Welcome Back from Break!

Here we are again...

1. Reminder that the Vacation Assignment packet is due on March 7th.  Please do not leave this until the weekend!
2. We looked at the fruit flies that mated over the break.  We got to see both larvae and pupae as we await the hatch!
3.  The rest of the class time was spent going over the assessment of Chapter 14 and 15.  You will find grades (out of 21) already posted.

HW: work on the Vacation Assignment packet!

Friday Before Break - Hello Drosophila!

Today we learned how to distinguish male from female fruit flies.  We also distinguished between the four fly types: wild, sepia, scarlet, and white eyes.

This was a lab book entry.  Title: Fruit Fly Lab.  Sketch of a male and a female fly.  Written description of the eye color of each of the fly variants.

At the end of class I collected the Self-Directed Biotech Tutorial.

Have a wonderful break!

Block Day before break

On block day I gave students time to work on their biotechnology self-directed tutorial.  See yesterday's entry for details.

Students also received the Diversity Unit Vacation Assignment.  This will be due MARCH 7th!  If you did not receive the packet you can pick it up after break.

Biotech Tutorial Day 1

We are working with our class textbooks and on our computers to learn about the techniques used in biotechnology.  It is REALLY important that you read the information in your textbook before viewing the animations.  Refer to the "Objective" statements in each section to make sure you have understood each technique fully.

The handout of summary questions that you received in class is due on Friday.

Self-directed tutorial on DNA Technology

DNA technology is an evolving field.  There are lots of resources available that will help you more than just reading in a book.  I’ve put together this tutorial to give you the opportunity to see the procedures in action through animations and, in some cases, to perform simulations.  These exercises are not meant to stand alone.  Use your book to support your understanding of the topics described in this tutorial as you proceed.  You may go at your own pace as long as you complete all activities by the due date.  There are several activities that we will be completing as a whole class. 

Topic 1: DNA Cloning (this topic is covered on pp. 385 – 392 of your text):

            Background: DNA cloning permits production of multiple copies of a specific gene or other DNA segment.  This can be accomplished using a bacterial plasmid, polymerase chain reaction, and a few other techniques we will leave for another course.  Why do scientists need to clone DNA?  Here are a few of the many reasons: to produce a protein product (ex. human growth hormone), to provide an organism with a new metabolic capability (ex. pest resistance), or to produce enough copies of the DNA for analysis (ex. at crime scenes). 

THE TECHNIQUES

Restriction Enzymes (p. 386) – these are needed to make DNA that contains nucleotide sequences from two different sources.  For example, if we want to insert a gene for human growth hormone into a bacterial plasmid we would use restriction enzymes.  The bacteria will then produce the human growth hormone, a protein, as part of its regular metabolism.

Objectives

After completing the restriction enzyme section (animation AND reading in the text) the student should be able to:

• Describe the natural source and function of restriction enzymes.
• The student should be able to understand why restriction sites need to be palindromic.
• The student should be able to explain how restriction enzymes can be used to combine DNA from two different sources to make recombinant DNA.

1.  Online go to http://www.dnai.org/b/index.html (you might want to bookmark this – we will be going back to it several times)

            At this website, click on “techniques” (the bottom middle button). 

            From there, click “cutting & pasting” at the top of the slide.

            a.   View the animation for “Cutting and pasting DNA”

b.   Then watch the animation of “Recombining DNA”. 

READ THE ACCOMPANYING TEXT to understand what is going on and why!!!

Bacterial plasmids (pp. 386-388) – these are small circles of extrachromosomal DNA found in many types of bacteria.  Plasmids are often used because they can be easily isolated from bacteria, manipulated to form recombinant plasmids by insertion of foreign DNA, and then reintroduced into bacterial cells.  Moreover, bacterial cells reproduce rapidly, multiplying any foreign DNA they carry.

