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Bruce Heyer - Biology

BIOL-6B: Cell & Molecular Biology

COURSE DESCRIPTION

This course is designed to introduce you, the student, to the study and understanding of the structure, genetics, biochemistry, and physiology of cells. The cell is the basic fundamental unit of life. All the processes of life, including harnessing energy, reproduction, inheritance of characteristics, and responding to the environment, can only be fully appreciated with an understanding of their cellular bases. Biol-6B will emphasize processes and structures common to most cells, and prepare you for more extensive, specialized upper-division work.  The development of the field of cell biology and the focus of current innovative research in molecular biology will also be discussed.  You will become more independent by learning to read, interpret, and evaluate original scientific papers. 

The laboratory portion of the course provides hands-on experience using the modern instruments and methods of molecular biology. These elegant techniques provide practical experience for those pursuing careers in biological research.


  • Required Text: Campbell Biology, 11th ed., Reese, J.B., et al; Pearson Education, 2017.
  • Required tutorial-homework-quiz website: Mastering Biology
  • Required Lab Manual: Biology 6B Laboratory Manual, Heyer, B., DeAnza College, 2016.

 


Catalog Information

BIOL 6B: Cell and Molecular Biology
  • 6 Units
  • Hours: Four hours lecture, six hours laboratory (120 hours total per quarter)
  • Degree Status: Credit course - Degree applicable
  • Transfer Status: CSU & UC
  • Grading Method: Letter Grade only

Description

Introduction to cellular structure and function, biological molecules, bioenergetics, molecular genetics, and cell proliferation. The laboratory includes extensive hands-on experimentation in molecular biology..

Student Learning Outcome Statement

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

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COURSE OBJECTIVES

By successfully completing and passing Biol-6B, the student will demonstrate by means of objective exams, essays, oral presentations, laboratory proficiency, and written research reports, a practical competency and fluent exposition of the following topics:

  • Biological chemistry - Explain the application of basic chemical principles to the complex chemistry of living systems. Understand the unique properties of water and carbon as they apply to organic chemistry. Know the classes of macromolecules and their biological significance.
  • Protein function - Describe the special significance of proteins in maintaining and regulating the complexity necessary for all living systems. Define the specific actions of different functional groups of proteins. Explain how the cellular environment modifies protein activity.
  • Molecular genetics - Explain how the structure of DNA relates to its function of storing and conveying information. Define a gene and describe the mechanisms for gene expression and how such expressions are regulated. Demonstrate how these genetic processes can be manipulated for the techniques of molecular biotechnology.
  • Cell structure - Contrast the structure of prokaryotic and eukaryotic cells. Elaborate how the cytoskeleton sustains and transforms cellular organization and provides motility. Identify the eukaryotic organelles and their functions. Illustrate the dynamic structure of cellular membranes and their vital roles in selective permeability and compartmentalization.
  • Inter-cellular communication - Describe the chemical and electrochemical mechanisms of cell-cell interaction. Compare the processes of paracrine and endocrine communication. Contrast the actions of membrane and nuclear receptors on cellular activities.
  • Cell cycle - Describe the processes of mitosis and cytokinesis in cell division. Explain the role of stem cells and regulation of the cell cycle in relation to proliferation, differentiation, apoptosis, and senescence. Postulate how aberrations of this regulation may lead to cancer.
  • Meiosis and sexual reproduction - Explain the modification of cell division for meiosis and gametogenesis. Explain how recombination affects the genome. Contrast the advantages of haploid versus diploid cells, and asexual versus sexual reproduction.
  • Inheritance – Compare and explain Mendelian, chromosomal, and epigenetic models of inheritance.
  • Bioenergetics - Describe how photosynthetic cells harness light energy to synthesize organic molecules, and how all cells use the chemical energy in these organic molecules to power biological processes. Elucidate the chemistry of proton gradients, redox reactions, and phosphorylations as they relate to extracting and distributing energy within the cell. Explain how chloroplast structure controls the chemistry of photosynthesis, and mitochondria structure determines cellular respiration.
  • Laboratory research - Perform routine procedures used in biological research laboratories, especially as related to the techniques of molecular biology. Demonstrate proficiency with standard protocols of lab etiquette, safety, hazardous materials handling, and documentation. Interpret published research articles to replicate their methodology and critique their interpretation of results.

