Bacteria, Gene Expression and Cancer.

We had a busy day in class today. You set up your LB plates for the bacterial growth, sampling from areas all around the Kirby Science Center.

After lab you shared your research on tuberculosis and we evaluated the credibility of your sources.  Following a quick review of gene expression in prokaryotes, we started to learn about gene expression in eukaryotes.

Homework: Read, annotate and answer the questions on pages 3-6 in the epigenetics packet.

Here are the links we looked at in class:
The epigenome at a glance animation.
GFP Gene control
HHMI Cell's Differentiation 
William Li's Can We Eat to Starve Cancer TED Talk

Evolutionary Arms Race

Today we started our work on bacteria by watching a clip from PBS's evolutionary arms race (below).
You developed a question from the video and your homework tonight is to find the answer to that question and write an annotated bibliography for your source.

What should an annotated bibliography contain?

• Complete bibliographic information
• Evaluation of why you feel this work is suitable for your topic.
• Some or all of the following:
• Information to explain the authority and/or qualifications of the author.  For example: Dr. William Smith, a history professor at XYZ University, based his book on twenty years of research.
• Scope and main purpose of work.
• Any bias that you detect.
• Intended audience and reading difficulty

Check out the Bunn Library Site for more information.

Homework for Tuesday

For Tuesday please complete the remaining questions for the Neuroses article.  In class you drew a line to indicate the questions that you had completed in class.  Be sure to complete these questions on your own.

A tiny test and a reading from Genome

Today you had a 'tiny test' (30 minutes) on restriction enzymes, gel electrophoresis and the relationship between genes and proteins.

After the tiny test we started to read chapter 5 from Matt Ridley's book Genome.

Below is a cheat sheet for words / concepts which he mentions.  Your homework is to read this chapter for class on Thursday.  As you read, annotate the chapter.

Consider the various hypotheses Ridley suggests for the prevalence of asthma.  On page 73, Ridley says "That same year a study of a mixed-race population in America...."  after you have read that paragraph, ask yourself "How could this be?!"  Write down your ideas and bring them to class on Thursday.

Page 65:
alkaptonuria - also known as black urine disease. The excessive acid produced by the body can cause damage to cartilage and heart valves.  It is most common in Slovakia and the Dominican Republic.  It is autosomal recessive (meaning it is not found on a sex chromosome and you need two copies of the recessive allele to have it).

Huntigton's chorea - a neurodegenerative disorder that is characterized by involuntary writhing movements.

"your peas are either wrinkled or smooth" - a reference to Mendel's genetic experiments

Page 66:
pleiotropy - the term for multiple effects of multiple genes,

Page 67:
atopy - a predisposition to a hypersensitivity to certain allergic reactions

eczema - the general term for swelling of the skin, sometime characterized by red, itchy skin

anaphylaxis - a serious allergic reaction that can result in death

immunoglobulin-E molecules - a class of molecules in the immune system that are only found in mammals.  They confer an immunity to parasites, especially worms.  They are a class of antibodies associated with allergic reactions.

asserts: to state or declare forcefully

illusory: based on illusion

Page 68:
isocyanates - highly reactive chemicals

trimellitic and phthalic anhydrides - chemicals used in the manufacturing of plastics

Page 69:
mycobacteria - a genus of bacteria known to cause disease.

Page 70:
non-specific urethritis - an inflammation of the urethra

histamines - released by your body when there is an 'invader.' Histamines can cause you to have a runny notes, watery eyes etc, basically it is your body attempting to flush out the foreign substance.

mast cells - part of your body's inflammatory response.

concatenation - series

Investigating Enzymes

Today we spent the first half of class completing the investigating enzymes lab.  Tomorrow you will collect the data and we will discuss experimental design.  On Saturday you will have a test.

What's going to be on the test? You spent the second half of the lab working in groups to review what we have learned since the first test.  Here's some of the things that you came up with:


Lab:
Gel Electrophoresis - placed in wells, the PO4 group is negatively charged so when you run an electric current through it the (starting at the negative side) the DNA segments move towards the positive side. Smaller pieces of DNA move to the positive side of the gel more quickly.

DNA Extraction

Articles:
William's Syndrome (lack of trust)
Stathmin & Timid Mice (fear)
Sports Gene - gene is ACTN3 and the protein is Alpha Actinin.  The traits are fast twitch or endurance.


Vocab and Concepts:
Chromosomes (homologous chromosomes)
Loci
Allele
Genotype
Phenotype
Recessive
Dominant
Punnet Square
Restriction Enzymes
Protein shape (how to build a protein)
Plasmids
Functions of proteins (for example receptors - PTC)
Homozygous and Heterozygous



An important note about dominance and recessive:  Read this article to help you understand what dominant and recessive really means.

Quiz Tomorrow

Tomorrow you will have a quiz on restriction enzymes, plasmids, gel electrophoresis and the timid mice article.

You will have 20-25 minutes for the quiz, then you will start to go over next week's lab.

