Exploring DNA Replication - ETHS

Sugat Dabholkar
Biology, Self-directed
90 Minutes
High School General Biology
v2

Overview

The DNA Replication Fork model helps students to simulate the process of DNA replication that occurs in every living thing as part of mitosis and meiosis. Students manipulate the simulation to see how different proteins work together to copy DNA. Students also learn how DNA relies upon patterns to replicate itself correctly and how mistakes in replication can sometimes occur.

Standards

Next Generation Science Standards
  • Life Science
    • [HS-LS3] Heredity: Inheritance and Variation of Traits
Computational Thinking in STEM
  • Modeling and Simulation Practices
    • Using Computational Models to Understand a Concept

Activities

  • 1. Challenge 1: Unwind the DNA
  • 2. Challenge 2: Unzip the DNA
  • 3. Challenge 3: Polymerize DNA
  • 4. Challenge 4: Completely Replicate DNA
  • 5. Part 2 - Challenge 5: Changing the Pace
  • 6. Part 2 - Challenge 6: Changing the Supply
  • 7. Part 2 - Challenge 7: Breaking the Rules

Student Directions and Resources


The DNA Replication Fork model helps students to simulate the process of DNA replication that occurs in every living thing as part of mitosis and meiosis. Students manipulate the simulation to see how different proteins work together to copy DNA. Students also learn how DNA relies upon patterns to replicate itself correctly and how mistakes in replication can sometimes occur.

You will need the following resources to complete this assignment.

1. Challenge 1: Unwind the DNA


Please read the instructions below, before you use the model.

Start by specifying the following settings in the simulator:

DNA-strand-length:  30                             Speed:  Normal

Enzyme labels: checked                           Substitutions:  unchecked

Nucleo labels: unchecked                         Free-nucleosides:  50                   Time-limit:  None
 

When you have chosen the correct settings, press SETUP.

The simulation setup shows the tools you will need to replicate DNA.  You have a strand of Condensed DNA, Free Nucleotides and Replication Enzymes:

Your GOAL  in PART 1 is to replicate (copy) a length of DNA by completing four CHALLENGES.

EXPLORE THE BIOLOGY:

Enzymes are proteins that perform chemical reactions in cells.  This simulation shows you four different enzymes that are integral to DNA replication. 

Press GO/STOP to start the simulation! 

You can drag and drop molecules inside the cell using your mouse cursor.


Question 1.1

Question 1:  Which enzyme unwinds condensed DNA? 

Hint: Try moving the different enzymes to the condensed DNA. 

[Note: you may have to “let an enzyme go” with your mouse in order to see the enzyme work.]

2. Challenge 2: Unzip the DNA


EXPLORE THE BIOLOGY:

DNA (DeoxyriboNucleic Acid) is made of two strands which wind around each other in a double helix.  When DNA is replicated, the DNA strands are separated and each serves as a template (i.e. the basis for a pattern) for a new double helix.

DNA-strand-length:  30                            Speed:  Normal

Enzyme labels: checked                           Substitutions:  unchecked

Nucleo labels: unchecked                         Free-nucleosides:  50                   Time-limit:  None

 

NOTE: Even though you are moving the proteins in this simulated cell by hand, in a real cell the proteins move randomly. This model allows the movement of molecules using the mouse to observe the effects faster. You would see the same behavior in the model but at a very slow pace if you do not move the molecules by hand.


Question 2.1

Question 2:  Which enzyme unzips the double stranded DNA? (Use the model to answer.)

3. Challenge 3: Polymerize DNA


EXPLORE THE BIOLOGY:

DNA is a polymer.  Polymers (poly = many) are large molecules made of smaller, linked units called monomers (mono = one). 

DNA is made up of many, individual nucleotides (monomers) that are connected to each other to form both single strands and helical, double strands (polymers).  Nucleotides are attached to a growing strand by an enzyme.    

DNA-strand-length:  30                               Speed:  Normal

Enzyme labels: checked                              Substitutions:  unchecked

Nucleo labels: unchecked                            Free-nucleosides:  50                   Time-limit:  None

 


Question 3.1

Question 3:  What enzyme will attach nucleotides to form double stranded DNA?

Hint:  You will need to move an enzyme and nucleotides into one place together to form new DNA.



Question 3.2

Question 4:  What do you notice about the shapes of the nucleotides? 



4. Challenge 4: Completely Replicate DNA


EXPLORE THE BIOLOGY:

Nucleotides are made of 3 parts: a sugar attached to a phosphate group and a nitrogen-containing base.  Human DNA is made of MANY nucleotides (about 3.2 billion base pairs) and there are different types of nucleotides because they are made with different types of bases. 

T = THYMINE G = GUANINE C = CYTOSINE A = ADENINE

DNA-strand-length:  30                              Speed:  Normal

Enzyme labels: checked                             Substitutions:  unchecked

Nucleo labels: unchecked                           Free-nucleosides:  50                   Time-limit:  None

Play with the model to answer the following questions: 


Question 4.1

Question 5:  Can polymerase attach any nucleotide, anywhere on a DNA strand?

(Hint:  Try out different bases at different locations; note what works and what doesn’t.)



Question 4.2

Question 6:  Which nucleotides (colors, labels) will pair together?  (Turn NUCLEO-LABELS on)



Question 4.3

Question 7:  Why do you think only certain nucleotides will pair up, but others won’t? 

