DNA Modeling Lab Advanced

What is DNA?

Hypothesis:

DNA has a very specific structure that allows it to replicate itself. Why does it replicate itself? Well, can you imagine only one cell in your entire body containing instructions of what to do? DNA must make copies of itself to ensure that every cell has a function, and that all functions are carried out properly. It is difficult to imagine what DNA looks like, let alone understand how its structure will help in DNA Replication. In this 3-part lab students will follow a similar procedure that the developers of the DNA model Francis Crick, James Watson, and Rosalind Franklin- used to create their model.

Important Concepts:
DNA stands for Deoxyribonucleic Acid De = Without oxy = refers to oxygen ribo = refers to the sugar molecule (deoxyribose in DNA ) nucleic = referring that it lies within the nucleus DNA is made up of many nucleotides. A nucleotide is a molecule made up of one phosphate molecule, one sugar molecule, and one nitrogenous base.

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DNA is the genetic material inside the nucleus of your cells; it is the instructions or blueprints to construct other parts of your body. o How do you have light hair but your friend has dark hair?

 A gene is a piece of DNA that makes a certain protein; proteins come together to form our traits! Everyones DNA has the same structure, but your genes are different because of the different nucleotide order, so when your nucleotides are ordered differently, your genes code for light hair, while your friends genes code for dark hair! DNA has only 4 Nitrogenous bases: Adenine, Thymine, Cytosine, and Guanine. Each base pairs with only one other base its complementary base. In DNA, Adenine only bonds with Thymine (and vice versa), and Cytosine only bonds with Guanine (vice versa). Each base is bonded to its complementary base through hydrogen bonds.

Materials: (group of up to 4)

1) DOTS Candy & Crows (also a product of Tootsie): ** NOTE: Material contains corn syrup! Green = Phosphate Black = Sugar (Use CROWS black licorice) Yellow = Adenine Pink = Thymine Orange = Cytosine Red = Guanine 2) 20 Toothpicks 3) 1 meter of yarn

Procedure (~30 minutes):

1. Take 12 green, 12 black, 4 yellow, 4 pink, 2 red, 2 orange candies and 20 toothpicks. 2. Cut all of your toothpicks in half you will use these to bond one candy to another 3. Set aside 6 green, 6 black, 2 yellow, 2 pink, 1 red, 1 orange (DOTS) you will use those later on. 4. With your remaining colors create 6 nucleotides. Each must have one black, one green, and either a red, yellow, pink, or orange, where the green one is on the outer part of the nucleotide, while the black is in between the base (pink, yellow, red, orange).
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http://academic.brooklyn.cuny.edu/biology/bio4fv/page/molecular%20biology/dna-structure.html

What three things is a single nucleotide made up of?

5. Once you have your 6 nucleotides, pick one randomly and according to the base that your chosen nucleotide has, find the nucleotide that has its complementary base. With the toothpicks bond the nucleotides, connecting bases (dont worry about correct number of base pairing bonds).

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Why is it important that bases are paired with their complementary base? 6. Choose another nucleotide. Attach this nucleotide to the already paired ones. Nucleotides are bound together through a phosphate. Make sure that the phosphate of the new nucleotide is not touching another phosphate, or sugar touching another sugar, and that the base is towards the center.

7. Continue attaching nucleotides until you have used your six nucleotides to make three (3) correctly bound pairs. DNA

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Compare your model to the diagram below. Does it look alike? Notice how one strand starts with phosphate but ends in sugar, while the other starts with sugar but ends in phosphate. Change your model so that the strands look like theyre going the opposite way. Why do you think they do that?

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http://www.biologycorner.com/resources/DNA_antiparallel.gif

In this lab you only made 6 nucleotides and three pairs. In real life, do you think DNA in your cells is made up of only 6 nucleotides? How many do you think there are?

1. Take the string of yarn. It should measure 1 meter. This is how long DNA would be in real life if you stretched it out. 2. Now, take the yarn and compact it so that it measures 1 millimeter, do you think you can do it? 3. Now try to make your 1-millimeter yarn 100 times smaller. This is the size of your cells nucleus: 10 microns long. It takes 1000 microns to make one millimeter. Try to squish this piece of yarn another 10 times (not possible, right?) DNA is 1 micron big inside the nucleus, which means its another 10 times smaller. Why do you think DNA is so small?

