Klug, Old Activity 11.1, DNA Replication
Klug, NEW Activity 11.1 DNA Replication
* In its revised format include parts 11.1.1 through 11.1.15. These parts should be
separated from the original tutorial then combined to form this new tutorial, Activity
11.1. 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 11.1, Semiconservative Model
Introduction (New 11.1.1.)
-This will not be programmed as part of the Flash animation.
-Use the final frame of the animation (static image) in the existing Introduction
(old 11.1.1) showing the three results of replication called Conservative,
Semiconservative, and Dispersive.
- Use the same static text (“Besides the semiconservative model…” ) as in old
11.1.
-This is the end of the introductory segment.
Animation (New 11.1.2) Meselson-Stahl Experiment
- Begin with the same image of the red flask as in old 11.1.2 and don’t start
the animation yet.
- Delete any hard stops between animation segments to come.
- Scroll the text of old 11.1.2.1 (“Mathew Meselson and Franklin Stahl…”)
from the bottom of the text window upwards until the first line reaches the
top of the text window. At this point, freeze the text, pause 2 seconds, and
dissolve to a scrolling of the second page of text, 11.1.2.2.
- When the top line of the second page of text (“Meselson-Stahl grew
Escherichia coli [Escherichia coli should be in italics]…”) reaches the top
of the text window, freeze the scrolling and start the animation after a 2
second pause.
- Dissolve and run the animation that ends with the red beaker and test tube.
Delete the old instructions of “To start the experiment”. Pause for 3
seconds and animate the eyedropper moving slowly over to the test tube,
and show red fluid appearing in the test tube automatically. Delete the
interactivity requirement for this to proceed. Delete the “thunk” sound
when the eyedropper reaches its destination. Bring up the word
“Centrifuge” as in the extant animation. This whole sequence we’ll call
11.1.2.3.
- Pause for 3 seconds after “Centrifuge” appears, and continue without stop
to the next sequence (11.1.2.4). Delete the instructions saying “Click the
centrifuge button” and delete required user interactivity.
- In 11.1.2.4, the test tube whirls around and stops as 15N/15N appears next
to the tube. Hold this final frame for 5 seconds and dissolve to the next
part of the sequence without stopping. Delete the instructions about
“Click to Play…”
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11.1.2.5 shows the test tube slide to lower left and red and blue flasks
appearing. Delete the instructions “Drag the dropper” and remove the
requirement for user activity. Hold at the tail of this sequence for 4
seconds, and dissolve to the next sequence (11.1.2.6) without stopping.
The movement of the eyedropper with blue fluid over to the test tube, and
the appearance of blue in the tube is sequence 11.1.2.6. Delete the
“thunk” sound but bring up the word “Centrifuge”. This is not a hot
button but merely the word ‘Centrifuge” since interactivity has been
removed. Delete the instructions that appear (“Click the Centrifuge
button…”). Pause for 3 seconds and continue to the next sequence.
Sequence 11.1.2.7 shows the test tube whirling to end up stationary with
the label 15N/14N. Delete “Click Play to Continue”. Hold the last frame for
4 seconds and dissolve to the next sequence, 11.1.2.8.
In 11.1.2.8, the test tube with the blue band move to center bottom and
another flask appears. Delete the “Drag the dropper instructions”and
pause for 3 seconds. Then continue automatically (without interactivity)
to the movement of the eyedropper in 11.1.2.9.
Show the eyedropper with blue fluid moving slowly over to the test tube
(11.1.2.9) and leaving blue fluid in the tube. Remove the “thunk” sound
as this happens, as well as deleting the text that comes up (“Click the
Centrifuge button”). Bring up the word “Centrifuge” but don’t make it a
hot button. Pause for 3 seconds before continuing to 11.1.2.10.
In 11.1.2.10, the test tube whirls around and stops with the double label
“14N/14N” and “15N/14N”. Delete the “Click to Play” instructions. Pause
for 4 seconds and dissolve to the next sequence, 11.1.2.11.
In 11.1.2.11, the third test tube drops to the bottom and the last flask and
dropper appear (Generation III). Pause 3 seconds here. Delete the “Drag
the dropper…” instructions.