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PREREQUISITES AND ADVISORIES

Biology-6B is the second part of the three-quarter introduction to biology series for college students majoring in biology or a related science. Completion of Biol-6A (organismal biology) with a grade of C or better is a prerequisite for Biol-6B. This series is acceptable for transfer to the University of California and California State University systems and most other colleges. This course is equivalent or exceeds the rigor and depth of the corresponding introductory biology courses at these universities. Since the precise sequence of presented topics differs among institutions, it is strongly recommended that you complete the whole series at one college.

The study of cell and molecular biology requires a comfortable familiarity with chemistry. To enroll in Biol-6B, you need to have passed Chem-1A or Chem-50 with a grade of C or better, or passed the Chemistry Placement Test administered by the Testing Center. You needed to meet this chemistry prerequisite before enrolling in Biol-6A, but Biol-6B is where you'll find that you really use it.

Using equations to calculate solution concentrations, conversions, and product yields in lab exercises requires above average math skills. Intermediate algebra equivalent to Math-105 or Math-114 is recommended.

Students will be writing essays and lab reports with an expected eloquence appropriate for scientific professionals. Coherent composition, accurate vocabulary, proper grammar, and correct spelling DO count! English skills equivalent to EWRT-1A or ESL-5 are highly recommended.

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TIPS TO HELP YOU DO WELL IN THIS COURSE

There is no question that this class can seem intimidating with novel concepts, new vocabularies, and applied chemistry and physics. You must be prepared to invest a substantial allotment of time and effort to this endeavor. Some keys to success and satisfaction are:

  • Attend every lecture and lab.
  • Be prepared! Do the text reading before you come to class. If my lecture is the first you hear of a topic, you'll likely get lost. Especially with the pace we fly through topics: unprepared = frustrated. Prepare questions for unclear material - questioning is a form of active learning.
  • Download and print out the lecture slides, when available, and bring them to class. But don't expect them to replace taking notes. Taking notes is another form of active learning.
  • Develop good study habits. Spend time studying outside of class every day. Do not let yourself fall behind! Review lecture notes after each lecture. Be able to explain the concepts for each diagram presented in your own words.
  • Construct study tools. Learning content-intensive material such as Biology often requires many steps: seeing, hearing, thinking, and doing. Create a list of terms in bold print presented in lecture. Write out flashcards and reorganize your lectures notes after each lecture as physical activities to help you process the material.
    I do not provide study guides for exams - that's your job! I will critique them though if you wish.
  • Form a study group! Repeated experience has shown that those who study collectively do better. A study group will help you get to know your fellow classmates and provide intellectual reinforcement as well as moral support. Come prepared to a group study session by reviewing lecture material on your own first. Compare notes and test each other. Learn by teaching: an excellent way to learn how well you understand a matter is by explaining it to someone else.
  • Review! The textbook supplemental CD-ROM and the publisher's MASTERING BIOLOGY website have flashcards, quizzes, games, and other tools to enhance your comprehension. They even have an online tutor to answer questions! Play the games with your study group. For access, follow the instructions on the first page of the textbook. You can go to the College Library or the Open Media Lab downstairs in Learning Center West for help with internet access.
  • Check for individual and group tutoring at the Math, Science & Technology Resource Center (MSTRC) located in S-43.  
    * A new resource available through the De Anza College student Portal is the Smarthinking Online Tutoring, including biology. For information, go to http://deanza.edu/studentsuccess/onlinetutoring/index.html.
             

 

Participation in this class is expected to proceed with professionalism and mutual respect. Questions and experiences you have to clarify or enlarge on the topics being discussed are welcome. Please do not be distracting to your colleagues (including me) in class. Students are expected to be familiar with the Student Conduct Code and College Policies on academic integrity and academic freedom stated in the De Anza College Catalogue. Individuals found engaging in cheating, plagiarism, or disruptive behavior will be expelled from the class, awarding a failing grade, and reported to the administration for further disciplinary sanctions.

