Klug, Old Activity 16.2 Polymerase Chain Reaction
Klug, NEW Activity 17.3 Polymerase Chain Reaction
* In its revised format include parts of old 16.2.1 through 16.2.6. These parts should be
separated from the original tutorial then combined to form this new tutorial, Activity
17.3. It will have it's own Introduction, Summary, and Post-quiz.
* Remove the screen that shows on selecting “module quiz” asking if the user wishes to
take the quiz.
New organization:
Activity 17.3, Polymerase Chain Reaction
Introduction (New 17.3.1)
- This will not be a part of the Flash animation, unless the text needs to be
scrolled.
- Use the image of the red DNA from 16.2.1.1. but delete the words “DNA
to be amplified” and “Cycle 1” from the image.
- Use the new title, “Polymerase Chain Reaction”
- Make a single window of text that combines “The polymerase chain
reaction (PCR) was developed….” with the next page of text “PCR allows
a direct amplification”, with paragraph break, if this will all fit. If it
doesn’t fit, scroll the text from the bottom to the top, stopping when the
bottom line clears the bottom.
- This is the end of the segment. The rest of old 16.2.1 will be made into the
following animation.
Animation (New 17.3.2) PCR Amplification
- This is the latter part of the old Introduction to PCR of old 16.2.1, but
renamed and renumbered
- Use the same diagram from 16.1.2.1 showing the “DNA to be amplified”
and the red 5’, 3’ DNA threads with “Cycle 1” over the top.
- Use the title “PCR Amplification”
- For the text of 17.3.2.1, write :
“There are three steps in the PCR process:
1. Denaturation of the Source DNA
2. Annealing of Primers
3. Extension of Primers”
-
-
Scroll this text from the bottom of the text window to the top, stopping
when the top line reaches the top. Pause 3 seconds and dissolve to
sequence 17.3.2.2.
In 17.3.2.2, the text dissolves to “Step 1 – Denature DNA….” Scroll this
text from the bottom of the text window to the top, stopping when the top
line reaches the top. Pause 3 seconds and start the animation of 17.3.2.3.
Run 17.3.2.3 showing the splitting of the red DNA lines in Step 1:
Denaturation. Pause 3 seconds and dissolve just the text to 17.3.2.4.
In 17.3.2.4, the text “Step 2 – Anneal Primers…..” should be scrolled from
the bottom of the text window to the top, stopping when the top line
reaches the top. Pause 3 seconds and start the animation of 17.3.2.5.
- The animation of 17.3.2.5 shows the green Primers annealing to the red
DNA. Pause 3 seconds at the end of this and dissolve the text to 17.3.2.6.
- Scroll the text of 17.3.2.6 (“Step 3 – Extend primers….”) from the bottom
of the text window to the top, stopping when the top line reaches the top.
Pause 3 seconds and start the animation of 17.3.2.7.
- Run 17.3.2.7 showing Step 3 and the extension of blue lines from the green
lines. Pause 3 seconds and dissolve the scrolling text of 17.3.2.8
- Scroll the text “Each set of three steps…” from the bottom of the text
window to the top, stopping when the top line reaches the top. This is
17.3.2.8. Pause 3 seconds and dissolve to the next text and image.
- In 17.3.2.9, bring up the image showing “Cycle 2” and the two
red./blue/green DNAs along with the text “Now, the next cycle – cycle 2—
begins….” Pause for 5 seconds, and dissolve to the new text of 17.3.2.10.
- Bring up –don’t scroll---“Step 1 – Denature DNA…” in 17.3.2.10 but don’t
scroll. Pause 3 seconds and start the animation of 17.3.2.11.
- Run 17.3.2.11 showing Step 1 Denature DNA of Cycle 2 with four DNA
strands on screen. Pause for 3 seconds and dissolve to the new text of
17.3.2.12.
- Scroll the combined text of 17.3.2.13 which includes both pages of text:
“Step 3 – Extend Primers…”) PLUS “After 2 cycles, there are 4 new
DNA…”. from the bottom of the text window to the top, stopping when the
line “After 2 cycles, there are 3 new DNA….” reaches the top. Pause 3
seconds and start the animation of 17.3.2.14
- In 17.3.2.13, the green primers anneal to the 4 DNA strands.
- This is the end of the segment.
