Presentation of DNA Replication Models

Thank you for sharing all of your hard work on your DNA Replication models!  There were several outstanding pieces of work!  See just a couple of representatives below.  I will try to post the others someplace on line.  Suggestions?

There is no homework tonight (only because the presentations took the entire period and then some!).  We will be starting Ch. 17 on block day, so feel free to read ahead!

On block day you will also have the opportunity to earn a couple of points added to the test score from Monday.  I will be giving you 15 pictures of cells in various stages of division.  Your task will be to 1. decide which cells show mitosis and which are meiosis and 2. put them in order for their respective cycles. 
After the extra credit opportunity I will be giving you a former AP free response question on DNA.  We will also discuss telomeres and then we will begin Chapter 17.

Test Day - Meiosis and Replication

We took a 31 question multiple choice test on these topics in  class.  If you were absent it is your responsibility to arrange a makeup time with me on the day you return to class!

Following the test I gave out an article to read entitled, "Are Telomeres the Key to Aging and Cancer?"  A link can be found here.

Homework is to finish the DNA Replication Interactive Model / Poster to present in class on Tuesday.

Plan for This Week

I hope you all had a good Thanksgiving with lots of good food and plenty of time with your loved ones!

Here is the plan.  I have decided to have our test on Monday.  The project will be due on Tuesday.

Once again, that's:
Test - Monday
Project due - Tuesday

I look forward to seeing your rested and refreshed faces in class on Monday.  Enjoy your weekend!

Preparing for Test on Chapters 13 and 16

Update as of 8 pm Monday.
Thank you to all of you who have sent me updates about tomorrow's late start schedule :).

Assuming that we have school tomorrow we will still be taking the test, but it will be a shortened version.  If we do not have school tomorrow we will have the test on Wednesday, but it will be a shortened version.  If we don't have school tomorrow or Wednesday then enjoy your Thanksgiving and we will just figure it out when we get back to school.

(today's powerpoint is in a different blog entry)

In addition to the test tomorrow you will be asked to commit to a category in which I will enter your DNA model grade.  Once you have made your selection it can not be changed.  Remember that our test category is 70% of your total grade, labs are 20 % and homework is 10%.  If you choose the test category your model will be worth about 1/2 of a test, or 18 points.  If you choose the lab category it will be worth about 20 points and if you choose the homework category it will be worth 40 points.  Choose wisely!


Now that we have worked with the concepts of DNA Replication you should definitely go back and read 16.2 of your textbook.  Also review the animations that have been posted on the blogs from the last two class days.

There will be a bonus question asking you to put 15 diagrams in order.  4 of them show steps of mitosis and 11 are meiosis. 

Think about the following with regard to meiosis:

1. How does the genetic material of the daughter cells compare to the parent cells?  To each other?  How many cells are formed?
2. What is the goal of Meiosis I?  Meiosis II?
3. Is DNA replicated for meiosis?  If so, in which stage?  What happens to the amount of DNA in the nucleus as the cell goes through the cell cycle followed by meiosis?
4. What is the order of events that occur during meiosis?  (for example: synapsis, crossover, separation of homologous chromosomes, separation of sister chromatids, formation of 4 new nuclei, etc.)
5. What are the similarities between meiosis and mitosis?  What are the differences?
6. What does 2n = 46 mean? How many chromosomes would be in a body cell?  In a gamete? 

Think about the following with regard to DNA structure:

1. What did Griffith discover from his work with pneumonia and mice?
2. How did Rosalind Franklin contribute to discovering the structure of DNA?
3. Describe the experimental setup of Hershey and Chase's experiment with bacteriophages.  What did the results show them?
4. What are the base pairing rules?
5. How many rings do purines have?  Which nucleotides are examples?
6. Describe the experimental setup of Meselson and Stahl's experiment using E. coli.  What did the results show them?
7. Practice labeling a DNA diagram.  Make sure you know purines vs. pyrimidines, how to ID the bases, numbering the carbons in a sugar, labeling 5' and 3' end, parts of a nucleotide.

Think about the following with regard to DNA replication:

1. Why do eukaryotes have multiple origins of replication?
2. What is the function of DNA polymerase III, DNA polymerase II, DNA polymerase I, ligase, the primers, helicase, single-strand binding protein and topoisomerase?
3. If DNA has 12% thymine, what percentage will be cytosine?
4. Why do Okazaki fragments form?
5. New nucleotides are attached to which end of the existing nucleotide strand?
6. Why is synthesis of the leading and lagging strands different?

