<%@ Language=JavaScript %> Introductory Genetics -- Fornari

Biology Dept.

DePauw University

Fall 2013
Instructor: Fornari

BIO 215A
Introduction to

 Cells & Genes

Lecture - MWF 2:50-3:50 PM in
 *Olin 241*

click here for all resgistration information

Instructor: Chet Fornari
Olin 232; e-mail: cfornari

1040  BIO 215B 


(1) Essential Cell Biology, Third Edition

NOT required (only for review if you need it): (2) An Itnroduction to Chemistry for Biology Students

"The key to every biological problem must finally be sought in the cell,
for every living organism is, or at sometime has been, a cell."
--E.B. Wilson, cell biologist (1925)

"Molecular Biology is the art of the inevitable. If you do it, it's inevitable you will find out how it works - in the end."
--Sydney Brenner, molecular biologist

"Science should be as simple as possible but not simpler."
--Albert Einstein

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." 


*COURSE OBJECTIVES* to learn and understand the basics of cell biology and molecular biology; to develop scientific attitudes and skills in problem-solving, and the creation and testing of hypotheses; to gain a greater appreciation for the beauty, logic and interconnectedness of the general principles and concepts underlying the biological sciences.

*RATIONALE for Course Design and Organization*

The contents of biology courses typically span atoms to biospheres; the topics covered and the sheer amount of information, details and data may seem overwhelming. This apparent burden is a reflection of the great and exciting diversity of the biological world. Basic principles, or "unifying themes" underlie this diversity, and serve to organize the biological world into a coherent science with all its concepts, laws and theories. Although biology courses have different names and emphasize different sub-fields, biological science is based on a set of common (mainly genetic, evolutionary, and biochemical/physical) principles. You should pay close attention to these "unifying themes" of biology and concentrate on making broad connections among the various subfields. Doing so will enable you to get out from under the mass of information, and make some sense of it all; then and only then will you come to appreciate the overall unity lurking within a wonderful diversity. 

BIO 215 is an introduction to both cell biology and molecular biology, and is a required course for the Biology and Biochemistry majors. Several upper-level courses require BIO 215 as a pre-requisite course. The pre-req course for BIO 215 is CHEM 120.

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*Tips for Success in BIO 215*  

How not only to survive BIO 215 but also to thrive and do well (i.e. learn more biology and accomplish the course objectives; WSS = web site syllabus): 

1. Attend Lectures, Know your syllabus, Follow my Organizational Plan: Use lecture discussions and your syllabus to keep track of the topics, and to organize the information into efficient study plans. Pay careful attention to how I organize each lecture, in terms of the sequence of topics and the relative time/emphasis placed on each topic. Refer to the text to read the assigned pages preferably BEFORE coming to the lecture (the reading assignments will be announced in class and summarized on the first slide of any new slide set and on the Web-site syllabus, or WSS). Other reading assignments (e.g., from Scientific American articles or other sources) will also be posted on the WSS. All lecture slides and handouts and articles can be found in your I:/drive folder for BIO 215 (see separate 1st-Day handout)

2. Prepare for class: Check the WSS, and my recommendations from the previous lecture, for reading assignments before coming to the subsequent lecture, and read the assigned text pages and/or articles. Do not expect to fully understand a reading assignment or lecture the first time you read/hear it; in other words, do not expect instant comprehension of all the topics read/discussed all the time. Think about the content, and learn to take effective notes, AND BY ALL MEANS ASK QUESTIONS!!!!! My task is not to present static information to you so neatly and so slowly that you can record every word that I say, and then have you transfer it back to me word-for-word through exams. My task is to help you in learning "how to learn" by challenging you to think about new knowledge and ideas; my task is to help you understand and apply new concepts and knowledge through the use of relevant discussions, examples and problems. 

To summarize, effective class preparation includes reading and scanning  the assigned pages, text figures and handouts, reviewing your previous notes, adding new notes from your text and handouts, and then reviewing the revised notes. Use this study strategy on a regular, daily basis. Be sure to ask questions whenever you do not understand the material.

Click this page site for some excellent advice from the authors of a text: To The Student

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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." 

*Attendance and Grading policies*

 Attendance in lectures is highly recommended. No make-up exams will be scheduled. If you are unable to take an exam because of an emergency or other disaster, then you must make every effort to inform Prof. Fornari and the Student Affairs Office before the scheduled exam.