 

Science majors are also expected to have read the BHES Division Student Handbook for additional advice and standards. The Handbook may be downloaded from http://bhs.deanza.edu/StudentHandbook.pdf .

 

 

SUPPORT SERVICES

The college has a wide range of support services to provide students with assistance.  These services range from tutoring and special short courses in reading and writing skills to financial aid and special programs for educational transition, reentry, and disabled students.  If you would like to see if any of these programs would be of help to you, please check with the Counseling and Advising office in the Registration and Student Services (RSS) building. Consult your class schedule for a list of telephone numbers, or go to the Student Services website at http://www.deanza.edu/studentservices .

If you need a special accommodation for a physical or learning disability, please talk to me after the first class session so that I can make appropriate adjustments in the class to meet your needs.  Visit Disability Support Programs & Services (DSPS) and the Educational Diagnostic Center (EDC) in Learning Center West, room 110 for testing, advice, assistance, and special programs. Consult the Disability Information Student Handbook (DISH) at http://www.deanza.edu/dsps/dish/ .

 

SAFETY

The laboratory portion of Biol-6B is much more technology-oriented than was Biol-6A, requiring the use of high-voltage instruments and potentially toxic or infectious materials. All students will be required to read and sign to affirm their understanding and acceptance of the "Standard Operating Procedures" form prepared by the Biology Department. Any student who knowingly or recklessly endangers anyone's safety, or who repeatedly violates laboratory safety rules will be expelled from the class and possibly face further disciplinary actions at the instructor's discretion. If you observe any activity or situation that you think might be unsafe, please let talk to the instructor about it. Beyond this course, developing excellent lab safety habits is essential to your academic progress and scientific career.

Since De Anza College is located in a seismically active area, students should give forethought to catastrophic emergency actions. If a significant earthquake occurs during class, move away from the windows and stay indoors. If you are in lab, disconnect any gas lines or electrical devices, secure glassware, and take shelter under the lab bench.

In the event of an emergency that requires the evacuation of the room, we will exit the building and regroup outside for roll call and further instructions. Be careful to avoid traffic lanes. Do not leave campus until you have been instructed to do so by your instructor or by emergency personnel!

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LABS

Biol-6B strongly emphasizes laboratory-science skill development necessary for biology major degree programs.
Therefore:

  • Participation in all labs is expected and you must pass the laboratory portion to receive credit for the course.  Your aptitude in the laboratory component will be evaluated by weekly online lab quizzes, the five lab project reports, and the cumulative lab exam.
  • Any missed lab will result in a proportional loss of points on the lab report for that day's project or projects.
  • If you miss any three labs you may be dropped from the class or awarded a failing grade.
  • Non-participation is considered equivalent to non-attendance.  Non-participation may be defined, at the instructors discretion, as not actively contributing to all aspects of the activities - including the techniques, calculations and discussions; violating laboratory etiquette or compromising lab safety; focusing on non-class related activities including other classwork, social media or irrelevant online sources; engaging in distracting nonproductive behaviors; or by arriving to lab late or leaving early.

Read the lab experiments before you come to class and come prepared to begin work. It is next to impossible complete a lab exercise and learn anything from the process if you are reading the instructions for the first time. The safety of you and your classmates may depend on your preparedness when we are using hazardous materials.

The activities explored in lab build upon concepts presented in lecture, but they do not correlate with the sequence of topics as they are featured in lecture. The laboratory procedures used will emphasize the modern tools and techniques of molecular biology that are used to study cell biology, as well as many other aspects of life sciences.

The course lab exercises are organized around five lab project reports. Each report will be a group project and cover experiments conducted over several lab periods. The students at your lab table are your lab partners, and your group will turn in one report for each project.

Each project may include different kinds of experiments over several lab periods, and more than one project may overlap on the same lab period. So you will need to have very good organizational and note-keeping practices to keep track of which experiment relates to which project. The projects will become increasingly complex as the quarter progresses, and techniques that are used repeatedly will need to be accomplished with greater efficiency. At first, the instructor will give more detailed instructions on what to do and how to organize your time. But by the latter portion of the course, you will be expected to interpret the instructions and budget your time effectively within your group. It is important to finish each experiment to complete each project.  The better you get at planning and time management, the more opportunities you will have to repeat experiments if needed.

