Principles of Cell and Molecular Biology

BIOLOGY 202 PRINCIPLES OF CELL AND MOLECULAR BIOLOGY SECTION A01 SEMESTER SYLLABUS FALL, 2017

Rm. 32 WEYDT, MWF 125-215. Dr. Carl S. Luciano, 19 Weyandt, 357-4462, [email protected]

I. Course Description and Philosophy

Biology 202 is a freshman-level course designed to introduce students to a variety of basic concepts in cell and molecular biology. BI 202 is thus expected to provide the logical foundation for further studies in zoology, botany, microbiology, genetics and other branches of the biological sciences. Because BI 202 is an early biology course for most students, it is also intended to introduce students to biology as a discipline and the many ways in which people study biology. The course also helps to introduce first year students to the scientific method and its applications to biological systems.

The lecture portion of the course is organized into three units. The first unit concentrates on the basics, including cellular chemistry and cell structure and it establishes a vocabulary for the balance of the course. The second unit emphasizes energy flow and the mechanics of cell function. It also emphasizes the power of proteins as chemical reagents capable of doing almost any imaginable cellular job. The third unit stresses the importance of information as an organizing principle and as a source for the structure of proteins. Each unit concludes with a non-cumulative ho0ur exam. See the class calendar for more details.

To the extent that it is possible in a large group, BI 202 students are expected to participate actively in the class. We will, from time to time, organize class discussions and question/answer sessions with students working in medium-size groups. You are encouraged, at all times, to ask questions about class material.

II. Lab Activities

You will get a separate laboratory syllabus that will describe procedures and grading policies for your laboratory section. Your lab instructor will distribute this syllabus. Labs for Fall 2017 will run differently than in the past. Rather than breadth and a variety of short experiments we will focus instead on a single task throughout the semester. This task

1 is a full semester research project on the viruses that infect certain bacteria. In this project student teams will isolate a new virus (aka “bacteriophage”) from soil samples and grow it in the laboratory in its bacterial host. Teams will then purify DNA from the virus and at the end of the semester send one DNA sample away for sequencing. This part of the research project is called “Virus Discovery”. Next semester you will continue the project by analyzing the DNA sequence in BIOL 203 lab. You will identify the genes in “your” DNA, try to determine their functions and their relationships with other genes, then compare the DNA with others in the international databases. This two-semester project is sponsored by the Howard Hughes Medical Institute and is known as SEA-PHAGE.

In order to accomplish the Virus Discovery project this fall, the lab schedule will be somewhat flexible and teams may need to work independently.

III. Instructor

Dr. Carl S. Luciano, Room 19 Weyandt, 357-4462, [email protected] Instructor Web Site: http://nsm1.nsm.iup.edu/luciano/index.shtm Course Web Site: http://www.people.iup.edu/luciano/

IV. Office Hours:

Fall 2017: MW 230-400, T 130-330

My office is located in the basement of Weyandt Hall on the side that is away from Oakland Avenue. You should feel free to stop in at any time if you have a question or a problem with Biology 202 material.

If you have a question which can be answered over the phone or by e-mail, don’t hesitate to call or write.

V. Required Texts:

(1) Campbell Biology, 10th ed. by Reece et al. (2) Laboratory Manual: Phage Discovery Guide available for free download. Watch your email for updates on lab!

VI. Other Required Materials

(1) Supply of index cards for lecture (see below) (2) Access to electronic communication (3) Your lab instructor may require additional items.

2 VII. Attendance

I will keep a record of your attendance in lecture but will not it as a way to determine your grade. Nevertheless, I expect students to attend all lecture meetings. A missed in-class assignment will be given the grade of zero and may not be made up except in emergency situations (decisions made on an individual basis) or with a physician's excuse.

I will be making important course announcements in class from time to time during the semester. These announcements are likely to affect your grade. Therefore it is important that you attend all regular class meetings.

We will follow the official IUP policies on class attendance as outlined in the undergraduate catalog.

VIII. Policy on Repeat Students

Students who are repeating the course must also repeat the lab.