- Set Scroll flags: “C1Step1” at 17.3.2.2, “C1Step2” at 17.3.2.4, “C1Step3”
at 17.3.2.6, “C2Step1” at 17.3.2.10, “C2Step3” in 17.3.2.12
Exercise(New 17.3.3) Virtual PCR Lab
- Begin with the same image of beakers and eyedroppers and the ”Virtual
PCR lab” title.
- Combine the two pages of text into one presentation, with paragraph break
(“Welcome to the Virtual PCR lab….”) PLUS (“You have
painstakingly….”). This should all fit on one page, especially since it
looks like the font size is bigger than normal and can be reduced to the
size for text in other activities. Change the last line of the last paragraph
which says “Press “play’ to give it a try” to “Click on NEXT to give it a
try”.
- Add a NEXT button to the bottom of the text screen in 17.3.3.1.
- When the user clicks NEXT, dissolve to the interactive screen with the test
tube and words, which we’ll call 17.3.3.2.
- Delete the Usage and Textbook buttons.
-
Delete the Exercise Instructions box and instead move the directions
“What are some of the things you need….” to the Interaction Instructions
box.
- Use the same or similar color coding of words so the user knows which
sets of words are to be dragged to which Answer box.
- Delete the requirement to finish the exercise before being able to move to
the next segment.
- Delete the Alert! Box that comes up when several answers are missed.
- Use the same interactive feedback boxes that pop up now.
- Delete the final box that comes up when the user is finished which reads
“That concludes this exercise….” and also delete the Continue button.
- This is the end of the segment.
Exercise (New 17.3.4) PCR: Thermocycler set-up
- Begin with the same image of the test tube and the ”Virtual PCR Lab…”
title.
- Use the text “Don’t take off your gloves…” with a NEXT button at the
bottom. Add the line “Click NEXT to go to the amplification stage of the
PCR reaction.”
- Add a NEXT button to the bottom of the text screen in 17.3.4.1.
- When the user clicks NEXT, dissolve to the interactive screen with the
Thermocycler Program entry boxes which we’ll call 17.3.4.2.
- To the Interaction Instructions box put the words “Fill in the names of the
steps (anneal, elongate, or denature) that match the descriptions of these
steps. Then type in the answers to the questions under the Thermocyler
Program. Click on Submit when you are ready to be scored. Press Reset
to start over.”
- Use the same interactivity which places an X over wrong answers and the
popup box reminding the student to review the textbook.
- Delete the requirement to finish the exercise before being able to move to
the next segment.
- Change the box that comes up saying “That’s the maximum number of
tries…” and offers a Continue button to leave. Delete all this text and the
button and change the box instead to say: “Remember to spell the stages
of the thermocycler program exactly the way the instructions show them.
The length of each cycle should be the sum of all the individual cycles.
The total incubation should be 25 cycles times the length of a single cycle.
Add the number of hours and minutes of the incubation onwards from 1
pm to see if you will finish in time.”
- This is the end of the segment.
Exercise (New 17.3.5) PCR Incubation
- Begin with the same image the white box with dotted lines and the graph
grid below. Use the same title “Virtual PCR Lab: Reaction Progress”.
- Delete the onscreen instructions (“Above, the plot will show the
temperature…”
- Add a button that says “Initiate Cycle” which serves as the old play button
to move the user from screen to screen.
-
Into the Interaction Instructions box, write “Press the Initiate Cycle button
to cause the thermocycler to begin another reaction cycle. The upper
diagram shows the temperature changes in the reaction tube for each
cycle. Press the Plot button next to the graph below to plot the number of
DNA copies per reaction cycle. Continue initiating a new cycle until the
whole incubation is complete.”
- After the first cycle is initiated, the text of 17.3.5.2 should say “Assuming
we started with 1 DNA molecule….” But delete the second line, :”Press
play…” Allow the graphs to change as in the extant tutorial.
- The text of 17.3.5.3 should say “After the second cycle…” but delete the
second line, :”Press play to see…” Allow the graphs to change as in the
extant tutorial.
- The text of 17.3.5.4 should say “After the third cycle…” but delete the last
line: “Press play to continue”. Allow the graphs to change as in the extant
tutorial.
- The text of 17.3.5.5 should say “After 4 cycles…” but delete the last line:
“Press play to see”. Allow the graphs to change as in the extant tutorial.
