Dr. Ruth BallardPage 111/07/18
BIO 2 SyllabusFall 2008
CALIFORNIASTATEUNIVERSITY, SACRAMENTO
Department of Biological Sciences
BIO 2: CELLS, MOLECULES, AND GENES
Fall, 2008
Lecture: MND 3011, M/W/F 8:00-8:50 AM
Lab: SQU 208, M 9:00-11:50 AMor M 2:00-4:50 PMor W 9:00-11:50 AM
Activity: SQU 452, W 1:00-2:50 PM;orHMB 102, F 9:00-10:50or F1:00-2:50 PM
INSTRUCTOR: Dr. Ruth Ballard ()
(Lecture and Labs) Professor of Biological Sciences
INSTRUCTORS:Dr. Melanie Loo ()
(Activities)Professor of Biological Sciences
Colin Contino()
Graduate Teaching Assistant
LAB TECHNICIAN:Rachel Douglas ()
LAB TEACHING ASSISTANTS:Kristen Greene ()
Abraham Stein-Freer ()
Audrey Guillermo ()
Crystal Yu ()
Gerald Busby ()
REQUIRED TEXTS:Biology, Seventh Ed., Campbell and Reese (Hornet Bookstore);BIO 2 Laboratory Manual, Fall 2008 (available for free download from the course website)
REQUIRED FOR LAB: Lab fee; Laboratory notebook
PREREQUISITES: BIO 1 and CHEM 1 A (or equivalent)
CONTACT INFORMATIONFOR DR. BALLARD:
OFFICE HOURS: F: 9:00 AM to 12:00 PM
OFFICE: 120-B Sequoia Hall
RESEARCH LAB: 108 Sequoia Hall
RESEARCH FOCUS: DNA forensics; Human molecular genetics
PHONE: (916) 278-6244
WEB SITE:
CATALOG DESCRIPTION
BIO 2. Cells, Molecules, and Genes. Introduction to molecular and cellular biology and genetics. Topics include biomolecules, cell structure and function, cellular energetics, molecular flow of information, cell division, and genetic inheritance. Development of scientific skills and a scientific mindset will be emphasized throughout the course, particularly in lab exercises and activities. Designed for science majors. Lecture three hours, laboratory three hours, activity 2 hours. Prerequisites: BIO 1 and CHEM 1A. 5 units.
COURSE POLICIES
I. EVALUATION OF STUDENT PERFORMANCE
The course has three components: lecture, laboratory, and activity (discussion). During the semester, student performance(NOT EFFORT) will be evaluated in eachcomponent separately. However, at the end of the semester, the scores earned in each component will be combined and students will receive a single grade for the course.
Please note, however, that in order to pass the course, students must receive a score of at least 60% in each component, regardless of their scores in the other components. Students who fail to do so will receive an “F” grade, even if their combined score is above 60%.
- Lecture
Students may earn a total of 440 pointsin thelecture portion of the course (55% of the total points in the course), with the points distributed as follows:
Lecture exams (3 @ 100 pts each)300
Homework (14 @ 10 pts each)140
TOTAL 440
Lecture exams will be non-cumulative and will be based on lectures and assigned readings. Homework will be distributed every Monday in lecture (starting 9/8) and will be due the following Monday in lecture (including exam days). Late assignments will not be accepted. If you must miss lecture, you may e-mail me your homework and I will accept it as long as the e-mail arrives before the beginning of the class period.
Students who need to make up an exam due to illness or another documented excuse will be given the opportunity to do so during finals week ONLY. Make-up exams will not be administered at any other time during the semester.
- Laboratory
Students may earn a total of 220 points in the lab portion of the course (27.5% of the overall grade), with the points distributed as follows:
Lab quizzes (12 @ 10 pts each)120
Lab Practical Exam (comprehensive)100
TOTAL 220
Lab Quizzeswill be administered during the first 15 minutes of each laboratory period. Students who arrive after the quiz has been handed out will not be permitted to take the quiz. Lab quizzes cannot be “made up” as they are designed to encourage students to arrive in lab on time and be prepared for the day’s work. Students may refer to their laboratory notebook (but not their lab manual) during the quizzes to help them answer questions.