Gel Electrophoresis

Yesterday you were able to practice micropippetting so that today when you did the gel electrophoresis using restriction enzymes you already had some experience.  While your gels were running, we reviewing the Williams Syndrome Article and watched this clip fromABC News about what it is like to have this genetic disorder.  Diving in deeper to protein structure you made wire models of proteins and worked with Fold.it to practice unraveling proteins. While you were at lunch the gels were stained in Gel Red and after lunch I went back and took pictures of the results. Below is part of one of the best gels.  Does it belong to you?  Find out tomorrow!

Restriction Enzymes and Gel Electrophoresis

Today in class you learned about restriction enzymes and gel electrophoresis. Tonight for homework complete the virtual gel electrophoresis lab here and answer the questions below.

1. Draw a gel with the wells and label which side has the positive electric current and which side is negative.
2. When the segments of DNA move through the wells, how are they sorted?

The virtual lab: go through the five steps for the virtual lab.  Briefly summarize what happens at each of the five steps.

Homework for Tuesday

Use pages 208-211 and 215-218 to help you answer the question on the worksheet. This homework should take you no more than 20 minutes.

Use the remaining ten minutes of homework time to watch the crash course video on heredity below.

Timid Mice and Heritablity

Today we had a busy day in class.  You extracted DNA from strawberries, then we read the NYT article "Timid Mice Made Daring by Removing One Gene" as well examined the abstract and graphs from the original article in Cell.  You spent the remaining time in class working on the timid mice questions that will be used for the group grade among the 2FS teachers.

Tonight for homework, please the Utah Genetics Heredity and Traits Site  Click on "what is a trait?" (the blue box on the left side of the page). You need to spend 30 minutes working through the animation.  Do not take any notes, pretend like you are watching a movie.  Depending on quickly you read, you may go through the animation up to three times.

Test Today and DNA Extraction

Today you had a test on cells, DNA, transcription and translation. Tonight for homework please read the DNA extraction lab protocol.  In addition, please read the FAQ's about DNA extraction from Utah Genetics here.

Born to Run Article

Tonight for homework, study for you test.  Tomorrow you will get a copy of the Born to Run Article.

Microscope Lab

Today you worked with microscopes to examine different types of cells.  Kudos to Mike and Daniel who went the extra mile and were very inquisitive about other things which they could look at underneath the microscope.

Quiz, Central Dogma & Microscope Prelab

Today you had a quiz on cells, DNA structure and DNA replication.  For class on Thursday, read pages 1 and 2 of the microscope prelab.  You'll have a short quiz on how to correctly use a microscope at the start of lab.  If you're confused about some of the terminology in the prelab, check out this video below.

DNA replication

Today we review DNA replication and you had a pop quiz on the structure of DNA.  Some of you asked how long does it take to replicate DNA?  Click the picture below to try it for yourself and find out.

Homework: On Tuesday you will have a 20 minute quiz on cells, DNA structure and DNA replication.

DNA Structure and Replication

Today you learned about the structure of DNA.  Use this silly replication animation to complete the worksheet on DNA replication. 

More than a Membrane

Today you learned about the organelles inside an animal cell as well as review the structure of a cell membrane.  We wrapped up class with each of you sharing a Want Ad for a part of the cell.

Tonight for homework click on the picture below to link to the Utah Genetics site.  First go through the What's is DNA section then go through the What is a Chromosome section and answer the questions below.

If you are running out of internet time you can download the tour (although the site should be cleared through IT).

Questions for What is DNA

1. How many total chromosomes does a human have?

2. What are the four bases in DNA?

3. DNA must follow certain base paring rules.  Write each letter with its corresponding pair.

4. Draw the structure of DNA.  Be sure to label the following parts: hydrogen bonds, sugar phosphate backbone, and include all four correctly paired bases.

5. What do the DNA bases (code letters) stand for?

6. Each of the words in a DNA "sentence" contains ____ letters.

Questions for What is a Chromosome

1. Suggest a reason why DNA needs to be packaged into chromosomes.

2. What can you learn from looking at a picture of chromosomes?

3. What are the sex chromosomes for a female? What are the sex chromosomes for a male?

After seeing this brief preview of DNA and chromosomes, write down three questions you have about DNA and/or chromosomes.  These could also be questions about something you'd like to learn more about. 

Welcome Back to the Blog!

We've returned to the blog...for now.  We may be using a page through Veracross eventually, but for now, you'll find your assignments posted here.

Homework: Read sections 6.1 and 6.4  You should briefly annotate as you read, but you do not need to take notes.

Our central question for this term is:

Is Biology Destiny?

Is Biology Destiny?:
Yes! - 4
No! - 2
Mayyyybee.... - 6

This question could also be asking:
....Is life the most that universe can achieve (WC)
....Does biology and genetics determine the life of a living thing (KP)
....Is biology a predetermined factor in life? (JL)
....Does DNA in people control their thought process or decisions (SS)
....Does biology determine what happens to me, for example diseases (EM)
...Is biology the key to our future (MS)
....How many variables are there that affect my life that I can't control or change? (SM)

For the most part it is predetermined, but there are things that can change the outcome.
Nature vs. Nurture
No, it's not destiny for human future.