IX. Grade Derivation

For purposes of grade calculation, the course is divided into lecture and laboratory components. This distinction is artificial and is used for convenience only and is not meant to represent modern biology as being separate from experimental work in any way.

(A) “Laboratory”

Your grade in the laboratory component of the course will count as 25% (1/4) of your overall grade in BI 202. The derivation of your laboratory grade is covered in detail in your laboratory syllabus. Your lab grading procedure will be described by your lab instructor.

(B) “Lecture”

Your grade in the lecture component of the course will count as 75% (3/4) of your overall grade in BI 202. Three equally-weighted non-comprehensive hour examinations (including one to be administered during Finals Week) will account for 60% of your overall grade. Class participation and answers to in-class, take-home or e-questions will account for the final 15% of your overall grade.

IN-CLASS TAKE-HOME or E-QUESTIONS: You will occasionally be asked to write a response to a verbal or written question and turn in your response on a 4” x 6” index card. In some cases, simply turning in a reasonable or logically-defensible answer will result in full credit for the assignment. In other cases, the answer which coincides with that generally accepted by the scientific community (i.e. the “correct” answer) will be required

3 in order for you to receive full credit. Partial credit may be awarded for any answer. Some of the take-home questions may involve a specific reading assignment.

In order to receive credit, your answer must be on a 4” x 6” index card. Your name and the date (printed legibly) must appear at the top of the card. Answers not adhering to the format will not be read and thus will receive a grade of zero.

As soon as I can set up a communication system, you may submit some of your answers via e-mail, hence the name “e-questions”.

EXAMS: Exams will be comprised of two sections. The first section will consist of about 50 multiple choice questions to be answered on a standard IUP answer sheet (bubble sheet). Each question will count as one point and so the first section will be worth about 50 points.The second section will consist of 4 or 5 questions to which you will be asked to respond with a short answer, essay, a calculation, a diagram or a one or two-sentence answer. The second section will be worth about 40 points.

Exam questions will be designed to test how well you have achieved the goals described in Section II of this syllabus. Therefore some of the questions, especially some of the multiple choice questions, will simply require you to repeat terms, definitions and characteristics that you have memorized. These are the questions that students usually consider to be “easy”. These questions will predominate on the first exam but will decrease progressively in frequency on the second and third exam.

Other questions, including both multiple choice and short answer questions, will demand more than a superficial understanding of the material. They will require understanding in some depth and will require more thought and effort on your part. They will test your ability to explain as well as your ability to memorize. They will test your ability to pull together information from separate parts of the course in order to generate an answer (a process known as synthesis). Finally, they will test your ability to apply what you have learned to new and unfamiliar situations. In my experience, students usually consider these to be “difficult” questions. They will not be frequent on the first exam but will increase in frequency on the second and third exams.

Please note that in any cases of possible plagiarism or academic dishonesty I will adhere to university policies as outlined in the current undergraduate catalog.

X. Grading Scale

In the absence of unusual circumstances, such as a highly skewed grade distribution, I will adhere to a standard 90/80/70/60/50 grading scale for A/B/C/D/F letter grades. I do not intend to use a “curve” for grade determinations.

XI. Late Submission/Makeup Work

4 Without the instructor's permission, no assignments whatsoever may be turned in after the due date and time. I will make all decisions about makeup work on a case-by-case basis, taking into consideration circumstances such as illness, emergency and so on. See me if you have questions.

IF YOU KNOW YOU MUST MISS AN IMPORTANT CLASS MEETING, YOU ARE MUCH BETTER OFF TO LET ME KNOW IN ADVANCE!!!!!!!

I will judge requests for make up work on a case by case basis and will expect to see solid documentation for issues such as student or family illnesses, university business, military assignments, court dates, deaths and funerals and so on. Issues such as broken printers, printers out of ink/paper, forgotten assignment and so on will not provide you with much support and are liable to be charged a late penalty of 20% per day late.

If you know that you have to be away on an important date (for example-on university business) it is better to let me know in advance so that we can work out arrangements for make up work without a rush.