Studentswill be required to keep a detailed Laboratory Notebook. For specific instructions on what type of notebook to buy and how to properly maintain your notebook, see the “BIO 2 Laboratory Notebook Instructions” handout. Students are expected to write up their protocols for the lab in detail before coming to lab. Students who fail to do so will not do well on the lab quizzes and will also have trouble completing the labs in the allotted time.
During the week before finals, students will take a Cumulative Lab Practical Exam. Information on the format and content of the exam will be provided to students well in advance of the exam date.
Students are expected to arrive in lab on time and to remain until they are excused.
Students may miss three laboratory sessions during the semester and do not need to provide me with a documented excuse. However, students who miss more than three lab sessions will receive a grade of “WU” for the course and will not be allowed to continue attending class. THERE WILL BE NO EXCEPTIONS TO THIS POLICY.
- Activity (Discussion)
Activity will be worth 17.5% of each student’s final grade in the course. The Activity instructors will provide students with specific guidelines for how they will be evaluated in their sections. At the end of the semester, the Activity instructors will send me the percentages for the students in their sections and I will factor that percentage into each student’s final grade such that Activity accounts for exactly 17.5% of the total.
II. STUDENT CONDUCT
Electronic Devices
My BIO 2 lecture and lab sections are “technology free” zones. Students are required to turn off or silence all electronic devices (including cell phones, laptops, iPods, CD-players, etc.).Activity instructors will let students know the policy for their individual sections.
Communication with the Instructor Outside of Class
All outside of class communications from me (the instructor) to you (the student) will take place through My Sac State. Be sure to log onto My Sac State regularly to check for messages.
Students should communicate with me via e-mail rather than by telephone, using the e-mail address provided on the first page of this syllabus. I do not reply to e-mails that fail to follow the rules of “e-mail etiquette” listed below. I strongly suggest that you get in the habit of using these same rules when communicating with all of your professors.
1.Address your professors as “Dr” or “Professor” unless they expressly tell you otherwise. You will never offend an instructor by being formal and respectful. However, you may well offend an instructor by using his/her first name without permission.
2.Write in complete, grammatically correct sentences (to the best of your ability).
3.Sign e-mails with your full name, particularly if your e-mail address does not include your full name.
4.Drop the “cutesy” e-mail address for school purposes. Using an address like is not professional and can be off-putting to many professors (not to mention prospective employers, medical school admissions committees, etc.) It is best to choose an address that includes your full name, such as .
5.Before sending an e-mail, try to answer the question or solve the problem on your own. For example, don’t write me an e-mail asking me when I hold my office hours or if BIO 150 is a requirement for the Forensic Biology concentration. This information is readily available online, and I will not answer e-mails of this kind.
6.Respect the fact that your professors have already set aside time for office hours every semester. Do not request to meet with a professor outside of these hours unless (1) You are at work or in class during the professor’s office hours and (2) Your questions pertain specifically to a course taught by that instructor or to an advising issue that can only be answered (or is clearly best answered) by that professor.
7.Do not assume that professors are available 24/7. Some do not answer e-mail over the weekends or in the evenings, and many go home at 5 PM. Limit your communications and requests for meetings, as much as possible, to reasonable business hours.
Cheating
No communication is permitted between students during the lecture exams, lab quizzes or the lab practical exam. No materials other than the students’ writing implements, a calculator, and quiz/exam materials may be used during a quiz or during the lab practical exam, with the exception that students may refer to their laboratory notebook during the lab quizzes. Students may not leave the room during a quiz or exam without my permission.Since the lecture exams are only 55 minutes long, I expect students to use the restroom prior to the exam, and I will not allow students to leave the room for “bathroom breaks” during an exam. If you have a medical condition that may require you to leave during the middle of exam, you need to tell me beforehand so that I am prepared to deal with the problem.If I obtain evidence of cheating on the exam, I will report the incident to the Department Chair and the Dean of Students for disciplinary action.
Although students are strongly encouraged to study in groups and to discuss homework problems freely, students must write up their homework in their own words. If I receive two homework papers that contain identical wording, both assignments will be given a grade of “0”. If the pattern continues, I may also refer the students involved to the Dean of Students for disciplinary action.
