In case you are feeling motivated!

Merry Christmas Eve or Happy Holidays or Jolly Vacation!

I've been remiss in checking email over break and I found that several students were asking what they can be working on... such a motivated bunch!

When we get back to school we will be learning about gene regulation in prokaryotes.  You can find this information in the second half of Chapter 18.  We will then progress to gene expression in eukaryotes, which is described in all of Chapter 19.

If you are more interested in reading some of the topics we will be rushing through later in the year I advise you to look at the circulatory system, respiratory system, digestive system and development.  Unfortunately I don't have a book in front of me to see what chapters these are in, but there is a great section called the "Table of Contents" included in all newer textbooks :).

Enjoy the rest of your break and I will see you in the new year!

Mrs. Sutton

Mutations

Today's focus was on mutations to the DNA.  The two main categories for mutations are base-pair (or point) mutations and insertions/deletions.  Base pair substitutions may result in silent, missense or nonsense codons.  Insertions and deletions (unless they involve multiples of 3 nucleotides) result in a frameshift.  The impact of mutations depends upon the type and location of the mutation.  Several examples of genetic diseases based on missense mutations were discussed.  A few that were named were: sickle-cell anemia, cystic fibrosis and Tay-Sachs.  You can learn more about each of these genetic diseases, as well as others at http://www.ygyh.org/

Here are some great links about mutations:

• A very nice look at why a base-pair substitution may occur.
• http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter11/animation_quiz_3.html
• An explanation of deletions and insertions
• http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter11/animation_quiz_4.html 
• A focus on thymine dimers caused by UV light.
• http://highered.mcgraw-hill.com/sites/0072556781/student_view0/chapter11/animation_quiz_5.html

Homework
Your homework tonight is to read pp. 359-361 and then take a look at the animations (there is also a good one in Ch. 19 of your textbook's website).  Then answer this one question: How does all of the DNA fit into the nucleus in an organized way?

http://www.pbs.org/wgbh/nova/genome/dna.html
http://www.biostudio.com/demo_freeman_dna_coiling.htm

Chapter 17 Quiz

Today we took a 17 question multiple choice quiz on Ch. 17 through 17.5.  I had 15 people absent!  See me as soon as possible to make up this quiz if you were excused absent today. 

I collected the Bioflix worksheet from last week for credit.

Homework is to read 17.7 on Mutations.

Protein Synthesis Part 2

Important Notes:
The Quiz on Ch. 17 is on Monday.  It will be 15 multiple choice questions.
Test Corrections from the last test are due on Monday at 3:05.
Bring in any coats you want to donate to the Coat Drive!  These will be donated to needy Bellevue families on December 15-17.

(for videos and notes on Transcription and Transcript Processing see Blog entry from Wednesday, Dec. 8th)

Translation
Watch the video below and then construct your understanding of translation using the following key words: small ribosomal subunit, large ribosomal subunit, tRNA, amino acid, codon, anticodon, A and P site, release factor.  Note that the process of translation is separated into initiation, elongation and termination.  Make sure that you know the key events of each stage.

Post Translational Modification
You will not be quizzed on this, but you should understand that proteins are not "ready to go" when they come off the ribosome.  They often need specialized assistance in folding, removal of certain segments, addition of chemical groups, like sugars or phosphate groups and they may need "tags" that identify where the protein needs to go.  The best way to learn more about this process in on pp. 325-6 of your text.

Important Notes:

The Ch. 17 Quiz has been moved to MONDAY

Test Corrections for the last test are due Monday at 3:05

Today in class we did a lot of learning!  Starting with a discussion of the concepts from yesterday's assignment on DNA From the Beginning (dnaftb.org).  From Concept 21 I focused on making sure students understand the differences between DNA and RNA, the composition of a ribosome, and the attachment of amino acids to a specific transfer RNA (tRNA) molecule by an enzyme.  From Concept 22 I chose to highlight the 3-letter codon and how to use a codon chart, as well as the basic structure of tRNA.  I will not be collecting this assignment.

Students were asked to make a long notes sheet by attaching two pieces of paper end-to-end.  The paper should have the Central Dogma drawn at the top (DNA --> mRNA --> protein) with lots of space.  I asked students to create 5 columns, corresponding to the sections of the Central Dogma.  The first column will stay blank.  The second column is titled "Transcription" the third column "Transcript Processing" the fourth column "Translation" and the fifth column "Post-Translational Modification."

Transcription

Watch the video below and then construct your understanding of transcription by applying the following terms in a written explanation: Promoter, TATA box, Transcription Unit, Transcription Factors, RNA polymerase, Termination.  The other terms used in the animation are beyond the scope of this course.



Extension to transcription explanation: multiple mRNAs can be transcribed at the same time, following each other like trucks in a convoy.