Part 2 Replication Process

Important Concepts:
The replication process allows a cell to divide in order to create copies of itself for new cells. DNA Helicase: An enzyme in DNA that cuts or unzips the double-stranded DNA into single strands in preparation of the replication process

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Replication Fork: The meeting point between the unwound part and the open part.

http://faculty.clintoncc.suny.edu/faculty/michael.gregory/files/Bio%20100/Bio %20100%20Lectures/DNA/dna.htm

DNA Polymerase: A DNA enzyme in charge of attaching or completing the complementary bases of the single strand. It moves along the single strands. Lagging and Leading Strand: The leading strand is the side that has phosphate closest to the replication fork. It is called this way because Polymerase always moves faster on this strand. The lagging strand is the side that has phosphate farthest from the replication fork Polymerase moves slowly in this direction so this strand is always lagging behind while the leading strand is finished in less time.

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Materials:
DNA Model 1 pair of Scissors Remaining 2 pink, 2 yellow, 1 orange, 1 red candies. Remaining toothpicks

Procedure (~15 minutes):

1. Take the Scissors and from bottom to top, cut your model through the middle, separating the first two base pairs but leaving the top base pair intact. What part of the replication process do the scissors represent? 2. Start with the Leading Strand (the one that has sugar farthest from the replication fork) and from bottom to top complete the DNA strand by attaching the complementary base to each splintered end, and then adding the sugar and phosphate (if you have A on one side, you are attaching T, and make sure you are using the right color candy!) What enzyme are you representing now? 3. Once you have completed one side, go to the next but start from top to bottom. This is the lagging strand. What characteristic makes it be called lagging? 4. Now you should have two emerging DNA strands, even though you started with only one! Now separate the remaining base pair and complete both strands. How many complete DNA strands do you have now?

Concept Questions:
1) True / False , the purpose of the replication process is to create new cells with DNA. 2) What is DNA made up of? 3) Approximately how big is DNA? 4) Pair these letters with their correct pairing letters: A A C T A A G G T A C A A T C C G C A 5) What do you think would happen to your genes if the bases in your DNA were not paired correctly?

PART 3 DNA & RNA

Where is DNA found & how is it used? Hypothesis:
Important Concepts:
There are two types of cells; Prokaryotic cells and Eukaryotic cells. While Eukaryotic cells have a protected nucleus and many organelles (specialized parts inside a cell), Prokaryotic cells dont have a nucleus, and have very few organelles. Human cells are Eukaryotic, so they have a cell membrane, cytoplasm (a jelly-like substance inside where the organelles are all spread out), and a nucleus in the center.

http://2.bp.blogspot.com/_lcqHdkGk3cs/Sdt9Oqn-5FI/AAAAAAAAATs/veXMRCgL_94/s400/human-cell.jpg

RNA is a single-stranded molecule that contains the same structure and information as DNA. It is also composed of a sugar (ribose), phosphate, and has 4 types of bases, though instead of having A, T, C, G, it has U in place of T. DNA RNA

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http://1mkturin.files.wordpress.com/2009/03/dna-colored.gif

http://www.biologycorner.com/bio1/DNA.html

RNA moves across the nucleus into the cytoplasm to transport the code from DNA for the creation of proteins. Proteins are what come together to form our traits, without them there would be something seriously wrong with us.

http://www.biologycorner.com/bio4/notes/gene-expression.php

Materials:
DNA model 1 large container Water Source 1 sandwich bag Procedure: 1. Which item represents which part of the cell? (Draw a line matching the material to the cell part) 1. Large Container 2. Sandwich Bag 3.Water a. Cytoplasm b. Nucleus c. Cell Membrane 1. 2. 3. 4.

2. Pour water into the large container (for the sake of precautions, fill only halfway) 3. Place the DNA model in the plastic bag (dont close it yet). What do you think the nucleus role is? Where is DNA stored? 4. Place the plastic bag in the water-filled container and when the bag is underwater, remove all air and water from bag and then seal the bag tightly. In this lab you placed the DNA inside a plastic bag before placing it in the liquid. Why do you think DNA is not found floating around in the cytoplasm?

5. Cut a hole 6 cm wide on a corner of the sandwich bag. The nucleus inside a cell does not open and close at all, instead, it has small pores on its surface. 6. Without tearing a bigger hole, try getting your entire DNA model out of the bag. Does it fit? What do you think you should do to get your DNA model out? 7. Gently, pull out only half of the DNA model through the hole. What do you think this single-stranded molecule could be? Why does DNA have small pores?

Concept Questions:
1) Name 3 differences between RNA and DNA: 2) DNA is found anywhere inside the human cell: TRUE / FALSE 3) The purpose of RNA is to: a. Eliminate DNA b. Provide nutrients to the cell c. Transfer the code in DNA out of the Nucleus d. Make a party