse Genetics
Problems: solved problem #1; 14

Part V - Gene Regulation, Theory and Applications

Ch.14	Regulation of Gene Expression (Prokaryotes) (# lectures) p. 434-436: Gene Regulation in Prokaryotes, structural considerations p. 436-439: The Lactose Operon, functional considerations p. 439-442: Genetics of the Lac Operon p. 443-446: Summary of the Lac Operon p. 446-448: The Arabinose and Trp Operons Regulation of Gene Expression (Eukaryotes) (# lectures) p. 448-451: Overview and Structure, Function, and Organization of Transcription Initiation p. 451-453: Tissue-specific Regulation of Transcription. p. 456-459: Steroid Hormones and Gene Expression. Problems: 1, 2, 4, 7-11
Ch.15	Regulation of Cell Number: Normal and Cancer Cells p. : p. : Problems:
Ch.16	The Genetic Basis of Development p. : p. : Problems:

PART VI - Population/Evolution Genetics

Ch.17

Population and Evolutionary Genetics (# lectures)
p. 536-537: Basic Principles of Evolution and Population Genetics
p. 537-541: Variation and its measurements; allele frequencies, heterozygosity, polymorphisms of various types

p. 541-542: DNA Sequence Polymorhisms

p. 542-544: Summary of Variation and its application to Human Populations

p. 544-546: The Hardy-Weinberg Law

p. 546-549: basic Sources of Variation: mutation, recombination, and migration
Problems: solved problems; 1-7; 17,18

Ch.18

Quantitative Genetics
p. :
p. :
Problems:

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Grades will be based on the following (subject to change with prior notice):
4 in-class tests and 1 test equivalent from lab work and reports: 4 in-class tests cover about 9 lectures each; one test-equivalent grade will be assigned to each lab/study group for that group's work and lab reports.
(test dates: Sept. 21st, Oct. 19th, Nov. 16th, Dec. 15th at 8:30am)
Grading Scale

Office Hours for discussing course-related issues with me:
Always contact me by e-mail to arrange a mutually compatible time for a meeting. I check my e-mail often enough to arrange a meeting within one or two days. In your e-mail briefly state the problem and propose a time for our meeting. Sometimes we can resolve problems or questions by an e-mail exchange only, so contact me anytime with concerns or questions.
cfornari@depauw.edu

*A Word to the Wise*: The study of Genetics can often be a particularly troublesome endeavor; an anxious struggle, in other words. Some of the most fundamental genetic concepts are difficult to grasp and it often takes much longer than you expected to become thoroughly comfortable and confident with these concepts. In order to do well in the course, you will need to achieve a certain, minimum level of understanding and to develop competence in applying concepts to the solution of problems. One certain way to achieve these goals is to study regularly and keep up with the material. Towards this end, I have devised two approaches in which you will all participate:

1.) the regular completion of homework problems, some of which will be discussed and presented in the lab sessions; there will be approximately 8 problem assignments (about every two weeks). The exams will reflect the types of problems found in the problem sets.

2.) the formation of study groups; each study group will have 3 students and will choose a study group leader. The study groups will meet regularly, especially after you have attempted to do a problem set. You may discuss whatever problems you are having with the problem sets in your study group and try to solve them as a group.

I strongly encourage you to meet regularly with your study group and to thrash out whatever problems you may be having with the understanding of concepts or the solution of problems. You will then discover that your understanding of the course material and your ability to solve the problems (in the problem sets and on the exams) will come at a more rapid rate. Thus you will avoid the intense anxiety that comes from discovering the night before the exam that you do not understand the fundamental concepts. You will also, by following these recommendations, become deliriously happy with your new knowledge and understanding of one of the most exciting sciences in our world today.