Molecules,Cells & Genes

*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 101 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 101 as a pre-requisite course.

*Tips for Success in BIO 101*  

How not only to survive BIO 101 but also to thrive and do well, i.e. learn more biology and accomplish the course objectives in the most efficient way;(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 class session, 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 101 (see separate 1st-Day handout) or the Box.

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 understand fully 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 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. In this regard, I will be asking you lots of questions in our class sessions.

To summarize, effective 'homework' and class preparation include the scanning and reading of any 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 link, Academic Expectations, for some excellent advice about college work in general; and from the authors of a popular biology-text: To The Student

*Attendance and Grading policies*

 Attendance in lectures is highly recommended. 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.

Grades will be based on the following:
BIO 101 exams (80%):
Exam #1 - Sep 27th
(Fall Break - October 12 - 20)
Exam #2 - Oct 30th
(Last Day of Classes - Dec 6)
Exam #3 - Dec 13th, 9:00 AM

BIO 101 labs (20%); see separate schedule

Grading Scales

Office Hours for discussing course-related issues with me:
Always contact me by e-mail or after class to arrange a mutually compatible time for a meeting. 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

Note 1: The lecture sessions address three main topic sections : (I) Molecules (chs. 2-6); (II) Cells/Genetics (chs. 7-14), and (III) Genes (chs. 15-19); and some Introductory Genetics in chs. 13 and 14. A good understanding and appreciation of both cell biology and molecular biology depends on knowing some chemistry, especially of macromolecules (chs. 2-6)

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 can consult it often for updates and current assignments.

Reading Assignments, Slides, Handouts, and Problems*
(Problems are all answered in the back of your text, and reviewed in class - not assignments for handing into me, unless the assignment is an OOPA (Optional One Point Assignment, and see study strategy)

Biology and the Tree of Life; Inside the Cell:
Sections 1.1-1.5; Sections 7.1, 7.2, 7.6  
(a) 1.1: Hierarchy and Properties of Life, Emergent Properties; "It's alive, it's alive.....!"
(b) 1.2: Cell Behaviors; Grand Theory 1: the Cell Theory, and "Omnis cellulae e cellulae"
(c) 1.3, 1.4, 1.5: Grand Theory 2: Natural Selection; organizing it all into Taxonomy, Classification, Phylogenetic schemes & Evolution
(d) 1.6: Doing Science: the Hypothetico-Deductive method of science; pattern and process: p. 9, 13 only, focus on slides
(e) Connecting Concepts: Doing Biology, p.16-17 for the 'Big Picture'
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(a) 7.1, 7.2: Review of Cell structures (prokaryotes and eukaryotes; the endomembrane system, structure & function)
(b) 7.6: Components of the Cytoskeleton (for Cell Culture/Wounding labs only!!)

ch1: 1-3; 5,7,11,12,14,15
(and see first slide of slide set for both specific reading assignments - RAs - and all assigned problems)zzzz; ch7: 1,2,3,5,6,7,8,10,12

Water and Carbon - The Chemical Basis of Life*:
Sections 2.1, 2.2, 2.5
(a) 2.1, 2.2: Chem review (p.55-67, selected slides); bonding theory; water and pH
(b) 2.5: carbon chemistry & functional groups
(c) p. 140-141 for the 'Big Picture' and Introduction to Macromolecules

1,7-10; 12,14,15,16

*Some review Only!

(3) Protein Structrue & Function; (4) Nculeic Acids and the RNA World
Sections 3.1-3.4; Sections 4.1-4.3
(a) 3.1: Small monomer structure; amino acid chemical categories and R-group structures; Monomers to Polymers (some polymer theory, applies to the 4 major macromolecular types)
(b) 3.2: protein structure, primary (1o) to quaternary (4o); importance of weak bonds for macromolecular structure and function
(c) 3.3: The shape and structure of folded proteins; structure-function relationships
(d) 3.4: The many functions of proteins
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(a) 4.1: DNA and RNA structures; monomer-polymer theory applied to nucleic acids
(b) 4.2: Essentials of DNA structure-function relationship; Watson and Crick paper in Nature
(c) 4.3: What distinguishes RNA from DNA? RNA is more than an 'informational' molecule...

