Biology 6B Syllabus, Winter 2020

Brian McCauley

Biology 6B is part of a three-quarter-long introduction to biology for students who are planning to major in biology or a related field. Bio 6A, organismal biology, is a prerequisite for 6B. Bio 6B will focus primarily on cell biology, including some chemistry, genetics, and molecular biology. For a more detailed list of the topics covered, see “course objectives” below. By the time you have successfully completed Biology 6A,B, and C, you should have a clear understanding of some of biology’s fundamental ideas, with sufficient depth to prepare you for upper-division courses at a university or for other course work related to life sciences.

Course objectives

By the time you successfully complete this course, you should have a good understanding of the following topics:

Biological Chemistry
How the principles of basic chemistry can be applied to the complex chemistry of living systems. The importance of water in biology. Classes of macromolecules and their biological roles. Cell Structure The structures of cells and their functions. The organization of prokaryotic and eukaryotic cells. The evolution of organelles.
Membrane Structure and Function
The chemical structure of biological membranes and the mechanisms by which this structure allows membranes to function in homeostasis, control of biochemical processes, cell signaling, and other processes.
Respiration & Fermentation
How cells harvest energy from organic molecules and convert it to usable chemical energy. How cell structures, particularly mitochondria, allow efficient control of the redox processes essential to life.
Photosynthesis
How cells harvest light energy and use it to create a proton gradient and synthesize organic molecules. How chloroplast structure functions in controlling the chemistry of photosynthesis.
Molecular Genetics
The structure of DNA and how it carries genetic information. Definitions of genes. The mechanisms of gene expression, and the modes of control of those mechanisms. Includes the control of eukaryotic gene expression and viruses.
The Cell Cycle and Cancer
How cells make new cells. The stages of mitosis. The molecular control of cell fate, including proliferation and differentiation. Cancer as a set of diseases resulting from defects in the control of the cell cycle. The roles of mutations, cell cycle checkpoints, apoptosis, and senescence.
Sexual reproduction and Meiosis
Meiosis as a variation on mitosis. The effects of meiosis and fertilization on genomes. Mendelian genetics A brief overview of how genes are passed from parent to offspring.
Cell communication
This section of the course will cover a variety of topics related to interactions among cells. Hormone action, cell-cell contacts, nerve cell function and other topics.
Laboratory research in molecular biology
How it’s done, in theory and in practice.

You can see the complete official De Anza College Bio 6B Course Outline here.

Course logistics

Class meetings

Biology 6B is a 6-unit course, with 4 hours of lecture and 6 hours of lab per week. For my Winter 2020 class, the meeting times will be:

Lecture:
Monday & Wednesday, 12:30-2:20.
Laboratory:
Tue & Thu, 9:30-12:20 or 1:30-4:20, room SC 2118.
Office hours:
Monday & Wednesday, immediately after lecture in my office: room SC1230 (Science Center faculty office suite, upstairs from the Science Center lecture hall.) Tuesday & Thursday, between labs: 12:20-1:20, room SC 2118 (the lab room).

Grading

You will receive one grade for lecture and lab combined. Grades will be calculated as follows (all scores will be converted to %):

Midterm average 30% of overall grade
Lecture final 30%  
Quizzes & assignments 10%  
Lab final 25%  
Lab participation 5%  
Total:  100%  

All your scores will be converted to percentages, so that if one quiz has 10 questions and another has 45, both will make the same contribution to your grade.

Your grade will be calculated according to this scale:

Grade Overall %
A+ 94
A  90
 A-  87
 B+  84
 B 80
 B- 77
 C+ 74
 C  70
 D  60
F below 60

Your overall percentage score for the quarter will be rounded off (by Excel) to two significant figures for determining your grade. If your score comes out to be 89.7%, Excel will display that as 90% and you’ll get an A.

