DNA Lab Teacher

What is DNA?

Hypothesis:

(Here students write what they think DNA might be)

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

QuickTime and a TIFF (Uncompressed) decompressor are needed to see this picture.

http://www.mhhe.com/biosci/esp/2001_gbio/folder_structure/ge/m4/s1/gem4s1_1.htm

How is DNA related to our body? DNA is the genetic material inside 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? [Advanced]: 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 due to the varying sequence in nucleotides. So, although you and your friends DNA structure is the same, your nucleotide sequence is different, and while your genes code for light hair, your friends genes code for dark hair! DNA has only 4 Nitrogenous bases: Adenine, Thymine, Cytosine, and Guanine. Each base corresponds 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. Adenine and Thymine are bonded with two bonds, while Cytosine and Guanine are bonded by three.

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/B/BasePairing.gif

DNA has a double-helix structure, meaning that when both sides of DNA come together, the strong energy and force of the hydrogen bonds between bases will cause the DNA to coil.

QuickTime and a TIFF (Uncompressed) decompressor are needed to see this picture.

http://ft.ornl.gov/~kspafford/projects.html

1) DOTS [2 boxes of 5 colors] & Crows candy [only 1 box] - (appx. $5 total at Walgreens) ** NOTE: Material contains corn syrup! Green = Phosphate Black = Sugar (Use CROWS black licorice) Yellow = Adenine Pink = Thymine Orange = Cytosine

Materials: (group of up to 4)

Red = Guanine 2) 20 Toothpicks [One Box of 250 Toothpicks (any kind but round is preferred) = $1.50] 3) 1 meter of yarn (single pack 6 oz. @ Jo-Ann Crafts store ~$4) Total Cost: $10.50

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 a double-helix even looks like (the structure of DNA), let alone understand how its structure will help in DNA Replication. In this 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.

Procedure (~30 minutes): Group of up to 4

1. Each group must Take 12 green, 12 black, 4 yellow, 4 pink, 2 red, 2 orange candies and 20 toothpicks. 2. Cut all of the toothpicks in half students 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).
P OP H SH AT E

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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? A phosphate, sugar, and base. 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).

6.
http://1mkturin.files.wordpress.com/2009/03/dna-colored.gif http://intra.stgym.dk/sa/3_chem1.gif

Why is it important that bases are paired with their complementary base? It is important that the bases are paired correctly because otherwise the DNA sequence would be incomplete and misinterpreted. If it is in charge of the production of a certain protein but the cell does not understand the instructions, then that protein will be manufactured incorrectly or not at all. The sequence will be incorrect if two bases cannot come together. 7. Choose another nucleotide and attach it 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-sugar bonds. Make sure the base is towards the center of the molecule, aligned with the other bases.

http://www.tutorvista.com/content/biology/biology-iii/nucleic-acids/deoxyribose-nucleic-acid.php

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

http://picsdigger.com/domain/studentsguide.in

9.

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. If necessary, change your model so that the strands look like theyre going the opposite way. Why do you think they do that? DNA is anti-parallel, meaning that both strands are parallel but face opposite directions.

n Ta ennicmtose d d cic pes o IF (Uud T r eseth ep mre s r F Qe kd a da o im r ec e p es e ) is o tur .

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

In this lab you only made 6 nucleotides and made 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? DNA continues on infinitely because it is made up 3.4 billion pairs of nucleotides in human DNA. Thats part of the reason why DNA coils to fit better inside the nucleus.

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 DNA strands in preparation of the replication process

QuickTime and a TIFF (Uncom pressed) decom pressor are needed to see this picture.

http://4.bp.blogspot.com/_8Rm_kFNfDDg/SadUClLoQ7I/AAAAAAAAA98/oWWpjdvvzwc/s400/DNA_ unzipping_Efjc_Ewlc.png

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. [Advanced]: 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.

1) 2) 3) 4)

Materials:
DNA Model students just created 1 pair of Scissors Remaining 2 pink, 2 yellow, 1 orange, 1 red, 6 green, 6 black candies Remaining toothpicks

Procedure (~30 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? Helicase unwinding DNA 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? DNA Polymerase 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? DNA Polymerase cannot go in this direction as easily as you can. 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? Students should have 2 complete (and separate) DNA strands.

Concept Questions:
1) True / False , the purpose of the replication process is to create DNA for new cells. TRUE 2) What is DNA made up of? Many many sequences of nucleotides, and each nucleotide is made up of one phosphate, one sugar, and one base. 3) Approximately how big is DNA? DNA is one millionth of a meter a micron long, and the nucleus is about 10 microns big 4) [Basic]: Your DNA is different from everyone elses True / False TRUE one variance in sequence of nucleotides makes everyone different. 5) [Basic]: DNA stands for: a. Dumb Newt Association b. Demoniclyrapid nickel Acid c. Deoxyribonucleic Acid d. Deoxygenated ribose in Nucleus Acid 6) Pair these letters with their complementary ones,(these have their correct number of bonds): A A C T A A G G T A C A A T C C G C A || || ||| || || || ||| ||| || || ||| || || || ||| ||| ||| ||| ||

T T G A T T C C A T G T T A G G C G T 7) [Advanced]: What do you think would happen to your genes if the bases in your DNA were not paired correctly? The sequence would be incorrect, so the instructions could give the wrong message. The instability of the cells could cause a mutation, although there is also a chance that nothing may be wrong, because one or two mismatches may not necessarily result in a physical mutation.

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

Q uickTim and a e TIFF (Uncom pressed) decom pressor are needed to see this picture.

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? The nucleus protects DNA and controls its movement, this is where DNA is 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? DNA is not able to exit the nucleus, and the cells cytoplasm is damaging to DNA.

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? Make a Hole. 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? To restrict the passage of large molecules such as DNA, but allowing smaller ones, like RNA to go through.

Concept Questions:
1) Name 3 differences between RNA and DNA: Possible Answers Structure: single-stranded vs. double-stranded Nucleotides: RNA has U instead of T as in DNA Mobility: RNA can transfer genetic code out of nucleus 2) DNA is found anywhere inside the human cell: TRUE / FALSE FALSE DNA is only found in the nucleus in human cells 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