First Post of Second Semester

I got out of the habit of updating the blog each day; sorry about that!

Today we went over inheritance when there are multiple (more than 2) alleles for a certain gene in the population.  The ABO blood group is a perfect example of this.  Alleles A and B are codominant and they are both dominant over allele O.  In addition, we discussed the Rh blood group which determines if someone is + or - (for example, I am O+).  I explained that + and - are based on a different gene from the one that determines ABO and that this gene codes for a protein called the Rh factor.  Rh+ is dominant over Rh-.  Then we took a few minutes to talk about blood compatibility for transfusions and the role of the immune system.  We established why O- is the universal donor while AB+ is the universal recipient.

If you are interested in learning more about blood groups start by looking at Wikipedia http://en.wikipedia.org/wiki/ABO.  Check the References and External Links at the bottom. 

Once we completed our discussion of multiple alleles I presented the case of Evan and Alexia and the mystery of their brown eyed son.  Groups answered 7 questions for Part 1, which we will discuss at the beginning of class tomorrow.

HOMEWORK:
Read 14.3 and 14.4.  You do not need to answer questions, but you never know when we may have a quiz.

Last post before Semester Final Exam!

Look back at the topic list from a few posts ago; it has now been updated to reflect what is actually going to be on the test!  You're welcome.

By the way, you will have an assignment to complete once you are done with your test. Once again, you're welcome.

Thanks for being so understanding about my ongoing laryngitis.  Hopefully these days of testing will allow me a full recovery.  Good luck on any tests you have before I see you!

Reviewing for the Semester Final

Today in class you had the opportunity to revisit our past exams.  Students were allowed to write down information, but no tests could leave the room.  Depending on how I feel tomorrow this process may continue.

Guest Speaker: Dr. Max Robinson Part II

Today Dr. Robinson continued his talk about atherosclerosis.  The focus was on how the gene, ABCA1, is regulated.  He also discussed some of the techniques used to discover which proteins act as transcription factors of this gene. 

There is no specific homework due on Tuesday, but if you haven't looked at the epigenetics resources from Wednesday I advise you to take a look at them.

Enjoy your three days!

Ghost in Your Genes - NOVA

Although many were disappointed to be in school today, they seemed to perk up when they learned we were watching a DVD entitled, "Ghost in Your Genes."  A link to the accompanying website can be found here: http://www.pbs.org/wgbh/nova/genes/.  We followed the film with a discussion that included the Epigenetics article you read over the weekend.

Some additional resources on epigenetics are at this site:
http://learn.genetics.utah.edu/content/epigenetics/
This is the curriculum that I worked on at the University of Utah 2 summers ago!   I especially like the activity entitled "Lick Your Rats."  Even Mr. Wellington has given this interactive a try and would be happy to talk to you about it!

And there are several articles that are interesting to read.  I've linked a few of them here:
The Sea Change That's Challenging Biology's Central Dogma
Now the Rest of the Genome
How Acquired Diseases Become Hereditary Illnesses
The Promise and Power of RNA
Tug of War Pits Genes of Parents in the Fetus
PreNatal Exposures Prompt EPA to Re-examine Chemical Regulations
Are Contaminants Silencing our Genes?

Topic List for Semester Final

This is a list of topics that you should know for the Semester Final!

Ecology
Gross vs. Net productivity
Pyramids of biomass, energy (10% rule), trophic levels
Community relationships - predator-prey, parasitism, mutualism, commensalism, camouflage, mimicry
     Producers, consumers and decomposers
Carbon and nitrogen cycles
Carrying capacity
Exponential growth
Food webs
Organizational Hierarchy - Biosphere, Community, Population, Organism

Biochemistry
Hydrolysis vs. dehydration synthesis reactions
The properties, building blocks, elements, and examples within each of the biomolecule groups: carbohydrates, lipids, proteins and nucleic acids
Enzymes - catalyst, substrate, active site, induced fit, how enzymes speed up reactions, activation energy, effect of pH, temperature, cofactors, inhibitors.  Allosteric regulation: comptetitive vs. non-competitive inhibitors.