Powerpoint from today's simulation of DNA Replication

The slides from today's powerpoint are to remind you of some of the key elements of DNA replication.  Please use your own materials and ideas if you are creating an interactive model.  BE CREATIVE!  Think about ways you can represent the concepts of class.  Molecules do not need to be represented in the shapes that they appear in the textbook.  No materials need to be purchased.  You can be creative with paper, paper clips, safety pins, cotton balls, toothpicks, tape, and so many other items you probably already have in large supply at home.

Have fun with it!

Extra Credit Assignment Description

If you choose to complete this extra credit lab it will be due on Monday, November 29th (that is the Monday AFTER Thanksgiving). 

1.  Find a protocol for completing a DNA extraction at home. Hint: do a Google search for "DNA extraction at home" :)
2.  Complete the protocol. 
3.  Provide evidence that you completed this lab by taking pictures or video that show YOU doing the lab.
4.  Submit your protocol and evidence on Monday, November 29th. 
* if you would like, I can provide you with a small vial in which to keep your DNA!

This will be entered in your lab category.

Intro to DNA Replication

1.  The new due date for the DNA replication model is Wednesday, Nov. 24th.
2.  The test on Meiosis (Ch. 13), DNA Structure (Ch. 16.1) and DNA Replication (Ch. 16.2) is still on Tuesday.
3.  Remember that on Wednesday we have a wonky schedule with 39 minute classes.

Today in class we started with a warm up to review basic DNA structure. 
We then spent a little time clarifying expectations on the DNA replication model.
Finally we began our discussion of DNA Replication.  We looked at the experiments of Meselson and Stahl which confirmed that DNA replication is semi-conservative, that is, the two strands of DNA separate and then are used as templates for complementary strands.  You can review this experiment here or here.

We will be examining the details of DNA replication together on Monday.  To prepare for our conversation here are some animations:
McGraw-Hill
Wiley
HHMI BioInteractive
Coordination of Leading and Lagging Strand
Movie of the process

See you Monday!

DNA REPLICATION MODEL RUBRIC

If you are looking for the post from class on Thursday, Nov. 18 go to the post titled "DNA Structure"

This project will be due on Tuesday, November 23^rd.  Depending on the grade you want, you can choose the level that you complete.  Please notice that to get credit for each level you must complete the level prior.

If you complete:

Level 1 you may receive up to 50%

Level 2 you may receive up to 70%

Level 3 you may receive up to 82%

Level 4 you may receive up to 92%

Level 5 you may receive up to 100%

DNA Replication Process Rubric for Interactive Model/Poster.                           Name: ______________________

Note: you will receive the grade for the lowest level that is complete.

Level 1: DNA Structure Not Interactive

Nitrogenous bases A,T,G, and C                                                       _____

5’ and 3’ ends labeled                                                                        _____

Antiparallel strands                                                                             _____

Hydrogen bonds (2 vs. 3)                                                                   _____

Purines (2-ring) and Pyrimidines (1-ring)                                         _____

Phosphates labeled                                                                             _____

Correct base-pairings shown                                                             _____   

Level 2: Replication on the Leading Strand. All of the above, plus:

Multiple Origins of Replication/Bubbles                                         _____

Helicase shown                                                                                    _____

     Explained                                                                                         _____

Topoisomerase shown                                                                        _____

     Explained                                                                                         _____   

Single-strand binding proteins shown                                              _____

     Explained                                                                                         _____

5’ and 3’ end labeled                                                                          _____

Replication on the Leading strand

     Leading strand labeled                                                                  _____   

     5’ and 3’ ends labeled on old and new                                       _____

     DNA polymerase III shown                                                         _____

          Explained                                                                                    _____

     Primer shown at start                                                                     _____

     Next incoming nucleoside triphosphate shown                        _____

     DNA polymerase I shown                                                             _____

          Explained                                                                                    _____

Level 3: Replication on the Lagging Strand. All of the above, plus:

Shows a specific DNA sequence                                                       _____

Replication on the Lagging strand  

     Lagging strand labeled                                                                  _____

     5’ and 3’ ends labeled on old and new                                       _____

     Okazaki fragments shown                                                            _____

          Explained                                                                                    _____

     Primers shown                                                                                _____

          Explained

     Ligase shown                                                                                   _____

          Explained                                                                                    _____

     DNA polymerase I shown                                                             _____

          Explained                                                                                    _____