The topics for the five lab project reports are:

  1. DNA restriction digest, ligation, & electrophoresis. Use enzymes to cleave DNA at specific sites and electrophoresis to analyze the cleavage products. This project will take 2 lab periods.
  2. Bacterial conjugation. Use direct and indirect methods to assess the transfer of genes from one kind of bacteria to another by culturing them under different conditions and observing the acquisition of heritable survival characteristics. The project will take all or part of 2-3 lab periods.
  3. pGLO. Insert a foreign gene into bacteria, isolate the new protein gene product from the bacteria, and identify the DNA of the transferred gene in the bacterial DNA. This project will take all or part of about 7 lab periods.
  4. PV92 polymerase chain reaction (PCR). Rapidly copy a part of your own DNA. Compare your DNA with the corresponding part of the DNA of others in the class. This project will take 2 lab periods.
  5. Bacteriophage. Infect bacterial cells with bacteriophage virus. Collect the virus from infected cells and use it to infect more cells. Use molecular techniques to identify the viral DNA from the dead bacterial cells. This project will take all or part of about 4 lab periods.

The project instructions in the Lab Manual include directions for how each report should be composed.

Each report shall be graded on a scale worth 20 points. Each student's score shall be a portion of those points based upon attendance, participation, and contribution to the group effort for that project.

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ASSIGNMENTS & GRADING


ONLINE LAB QUIZZES

To test your progress in the theory and practice of experimental methods, each week a quiz will be posted on the Mastering Biology website covering topics presented and used in the previous week’s labs. Usually the quizzes will be posted Monday afternoon, and due by Wednesday morning — including on weeks with a Monday holiday. The quizzes are time-limited: i.e., once you start the quiz, you have a time limit (usually 30 minutes) to complete it.


LAB EXAM

The final lab class will consist of a comprehensive lab exam derived from all of the lab projects and methodologies. Bring a BB-8 (large) Examination Blue Book for the lab exam essays and illustrations.


ONLINE HOMEWORK EXERCISES

Each lecture topic coincides with tutorials and graded textbook problem sets presented on the Mastering Biology website. These have been selected to enhance your comprehension of the complex concepts that may be presented too quickly in lecture. Be sure to allow sufficient time to derive the maximum benefit from these exercises. Your total score of all these graded problems will be used to calculate your percent score. These homework sets are generally posted weekly on the Mastering Biology website after Thursday’s lecture, and are due before the next Tuesday’s lecture.  If you score less than 90% on any homework set, Mastering Biology will offer some additional questions (ungraded) to help you strengthen your comprehension in the areas you missed. After the due time has passed, the entire problem set will again become available for non-graded practice.


LECTURE EXAMS

There are three exams based upon material covered in lecture. (The final exam is Exam 3.) These exams are non-cumulative and will be composed of multiple choice and matching questions and diagram interpretations. A new (clean and unwrinkled) Scantron Form # 882-E (green) answer sheet and a #2 pencil will be needed for each lecture exam.

Please note the dates of all exams. If you are sick or have an emergency, contact me BEFORE the exam and special arrangements might be made in extenuating circumstances. Vacation plans are not extenuating circumstances! If a last-minute crisis occurred on the way to the exam, contact me before the end of the day.


GRADING

  • Lab Project Reports: Five reports; each report counts 20 points. (5 x 20 = 100 points)
  • Online Homework & Quizzes: Cumulative % score of all exercises and quizzes counts 100 points.
  • Lab Exam: One exam; counts 100 points.
  • Lecture Exams: Three exams. Each exam counts 100 points. (3 x 100 = 300 points)

The final class grade will be determined as a percentage of the maximum total 600 points:

92-100% = A

89-91% = A-

86-88% = B+

80-85% = B

77-79% = B-

74-76% = C+

65-73% = C

53-64% = D

<53% = F

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Last Updated: 9/5/17