The University policy on academic dishonesty can be reviewed at the following web link: If you have never read this policy, take the opportunity to do so because it will help you avoid inadvertently engaging in plagiarism or other forms of academic dishonesty in all of your classes, not just this one.
Safety
Students must follow all laboratory safety rules and must come to lab prepared and ready to work safely and efficiently. Laboratory safety rules will be covered during the first week of class and will be emphasized in each laboratory as needed.
III. ADD/DROP POLICY
The Add/Drop policy will be followed as detailed on the campus website. For a direct link to the policy, go to The one exception is that the Department of Biological Sciences allows students to drop a course up until the Census date without providing “serious and compelling reasons” for doing so. Please note, however, that afterthis date, students will be required to produce convincing documentation of a serious and compelling reasonfor dropping the course. Please see me if you need to drop the course after this date.A low grade in the class is not a sufficient reasonto drop the course after the census date.
UNIVERSITY POLICY STATES THATDROPS DURING FINALS WEEK WILL NOT BE PERMITTED FOR ANY REASON. Students with an emergency during this time can request to be assigned a grade of “I” in the course and must make up the missed assignments/exams within 12 months or the “I” grade will automatically become an “F”.Special forms are required and are available in SQU 202 (Dept office).
BIO2 LEARNING OBJECTIVES
After completing BIO 2, students should be able to:
- Explain the cosmic origin of the atoms and molecules upon which life depends.
- Articulate the differences between living and non-living things.
- List the major facts supporting the theory that evolution by natural selection accounts for the origin and diversity of living organisms.
- Draw the chemical structures of the “building block” molecules of life, nucleotides, sugars, amino acids, and simple lipids.
- Draw the chemical structures of life’s important macromolecules, nucleic acids, carbohydrates, and proteins, and describe the importance of polymerization in forming these molecules.
- Explain how cells separate “self” from the environment and other living organisms.
- Describe the differences and similarities between prokaryotic and eukaryotic cells.
- Describe the structure and functions of the cell membrane.
- Describe the structure and digital nature of life’s information molecule, DNA.
- Explain how the information stored in DNA is used to drive cell processes through transcription and translation.
- Explain how genetic information is replicated and transmitted to daughter cells or offspring through both asexual and sexual reproduction.
- Explain how cellular diversity arises from the inexact copying and transmission of digital genetic information.
- Describe how organisms fight the entropic nature of the Universe by harvesting energy through the processes of photosynthesis and respiration.
- Articulate the importance of enzymes and ATP in driving and maintaining order in the cell.
- Explain how the scientific method works and how it differs from other ways of gaining knowledge.
- Design and execute a scientific experiment, starting with a hypothesis and using proper controls.
- Use the basic scientific tools of cellular and molecular biology.
- Performroutine scientific calculations accurately and reproducibly.
- Explain how scientists communicate with one another, in both formal and informal ways.
- Express and support informed personal views on some of the current applications of cellular and molecular biology, particularly those with bioethical implications.