 Next incoming nucleoside triphosphate shown                            _____

Explanation of where energy comes from to create growing strand         _____

Explanation of why replication on the lagging strand is discontinuous    _____

Level 4: Interactive! Leading Strand. All of the above, plus:

Model can be used to show how replication occurs on the leading strand.  Must include accurate application of:

New nucleotides arrive as triphosphates that lose two phosphates before they can bond                    _____

Attachment to growing DNA strand             _____

DNA polymerase III          _____

Primer            _____

Level 5: Interactive! Lagging Strand. All of the above, plus:

Model can be used to show how replication occurs on the lagging strand.  Must include accurate application of:

New nucleotides arrive as triphosphates that lose two phosphates before they can bond       _____

DNA polymerase III         _____

Primers                  _____

DNA polymerase I           _____

Ligase                     _____

Okazaki Fragment         _____

DNA Structure

Today and yesterday were block day classes.  We began the class with Watson and Crick's original publication in Nature from 1953.  You can look at it again here where you will also find links to several other significant papers from that same era.  Notice that an article by Wilkins and one by Franklin also appeared in the same issue!

I asked students to identify, in the brief Watson and Crick article, the significant descriptors of DNA.  We were able to find approximately 15 specific items.  Those were then used to fill in a blank diagram of part of a DNA molecule.  We were able to locate phosphates, sugars and bases, label the carbons of deoxyribose, discuss the difference between deoxyribose and ribose, label the 5' and 3' ends of the molecule, correctly tag cytosine, guanine, adenine and thymine based on their size and # of hydrogen bonds, differentiate between purines and pyrimidines (PuAG2!), learn that the helix shows a full twist every 10 nucleotides and that nucleotides are 0.34 nm apart.  We also added that the two strands of DNA run anti-parallel, that it is double-stranded and the width of the molecule is 2nm. 

Here is a blank DNA diagram so that you can practice
With limited time remaining in class I introduced several upcoming items:
1. We have a test coming up next week.  I am now planning for TUESDAY.  It will cover Ch. 13 (meiosis and sexual reproduction), Ch. 16.1 (DNA structure) and Ch. 16.2 (DNA replication).  You will definitely see a reproduction of the DNA diagram we used today in class on the test.
2.  There is an opportunity for extra credit, which would be due on Monday, 11/29.  This assignment will be described in another blog entry, titled "EXTRA CREDIT DESCRIPTION"
3. I am assigning a project on DNA replication.  I am now planning that it will be due on TUESDAY.  This project will be described in greater detail in another blog entry, titled "DNA REPLICATION MODEL."

Your homework tonight is to skim the section (Ch. 16.2) on DNA replication.  Make a list of the following enzymes and explain what they due during DNA replication (note, if you are in 2nd or 3rd period this same list is on your reading guide and you may just fill it out there)

• helicase
• topoisomerase
• single-strand binding proteins (not really an enzyme, but we will include it anyway)
• DNA polymerase III
• DNA polymerase I
• ligase

In addition, you may want to take a look at one of the following animations of DNA replication.
McGraw Hill - select the first and last animations in the list

Discovery of DNA Structure

We began class today by going over some of the conceptions in Meiosis that I saw in the paragraphs you wrote for me yesterday.  The most common mistakes were seen in the events of Prophase I.  I drew pictures and a flow chart on the board which I asked students to copy into their notes.  I also pointed out some other areas of confusion, such as when chromosome duplication happens (it is in the S phase of interphase, just like before mitosis) and how haploid cells relate to gametes (the haploid cells at the end of meiosis will be modified to become functional gametes).

Another great review of the whole process of meiosis can be found here

We then discussed the significance of Griffith's experiments with pneumonia and mice.  The conclusion he was able to draw was that a specific molecule is responsible for genetic traits.  However, his work did not show that this molecule was DNA.  Most scientists still believed that proteins were the more likely candidate.

Your book does not spend much time discussing the significant contributions of Avery, McLeod and MacCarty so I gave each table a worksheet that gave an overview of their experimental design and a picture of the results they received.  Students drew conclusions based on this information and determined that this experiment showed that DNA must be the transforming agent in Griffith's work.

The homework for tonight is to review the structure of DNA. 
Then watch the animation describing DNA structure HERE.
And examine DNA structure at DNA Interactive.  At DNA Interactive examine the module titled "Finding the Structure."  Use the tabs at the top to navigate.  When you look at "pieces of the puzzle" take some time to read about Rosalind Franklin's X-ray and Pauling's triple helix. 

• What two things did Watson and Crick learn from her X-ray?
• Why was Pauling's triple helix impossible?