Transcript Processing

Watch the two videos below and then construct your understanding of transcript processing by applying the following terms in a written explanation: 5' cap, 3' poly-A tail, spliceosome, intron, exon.  The other terms used in the animation are beyond the scope of this course, as are the specific mechanisms for removal of nucleotide segments.

Your homework tonight is to complete the handout from class using the Bioflix animation on the texbook website.   http://wps.aw.com/bc_campbell_biology_7  Look in the left column for Bioflix.  It is the one for Chapter 17 Protein Synthesis.  If you need the handout you can print your own from the animation site.  It is listed as the Study Sheet.  If you cannot access the textbook link you can fill out the handout using your textbook (but the animation is really helpful and clear!)

Some great resources for Transcription and Translation

http://learn.genetics.utah.edu/content/begin/dna/

• Select TRANSCRIBE & TRANSLATE A GENE and WHAT MAKES A FIREFLY GLOW?

http://www.youtube.com/watch?v=u9dhO0iCLww

Your homework due on the block day is to finish the questions from the DNA From the Beginning web site: http://dnaftb.org/15/concept/

The questions are below, in case you don't have your sheet.

Questions from DNA from the Beginning Concepts 21 – 24.

#21. RNA is an intermediary between DNA and protein.

1.      What is the "Central Dogma?"

2.      What is the difference between transcription and translation of the DNA message?

3.      From the PROBLEM section: How would you describe two types of genetic mutations? How do the mutations change the protein product?

#22. DNA words are three letters long.

4.      How does a three-letter code make it possible to make 64 different combinations?

5.      Why was it believed that it was necessary to have a three-letter code?

6.      What is a codon?

7.      From the PROBLEM section: Why can there be more then one possible mRNA sequence for a peptide sequence?

#23. A gene is a discrete sequence of DNA nucleotides.

8.      How would you define a gene?

9.      What is DNA sequencing?

10.  From the PROBLEM section: How do you read an autoradiogram of a gene sequencing gel?

#24. The RNA message is sometimes edited.

11.  What happens to mRNA when there is no binding region of DNA to match?

12.  What is the difference between an intron and exon?

13.  From the PROBLEM section: What causes a doublet to form in a gel sequence?

14.  From the PROBLEM section: How can you detect the exon regions on an electron micrograph of a DNA/RNA hybrid?

Introducing Gene Expression

The focus of today's lesson was on gene expression.  We began our discussion by discussing Garrod's study of alkaptonuria and how that led him to deduce that a gene error is responsible for an enzymatic malfunction (he hypothesized that genetic diseases are inborn errors of metabolism).  Beadle and Tatum's work with neurospora supported Garrod's hypothesis by using mutant strains grown in minimal media.  Here is a link to a great animation about this experiment: Dolan DNA Learning Center.

In the last 15 minutes of class students were given time to look over last week's test on DNA Replication and Meiosis.  Test corrections will be due Monday, December 13th at 3:05.

There is a quiz on Chapter 17 planned for Friday, December 10th.

Introducing Gene Expression

We started class today by making holiday cards for Gary.  Thank you to everyone who participated!  I don't think we often appreciate how much our community means to Gary and how much he means to us.  Hopefully our cards will bring him smile over the December break.

In all classes except third I gave you a pre-test on the concepts of gene expression.  This did not count, but served as a gauge for how much students remember from their Biology class.  Based on what you learned by taking the pre-test I asked students to look back over 17.1 and 17.2 to make sure you had a general understanding of how DNA is used to make protein.

Third period was able to begin a discussion of the one-gene-one-protein hypothesis by examining Beadle and Tatum's experiment with Neurospora.  Other classes will begin this on Monday.

Have a great weekend!  Good luck to football at State!  And if you are in the school performance of Sight Unseen "break a leg!"

Wrapping Up DNA Replication

To start class today I gave students a chance at some extra credit on Monday's test.  Each student was given a set of 15 pictures to first separate into mitosis and meiosis and then put in order.  See me as soon as possible if you were absent for this opportunity!

We finished our discussion of DNA replication by discussing how errors are minimized.  This is addressed on p. 305 of your textbook.  Next we talked about why the ends of chromosomes shorten with each replication.  The process is summarized on p. 306.  Our conversation extended to the ethical implications of using telomerase as a treatment for disease and/or aging.  It is an interesting area to think about and one that we will likely be hearing more about in the next decade!

Toward the end of class I shared an AP Free Response question on the topic of DNA structure and replication.  The question is below:

Scientists seeking to determine which molecule is responsible for the transmission of characteristics from one generation to the next knew that the molecule must (1) copy itself precisely, (2) be stable but able to be changed, and (3) be complex enough to determine the organism's phenotype.

• Explain how DNA meets each of the three criteria stated above.
• Select one of the criteria and describe experimental evidence used to determine that DNA is the hereditary material.