If you are absent unexpectedly and want to make up missed work then you must take the responsibility to initiate a plan for the make up work by contacting me, within one week of the missed assignment.

We will handle arrangements for make up work using email to confirm discussions and plans. This way we will all have an electronic copy of all conversations and decisions.

I will not give a high priority to make up requests that involve vacations, social events, family gatherings or a desire to leave town early at the end of the semester or before a holiday.

If you miss an exam or part of an exam and I agree to let you take a make up exam (due to strong documentation) then your make up exam may have a different format from the regular exam.

XII. Reading Assignments

Reading assignments in the “Campbell” text are made on the calendar below. Additional assignments may be made from time to time. Although your exams will emphasize material from lecture, you are also responsible for the assigned reading in the text, unless otherwise notified. In some cases lecture topics may not exactly coincide with text chapters. If this is the case, use the Index to find additional reading. I will make more detailed reading assignments as we move through the course.

XIII. Review Sessions

5 At student request, at least one review session will be scheduled before each exam, including the exam scheduled at the end of the session.

XIV. Tentative or Approximate Class Calendar for Fall, 2017

Date Topic (tentative) Main Reading Assignment (Campbell Chapter #) August 28 Introduction 30 Tour of Cells and Organelles 6

September 1 Tour of the Cell and its Organelles 6 4 Labor Day Holiday-No Class 6 Water, Carbon and Molecular Diversity 3,4 8 Macromolecules 5 11 Macromolecules 5 13 Macromolecules 5 15 Macromolecules 5 18 Membrane Structure and Function 7 20 Membrane Structure and Function 7 22 Enzymes and Metabolism 8 25 Enzymes and Metabolism 8 27 Enzymes and Metabolism 8 29 Hour Exam #1

October 2 Cell Respiration/Fermentation 9 4 Cell Respiration/Fermentation 9 6 Cell Respiration/Fermentation 9 9 Cell Respiration/Fermentation 9 11 Photosynthesis 10 13 Cell Communication and Signalling 11 16 Cell Communication and Signalling 11 18 Cell Communication and Signalling 11 20 Cell Division and the Cell Cycle 12 23 Cell Division and the Cell Cycle 12 25 Cell Division and the Cell Cycle 12 27 HOUR EXAM TWO 30 DNA Replication and Repair 16

November 1 DNA Replication and Repair 16

6 6 DNA Replication and Repair 16 8 Gene Expression and Regulation 17, 18 10 Gene Expression and Regulation 17, 18 13 Gene Expression and Regulation 17, 18 15 Gene Expression and Regulation 17, 18 17 Gene Expression and Regulation 17, 18 20 Thanksgiving Holiday-no class 22 Thanksgiving Holiday-no class 24 Thanksgiving Holiday-no class 27 Gene Expression and Regulation 17, 18 29 Viruses and Pathogenic Microbes 19, 27

December 1 Viruses and Pathogenic Microbes 19, 27 4 Viruses and Pathogenic Microbes 19, 27 6 DNA Tools and Biotechnology 20, 21 8 DNA Tools and Biotechnology 20, 21 11 DNA Tools and Biotechnology 20, 21 13 HOUR EXAM THREE at 0800-1000 AM in Rm 107

This approximate schedule will be adjusted during the semester.

XV. Summary of Exam Dates

1. Exam One: Sept. 29 2. Exam Two: October 27 3. Exam Three: Wednesday December 13 1230-230 PM. Exam 3 is not cumulative. NO EARLY EXAMS GIVEN

The first two hour exams are scheduled on a Friday. Depending on our experimental schedule, the exams may be given during our “lab” period. This will also allow you more time to complete the exam.

XVI. How to Study Science

For advice on how to succeed as a student in a college science course, see How to Study Science, 4th ed. By Fred Drewes and Kristen Mulligan.

Find out what kind of a learner you are by answering Richard Felder’s Index of Learning Styles questionnaire at: http://www.engr.ncsu.edu/learningstyles/ilsweb.html

7 This is a 44-item questionnaire that may help you to recognize your study strengths as well as areas where you need some work.