Lipids, Membranes & the First Cells
Sections 6.1-6.4
(a) 6.1, 6.2: Lipid structure & function, and the lipid bilayer in Membrane structure
(b) 6.3: biophysics of Membrane transport; semi-permeable membranes
(c) 6.4: Membrane proteins; carrier and channel proteins and their functions

1,2

1,2

1,2

(2), Section 2.3 - Chemical Reactions & Energy; (8) Energy & Enzymes - An Introduction to Metabolic Pathways; (9) Cellular Respiration & Fermentation
(a) 2.3, 8.1: Energy transformations in chemical reactions; basic Thermodynamics; spontaneous & non-spontaneous reactions
(b) 8.2: What about non-spontaneous reactions?
(c) 8.3, 8.4: How do enzymes work, and what affects their functions?
(d) 8.5: The Biochemical Pathway
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(c) 9.1:Overview of Metabolism; 'activated' carrier molecules
(b) 9.2-9.5: Glycolysis & TCA & electron transport; Oxidative phosphorylation & proton motive force

(10) Photosynthesis; Sections 10.1, 10.2
(a) How does Photosynthesis work: light to chemical energy
(b) How does Photosynthesis work: photosynthetic pigments

(12) The Cell Cycle
(a) 12.1, 12.2: Basic mechanics of the cell cycle in nuclear (mitosis) and cell division (cytokinesis)
(b) 12.3, 12.4: Control of the cell cycle, and what happens when it 'breaks bad'

(13) Meiosis; (14) Mendel and the Gene
(a) 13.1: Meiosis and its phases; making gametes; meiosis & mitosis compared
(b) 13.2, 13.3: Chromosome dynamics to explain Segregation & Independent Assortment (Mendel's First & Second rules or Laws of Inheritance - the Chromosome Theory of Inheritance); crossing over and its implications for genetic variation
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(a) 14.1, 14.2, 14.3: the brilliance of Mendel's experimental system, and how the results of his mono- and di-hybrid crosses could be explained by the dynamics of chromosomes during meiosis (see Ch.13 sections)
(b) Chromosome Theory of Inheritance; summing it all up: chromosome dynamics, Mendel's results

(15) DNA and the Gene - Synthesis & Repair; (16) How Genes Work
(a) 15.2: the semi-conservative nature of DNA Replication (first component of the 'central dogma')
(b) 15.3: biophysics & biochemistry of DNA Replication on leading and lagging strands at replication forks
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(a) 16.2: the Central Dogma of Molecular Biology: Replication, Transcription, Translation
(b) 16.3, 16.4: the Genetic Code; theory and practice of mutations
(c) Connecting Concepts: Transcription to Translation to point mutations, to What's a Gene?.

(17) Transcription, RNA Processing, and Translation
(a) 17.1, 17.2: Making RNA transcripts in bacteria & eukaryotes (second component of the 'central dogma'); the 4 steps of processing RNA transcripts in eukaryotes
(b) 17.3, 17.4, 17.5: Translation (third part of 'central dogma'); the 'bi-lingual' tRNAs, and the structure & function of ribosomes

(18)Control of Gene Expression in Bacteria; (19) Control of Gene Expression in Eukaryotes
(a) 18.1: Enviromental & nutritional control of genes in bacteria; the lac operon's genetic structure & functions
(b) 18.3, 18.5: Operons & Regulons
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(a) 19.1: An introduction to the complexities of gene regulation in eukaryotes
(b) 19.2, 19.3, 19.4: the problems and solutions of initiating transcription in eukaryotic genes; what is alternative splicing?
(c) 19.5, 19.6: comparison of gene regulation proks and euks; the genes for cancer

(20) Analyzing and Engineering Genes
DNA Technology:
(a) Analyzing DNA molecules
(b) Nucleic Acid Hybridization
(c) DNA cloning
(d) Genetic Engineering

(a) to be announced