Objectives

After completing the restriction enzyme section (animation AND reading in the text) the student should be able to:

• Explain how vectors are used in recombinant DNA technology
• Suggest limitations of using bacterial vectors to create mammalian proteins

1.  Online view the animation about cloning genes using bacterial plasmids at   http://www.sumanasinc.com/webcontent/animations/content/plasmidcloning.html

2. (practice it) Read and complete the Worksheet entitled “Gene Cloning”

3.  Online, learn about cloning genes by going to http://www.dnai.org/b/index.html

            Once again, click on “techniques.”

            From there, click “Transferring and Storing.”

            Watch the animation for “Transformation.”

Forming cDNA (p. 390) – one of the problems with using bacteria to produce human proteins is that bacteria do not have introns within their genes.  They do not have a mechanism to get rid of the introns that are within the human gene.  To get around this, scientists produce complementary DNA (cDNA).  This process uses a messenger RNA transcript from the gene (so the introns have been removed) and the enzyme reverse transcriptase to produce DNA. This can then be inserted into the plasmid.

Objectives

After completing the restriction enzyme section (animation AND reading in the text) the student should be able to:

• Give a step-by-step description of how cDNA is created.
• Explain why we need to use cDNA when bacteria are the vector
• Explain the role of reverse transcriptase in creating recombinant DNA

Creating a DNA Library (pp. 388-390) – a DNA library, or genomic library, is the complete set of plasmid clones, each carrying copies of a particular segment from the initial genome.

Objectives

After completing the restriction enzyme section (animation AND reading in the text) the student should be able to:

• Define and distinguish between genomic libraries using plasmids, phages, and cDNA.

1.  Here is how it is done (click on either “step through” or “narrated”): http://www.sumanasinc.com/webcontent/anisamples/nonmajorsbiology/dnalibrary.html

2.  And another one:   http://www.dnai.org/b/index.html

            Once again, click on “techniques.”

            From there, click “Transferring and Storing.”

            Watch the animation for “Storing”

PCR (pp. 391-392) – Polymerase Chain Reaction allows for very quick amplification (many copies) of any specific DNA target segment.  The process takes place in a test tube, so no living organisms are required.  With automation, PCR can make billions of copies of a target segment of DNA within a few hours.

Objectives

After completing the restriction enzyme section (animation AND reading in the text) the student should be able to:

·         Describe the polymerase chain reaction (PCR) and explain the advantages and limitations of this procedure.

1.  Online, click the “PCR simulation” in the text at http://www.amnh.org/learn/pd/genetics/pcr/

2.  Then try this other simulation at http://www.dnai.org/b/index.html

            Click on “techniques” then “amplifying.”

            Perform the interactive tutorial entitled “Making Many Copies of DNA”

Topic 2: Restriction Fragment Analysis (pp. 392-394) –

            Background: This can be used to detect DNA differences that affect restriction sites.  Some applications of restriction fragment analysis are: to look for variations in genes from person to person, to identify whether a particular allelic change is associated with a hereditary disorder, to find where a gene is located in the genome, and to compare the same gene from species to species to investigate evolutionary relationships.

THE TECHNIQUES

Gel Electrophoresis –this process is used to separate molecules based on size and charge.

Objectives

After completing the restriction enzyme section (animation AND reading in the text) the student should be able to:

·         Explain how gel electrophoresis is used to analyze nucleic acids and to distinguish between two alleles of a gene.

1.          Online, review gel electrophoresis by going to http://www.dnai.org/b/index.html

            Click on “Techniques” and then the “sorting and sequencing” button.

            Watch the animation titled “gel electrophoresis.”

2.         (Practice It) Complete the activity “DNA Goes to the Races”

3.         (Practice It) Complete the questions from the worksheet entitled “Restriction Maps and Logic Puzzles”

Southern Blot – this technique uses a combination of gel electrophoresis and then a specific probe to identify sequences within the DNA.

Objectives

After completing the restriction enzyme section (animation AND reading in the text) the student should be able to:

• Describe the Southern blotting procedure and explain how it can be used to detect and analyze instances of restriction fragment length polymorphism (RFLP)

1.  Watch and read this animation that follows both gel electrophoresis and southern blotting: http://bcs.whfreeman.com/thelifewire/content/chp16/1602001.html

2.  Try your hand at the following online quiz after watching the animation http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter14/animation_quiz_5.html

Topic 3: Genomics – this is the study of whole sets of genes and their interactions.