Midterms
There will be 3 midterm exams. They will include essay, diagram, and multiple-choice questions. There will be study guides on this site.
Lecture Final
Will contain both new material from the last part of the course and review material covered in the midterm study guides. The date and time of the lecture final will be as stated in the schedule of classes.
Quizzes
Expect frequent quizzes. They will come in a variety of formats, including multiple-choice (Zipgrade), short answer, individual and group work. Quiz dates won’t necessarily be announced ahead of time; bring a calculator to lab every day, because you may want it for a quiz. Quizzes may include lab or lecture material. Be sure you keep up. You may be tested on material for a lab on the day you start that lab – that is, before you actually do the lab. Be sure you’ve read the lab pages before showing up for lab.
You may need to print and bring your own Zipgrade forms. I will explain this in class.
In calculating your quiz average, I will first convert all the point scores to percentages. It doesn’t matter if the number of questions varies among quizzes; all will be converted to percent. I will drop your lowest quiz score and take the average of the remaining percent scores.
Lab Final
Will be given during the last lab period. It may cover anything from the quarter’s labs, the lab manual, or information presented during lab.
Lab participation
is just that – showing up and participating in lab. If you miss labs, are frequently late or unprepared, or don’t work with your partners, you will lose points. If you spend your lab periods sitting and not doing lab work, you will lose points. You’ll also lose points if you consistently leave a mess in lab, misuse equipment, or fail to take proper safety precautions. If you come in late, I might have already marked you absent; if so, it’s your responsibility to make sure I know you are in lab. If you came in late and were marked absent, it’s as if you didn’t attend lab. If you don’t let me know that you have arrived, it’s possible that you will fail the course due to missing too many labs.
Lab participation also includes cleaning up the lab when you're done. If you leave a mess, your score will be reduced. If the lab is consistently left messy, with equipment not put away properly, I may lower the lab participation score for everyone in the lab section.

Missed labs and make-ups: Lab attendance is required. Missing one lab won’t necessarily lower your grade, but missing more than one lab will. If you miss miss three labs, you may be dropped from the course, if the drop deadline has not passed. In some cases you may be able to attend the other lab section, but only with the instructor’s permission in advance.

Peer evaluation: I will ask you to evaluate the contribution of your fellow lab group members to your lab work and report writing. I will use your evaluations, along with my own evaluations, to help determine individual lab report and participation scores.

Make-up exams and quizzes: make-ups will generally not be given.

Student Conduct: Students in this course must abide by the rules set out in the  De Anza Academic Integrity policies and the Student Code of Conduct.  Any student who endangers others, fails to follow lab safety rules, or repeatedly disrupts the class may be dropped from the course, possibly receiving a grade of F.

Cheating: cheating in any form is a serious offense. Any student caught cheating will receive a zero on the exam. Cheating includes accessing any electronic device, having any extra papers visible or available during an exam, communicating with anyone, or anything else that could potentially give you an unfair advantage – even if you didn’t intend to cheat. If you are looking at notifications on your phone or other device during an exam, that is considered cheating, regardless of your intent or the content of what you look at.

Other rules for exams and quizzes: Be on time. Arriving late to an exam is disruptive to other students and unfair to your group members if it’s a group quiz. If you are  late for a quiz, I might not let you take it, depending on the nature of the quiz. If it's a group quiz and your lab partners have already done much of the work, you can't show up late and copy their answers. For lab quizzes I will typically show the questions on the screen; if you're late and you miss some questions, you'll need to leave those blank. You may not leave the room and return to finish your exam. For lecture exams, if you are so late that another student has already completed the exam and left, I will not allow you to take the test. It is your responsibility to use multiple choice forms correctly so they can be scored automatically; please don't ask me to re-score them manually if you fail to properly fill in the boxes. Use a soft pencil and bring a good eraser.

Enrollment: I will not add you to the class after the add deadline has passed or drop you after the drop deadline has passed. If you decide to drop the course, that's your decision and your responsibility; if you stop attending but do not drop, you might end up with an F for the class.

Prerequisites and advisories

Biology 6A or the equivalent is a prerequisite for Bio 6B. In 6B, I will assume that you have some basic chemistry knowledge; if you fulfilled the chemistry prerequisite for 6A, you should be adequately prepared. This course also requires a lot of reading and writing; English skills equivalent to eligibility for English 1A are strongly recommended. A substantial part of your grade will be determined by essay exams, and the ability to write clearly will be essential. You’ll also need to read and write quickly.

