Klug, Old Activity 10.1, The Structure of DNA
Klug, NEW Activity 10.1 DNA Structure
* In its revised format include parts 10.1.1 through 10.1.10. These parts should be
separated from the original tutorial then combined to form this new tutorial, Activity
10.1. 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.
* Change the name of this Activity to DNA Structure
New organization:
Activity 10.1, DNA Structure
Introduction (New 10.1.1.)
-This will not be programmed as part of the Flash animation.
-Use the final frame (full build) of the animation in the existing Introduction (old
10.1.1) showing the deoxyadenylic acid already zoomed forward with labels.
- Use the same static text (“Nucleic acids are molecules…” as in old 10.1.
-This is the end of the introductory segment.
Animation (New 10.1.2) Nitrogenous Bases
- Begin with the same image of the pyrimidine and purine ring as in old
10.1.2 and don’t start the animation yet.
- Delete any hard stops between animation segments to come.
- Scroll the text of old 10.1.2.1 (“Nitrogenous bases are one of three
essential…”) 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, New 10.1.2.2
- When the animation revealing cytosine, thymine, and uracil (10.1.2.2)
completes, pause for 2 seconds and start the animation of 10.1.2.3 (brings
up the purines Adenine and Guanine).
- Set up Scroll flags at the following names and at the following locations:
“Pyrimidines” at the start of the animation of 10.1.2.2, and “Purines” at
the start of 10.1.2.3.
- This is the end of the segment.
Animation (new 10.1.3) Pentose Sugars
- Begin with the same image of the Ribose and 2-Deoxyribose as in old
10.1.3.1 and the same title in the graphics window, and don’t start the
animation yet.
- Delete any hard stops between animation segments to come.
- Scroll the text of old 10.1.3.1 (“A pentose sugar is the next essential…”)
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, 10.1.3.2
- Run the animation of the flashing red arrows (10.1.3.2) to the end.
- This is the end of the segment.
- Set up a Scroll flag at the following name and at the following location:
“Carbon 2’” [note the single apostrophe after the number 2] at the start of
the animation of 10.1.3.2.
Animation (new 10.1.4) Nucleosides and Nucleotides
- Begin with the same image of Deoxyriboguanosine as in old 10.1.4.1 and
the same title in the graphics window, and don’t start the animation yet.
- Delete any hard stops between animation segments to come.
- Scroll the text of old 10.1.4.1 (“When a pentose sugar and a nitrogenous
base…”) 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, 10.1.4.2
- Run the animation of the orange ball appearing on the left (10.1.4.2) to the
end, pause 3 seconds, and dissolve to the next graphic and text of 10.1.4.3
- Bring up the table entitled “Types of Nucleosides and Nucleotides” with
the static text associated with this (“This table shows the different
types….”).
- This is the end of the segment.
- Set up Scroll flags at the following names and at the following locations:
“Phosphate” at the start of the animation of 10.1.4.2, and “Types” at the
start of 10.1.4.3.
Animation (New 10.1.5) Nucleoside Triphosphates
- Begin with the same image of Deoxyadenylic acid as in old 10.1.5.1 and
the same title in the graphics window; don’t start the animation yet.
- Delete any hard stops between animation segments to come.
- Scroll the text of old 10.1.5.1 (“Since a nucleotide is composed of a…”)
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, 10.1.5.2
- Run the animation showing the orange ball becoming three linked orange
balls (10.1.5.2) to the end.
- This is the end of the segment.
- Set up a Scroll flags at the following names and at the following locations:
“Triphosphates” at the start of the animation of 10.1.5.2.
Animation (10.1.6) Polynucleotides
- Begin with the same image of two nucleotides as in old 10.1.6.1 and the
same title in the graphics window (“Linkage of Two Nucleotides”); don’t
start the animation yet.
- Delete any hard stops between animation segments to come.
- Scroll the text of old 10.1.6.1 (“Polynucleotides are formed by linking…”)
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, 10.1.6.2
- Run the animation showing the linkage reaction (10.1.6.2) to the end,
pause 3 seconds, and dissolve to the graphic showing a chain of
nucleotides and the title “Polynucleotide Chain Shorthand Notation”,
keeping the same text in the text window.
- This is the end of the segment.
-
Set up Scroll flags at the following names and at the following locations:
“Linkage” at the start of the animation of 10.1.6.2 and “Notation” at the
dissolve to the graphic of 10.1.6.3.
Animation (new 10.1.7) Watson and Crick Model
- Begin with the same image of a pink coiled DNA molecule as in old
10.1.7.1 and the same title in the graphics window (“Schematic Structure
of DNA”); don’t start the animation yet.
- Delete any hard stops between animation segments to come.
