BIOL 219 – The Living Cell: 2008 Syllabus

Texbook - Cell and Molecular Biology: Concepts and Experiments by Gerald Karp.

To visit the student companion site you can click the link above. If you bought a copy of the text, you should be able to log in and access the resources. There are many, many student resources available including additional websites, tutorials, animations, answers to text questions, self tests, etc.

 

You will need Windows Media Player and/or Quicktime Movie Player to view some animations found below.

You can use Microsoft Office Powerpoint (not free) or OpenOffice (FREE) to view the lectures.

 

Writing these lectures is a dynamic process. Please be aware that the lectures and links posted here may change and may be added to. Check back frequently.

 

Final Exam Schedule (missing from the syllabus)

Section 001 (9:30 am MWF) - 8 am, Thursday, December 11, 2008

Section 002 (8:30 am MWF) - 11 am, Tuesday, December 9, 2008

The official WVU exam schedule for Fall 2008

 

Common questions and my answers. In a class of some 350+ students, I tend to get the same questions from multiple individuals. To help me avoid writing or saying the same thing repeatedly, please review this list of questions and answers before asking.

1. When is the test? Please consult the syllabus linked at the top of this page.

2. What should I study? I try not to get annoyed at this one but often fail because I answer it at least three days per week for ~100 minutes each day (50 minutes from 8:30-9:30 and 50 minutes from 9:30-10:30). The whole point of the lecture is to communicate to you what you should study.

3. How should I study? Every person has different learning styles. What works for me may be ineffective for you and may actually hinder your learning. To avoid this problem, I abstain from answering this question directly. However, I can tell you that the lecture notes serve as a guide. You should also be sure to attend class, read the text, discuss the information with other students, ask questions, consult outside sources, etc. In other words, make every reasonable effort to confirm that you understand the concepts presented.

4. Should I read the book? Yes.

5. Should I study the notes? Yes.

6. What should I concentrate on? See question number 2.

7. Should I study X that you presented in class? Yes.

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Chapter 10 - The Nature of the Gene and the Genome - Chapter 10 Powerpoint

- For more information about calculating probabilities in basic genetics go to this page.

- A tutorial on simple genetic crosses like the ones Mendel performed.

- More complex crosses.

- The Hershey-Chase experiment.

- Some very good information on DNA Fingerprinting and its applications is available on this site.

- For you forensics types, here are the 13 CODIS loci and additional information.

- The transposon animation shown in class. If you get past the first animation, there are several more illustrating how DNA transposons can alter significantly alter genome structure.

- This animation illustrates the complex nature of the human genome by looking in detail at 1/5000th of it.

Chapter 11 - Gene Expression: From Transcription to Translation - Chapter 11 Powerpoint

- The animation discussed in class illustrating transcription. This animation is also part of the textbook website.

- The coordination of transcription factors to initiate the production of an mRNA is illustrated here.

- This site provides detailed information on the transcription factor animation above.

- The addition of the 5' cap and poly-A tail are detailed by this animation.

- Again, the details of the above animation are provided here.

- Finally, this link goes to an animation of the mRNA splicing process/

- Details of mRNA splicing.

- This animation illustrates translation. It is also part of the textbook website.

- An alternative animation of translation can be found at this link.

- With the associated details.

- This very large file (40 Mb) illustrates the details of translation in bacteria.

- This one is even larger (109 Mb) but clearly illustrates the details of elongation discussed in class.

- This animation was created by a high school biology class but is easier to dance to.

- The RNA splicing animation shown in class.

- Protein synthesis as presented by a group of flower children in 1971. Skip the boring intro and go straight to 3:12.

Chapter 12 - The Nucleus and Control of Gene Expression - Chapter 12 Powerpoint

- DNA packaging movie

- The first minute or so of this one illustrates DNA packaging. The rest is stuff from before or for later in the class

- The evolution of human chromosome 2 (original YouTube link) and the paper mentioned in the video

- Telomerase animation

- Lac operon animation and movie

- More Lac operon stuff

- Trp operon animation and movie (containing information on attenuation not discussed in class)

- A simplified but pretty complete picture of gene expression

Chapter 13 - DNA replication and Repair - Chapter 13 Powerpoint

- The Meselson Stahl Experiment animation and quiz

- The Meselson Stahl Experiment animation from class

- Why is knowledge of the molecular processes important? Ever taken an antibiotic? Refer to slides about DNA gyrase.

- DNA replication and the leading and lagging strands (click the first link)

- Simple animation illustrating the extension of a DNA strand from the 3' end.

- Another simple animation illustrating the action of the DNA polymerase complex at the replication fork.

- One of the coolest and most accurate animations of DNA replication I've ever seen.

- Yes, it's true - the DNA replication rap

- Another group take a more 'boy band' approach

- This animation from the Nature website illustrates one version of Nucleotide Excision Repair.

- This little movie also illustrates NER.

- Finally, this animation is essentially useless as far as depicting NER. However, if you like mice wearing t-shirts....

- Here is the 2006 practice test. Please read the instructions before beginning. This is purely for you to get an idea of the kind of tests I administer. This is an exam from a previous semester. There is information on here that you may be tested on but there is also information that will not be on the exam.

Course information from 2007

Finally, evolutionary theory is not explicitly covered in this course but the reasoning implicit in this unifying theory behind all of Biology is a recurring theme. A hobby of mine is to follow the attempts by creationists, intelligent design advocates and others to replace evolutionary theory, an idea that has been throroughly documented and tested, with non-scientific alternatives in the science classroom. Please don't get me wrong. I have no problem with religion. I just don't like it when people try to replace science with their particular religions ideas. If you are also interested in this topic or are just curious, please take a look at the following links.

- The Panda's Thumb - a blog dedicated to "giving another voice for the defenders of the integrity of science."

- 15 Answers to Creationist Nonsense - the title is self explanatory

- An Index to Creationist Claims - a comprehensive rebuttal of nearly all creationist arguments against evolutionary theory

- Understanding Evolution - a basic guide to evolutionary theory and its impact on our lives

- The Kitzmiller Decision - the complete text of the ruling by a U.S. District Judge on the 2005 Pennsylvania case in which the Dover school board required a disclaimer on Evolution be read in Biology classes. Read the whole thing if you like (I have) but I think the important points start being made on page 64.

- "I get frustrated..." - A great response to the statement, "I get frustrated when you guys can't see the impossibilities of evolution."

- The Clergy Letter Project - on which I am listed as a scientific consultant.

- The Church of the Flying Spaghetti Monster

Enjoy.