Cell Parts
Eukaryotes vs. Prokaryotes
Plant cells vs. animal cells
Functions of cell parts
Endomembrane transport. Example: Rough ER --> vesicle --> golgi --> vesicle --> cell membrane
Cytoskeleton: microfilaments, intermediate filaments, microtubules
Structure of cilia and flagella

Cell Transport
Structure of cell membrane
     Role of phospholipids, proteins, cholesterol
Active vs. Passive transport
Osmosis and direction of water movement
How the properties of molecules determine how they cross the membrane
Hypertonic, hypotonic and isotonic solutions

Cell Communication
Signal reception, transduction and response
communication at various distances: cell-to-cell, local and long-distance

Mitosis, Cytokinesis, and the cell cycle
Purpose/ outcome of mitosis
Stage at which DNA is replicated
Somatic cells vs. gametes
Process of mitosis, stages and main events
Key events of the cell cycle
Amount of DNA at each stage

Meiosis
The goal of the complete process, goal of meiosis I, goal of meiosis II
Stages and main events.
Comparison of mitosis and meiosis
Variation due to meiosis - crossing over, independent assortment, fertilization
Haploid vs. diploid
Replicated vs. unreplicated chromosomes
Amount of DNA at each stage

DNA Structure
Contributions of: Franklin, Chargaff, Hershey and Chase, Watson and Crick
Know the diagram!  Be able to label 5' and 3', purine vs. pyrimidine, H-bonds, TCGA, parts of a nucleotide, # the carbons of deoxyribose

DNA Replication
Comparison of DNA to RNA
Contribution of Meselson and Stahl
Roles of the following: helicase, topoisomerase, single-strand binding proteins, DNA polymerase I, DNA polymerase III, ligase, primers
Directionality of replication
Continuous replication on leading strand vs. discontinuous replication on lagging strand
Okazaki fragments
How errors of replication are minimized

Gene Expression
Transcription vs. Translation
Codon and why it contains three nucleotides
Using the codon chart
mRNA, tRNA, rRNA
Mutations: Point (silent, nonsense or missense) or Frameshift (insertion or deletion)
Transcription factors, promoter, RNA polymerase
mRNA processing - introns vs. exons, 5' cap, 3' poly-A tail
Stop codon/ release factor

Control of Gene Expression
Operon theory in prokaryotes:
Roles of promoter, operator, repressor, regulatory gene, corepressor (ex. tryptophan), structural genes
Inducible vs. Repressible operons
Goal of trp vs. lac operons
Active vs. Inactive Repressors and the effect on the operon

Completion of Control of Eukaryotic Gene Expression

With our assembly we had classes of varying lengths today.  Our main task was to complete the sharing of information on our posters of gene expression.  In some classes we began a discussion of the epigenetics article, but this topic will be our main focus on the block day.

There is no new homework tonight. 

I will be posting the topics that are fair game for the semester Final exam soon.

Guest Speaker: Dr. Max Robinson

Our guest speaker came to us from the Institute for Systems Biology in Seattle.  Atherosclerosis was the focus of his talk, with a special emphasis on dietary influences on the good cholesterol (HDL) and bad cholesterol (LDL).  Dr. Robinson may post comments, so check below to see if he has chimed in about his talk!  On Friday Dr. Robinson will return to use the atherosclerosis model to more specifically describe how one gene involved in the pathway to disease (and health!) is regulated.

Tonight's homework is on the topic of epigenetics.  You will be reading an article from NewScientist and then responding to the questions below.  The title of the article is Rewriting Darwin: The new non-genetic inheritance.  I will also email the document to you.  As you are reading:

1.  Be ready to discuss the difference between the genome and the epigenome.
2.  Describe at least three examples of characteristics or diseases that are influenced by the epigenome. (in humans or other organisms)
3.  How does the study of the epigenome influence the "nature vs. nurture" debate?
4.  How might this study spark new treatments?
5.  Select THREE sentences in the text that you feel share the most important concepts of the reading.

Group Teaching about control of eukaryotic gene expression

Students first met with other students who had been assigned the same section of the reading.  I met with each group to clarifiy concepts and answer any questions.  Next we moved back into the small groups assigned yesterday.  Students reproduced the diagram from p. 362 on poster paper.  Next team member 1 explained their section.  A different member of the group then summarized the explanation on the poster.  The next team member then explained their section.  Most groups only got through the first two sections.  We will finish this poster and discussion on Tuesday.

No homework this weekend, but there are a couple of things to note:

1. We will have a guest speaker on Monday, Dr. Max Robinson from the Institute for Systems Biology.
2. We have an assembly on Tuesday for MLK Jr. Day.

Checking your understanding of operons

All classes are registering for AP tests at the computer lab during the block day.

Class began with a short check of your understanding of operons.  This was followed by an assessment to see how students manipulated their lac operon models in response to environmental conditions.

We discussed the positive regulation of the lac operon, as described in 18.4.  Key points:

• Lactose is a secondary energy source that will only be used when glucose is low.
• CAP is an activator of the lac operon.
• CAP will only work if cAMP is bound to it.
• Low levels of glucose lead to high levels of cAMP and therefore, high levels of active CAP.
• Without CAP, even if the repressor is inactive, the lac operon will transcribe only in very small amounts.

