Epigenome

IDENTICAL TWINS: PINPOINTING ENVIRONMENTAL IMPACT ON THE EPIGENOME
1. Often, the physical characteristics of genetically identical twins become increasingly different as they age, even at the molecular level. Explain why this is so.
As people age, the a greater difference in environmental occurs. While they are younger (birth to toddling ages), they are more closely related because they haven't really had the time to see more of the world and make their own decisions and develop different habits.

2. Name 3-4 environmental factors that influence the epigenome.
Diet, habits (exercise or tv), toxins (smoking), and stress amounts.

3. What is an imprinted gene?
An imprinted gene is a epigenetic tag that instead of being erased during the first days after fertilization, are kept and the child is born with these tags turned on or off.


YOUR ENVIRONMENT, YOUR EPIGENOME
1. Discuss factors in your daily life (ie. Diet, exercise, stress etc.) that could be affecting your epigenome
The fact that I don't like bananas (awful little things) is probably not doing me any good because it means I won't be getting potasium, whatever that is. But the fact that I listen to my music out-loud when I can and as low as it can go will lead me to have less of a risk of hearing-impairment problems when I'm older.


LICK YOUR RATS
1. Explain how a high-nurturing mother rat shapes her pup's epigenome, and what that pup's response to stress will be.
A rat mother who constantly licks her pups will produce cortisol more readily which will bind to GR protein and calm the wel nurtured rat quicker than the neglected rat.

2. In rats, does licking by the mother activate, or deactivate her pup's GR gene?
It will activate the gene.

3. Explain how cortisol and the GR protein work together in the brain to relax a rat pup. You may draw a diagram.
When rats are agitated, animals go into this fight or flight instinct, where they will flee from the danger or fight it. However, with well nurture rats, soon after the danger has passed, more cortisol is released which binds to the GR protein which will then send out calming signals to the rat. Where a maltreated rat will take longer to calm down because less cortisol is released.

4. The rat nurturing example shows us how parental behavior can shape the behavior of their offspring on a biochemical level. Relate this to humans and think about the personal and social implications. Record your thoughts.
Now a days, the more open, fun, and accepting a family is, the kid is more confident, chirpier, and accepting as well. The page kind of gave an example of this with the rats. A well nurtured rat in human society would fit in nicely and be sociable, whereas a low-nurtured rat would have a harder time fitting in because it would be anxious and paranoid. However, in the wild, it is a good thing to be anxious because those rats are more alert to danger in a land of scarce food vs. a happy-go-lucky rat. So low nurtured rats would make poor humans and high nurtured would good people.

NUTRITION & THE EPIGENOME
1. Explain how the food we eat affects gene expression.
Extracted nutrients are manipulated, modified, and molded into molecules, sometimes that molecule is important in making epigenetic tags that turn off genes. The molecules that will be helping epigenetic tags go through the methyl pathway in the metabolism who, in the end, put the modified molecules into our DNA.
2. Can the diets of parents affect their offspring's epigenome?

Yes, they can. For example, a lack of methyl-donating folate or choline during late fetal or prenatal development in a child leads to a methyl deficiency for life. With rats, a mother can malnourish her rats without eating methyl for the agouti gene which will cause her pups to have a yellow coat and be fat. Whereas healthy, methyl nourished pups will be thinner and have a brown coat.


EPIGENETICS & THE HUMAN BRAIN

1. How does Dietary methyl influence gene expression?
A higher level of methyl leads to a less active RNA, leading to a less active ribosome, meaning less protein which occurs in a greater number of people who commit suicide. Those who commit suicide have a gene for REEELIN protein which has less methyl (so is more active) that normal schizophrenic brains. This protein is crucial for the shaping of the brain in the early years and later on for learning.

2. Why do Toxins affect gene methylation?
Some toxins affect methylation because they treat the mental illness by changing the gene expression. The expressions are then stabilized through "epigenetic mechanisms" (DNA methylation and histone modification) which will reverse the effects of the disease. Harmful drugs, such as cocaine, will cause epigenetic changes in specified brain regions which will affect hundreds of genes in one go. Some of these changes are irreversible and are for life, even after the lack of exposer to the drug. It's theorize that long-term effects of drug abuse, addiction, and high rate of relapses is due to the epigenetic code.

DNA Fingerprinting

Create a DNA Fingerprint ( http://www.pbs.org/wgbh/nova/sheppard/analyze.html )

Introduction:

1. DNA is unique for everyone. The only exception is if a person has what?
An identical twin would be the exception.

2. What are DNA fingerprints used for?
Determining a biological mother or father.

Part 1 “It Takes a Lickin”

3. What “crime” was committed?
Jimmy Sweet's lollipop was licked by someone other than himself. Supposedly, one of his seven sisters.

4. What bodily fluid was removed from the “crime scene” to get DNA?
Saliva.

Part 2 “DNA Fingerprinting at the NOVA Lab”

5. What does a restriction enzyme do?
It cuts the long strands of DNA into different sections, and the length of those fragments will determine who ate the lollipop because everyone's DNA is different and will be cut differently.

6. What is agarose gel?
A thick, pours, jello-like substance that will act as a molecular strainer and allow the smaller pieces of DNA to move through more easily.

7. What is electrophoresis?
The process of moving molecules with electricity. THe DNA fragments have a negative charge and therefore move to the positive charged end.