- The text of 17.3.5.6 should say “After 5 cycles…” but delete the last line:
“Press play to see”. Allow the graphs to change as in the extant tutorial.
- The text of 17.3.5.7 should say “Now, after 10 cycles…” but delete the
last line: “Press play to see”. Allow the graphs to change as in the extant
tutorial.
- The text of 17.3.5.8 should say “After 15 cycles…” but delete the last line:
“Press play to see”. Allow the graphs to change as in the extant tutorial.
- The text of 17.3.5.9 should say “At the end of 25 cycles…” but delete the
last line: “Press play to continue this module”. Allow the graphs to
change as in the extant tutorial.
- This is the end of the segment.
Summary (New 17.3.6)
-This will not be programmed as part of the Flash animation.
- Convert this page to our new format.
Post-quiz (New 17.3.7)
-This will not be programmed as part of the Flash animation.
- Delete screen asking if user wants to take the quiz.
-
First Pass Comments from Eric Stavney 10/28/03
1. In 17.3.2 please fade out the old text before beginning the scrolling of the next
text at the Scroll Flag C1Step2.
[Andy 10/29: Please make these corrections.]
2. Please put a space between the words in the 17.3.2 Scroll flags—eg. “C1Step 1”
should be “C1 Step 1” etc.
[Andy 10/29: Please make these corrections.]
3. In 17.3.2 please fade out the old text before beginning the scrolling of the next
text at the Scroll Flag C1 Step3. Please do this for all the transitions marked
by scroll flags.
[Andy 10/29: Please make these corrections.]
4. In 17.3.2, during the C1 Step 3 scroll flag sequence and the C2 Step 3 sequence,
we need a correction in the first line of text. The word “Taq” needs to be
italicized so that the sentence reads: “A heat-stable form of DNA polymerase
(Taq polymerase, an…..”
[Andy 10/29: Please make these corrections.]
5. Exercise 17.3.3 doesn’t work yet, as acknowledged.
[Andy 10/29: Please correct. Also, by default, the instructions boxes should be open
at the beginning and close after a few seconds.]
[Andy 10/29: Also, the spacing of the words on the Thermocycler Program screen is
too crowded. There is room to the left and right so adjust the content to optimally use
the real estate. This will help to prevent the “Submit” and “Reset” buttons from
crashing into the blue control bar at the bottom of the screen.]
6. I had to click on “Initiate Cycle” three times in Exercise 17.3.4 to get any visible
change in the PCR graph. Let’s change this so that the user gets results (1st cycle)
after a single click. Furthermore, no amount of clicking “Initiate Cycle” will start
the animation as long as the Interaction Instructions window is still up. Let’s fix
this.
[Andy 10/29: I think the “Next” button is necessary. This allows the user to read the
text associated with each step. Auto-play would make it difficult for those of us that
ready slowly. Keep the Next buttons but format the text sot that is doesn’t crash the
other parts of the screen.]
[Andy 10/29: In addition, I do not understand the purpose behind the Plot, Hide, and
Reset buttons. They don’t do anything important so delete them. The graph should
be on by default. After the 5th cycle the graph changes, which is should do with the
click of the Next button. The graph should NOT disappear. Each time the graph
changes, show it.]
Second Pass Comments from Eric Stavney 11/5/03
1.In 17.3.3.1 we need a period at the end of the last sentence of the last paragraph that
comes up as the user arrives at this exercise. The period should follow the word
"try".
[Andy 11/5: Please make this correction.]
2. In 17.3.4.1 it takes TWO, not ONE click of the NEXT button to move to the
second screen. Let's please change this so the NEXT button works on the first click.
[Andy 11/5: Actually, the code appears to be inactive until the instructions close. The
“Next” button needs to work even if the instructions panel is open. Please correct.]
3. In 17.3.4.2 I clicked the Reset button after an incorrect attempt and could not get
any further interactivity upon clicking the SUBMIT button with a second try. The
button goes down but the interactivity appears to be hung. Can you look at this?
[Andy 11/5: I could not reproduce the behavior that Eric describes. Please check this
on a Mac to see if there is a deeper issue. Also, please delete the Alert box and it’s
text. It’s of no use and likely to be viewed as condescending.]