Exploring Proteins with Molecular Workbench

You will use the Molecular Workbench software to explore protein structure and the processes of transcription and translation.

The homepage of the molecular workbench software is: http://mw.concord.org/modeler/

You can run/install the software from that page.  After you install and run the software, sign in and you should see a list of activities for my class.  The protein structure activity is number 12.  The DNA to Protein activities are the top two items.  You should answer the questions throughout each activity and submit a report online to me at the end of each activity.

I would recommend the following order:

  1. Molecular Workbench – DNA to Proteins Part 1 (#1) = see how DNA codes for proteins
  2. Molecular Workbench – Four Levels of Protein Structure (#12) = gain a deeper appreciation for protein structure
  3. Molecular Workbench – DNA to Proteins Part 2 (#2) = see what happens to protein structure when you mutate the DNA

Due:  Monday, 3/25/13

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Proteins: The Structures of Life

Read the book The Structures of Life.  You should type the answers to all the “Got It” questions at the end of each chapter.  Also, you should read page 86 in the class textbook (in chapter 3) and summarize the cause of cystic fibrosis in 2-3 sentences in the same document as the “Got It” answers.   Remember, you can view the book online or download a free pdf version of this book or order a free print version from the NIGMS website.

Due: Wednesday, 3/19/13

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When Whole Grain is Not Telling the Whole Truth

Food companies can say lots of things on their labels that might mislead the shopper into thinking they are buying healthy items when they are not.  One of these issues revolves around whole grain foods.  Read this article to learn what terms have a legal meaning and which do not.  Be sure to check out their guide to decoding ingredients in grain products too.

Then go to the DNA page on my wiki and complete the section under ‘Extracting DNA’.  Be sure to understand the parts of the wheat seed.

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Karyotype Homework

Complete the following to deepen your understanding of karyotypes:

  • Go to my wiki karyotype page, read it and complete the practice link at the bottom of the page
  • Complete the instructions in the Going Further section of the Karyotypes activity given in class.  Those instructions are…
    • Using reference material, research the following human genetic disorders: Patau syndrome, and Edwards syndrom.  For each disorder find the cause, type of mutation, and characteristics.  Construct a karyotype for each.
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DNA Model

Your task is to create a DNA model. You may use any materials you wish when constructing your model, except food items. The model should be at least one foot long and be as realistic as possible. It should show the sugar (shaped correctly), phosphates, bases, the anti-parallel nature of the two strands, the 3′ and 5′ ends (structurally correct), the number of bases per turn, the correct base pairings, the hydrogen bonding between bases (2 or 3 as appropriate), etc… At least part of the model must be twisted in the helix shape.  You also must include a ‘key’ that explains what each item is.  There are examples in class for you to view.

Due: Monday, 3/11/13   Wednesday, 3/13/13 (due to Junior Research)

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DNA Structure (JMOL)

Go to my wiki page located here.  You will see two links (Exploring DNA and DNA Structure).  You should visit these pages in the order presented and view the JMOL interactive models at those sites.  These are very cool 3-D models that you can manipulate to understand the structure of DNA.  After you view the first site (Exploring DNA) and while you are viewing the second site (DNA Structure), you should answer the questions from the Question Sets you received in class.  A copy in pdf format can be found here.  Please don’t just rush to answer the questions.  Take your time to investigate and appreciate the beauty of DNA and of these modeling programs.

Due:  Friday, 3/1/13

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Biology Cell Test

You will have a test on the following:

  • cell organelles (identification and function)
  • animal vs. plant cells
  • cell cycle and mitosis
    • stages & events
    • identify pictures of various stages
  • microscopy
    • identify parts of a microscope
    • microscope usage
    • compare types of microscopes (light, electron, atomic force)
  • eye
    • identify parts of the eye
    • how vision works
    • vision problems as discussed in class

The test will be on Wednesday or Thursday, 1/9/13 or 1/10/13, depending upon your section

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Microscope Practical

You will have your microscope practical starting on Monday, 12/17/12.  The practical will consist of:

  • slide preparation
  • microscope usage
    • focus under low magnification
    • focus under higher magnification
  • locating an object using the scope
    • e.g. a cell in anaphase
  • depth of field
    • determining red/blue/yellow thread order
  • open question
    • I will ask a question about the microscope or magnification etc…
  • clean up
    • slide removal and cleaning
    • microscope off

There are certain mistakes that will result in an automatic zero, such as turning the course adjustment knob under any objective lens higher than 4x or the inability to find and focus an object under low power magnification.

You may practice during activity period, study hall or before school.  I will be testing neuroscience students after school so my room will not be available this week during that time.

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