Required materials

Textbook: Biology, current edition, by Campbell and Reece. It's in the De Anza Bookstore, or you can find it elsewhere. You don't need anything but the textbook itself. Other recent editions of this textbook will be OK, but I can't guarantee that there is no important difference between an older edition and the current one.

Lab website. There is no printed lab manual for my Bio 6B class. Instead, you'll use this website as your guide (see parts of this site). Be sure to look at the calendar page and especially at the lab guide page for the relevant reading for each day's lab. You'll need to have a way to read the day's lab procedures during lab. You can either print out the appropriate pages or use your laptop, phone, or other internet device during lab. There will be a couple of activities in which a laptop will be particularly useful. Also, when preparing lab reports, you will need to use the Bio 6B flickr site to download your photos from lab and compare them with other groups' results.

Special accommodations

Special accommodations can be made for disabled students or others with special needs. If you need any special accommodations, you must contact both the Disability Support Programs & Services office (864-8753) and the instructor, well in advance.

Lab

The laboratory is an essential part of this course. You'll spend more time in lab than in lecture, and the work you do in lab will be a large part of your learning experience and your grade. As with the lecture part of the course, the overall purpose of the lab is to prepare you for further work in biology, whether it’s taking other biology courses or working in any area of biological science. If you successfully complete the Bio 6B lab, you'll be well-prepared to do molecular biology lab work in a university or biotech industry setting. Even if you don’t do lab work in the future, if you are studying biology, you should have some sense of where the field’s knowledge comes from. Also, learning to do lab work is part of the foundation of learning to think scientifically, whether or not you ever use these techniques again.

Lab safety

By the end of this course, you should be prepared to work safely in a variety of lab settings. We will cover safe procedures for handling potentially dangerous chemicals and bacteria, and you’ll learn how to assess the safety of new techniques for yourself. Everybody who works in any kind of lab, for a class or a job, needs to know and follow basic safety procedures. Before you can participate in a biology lab at De Anza, you must read, understand, and sign the “Standard Operating Procedures” sheet prepared by the biology department. Any student who repeatedly violates lab safety rules may be dropped from the course, possibly receiving a grade of F.

Lab organization

The quarter’s labs will be organized around a series of multi-day lab projects, which you'll carry out in groups (one group per lab table).

The projects for the reports will become increasingly complex as the quarter progresses. At first, the instructor will show you exactly what to do and how to organize your time; by the end of the quarter, you’ll be expected to budget your own time as a group. It will be important to finish each experiment, and in some cases you will have time to re-do experiments if necessary. The topics for the labs are:

Plasmid biology: Conjugation, Transformation, and Gene Expression
You’ll use direct and indirect methods to assess the transfer of genes from one kind of bacteria to another. This will require culturing bacteria under specific conditions, purifying purifying DNA and analyzing it with restriction digests and electrophoresis. This will take multiple lab periods.
You’ll transform bacteria with a recombinant plasmid, manipulate the expression of a cloned gene, visualize a cloned protein expressed in the cells using electrophoresis, and purify and examine the recombinant DNA. This project will take multiple lab periods, overlapping with the conjugation lab.
PTC & PV92 Polymerase Chain Reaction (PCR)
You’ll use PCR to copy a specific part of your own DNA and compare it to the DNA of others in the class. The DNA in question is part of a gene that encodes a taste receptor protein; you'll analyze the connection between this gene and your ability to taste specific substances. This project will take 2 lab periods. 
Bacteriophage
You’ll infect bacterial cells with a virus known as a bacteriophage. Then you’ll collect the virus from infected cells and use it to infect other cells. Finally, you’ll use molecular techniques to identify the virus DNA from the dead bacterial cells. This project will take about 4 lab periods.

Student Learning Objectives (SLO)

The following SLO has been created for Bio 6B:

BIOL6B_SLO_1 Demonstrate the ability to use appropriate molecular biology techniques to answer research questions and to interpret and explain the results.

 

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