Proceed directly in 11.1.2.12 to animating the eyedropper moving itself
slowly to the right and adding a blue layer to the test tube. Bring up the
word “Centrifuge” without making it a hot button. Delete the instructions
about “Click the Centrifuge button”. Pause for 3 seconds, and continue to
11.1.2.13.
The whirling of the tube to end up with the two blue bands and double
label comprises sequence 11.1.2.13. Delete the “Click to Play” reference
at the end of this sequence. Pause 4 seconds and move to the next
sequence directly.
In 11.1.2.14, show the test tube moving down, dissolve to “Comparing
With Expected Results”, and bring up the text “Comparing the actual
results with the expected….” just as this happens in the extant animation.
This is thankfully the end of this segment.
Set up Scroll flags at the following names and at the following locations:
“Growing bacteria” at the start of the text scroll of 11.1.2.2, “Growth in N15” at the start of 11.1.2.3, “N-15 Centrifugation” at the start of 11.1.2.4,
“1st Gen N-14” at the start of 11.1.2.5, “Preparing 1st Gen DNA” at the
start of 11.1.2.6, “1st Gen Centrifugation” at the start of 11.1.2.7 (the
whirling test tube), “2nd Gen N-14” at the start of 11.1.2.8, “Preparing 2nd
Gen DNA” at the start of 11.1.2.9, “2nd Gen Centrifugation” at the start of
11.1.2.10, “3rd Gen N-14” at the start of 11.1.2.11, “Preparing 3rd Gen
DNA”, at the start of 11.1.2.12, “3nd Gen Centrifugation” at the start of
11.1.2.13, “Comparing Results” as soon as the full build (last frame) of
11.1.2.14 appears.
- This is the end of the segment.
Animation (new 11.1.3) Vicia faba
- Begin with the same image of the unlabeled and labeled chromsomes as in
old 11.1.3 and don’t start the animation yet.
- Delete any hard stops between animation segments to come.
- Scroll the text of old 11.1.3.1 (“The year before the results of the…”) from
the bottom of the text window upwards until the first line reaches the top
of the text window. At this point, freeze the text, pause 2 seconds, and
dissolve to a scrolling of the second page of text, 11.1.3.2.
- When the top line of the second page of text (“For semi-conservative
replication to occur…” reaches the top of the text window, freeze the
scrolling and start the animation after a 3 second pause.
- Dissolve away the text, as in the existing sequence for 11.1.3.3 and play
the animation sequence (New 11.1.3.3) to the end, building a full screen of
chromosomes with a photo.
- This is the end of the segment.
- Set up a scroll flag by the following name and at the following location:
“Labeling DNA” at the start of the animation of 11.1.4.2.
Animation (new 11.1.4) Bidirectional Replication
- Begin with the same image of the DNA circle as in old 11.1.4.1 and the
same title in the graphics window (Replication of E. coli).
- Delete any hard stops between animation segments to come.
- Scroll the text of old 11.1.4.1 (“John Cairns found the replication of E.
coli [put E. coli in italics]…”) from the bottom of the text window
upwards until the first line reaches the top of the text window. At this
point, freeze the text, and start the animation, 11.1.4.2
- Run the animation of the DNA circle peeling away to make two circles
(11.1.4.2) to the end, pause 3 seconds, and dissolve to the next graphic and
text of 11.1.4.3
- Bring up the table entitled “Summary of Replication of E. coli” with the
same text as in 11.1.4.2.
- This is the end of the segment.
- Set up Scroll flags at the following names and at the following locations:
“Bidirectional Replication” at the start of the animation of 11.1.4.2, and
“Summary” at the start of 11.1.4.3.
Animation (New 11.1.5) DNA Polymerase I
- Begin with the same image of the red and blue DNA fragment as in old
11.1.5.1 and the same title in the graphics window (“Chemical Reaction
Catalyzed…”); don’t start the animation yet.
- Delete any hard stops between animation segments to come.