THE TECHNIQUES

DNA Microarray (pp. 400 – 401) – consists of tiny amounts of a large number of single stranded DNA fragments representing many genes fixed to a glass slide in a tightly spaced array (grid).  This is used to measure the expression of thousands of genes at one time.

Objectives

After completing the restriction enzyme section (animation AND reading in the text) the student should be able to:

• Explain the purposes of gene expression studies. Describe the use of DNA microarray assays and explain how they facilitate such studies.

1.  Online, go to http://highered.mcgraw-hill.com/sites/0072437316/student_view0/chapter16/animations.html#

            Select “Microarray” from the list to see how a DNA microarray is created   (although all of the other animations are very good, too).

2.  Watch the interactive animation of the process at http://www.bio.davidson.edu/courses/genomics/chip/chipQ.html

3. Great interactive!  http://learn.genetics.utah.edu/units/biotech/microarray/

Revisiting Personalized Medicine

Today we went back to the personalized medicine case that we started way back in October.  The case dealt with two girls, Beth and Laura, who were both diagnosed with Leukemia.  Both girls were given the same treatment, but Laura almost died from it.  Through the case we learned that the drug interferes with DNA replication, but any excess is supposed to be converted to an inactive form and removed from the body.  The enzymes involved in the metabolic pathways are coded for by genes (of course). A small percentage of the population has a mutation to the gene that codes for the enzyme, TPMT, that breaks down the drug into its inactive form.  This means that excess drug remains in the body and interferes with DNA replication even in healthy cells.  This is most likely what is going on with Laura.

I did not give a homework assignment since I was not at school on Friday to get anything ready.  Enjoy it!

Quiz Day with a Substitute

Sorry I was out with a sick little boy :(

However, the quiz still went on!  If you were absent for the quiz you need to see me as soon as you get back to school so we can schedule a time for you to make it up.

Oh, by the way, I am throwing out question #5 since I accidentally forgot to include the correct answer.

Block Day - Wrapping Up Heredity

Today we applied the Chi-Square equation to some practice problems.  On our test you would be given the equation and a copy of the probability table.  You would be responsible for calculating the Expected Values, Calculating the Chi-Square value, determining degrees of freedom, interpreting the probability table and determining if your hypothesis should be accepted or rejected.

How to read the probability table: Once you have determined your chi-square value you must calculate degrees of freedom.  This is simply the number of classes (for example, there are 4 classes for blood type, O, A, B, and AB) and subtract 1 (for the blood type example the degrees of freedom is 4-1 = 3).  Then look at that column in the probability table.  In science experiments we only use the 0.05 probability row.  Compare the chi-square value to the number in the table.  If chi-square value is BELOW the number then we ACCEPT our hypothesis, if the chi-square value is ABOVE the number then we REJECT our hypothesis.  The interpretation of the table is that if our chi-square value is above this number then there is a 95% likelihood that our deviation from expected is due to something other than chance.

The second half of class was spent going over 15.4 which discusses chromosomal abnormalities.  Use your textbook to review these concepts if you are having difficulty with them.  Below is a picture from the power point that shows the rates of various chromosomal abnormalities.

LIST OF TOPICS YOU SHOULD KNOW FOR TOMORROW's TEST:

monohybrid crosses

incomplete dominance crosses

codominance crosses

multiple alleles (blood types)

pedigrees

dihybrid crosses

pleiotropy

epistasis

polygenic traits

linked genes

creating linkage maps from crossover data

sex-linkage

non-disjunction errors

deletion, duplication, inversion, translocation errors

Sordaria Crossover Data

Today in class we collected data on the rate of crossover in Sordaria.  We found that the distance between the centromere and the gene for spore color was approximately 28 map units.  If you were absent today you will need to get the data from a classmate.  For analysis of the lab I asked students to draw the chromosomes at the end of meiosis I and meiosis II when crossover has occurred.