(Hint:  Review your answer to Question 4 in CHALLENGE #3 on the page 4.)



Question 4.4

Reflection Question 1:

Before scientists had discovered that nucleotides form the base pairs you observed with the model today, one biochemist, Edwin Chargaff, discovered something unexpected.  He was studying DNA samples from humans, other animals and bacteria.  Chargaff discovered that, in every sample, the percent of cytosine was about the same as the percent of guanine AND the percent of adenine was about the same as the percent of thymine.  This observation became known as Chargaff’s Rule.

Explain how Chargaff’s observation relates to the base pairings you saw today.



Question 4.5

The percentages of A & T and C & G were about the same, but not exactly equal.  For example, in a sample of human DNA, Chargaff noted that the percentages of nucleotides were: Adenine = 30.9%    Thymine = 29.4%    Guanine = 19.9%    Cytosine = 19.8%

Why do you think the percentages of A & T and C & G are not EXACTLY the same? 



Question 4.6

Reflection Question 2:

In this model, you moved enzymes and nucleotides around to replicate DNA.  But, in real, living cells, no tiny person is there to move enzymes and nucleotides into position to replicate DNA.   

So, how do you think enzymes and nucleotides “know” where to go to create new DNA?  How do enzymes “know” what to do?  How does polymerase “know” which nucleotide is the right one to add to a growing DNA strand? 

5. Part 2 - Challenge 5: Changing the Pace


In PART 1, you replicated DNA but did not change any settings.  In PART 2, your GOAL is to investigate the effects of changing variables in the simulation on your DNA replication.  To complete this goal, you will need to complete a second set of CHALLENGES.

[NOTE:  If at any time in Challenges 5 through 7, you “run out of DNA” to replicate, just reset your simulation and continue with your challenge.]

1. Start by specifying the following settings in the simulator:

DNA-strand-length:  30                               Speed:  see below

Enzyme labels: checked                              Substitutions:  unchecked

Nucleo labels: unchecked                            Free-nucleosides:  150                    Time-limit:  No Limit

2. When you have chosen the correct settings, press SETUP. Press GO/STOP. 

3. Start DNA replication by unwinding and unzipping your DNA and attaching polymerase ONLY on the TOP strand.

4. First change the simulation speed by moving the slider to the left, to FASTER.

Do NOT move the nucleosides using mouse. Observe the random motion of nucleosides and DNA replication. 

6. After you replicate the top strand, decrease the simulation speed by moving the slider to the left, to SLOWER.

Attach the polymerase to the bottom strand.

Now, observe the replication bottom strand of DNA.  Press GO/STOP to end the simulation.

 


Question 5.1

Question 8:  How does increasing the simulation speed affect your DNA replication?  Is it easier or harder?  Why? Use your observations to justify the reason.



Question 5.2

Question 9:  How does decreasing the simulation speed affect your DNA replication?  Is it easier or harder?  Why? Use your observations to justify the reason.

6. Part 2 - Challenge 6: Changing the Supply


1.  Return the speed to NORMAL and SETUP the simulation, then press GO/STOP.

2.  Unwind the DNA, separate the strands and attach polymerase. Increase the number of free nucleosides to approximately 150 bases.

3.  Observe the replication the TOP STRAND of DNA ONLY.

4.  Now, decrease the number of free nucleosides to approximately 15 bases. 

5.  Attach polymerase to the bottom strand. Observe the replication the bottom strand of DNA now.  Press GO/STOP to end the simulation.


Question 6.1

Question 10:  How does increasing the number of nucleotides affect your DNA replication?  Is it easier or harder?  Why? Use your observations to justify the reason.



Question 6.2

Question 11:  How does decreasing the number of nucleotides affect your DNA replication?  Is it easier or harder?  Why? Use your observations to justify the reason.

7. Part 2 - Challenge 7: Breaking the Rules


1. Return the free nucleotides to approximately 50 and SETUP the simulation, press GO/STOP.

2. Unwind the DNA, separate the stands, attach the polymerase to the TOP strand ONLY. Observe the top strand of DNA, now.

~

3. After the top strand is finished, turn SUBSTITUTIONS to ON and attach polymerase to the bottom strand. Observe replication of the bottom DNA strand.

4. Press GO/STOP to end the simulation.

5. Check the readout boxes for your top and bottom DNA strands (as in the picture below)

. 

 


Question 7.1

Question 12:  Compare your top and bottom strands; what changed when you turned SUBSTITUTIONS on?    What do you think SUBSTITUTIONS means?

Hint:  You might want to compare this challenge to your results from Part 1 – Challenge 4.

Hint:  In order to see your DNA more clearly, press GO/STOP, change FREE-NUCLEOTIDES to zero, and move the enzymes out of the way, then press GO/STOP again!



Question 7.2

Question 13:  What nucleotide pairings do you observe in the bottom strand but not in the top strand?



Question 7.3

Reflection Question 3: The changes you observed in the sequence of nucleotides in your DNA strand are called mutations.  There are several different types of mutations.  You simulated substitution mutations, meaning that some nucleotides were paired incorrectly during replication, for example a Thymine might be substituted where a Cytosine should be, or a Guanine substituted for an Adenine.  As a result, the two, new DNA strands that you made in CHALLENGE 7 had different (mutated) sequences. 

 

What other kinds of mutations do you think might happen to change the sequence of nucleotides in DNA?