Scroll the text of old 11.1.5.1 (“The first enzyme isolated in DNA
synthesis…”) from the bottom of the text window upwards until the first
line reaches the top of the text window. At this point, freeze the text, and
start the animation, 11.1.5.2
- Run the animation showing the dNTP sliding in from the left, pausing,
finally joining the red line (11.1.5.2).
- This is the end of the segment.
- Set up a Scroll flags at the following names and at the following locations:
“Adding a dNTP” at the start of the animation of 11.1.5.2.
Animation (11.1.6) DNA Synthesis
- Begin with the same image of two yellow filled nucleotides as in old
11.1.6.1 and the same title in the graphics window (“5’ to 3’ Synthesis of
DNA.
- Delete any hard stops between animation segments to come.
- Scroll the text of old 11.1.6.1 (“The direction of DNA synthesis is…”)
from the bottom of the text window upwards until the first line reaches the
top of the text window. At this point, freeze the text, and start the
animation, 11.1.6.2
- Run the animation showing the linkage of 2 nucleotides and ending with
two labeled DNA strands. (11.1.6.2This is the end of the segment.
- Set up a Scroll flag by the following names and at the following locations:
“Chain elongation” at the start of the animation of 11.1.6.
Animation (new 11.1.7) Helical Unwinding
- Begin with the same image of a blue and green double strand with blue
blobs as in old 11.1.7.1 and the same title in the graphics window
(“Unwinding with DnaA…..”); don’t start the animation yet.
- Delete any hard stops between animation segments to come.
- Scroll the text (11.1.7.1) from the old text window saying “For DNA
replication to occur…” upwards from the bottom of the text window to the
top and freeze when the top line meets the top of the window. Pause 2
seconds and start the animation sequence of 11.1.7.2
- Run the animation of 11.1.7.2 showing the blue blobs grouping and an
orange DnaB blob opening up the DNA.
- This is the end of the segment.
- Set up a scroll flags by the following name and at the following location:
“DNA unwinds” at the start of the animation of 11.1.7.2.
Animation (new 11.1.8) Opposite Polarity
- 11.1.8.1 has an image of single double-stranded DNA (DNA template)
and the text “DNA replication requires a template”. Scroll the text from
the bottom of the text window until the top line reaches the top. When it
does, freeze the scroll, wait 2 seconds, and start the animation sequence.
- The animation sequence (11.1.8.2) shows the red double line forking open.
Keep the same text onscreen
- Set up a scroll flags by the following name and at the following location:
“Synthesis at fork” at the start of the animation of 11.1.8.2.
- This is the end of the segment.
-
Animation (new 11.1.9) Concurrent Synthesis
- 11.1.8.1 has an image of two blue balls and red DNA.
- Scroll the text (“both the leading and lagging strands of DNA…” from the
bottom of the text window until the top line reaches the top. When it does,
freeze the scroll, wait 2 seconds, and start the animation sequence.
- The animation sequence (11.1.8.2) shows the two blue balls moving to the
right.
- Keep the same text onscreen
- This is the end of the segment
- Set up scroll flags by the following name and at the following location:
“Simultaneous synthesis” at the start of the animation of 11.1.9.2.
Animation (new 11.1.9) Summary of Synthesis
- Begin with the same image of two red lines and the orange blob as in old
11.1.9.1 and the same title in the graphics window (“A Model of DNA
Synthesis”).
- Delete any hard stops between animation segments to come.
- Scroll the text of old 11.1.9.1 (“The basic steps of DNA synthesis…”)
from the bottom of the text window upwards until the first line reaches the
top of the text window. At this point, freeze the text, and start the
animation, 11.1.9.2.
- Run the animation which ends with the orange “rocketship” surrounded by
blue balls along the red lines. (11.1.9.2). Pause for 4 seconds, then
dissolve directly to the next sequence.
- Run the animation which ends with a doublet of blue balls moving to the
lower right (11.1.9.3). Pause for 4 seconds, then dissolve directly to the
next sequence.
- Run the animation which shows the “Okazaki fragments” being transiently
labeled (11.1.9.4).
- This is the end of the segment.