LECTURE SCHEDULE
Week
/ Date / Topic /Readings in Textbook
PART ONE: INTRODUCTION1 / 9/3 / Introduction to the Course
9/5 / Introduction to the Course (continued)
How scientists view the world / Concept 1.5, p. 19-26
2 / 9/8 / The Universe and its chemistry ; What is life? / Chapters 2, 26
9/10 / The chemistry of life: atoms, molecules, and bonds / Chapter 2
9/12 / The chemistry of life: water and pH / Chapter 3
3 / 9/15 / The chemistry of life: carbon and macromolecules / Chapter 4
9/17 / The chemistry of life: carbon and macromolecules / Chapter 5
9/19 / The chemistry of life: carbon and macromolecules / Chapter 5
PARTTWO: SEPARATING SELF FROM OTHER
4 / 9/22 /
A tour of the cell: prokaryotes
/ Chapters 6, 279/24 / A tour of the cell: eukaryotes / Chapter 6
9/26 / The cell membrane / Chapter 7
5 / 9/29 / Lecture Exam 1
PARTTHREE: LIFE’S INFORMATION MOLECULE AND ITS PERPETUATION
10/1 /
DNA structure
/ Chapter 1610/3 /
DNA replication
/ Chapter 166 / 10/6 /
DNA replication
/ Chapter 1610/8 /
Transcription
/ Chapter 1710/10 /
Transcription
/ Chapter 177 / 10/13 /
Translation
/ Chapter 1710/15 /
Translation
/ Chapter 1710/17 /
Translation
/ Chapter 178 / 10/20 /
Protein localization
/ Chapter 1710/22 /
The cell cycle
/ Chapter 1210/24 /
Mitosis and asexual life cycles
/ Chapter 129 / 10/27 /
Cell cycle control and cancer
/ Chapter 1210/29 /
Meiosis and sexual life cycles
/ Chapter 1310/31 /
Meiosis and sexual life cycles
/ Chapter 1310 / 11/3 /
Lecture Exam 2
11/5 /Mendel’s experiments and First Law
/ Chapter 1411/7 /
Mendel’s experiments and Second Law
/ Chapter 1411 / 11/10 /
Pedigree analysis
/ Chapter 1411/12 /
Chromosomes and genes
/ Chapter 1511/14 /
Chromosomes and genes
/ Chapter 15PART FOUR: FIGHTING ENTROPY
12 / 11/17 / Introduction to metabolism / Chapter 8
11/19 / ATP and enzymes / Chapter 8
11/21 / Cellular respiration / Chapter 9
13 / 11/24 / Cellular respiration / Chapter 9
11/26 / Cellular respiration / Chapter 9
11/28 /
THANKSGIVING HOLDAY – CAMPUS CLOSED
14 / 12/1 /Photosynthesis
/ Chapter 1012/3 /
Photosynthesis
/ Chapter 1012/5 /
Photosynthesis
/ Chapter 10PART FIVE: EVOLVING OVER TIME
15 / 12/8 /
Molecular basis for evolution
/ Chapters 23, 2512/10 /
Molecular basis for evolution
/ Chapters 23, 2512/12 /
Molecular basis for evolution
/ Chapters 23, 2516 / 12/17 /
Lecture Exam 3
(1 hr exam during final exam slot; 8:00 AM)
LABORATORY SCHEDULE
DATES / LAB # / TOPIC9/1, 9/3 / NO LAB DURING FIRST WEEK OF CLASSES
9/8, 9/10 / 1 / Measurement Madness & Diffusion/Osmosis/Tonicity
9/15, 9/17 / 2 / Introduction to Microbiology
Scientific Papers I: Hypothesis Development
9/22, 9/24 / 3 / Bacteria Colony Morphology & Mouthwash Experiment
9/29, 10/1 / 4 / Analysis of Mouthwash Experiment and EMB Plating ResultsDetermining Concentration of Bacterial Cultures
10/6, 10/8 / 5 / DNA Extraction from Bacteria Restriction Digestion of DNA
Scientific Papers II: Structure, Tense, and Voice
10/13, 10/15 / 6 / Agarose Gel Electrophoresis of Digested DNA & PCR Set-up
10/20, 10/22 / 7 / Agarose Gel Electrophoresis of PCR products
Scientific Papers III: Materials & Methods
10/27, 10/29 / 8 / Transgenic Plants I
11/3, 11/5 / 9 / Transgenic Plants II
Scientific Papers IV: Results
11/10, 11/12 / 10 / Human Genetics I: Simple and Complex Genetic Inheritance; Concordance, Twinning, and Cloning
11/17, 11/19 / 11 / Human Genetics II: Enzymatic Tests in Forensic Biology
11/24, 11/26 / THANKSGIVING WEEK – NO LABS
12/1, 12/3 / 12 / Human Genetics III: Detection of Spermatozoa in Forensic Biology; Infertility and Assisted Reproductive Technologies
Structure of Scientific Papers V: Discussions and Abstracts
12/8, 12/10 / COMPREHENSIVE LAB PRACICAL EXAM
12/15, 12/17 / FINAL EXAM WEEK - NO LAB