Toward the end of class I introduced Chi-Square statistical analysis.  This is a calculation used to determine if data collected differs significantly enough from the expected to indicate that our initial hypothesis is refuted.

There is no homework, unless you did not complete the chromosome drawings for the analysis of the Sordaria activity.

Don't forget the test on Ch. 14 and 15 this Friday!

Set up for Sordaria Activity

1.  I gave the answers to the homework document on gene linkage from Thursday.
2.  I announced a TEST for FRIDAY on Chapters 14 and 15.
3.  I assigned the HOMEWORK - read about X-inactivation on p. 284 and then read Ch. 15.4.
4.  We discussed X-inactivation

• X-inactivation is responsible for dosage compensation (the reason why males and females function basically the same even though females have twice as many X-chromosome genes)
• The inactivated X is called a Barr Body and can be detected as a black dot when seen through a microscope.
• X-inactivation happens early in embryonic development.  50% of the cells should shut down the maternal X and 50% the paternal X.  All cells created through mitosis from these will shut down the same X chromosome.
• Inactivation is accomplished through methylation.
• A small region, that has a homologue to a section of the Y-chromosome, remains active.

5.  We discussed Sordaria (fungus) and how it is used as a model organism to study crossover.  Go to the following link to remind yourself of what we learned today.  http://www.phschool.com/science/biology_place/labbench/lab3/concepts2.html
6.  After I presented the information students wrote explanations in their own words into their lab book under the title Lab 3: Crossover.

Linked Genes

We started class with a warm up asking you to write down everything you know about how we get our eye color.  If you want to learn more about some interesting genetics questions you can link to http://www.thetech.org/genetics/asklist.php. 

Next we discussed the reading, 15.1 and 15.2.  Most students did not have any questions from 15.1, but 15.2 was a struggle.  I went through an example on the board, first showing what would happen during meiosis if two genes were not on the same chromosome (not linked) and then repeated the exercise for when they are on the same chromosome (linked).  This resulted in two different expected outcomes of a cross.  I used this example to introduce crossover and explain how crossover during meiosis results in new combinations of alleles on a chromosome. 

Finally we went over how to determine the relative locations of genes on a chromosome based on their crossover rate. 

For homework I asked students to make sure they understood problems 1-5 (ignore #6) from the homework linked on the last post.

On Monday I will address any questions on the homework before we complete a lab activity (don't get too excited, it is based on pictures of fungal spores :))

Block Day - Eye Color Genetics

Was it hard to stay on task today or was it just me?

In class we mainly focused on finishing up the case of Alexia and Evan who are both blue-eyed, but have a brown-eyed child named Ryan.  The case revealed the multiple genes involved directly in eye color and suggested several others that could influence the final color seen.

While students were working on the case there were several side conversations that ventured into the areas of chimerism (and search for "I Am My Own Twin" which originally aired on the Discovery Channel), dermoid cysts, conjoined twins, and more.

For homework tonight I am asking you to read 15.1 and 15.2.  Then go to this LINK https://docs.google.com/document/d/1lIcrXCROg2eC5c8AURkO-Zp5EGifMbkJanF8ZTvMm5s/edit?hl=en&authkey=COKx_q0B and answer the 6 questions on the Chapter 15.2 Worksheet.

I am also linking you to a few excellent sources below:
BioCoach at http://www.phschool.com/science/biology_place/biocoach/inheritance/intro.html
Your textbook web site.  Go to Chapter 15 and go through Activity 15.2.
Lab Bench Activity reviewing Meiosis, Crossover and how this relates to Linked Genes.

Complexity of heredity

Today in class I did a reading check by asking students to define and give examples of:
complete dominance, codominance, incomplete dominance, pleitropy, epistasis, polygenic inheritance.
We then had a discussion of the last three terms using the examples of Marfan Syndrome and cystic fibrosis for pleiotropy, albinism for epistasis, and height and skin color for polygenics.

We ended by looking at the pedigree for hemophilia and having a quick discussion of its impact on history.

No homework tonight.  Enjoy it.