- Set up Scroll flags by the following names and at the following locations:
“Helix denatures” at the start of the animation of 11.1.9.2, “Replication
and gyrase” at the start of 11.1.9.3, and “Okazaki fragments” at the start of
11.1.9.4.
Animation (11.1.10) Replication of Telomeres
- Begin with the same image of the two red lines as in old 11.1.10.1 and the
same title in the graphics window (Replication at the End….).
- Delete any hard stops between animation segments to come.
- Scroll the text of old 11.1.10.1 (“In eukaryotes, at the end of the
lagging…”) from the bottom of the text window upwards until the first
line reaches the top of the text window. At this point, freeze the text, and
start the animation, 11.1.10.2
- Run the animation of the blue and green lines that draw themselves along
the red lines (11.1.10.2), pause 3 seconds, and dissolve to the next
animation sequence.
- Run 11.1.10.3 ending with “Gap b” along the bottom of the upper red line.
- This is the end of the segment.
Set scroll flags of “Strand synthesis” at the beginning of 11.1.10.2 and
“Appearance of gaps” at the beginning of 11.1.10.3.
Animation (11.1.11) Telomerase
- Begin with the same image of the one red lines as in old 11.1.11.1 and the
same title in the graphics window (Predicted Solution for Ends….).
- Delete any hard stops between animation segments to come.
- Scroll the text of old 11.1.11.1 (“Telomerase is an enzyme that allows….”
)from the bottom of the text window upwards until the first line reaches
the top of the text window. At this point, freeze the text, and start the
animation, 11.1.11.2
- Run the animation of the red line bending under in a hook (11.1.11.2),
pause 3 seconds, and continue to the next animation sequence.
- Run 11.1.11.3 ending with the red bent portion moving down to the lower
right of the graphics window.
- This is the end of the segment.
- Set scroll flags as “Adding repeats” at the start of 11.1.11.2 and
“Removing hairpin” at the start of 11.1.11.3.
Summary (New 11.1.12)
-This will not be programmed as part of the Flash animation.
Post-quiz (New 11.1.13)
-This will not be programmed as part of the Flash animation.
- Delete screen asking if user wants to take the quiz.
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First Pass Comments by Eric Stavney
1. The first scroll flag in 11.1.1 needs to be moved over so it comes up fully
onscreen. How about changing it to “Meselson-Stahl Expt.”?
[Andy: Please adjust the position of the scroll flags. No need to change the
wording.]
2. The whole tempo of 11.1.1 is a bit fast, now that we’ve connected all these
subsequences together. Can we slow down the tempo to fewer frames per second
so that the user can follow all this?
[Andy: Please adjust the timing to slow the presentation.]
3. Make this tutorial scaleable as we are with the other tutorials.
[Andy: Standard fix.]
4. Nice job getting in all the scroll flags in 11.1.1.
[Andy: …and miraculous too. ]
5. We need a full two seconds, maybe three seconds between the halting of the
scrolling text of 11.1.3.1 to 11.1.3.2. I’m not counting 2 seconds here but
something less.
[Andy: Please adjust the pause as directed.]
6. Correct the typo in the second scroll flag of 11.1.3 (Vica faba) – it should be
Labeling DNA, not Labelling DNA. [one “l” in labeling].
[Andy: Please correct as directed.]
7. Place dissolves between the changes of all the images in 11.1.4, not blunt cuts.
[Andy: Please correct as directed.]
8. Slow down the animation of 11.1.5, perhaps by reducing the tempo setting (you
can do this in Director I know, not sure about Flash).
[Andy: Please correct as directed.]
9. The caption at the bottom of the graphics screen in 11.1.7.2 saying “After DnaA
initiates helical unwinding….” is a bit tightly associated with the illustration
above it. Can we raise the whole animation upwards and pull this text downwards
to give it more breathing room?
[Andy: In stead of moving the graphic, put the text on 3 lines instead of 4.]
[Andy: In 11.1.8, Opposite Polarity, the animated segment should be under scroll
bar control. This also happens in many of the other segments. Please correct these
in all cases. The scroll bar should always control the action of the animated
graphic.]
10. 11.1.9 was very nice.