Grades will be based on the following:
BIO 215 exams:
Exam #1 - Oct. 2nd;  #2 - Nov. 11th; #3 - Dec. 20th

Grading Scales

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:



*Topics and Reading Assignments are posted weekly on this web-site*
Most Overheads and all PowerPoint Slides used in lecture will be placed in your I:/drive class folder; the first PowerPoint slide of a set repeats the reading assignments listed here:

Note 1: The lecture sessions address two main topic sections : (I) Molecular Biology (chs. 2-10), and (II) Cell Biology (chs. 11-20).

We can divide topic section (I) into sub-topics: I(A) for Basic Chemistry, & Chemical Components of cells (ch. 2); I(B) for Thermodynamics, Enzyme kinetics, & Protein structure (chs. 3 & 4); I(C) for DNA/Chromosome structures, DNA Replication, Transctription, RNA translation (chs. 5, 6, & 7 ); I(D) for Gene Regulation & Evolution (chs. 8 & 9); I(E) for Molecular and Biochemical Methods (ch. 10).

We can divide topic section (II) into sub-topics: II(A) for Membrane Structure & Transport (chs. 11 & 12); II(B) for Mechanisms for Energy transformations (chs. 13 & 14); II(C) for Intracellular and Intercellular transport and signal transductions (chs. 15 & 16); II(D) for Structures and Functions of the cell cycle (chs. 17 & 18); II(E) for Cell Divisions of Mitosis and Meiosis (chs. 19); and lastly, II(F) for applications of molecular and cellular biology to tissues and cancer (ch. 20).

Note 2: We cannot cover all the text topics in complete depth in one semester; hence I will assign specific pages for critical reading and for help in solving the assigned problems. This Web Site Syllabus, or WSS, is a dynamic document; I can modify it at any time and you should consult it often for updates and current assignments.

Topic Sections I: Molecular Biology and II: Cell Biology


Reading Assignments, Slides, and Handouts


IC = in chapter;
EOC = end of ch
Ch.1 Introduction and Orientation to BIO 215 Cells & Genes:  
(a) Hierarchy and Properties of Life, Emergent Properties, p.1-7 and slides
(b) Cell Behaviors; the Cell Theory, and "Omnis cellulae e cellulae" & cell division; p. 1-7 and slides
(c) Taxonomy, Classification, Phylogenetic schemes & Evolution; p.11-16, prokaryotes; p.16-27, eukaryotes; p. 26-35 for Model Organisms
(d) the Hypothetico-Deductive method of science: on slides
(e) Connecting Concepts: Central Dogma: p.4 fig. 1-2 & slides

(all EOC)
IC: 4


Topic Section I(A): Molecular Biology, ch. 2 Basic Chemistry & Components of Cells: from bonds to molecules to macromolecules
(a) Chem review: p. 39-40; Bonding theory: p. 40-48; H2O & pH: p. 48-50 (for an EXCELLENT review of some basic chemistry, see Panels 2-1 & 2-2 on p.64-67)
(b) Small monomer structure; amino acid chemical categories and R-group structures: p. 50-58; Panels 2-3 to 2-7, p.68 -77
(c) Monomers to Polymers (some polymer theory): p. 58-62
(d) Importance of weak bonds for macromolecular structure and function: p. 62-63

(1-9)*10 IC
15-22 EOC

*Review Only!


Topic Section I(B): Enzyme Kinetics & Protein Structure
(a) Essential thermodynamics:1st and 2nd Laws and the Gibbs Free energy; p. 82-88; 88-98;. and Panel 3-1, p. 94
(b) Diffusion Dynamics; Essential enzyme kinetics: p. 98-99; 99-102
Panels 4-3, p.160-161 of ch.4 on the centrifuge and types of centrifugation; handout on Svedberg equation, and Svedberg's famous experiment with hemoglobin to resolve the controversey about macromolecular structure
(c) The shape and structure of proteins: p. 119-143
(d) Structure-dependent protein functions:
p. 143-150
Control of enzyme functions: p. 150-158

3-4, 3-6, IC(ch3)
11-13,16,20-22 EOC(ch3);