8. Smaller fragments of DNA move ____________ than longer strands?
More easily.

9. Why do you need to place a nylon membrane over the gel?
Because agarose is hard to work with and the nylon is used to transfer the DNA from the aragose to the membrane.

10. Probes attach themselves to __________
The DNA fragments on the nylon membrane.

11. Which chemical in your “virtual lab” is radioactive?
Probes.

12. Sketch your DNA fingerprint.
It looks like a bar code you find on products in a store. There was a little more space between the black lines, but the idea of the bar code is the same. Out of curiosity, were bar codes developed before or after the DNA was discovered? If after, then was bar code copied after, and if before, then was it just a mere coincidence? There were 3 fat bars, one medium bar, 6 skinny bars, and 2 anorexic bars.


13. Based on your DNA fingerprint, who licked the lollipop?
Honey Sweet.


 

Click on the Link “DNA Workshop” (if this link won't load, scroll down to the bottom where it says "try the non-java script version)
Once you’re there, go to the link “DNA Workshop Activity” and practice with DNA replication and protein synthesis.

Browse the DNA Workshop site.


14. What kinds of things could you do at the DNA workshop?
DNA replication and protein synthesis.
 

 

Find an Article about DNA

Go to http://www.thegenesite.com/

15. Read an article about genetics at this site that you might find interesting, or use the "Search" box in the upper right hand corner to search for DNA fingerprinting.

Title of Article: CHEMISISTS CREATE DNA ASSEMBLY LINE Author and Date: SCIENCE DAYILY/MAY 14, 2010

Summarize what the article was about. Write this in a paragraph format.
Chemists created a DNA assembly line which consisted of three DNA machines are used in the DNA assembly line. The first is known as a DNA origami, which is a composition that involves a couple hundred short DNA strands to direct a long DNA strand to form to the desired shape. The next is known as a "cassette" which determine the cargo being moved in the DNA. Changing the sequence of the machines, scientists can enable to prevent the cargo being transported. The last is known as a "walker." This moves the assemble track and picks up the cargo at the priorly mentioned machines.

 

 

Mitosis Tutorial Virtual Lab

1. Which stage does the following occur
Chromatin condenses into chromosomes
PROPHASE
Chromosomes align in center of cell.
METAPHASE
Longest part of the cell cycle.
PROPHASE OR ANAPHASE, (DEPENDING ON IF YOU ARE INCLUDING PROMETAPHASE OR NOT)
Nuclear envelope breaks down.
PROMETAPHSE
Cell is cleaved into two new daughter cells.
CYTOKINESIS
Daughter chromosomes arrive at the poles.
TELOPHASE
Watch the video carefully.

2. The colored chromosomes represent chromatids. There are two of each color because one is an exact duplicate of the other.

--How many chromosomes are visible at the beginning of mitosis?
8

-- How many are in each daughter cell at the end of mitosis?
4

--The little green T shaped things on the cell are:
Centrioles

-- What happens to the centrioles during mitosis?
The fibers (with the chromatids attached) hook on to the centrioles who then travel to opposite poles of the cell and are split into each cell when it is divided. (Question: There were four in the mother cell, and two in each daughter cell. The next generation of cells from the daughter cell will have enough centrioles, but what happens after that? Each daughter cell would only have one centriole.)

3 . Identify the stages of these cells:
Interphase: When the cell is not experiencing mitosis.
Prophase: The nucleus dissolves and chromatin condense into chromosomes.
Prometaphase: Fibers elongate to attach to either kinetochores or chromosomes.
Metaphase: Chromosomes align at the equator of a cell.
Anaphase: Daughter chromosomes are pulled to opposite poles of the cell by shortening spindle fibers.
Telophase: Daughter chromosomes arrive at the opposite ends of the cell, and the fibers disappear.
Cytokinesis: A contracting rings severs the cell in two.

Another Mitosis Animation

Go to www.johnkyrk.com/mitosis.html

View the animation and sketch the cell in:
Prophase
Chromosomes condense and become visible while the nucleus dissolves. Centrioles appear and move to opposite poles on the cell. Spindle fibers form but do not latch on yet.

Metaphase
Chromosomes line up at the equator of the cell and spindle fibers attach onto their kinetochores (where the duplicated and original chromosomes are connected).

Telophase
The nucleus reforms after spindle fibers shorten, then dissipate. Then the chromosomes disperse. Cytokinesis, while not technically considered part of mitosis, would be when the equator of the cell is stretched and begins to squeeze into two cells, then splits. This creates the two, duplicated sister cells.


Onion Root Tip - Online Activity

http://www.biology.arizona.edu/cell_bio/activities/cell_cycle/cell_cycle.html

Read the introduction, then click the “next” button.

You will have 36 cells to classify. When you’re finished, record your data in the chart below.
| Interphase | Prophase | Metaphase | Anaphase | Telophase | Total
Number of cells | 20 | 10 | 3 | 2 | 1 | 36
Percent of cells | 56% | 28% | 8% | 6% | 3% | 100% (Technically, 101%, but I rounded)


Mitosis in Whitefish & Onion Roots

http://www.biologycorner.com/flash/mitosis.html

For each organism, identify the stage of mitosis.

Whitefish
View 1: Telophase
View 2: Metaphase
View 3: Prophase
View 4: Anaphase

Onion
View 1: Prophase
View 2: Metaphase
View 3: Interphase
View 4: Telophase
View 5: Anaphase