[Andy: Please review and correct the scroll bar control. See the segments labeled
“Helix Denatures,” “Replication and Gyrase,” and “Okazaki Fragments” as
examples of correct scroll bar implementation and control of the graphic.]
11. In 11.1.10, please put in dissolves, not blunt cuts, between the captions that
appear in successive sequences.
[Andy: Please correct as directed.]
12. In 11.1.11, please put in dissolves, not blunt cuts, between the captions that
appear in successive sequences. This is especially true during the transition to the
last caption at the bottom of the screen.
[Andy: Please correct as directed.]
Second Pass Corrections From Eric Stavney 10/24/03
1. Why are the plunger tops of the test tubes separated from the test tubes in 11.1.2
during the whole animation? In the original version, the plunger tops came down
to cap each test tube after the eyedropper added something and they tops stayed
on as the tubes were lined up along the bottom of the screen. Let’s recap our
tubes and kept them capped!
[Andy 10/30: Please make this correction. This appears to be intermittent and I
suspect that it’s because the capping animation isn’t under the control of the scroll
bar. If you move the scroll bar at the wrong time then the test tubes spin with an open
cap. Also, for each of the segments in the first animation, add the scroll bar flag title
as a screen title to correspond to the action. This should begin with “Growth in N15” and continue through “3rd Gen Centrifugation”. The last flag title matches the
screen title.]
[Andy 11/7: This has not be correct but it is an issue that we can accept in light of
the time required to make the correction and the lack of significance of the
concern.]
2. We got a small case of “moving” static graphics in 11.1.2 as the black arrows that
come up between the test tubes at the bottom of the screen move slightly right and
left in later sequences. Can we firmly position these black arrows so they don’t
dance around by a few pixels? Speaking of which, who asked for the black
arrows to be added to the lower series of tubes? These arrows are not in the
original animation and I think they should be removed.
[Andy 10/30: Please make this correction.]
[Andy 11/7: The 2 black arrows that appear between the test tubes (BEFORE the
last screen) need to be removed. It is correct to show 2 black arrows in the middle
row of test tubes on the last screen of but it is not correct to show the 2 arrows
that appear when each of spinning tubes drop.]
3. What happened to 11.1.3 (Vicia faba) – when I click NEXT from 11.1.2, all I get
is a white screen. Another click brings me to 11.1.4.
[Andy 10/30: Please make this correction. It sounds like a Mac coding issue.]
4. Is the scroll bar in the right place in this tutorial? There’s not supposed to be white
screen hanging out below the scroll bar. This is really obvious in 11.1.6 during
the very last animation when a DNA nucleotide flies in behind and under the
scroll bar to join the DNA onscreen! Obviously we gotta drop the scroll bar to the
bottom of the screen.
[Andy 10/30: Please make this correction.]
[Andy 11/7: This has not been corrected. Please see the animation titled
“Direction of DNA Synthesis” near the part where the 4th nucleic acid comes in
from the bottom. We should not see the objects below the blue scroll bar.]
5. In 11.17 (Helical Unwinding) I can’t seem to control the animation with the scroll
bar slider in the DNA Unwinds scroll flag section. In this same section, the words
DnaC and DnaB appear transiently at upper right for no reason, then reappear
again as labels with leader arrows (appropriately) next to certain molecules.
Delete the appearance of DnaC and DnaB by themselves (not pointing to
anything).
[Andy 10/30: Please make this correction.]
[Andy 11/7: Corrected.]
6. 11.1.9 needs a title in the top of the graphics window saying “A Model of DNA
Synthesis”.
[Andy 10/30: Add the title “A Model of DNA Synthesis” to the top of the screen.]
[Andy 11/7: Corrected.]
7. The first scroll flag of 11.1.9 should be “A Model of DNA Synthesis”, not “Cell
Cycle Times”.
[Andy 10/30: Please make this correction.]
[Andy 11/7: Corrected.]
8. There’s nothing onscreen when I click NEXT from 11.1.9. Where’s 11.1.10? I
can move
[Andy 10/30: I believe this is corrected now.]