HOMEWORK
Classes were split into groups of four.  Group members then numbered off 1-4.  Based on your number you are to read a section of 19.2 to read and then teach to your group in class on Friday.  If you were ABSENT for class, please read the section for group member 2.

Student number 1: Regulation of chromatin structure.  Special focus on histone modifications and DNA methylation.

Student number 2: Regulation of transcription initiation.  Special focus on transcription factors, enhancers/activators/repressors and coordinately controlled genes.

Student number 3: RNA processing and mRNA degradation

Student number 4: Initiation of translation and protein processing and degradation

Modeling the Operon

Class began with a warmup of the trp operon.  You were asked to explain what happens when trp is present in the cell using the terms: regulatory gene, structural genes, RNA polymerase, operator, repressor, promoter and transcription.

We then did a brief comparison of the lac operon to the trp operon.  The important differences are:

• the lac operon is INDUCIBLE (usually off, but is turned on by lactose) while the trp operon is REPRESSIBLE (usually on, but is turned off by tryptophan)
• the lac operon is for the breakdown of lactose, while the trp operon is for the construction of tryptophan.
• in the lac operon the repressor is constructed in an ACTIVE form (which is why the operon is usually off) while in the trp operon the repressor is constructed in an INACTIVE form (which is why the operon is usually on)

Students then made simple models of the lac operon that could be manipulated to show what happens when lactose is present or absent in the bacterium.  These models will be used on block day to demonstrate comprehension.

There is no assigned homework.  Our next topic is to expand our study of control of gene expression to eukaryotes.  We will also be talking about the positive control of the lac operon that also exists.

For class tomorrow, be prepared to answer these questions:

1. What is the function of the operator?
2. What is the function of the promoter?
3. What is the function of the repressor?
4. In the lac operon, is the repressor active or inactive when lactose is present?
5. In the trp operon, is the repressor active or inactive when tryptophan is present?
6. What does it mean when an operon is said to be "repressible?"
7. What is the product of the trp operon?
8. What is the product of the lac operon?
9. Name the specific organism we use to study the lac and trp operons.

Regulation of Gene Expression in Prokaryotes

Welcome back everyone!

Class began with a recap of our guest speaker's talk from the Friday before break, followed by a revisit of the quiz on Chapter 17 that we took the Monday before break.

Today's lesson focused on how E. coli regulate the production of tryptophan, an amino acid necessary for the production of many proteins. E. coli are found in our digestive tracts where tryptophan is present only occasionally, like when we consume meat products.  E. coli can create tryptophan from a precursor molecule through a series of steps, where each step is catalyzed by a specific enzyme.  Tryptophan, itself, acts as an inhibitor on this system, so if tryptophan accumulates in the cell it shuts down its own synthesis.  This is feedback inhibition.

Some key points of the trp operon:

1.      The genes that are functionally related, like the 5 genes for the enzymes to make tryptophan,  are grouped together into an operon.

2.      They can be served by a single promoter.  Therefore all of the enzymes necessary can be made at once.

3.      Just one mRNA is transcribed which contains all of the genes. (later is makes separate polypeptides from separate start and stop codes)

4.      There is a single "on-off" switch for the entire unit.  This is called an operator. 

5.      Operator controls access of RNA polymerase to the genes.

Trp operon (for tryptophan)

If the operator is the control point for transcription what determines if it is turned on or off?

·         Alone the operator is on and RNA polymerase can bind to the promoter to transcribe the genes.

·         The operator can be switched off by a protein called a repressor.  When the repressor binds to the operator it blocks access by RNA polymerase.

·         Repressor is made by a gene called the regulatory gene, located some distance away from the operon it controls.  It has its own promoter.

·         There are always a few trp repressor molecules present in the cell.  Why is the operon not switched off permanently?

·         Reversible binding to operator

·         Allosteric enzyme

·         Trp repressor is synthesized in an inactive form which does not bind well to operator. 

·         Tryptophan will bind to it and change it to the active form that can bind to operator.

·         Tryptophan = corepressor

·         Therefore the bacterium can respond rapidly to changing environment.

Here is a link to an animation of the process: http://bcs.whfreeman.com/thelifewire/content/chp13/1302002.html
HOMEWORK:
Read all about regulation of gene expression by bacteria in 18.4.  You can review the trp operon, but also pay special attention to the lac operon.  You will be asked to demonstrate understanding of the operon concept by using an interactive paper model of the lac operon that you will begin constructing in class tomorrow.