Try your hand at the "Base Pairing Interactive" under "Putting it Together."  After you have given up take a look at the clues. 

• Click through the Clues and write down the rules of base pairing that are given to you.

Finally, link HERE to read the original publication by Watson and Crick in Nature.  Note that this incredible breakthrough only took up ONE PAGE in the journal!  We will be talking about this in class tomorrow.

The Concept (Map) of Meiosis

Today in class we worked on Concept Maps of meiosis using the following 11 terms:

• haploid cell
• diploid cell
• meiosis
• meiosis I
• meiosis II
• prophase I
• gamete
• synapsis
• crossing over
• recombination
• homologous chromosomes

We shared these out on the overhead projector (kickin' it old school).  At the end of class I asked each student to explain the process of meiosis in a paragraph using each of the 11 terms.  I have now looked at some of your submissions and will be addressing the common misconceptions at this blog later this evening.

There is no new homework.  We did not begin discussion of Chapter 16 today so I will not collect the reading guide until tomorrow.  Please bring it with you to class. 

The Benefits of Sexual Reproduction

SEE THE NOTE ABOUT THE READING GUIDE HOMEWORK AT THE BOTTOM.

Today we focused on understanding why sexual reproduction is far more prevalent than asexual reproduction in organisms, although it is much less efficient.  The main factor we discussed as playing a role in sexual reproduction is variation (note: there are several different hypotheses suggested here).  That variation comes from the process of meiosis.  (see links to meiosis from earlier blog posts)

1. Meiosis begins with a single cell containing diploid replicated chromosomes.
2. In Meiosis I homologous chromosomes are separated, resulting in 2 cells containing haploid replicated chromosomes.
3. In Meiosis II sister chromatids are separated, resulting in 4 cells containing haploid unreplicated chromosomes.

The variation comes in at three points:

1. Crossover between non-sister chromatids of homologous chromosomes.
2. Independent assortment of homologous chromosomes at metaphase I.
3. Random fertilization.

On Monday we will be focused on the discovery of DNA structure.

Homework:
You received a reading guide for Ch. 16 in class today.  You only need to complete 16.1 for Monday! 

• If you are in 2nd or 3rd period you received the reading guide for the whole chapter, so ONLY COMPLETE 16.1. 
• 5th and 6th period only received the part of the reading guide that pertains to 16.1 so you must COMPLETE THE WHOLE THING.

See you Monday and have a GREAT 4 days off!!

Tomorrow we have a funky schedule.  Here it is:
1st 7:30 - 8:09
2nd 8:14 - 8:53
3rd 8:58 - 9:37
4th 9:42 - 10:21
5th 10:25 - 11:04
6th 11:08 - 11:47
7th 11:51 - 12:30

Today, once again, different classes did different things.  2nd and 3rd period went over the test.  2nd period had time to start a discussion of meiosis.  3rd period only had a 20 minute class due to the extended Veteran's Day assembly.  5th period we discussed Cell Cycle Controls and briefly introduced meiosis. 6th period we wrapped up our discussion of cancer and began a discussion of meiosis.  In all classes I collected the homework from yesterday's blog.

Tonight's Homework:
The main benefit of sexual reproduction, from an evolutionary standpoint, is the variation it produces.  Read Section 13.4 in your textbook to learn about the three main sources of variation resulting from meiosis. You should be able to discuss how each of the following contributes to variation: independent assortment, crossing over and random fertilization.

On your textbook website I highly recommend watching "13.4 Activity: Origins of Genetic Variation" and the Bioflix animation for Meiosis (select Bioflix from left menu and then go to Chapter 13 Meiosis).  Test your knowledge by completing the tutorials and self quiz after watching the Bioflix animation.

You do not need to submit an assignment to me.

Note: There will be homework over the 4-day break :(

Cell Cycle Controls, Going over Friday's Test, etc.

Today was a bit of a "mish-mash." See below to find out how we spent your class period.  HOMEWORK is at the bottom.  Please note the 9 questions I ask you to answer on paper.

I finally got a chance to grade Friday's test and the scores overall are much better!  The average has gone up by 15% , from 63% to 78%.  I still have great concerns about the 32 students who scored below 70%.  I would love to have an individual conference with each of these students to find out what we can be doing differently.  Please try to schedule a time during tutorial in the next few days so that we can talk.

In 5th and 6th periods I was able to discuss Friday's test.  6th period also began the discussion of cell cycle regulation.