9. The Conclusion page should be entitled “Conclusion”, not DNA Replication
Summary.
[Andy 10/30: Please make this correction.]
[Andy 11/7: Corrected.]
10. The term “Vicia faba” should be italicized at the end of the second paragraph on
the Conclusion page.
[Andy 10/30: Please make this correction.]
[Andy 11/7: Corrected.]
Second Pass Comments from Eric Stavney 10/29/03
1. In 11.1.2 the test tube that is moved downwards to the far left of the bottom row
loses its label because the 15N/15N sits off-screen. The label needs to be moved
and/or reduced.
[Andy 10/30: Please make this correction.]
[Andy 10/30: Also, the black arrows jump around on the screen. These should not
move.]
[Andy 11/7: I rescind this comment. The black arrows should not appear until the
very end. See Eric’s last review for directions.]
2. It’s maddening that the scroll bar still doesn’t control the animation completely in
11.1.2.--- there’s lots of drop out and incomplete movements when sliding the bar
manually.
[Andy 10/30: The scroll bar must control the action. In the case of 11.1.2, the only
action I observed that wasn’t under scroll bar control was the movement of the blue
line down the test tube. I don’t think this is an issue to worry about but there are
other instances that are a big deal. See the last part of Unwinding with DnaA, DnaB,
and DnaC. The action at the replication bubble MUST be under the control of the
user with the scroll bar.]
[Andy 11/7: Corrected.]
3. There is no bounding blue space above the white screen or stage in 11.1.2. Where
did this go?
[Andy 10/30: This .swf appears to be crashing the top part of the browser window
while the others push out the bottom. In several, I noticed that the “Next” was half
off screen. This should impact the final assembly of the tutorial but it looks odd.]
[Andy 11/7: Corrected.]
4. No visible segment comes up for 11.1.3 – Vica faba is still not visible to me using
a Mac G4 running OS X and Internet Explorer 5.2.
[Andy 10/30: I’m able to see the Vica faba segment (Taylor, Woods, and Hughes) on
my PC. This might be the same issue with the Mac that we encountered with 17.4]
[Andy 11/7: The scroll flag labeled Vica Faba should be italicized.]
5. The first scroll flag in 11.1.4 should be E. coli not E. Coli.
[Andy 10/30: Please make this correction.]
6. In 11.1.7 in the last scroll flag sequence the words DnaC and DnaB come on
screen briefly and then disappear, to show up a few moments later, pointing at
nothing obvious. Delete the first appearance of these two words and the second
time they come up, show the protein blobs and the leader arrows these words are
pointing to.
[Andy 10/30: Please make this correction. The DnaC and DnaB should only appear
with the leader line. This is in the segment titled “Unwinding with DnaA, DnaB, and
DnaC”]
[Andy 11/7: Corrected.]
7. In 11.1.9 (Concurrent synthesis) the text is too close to the graphic. Shrink the
graphic and move it leftwards.
[Andy 10/30: The art IS too close to the text but trim the left-hand side (by the 5’ and
3’ end) because I don’t want the art reduced.]
[Andy 11/7: Corrected.]
8. The scalability of this tutorial is kind of weird. I can’t get the NEXT hyperlink to
show in the bottom right of the browser window unless I enlarge the browser to
nearly full screen. In other words, even though the white screen does scale with
the browser window, it’s not a fully linked ratio and some vignetting occurs when
the browser window is small.
[Andy 10/30: I also noted this. This is probably due to the way the SWF is embedded
in the HTML. It shouldn’t be an issue once the tutorials are assembled.]
[Andy 11/7: This will be addressed in assembly.]
[Andy 10/30: The .swf file FOLLOWING “Chemical Reaction Catalyzed by DNA
Polymerase I” should be titled “Direction of DNA Synthesis”. Also note that part of
the DNA art hangs off the bottom of the screen and past the blue scroll bar. This is
awkward and needs to be corrected.]
[Andy 11/7: Corrected.]
[Andy 10/30: The .swf file FOLLOWING “Unwinding with DnaA, DnaB, and
DnaC” should be titled “Templates and Primers”.]
[Andy 11/7: Acceptable.]