Topic Sections I(B): Molecular Biology, ch. 3 Thermodynamics, Enzyme kinetics, and II(B): Cell Biology, chs 13 & 14 Mechanisms for Energy Transformations in Mitochondria and Chloroplasts
The shape and structure of proteins: p. 119-136
How proteins are studied : p. 156-168; Panel 4-2 Proteind Imaging, p.128-129; Panel 4-5, Chromatography & Electrophoresis, p.166-167; Probing Protein Structure, p. 158-160

Overview of Metabolism: p. 84-91;
Activated carrier molecules: p. 106-111
Glycolysis & TCA cycle & electron transport: p.425-450
(e) Oxidative phosphorylation & proton motive force:
p. 453-473
(f) Panel 14-1 for Redox potentials:
p. 467; -470-472
(g) Chloroplasts and photosynthesis: p. 482-486; fig. 14-37

1,2,7,8,9,10,12,14,16 (ch3)





Topic Section I(C): Molecular Biology, chs. 5, 6, & 7 DNA/Chromosome structure and functions
DNA and RNA structures: p. 169-171; 175-176
(b) Chromosome structures, architectures; nucleosomes:
p. 177-182; 184-187; 189-191 (chromatin remodeling and histone tail covalent modifications)
(c) DNA function: Replication:
p. 195-197; 201-207
DNA function: Transcription, p. 229-243
(e) RNA function: translation:
p. 243-245; 248-257
(f) Connecting Concepts: Transcription to Translation to point mutations, to What's a Gene?.

1,2, IC(ch5)

15,16,17 EOC(ch5)

20(a) (ch6)



Topic Section I(D): Molecular Biology, chs 8 & 9 Gene Regulation and Evolution; how Genes and Genomes evolve
(a) Introduction to Gene Expression: p. 267-270
(b) Transcriptional Switches and gene regulatory mechanisms: p. 271-280
(c) Combinatorial control and cell specialization mechanisms: p. 280-281; 285-289
(d) Molecular Mechanisms of genetic variation in genes & genomes: p. 293-
(e) The Tree of Life and its evolution: p. 304-310
(f) The Human Genome: p. 311-313; 316-319


Topic Section I(E): Molecular Biology, ch 10 Molecular & Biochemical Methods
(a) Analyzing DNA molecules
Nucleic Acid Hybridization
DNA cloning
Genetic Engineering



Reading Assignments, Slides, and Handouts
Problem assignments
Topic Section II(A): Cell Biology, chs 11 & 12 Membrane Structure and Transport
(a) The lipid bilayer and Membrane structure
(b) Membrane proteins
(c) Cell cortex and surfaces
(d) Principles of Membrane transport
(e) Carrier and channel proteins and their functions
1,2,3,5, 9abcdf, 10,11,12,18,19,20(ch11)

Topic Section II(C): Cell Biology, chs 15 & 16 Intracellular and Intercellular transport and signal transductions
(a) The general principles of cell communication by molecular signaling
The nature of signals and information transfer: what is Signal Transduction?
The basic modes of cell signaling between animal cells
(d) Intracellular signaling pathways: structure/function, signaling cascades
The 3 main classes of cell-surface receptors

1,2,3,5 IC(ch16)
11(abc),12-15,17,24 EOC(ch16)

Topic Section II(D): Cell Biology, chs 17 & 18 Cell Cycle Biochemistry & function
(a) tba (selected sections only, but HIGH PRIORITY for understanding mitosis and meiosis in the next section)


Topic Section II(E): Cell Biology, chs 19 & 20 Cell Divisions: Mitosis & Meiosis
(a) tba (selected sections only, but HIGH PRIORITY for explaining Chromosome Dynamics in gene transmission - essentially Mendel's First and Second Laws of Segregation and Independent Assortment)


Topic Section II(F): Cell Biology, ch 21 Applications of molecular and cellular biology to tissues and cancer
(a) tba (selected sections only)



Reading Assignments, Slides, and Handouts
Ch. DNA Technology:

Ch. The Genetic Basis of Development:


"And so in order to wake up, the one thing you need the most is not energy, or strength, or youthfulness, or even great intelligence. The one thing you need most of all is the readiness to learn something new." --Anthony de Mello, p.28 of Awareness 

And see: Merlyn's Advice

And see: Words of John Adams, American Revolutionary and 2nd President of the United States