In 2nd and 3rd period we discussed the details of cell cycle regulation, specifically clarifying the roles of cyclin and cyclin-dependant kinases. The synthesis of cyclin was linked back to cell communication in the form of growth factors that may lead to transcription of the cyclin-forming genes.  Additionally we clarified the roles of the three main checkpoints of the cell cycle. 

In all classes I collected the 6 questions on the Cell Biology and Cancer reading that was assigned Friday.

Tonight's Homework:
We are beginning our unit on Genetics, which begins with a look at how we pass on genetic information.  There are a few topics from Chapter 13 that deserve special focus.  The FIRST is the comparison of sexual life cycles.  We will review this during class.  The THIRD is the process of crossing over during synapsis.  We will be completing an activity in class on this topic.  The SECOND topic is meiosis.  The basics of this process can be studied on your own, outside of class. 

1.  Use your review book, textbook (pp. 244-245) to study the main stages and events in the process of meiosis.
2.  Watch the animation at http://www.sumanasinc.com/webcontent/animations/content/meiosis.html and select "Step Through."
3.  ON PAPER, answer the following questions about the most significant aspects of meiosis.
--All animations referred to below can be found at this link: http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter12/animations.html

After watching "Stages of Meiosis"
     1. What is the goal of Meiosis I?
     2. What is the goal of Meiosis II?
After watching "Unique Features of Meiosis"
     3. Explain synapsis.
     4. Explain homologous recombination.
     5. Explain reduction division.
After watching "Comparison of Meiosis and Mitosis"
     6. Make a list of similarities.
     7. Make a list of differences.
After watching "Random Orientation of Chromosomes During Meiosis"
     8. Why is random orientation of chromosomes during meiosis significant?
     9. The cell in the example had 3 pairs of homologous chromosomes.  Humans have 23.  How many different combinations of chromosomes can humans have in the gametes they produce?

REtake of Cell Test

I had a substitute today, as I had to attend a district meeting.
In my absence you were given the opportunity to show me that you now fully understand the concepts of cell transport, cellular communication and cell division.  I am excited to see the much improved scores on this test!

After the test you finished reading the Cell Biology and Cancer article that we began on Monday.  Your assignment was: AFTER reading each section to write a higher level question (not just recall) about the main concepts of that section.  The sections you needed to write a question for were:

• What is Cancer?
• Oncogenes and Signal Transduction
• Tumor Suppressor Genes
• DNA Repair Genes
• Cell Cycle
• Tumor Biology

An example of a higher level question would be, "how is ______ like _____?"  or "differentiate between ____ and ____."

I will see you on Monday!  Remember that we have a short week next week!

Follow up on Yesterday's Test

How should I begin?  The results from yesterday's test were... disappointing and surprising.  We spent the period today going through the questions from the test and discussing strategies for approaching the questions.

Here is what is going to happen: ALL STUDENTS WILL BE RETAKING THE TEST IN CLASS ON FRIDAY.  There will NOT be test corrections on this test.  After having spent 90 minutes going through the questions there is no excuse for not doing well.  The test will be the exact same format as the first time, but with slight tweaks to each of the questions.

Homework: Hmm.  Just make sure you are ready to discuss 12.3 in class.

Cell Test!

Today we spent a joyous class period demonstrating our knowledge about all things cell transport: cell membrane structure, cell communication and cell division.

Upon completion of our assessment we worked on a set of questions to accompany section 12.3: Cell Cycle Controls.

Homework is to complete the questions for 12.3.

Intro to Cancer and disruption of cell cycle control

I passed back the worksheet from Chapter 12.

We discussed what is going to be on tomorrow's test:

• All of Chapter 7 - membrane structure, transport (including water potential)
• Cell communication from blog on 10/
• Ch. 12.1 and 12.2 - cell cycle and mitosis, including cytokinesis adn binary fission
• Cancer as a disruption of cell cycle controls - roles of protooncogenes and tumor suppressor genes

We then read the beginning of the Cell Biology and Cancer packet and discussed what cancer is.  The focus questions for this reading were:

1. What is the normal role of a proto-oncogene?
2. What is the normal role of a tumor suppressor gene?
3. Why must there be mutations to both tumor suppressor genes and proto-oncogenes for cancer to occur?
4. Would you need mutations in both copies of your proto-oncogenes to cause a problem to the cell cycle?  Explain.
5. Would you need mutations in both copies of your tumor suppressor genes to cause a problem to the cell cycle?  Explain.

Your homework is to study for tomorrow's test!