- Scroll the text of old 10.1.7.1 (“In 1953, Watson and Crick proposed…”)
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, wait 3 seconds, and
dissolve to a scrolling of the second unit of text on 10.1.7.2
- Scroll the text (10.1.7.2) from the old second text window saying “The
nitrogenous bases of opposite chains…” 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 bring up the labels on the graphic (part
10.1.7.3).
- In 10.1.7.3, fade in the labels on the DNA picture as they do in the extant
animation. Pause after this for 5 seconds, and dissolve to the next
animation, 10.1.7.4
- In 10.1.7.4, a white box “X-ray” slides in and replaces the DNA molecule.
- This is the end of the segment.
- Set up Scroll flags at the following names and at the following locations:
“Base pairing” at the start of the text scroll of 10.1.7.2, “DNA
measurements” at the start of 10.1.7.3, “Closeup” at the start of 10.1.7.4.
Exercise (new 10.1.8) Nucleotide Pairing
- Delete the screen of old 10.1.8.1 showing the green and blue molecules
with the text “In these exercises….” and go directly to the exercise of old
10.1.8.2.
- Delete the Exercise Instructions box that pops up.
- Into the Interaction Instructions box, put the following”
- Drag and drop each base to match with its partner in order to maximize
hydrogen bonding.
- Maintain the same interactivity as in the current exercise. If the new
standards call for positive feedback in a green header box, move the
feedback, minus the word “Correct”, into such a popup.
- When the user completes the second match by dragging over the
appropriate box, put up another positive feedback box that says “That’s
right. Guanine and cytosine make three hydrogen bonds with each other,
and thus have a stronger base-pairing than an A-T base pair.” Hold this
feedback box for 5 seconds, then dissolve to the next phase of the
exercise.
- In 10.1.8.2, a line of colored boxes runs across the top of the screen filling
the whole window.
- Delete the Exercise Instructions box in 10.1.8.2.
-
Into the Interaction Instructions box (which now changes to new
instructions), place “Drag and drop each base to match with its partner
such that hydrogen bonding will be maximized.”
- Allow the same drag and drop interactivity as in the old exercise.
- When the user has dragged all the boxes correctly, put up a positive
feedback box with the words “Well done! You’ve correctly matched each
of the bases with its complement on the matching strand.”
- This is the end of the segment.
Summary (New 10.1.9)
-This will not be programmed as part of the Flash animation.
Post-quiz (New 10.1.10)
-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 (10/6)
Andy’s Comments 10/7:
1. Lengthen the time the Pyrimidines are on the screen by pausing at least 4 seconds
after the animation in 10.1.2.2 completes the build of Cytosine, Uracil and
Thymine.
[Andy 10/7: Yes, this section moves too fast. A longer pause is necessary. Also,
add a screen title at the beginning. This should be “Nitrogenous Bases” like the
first flag.]
2. Make the transition form 10.1.2.2 (Pyrimidines scroll flag section) to 10.1.2.3
(Purines scroll flag section) a dissolve instead of a hard cut.
[Andy 10/7: Yes, dissolve out then dissolve in. ]
3. The scroll flag at the start of 10.1.4 (Nucleosides and Nucleotides) should be
deleted. It currently says “Nucleosides and Nucleotides” and doesn’t even fit on
the screen entirely. Users already know they can rewind to the beginning to see
the segment from the top.
[Andy 10/7: No, leave the flag but make sure that it is all on screen. The flag
offers a quick indicator. ]
4. The text justification really makes a doozie in 10.1.5 by leaving a half-line gap
between the word “called” and “nucleoside”. Is there anything we can do about
this? I realize the problem is the following long word “monophosphates” that is
causing this to happen.
[Andy 10/7: Change the first sentence to read “Since a nucleotide is composed of
a nucleoside and a phosphate group, they can also be called nucleoside
monophosphates.” The change from “nucleotides” to “they” should allow the
word “called” to move up one line so that “nucleoside monophosphate” can fit on
a single line. ]
5. Make the play screen scalable and playable in the full screen of the browser.
[Andy 10/7: This is a universal request for all .swf files. ]
6. The first scroll flag in 10.1.5 should be deleted (“Nucleoside Triphosphates”) as it
barely fits onscreen and users know they can go to the top of the segment by
rewinding to the beginning. We don’t need flags at the start, in my opinion.
[Andy 10/7: No, I like the opening scroll flag. Adjust its position so that it is all
on screen. ]
7. The first scroll flag in 10.1.6 should be deleted (“Linkage of Two Nucleosides”)
as it doesn’t fit entirely onscreen and users know they can go to the top of the
segment by rewinding to the beginning.
[Andy 10/7: No, I like the opening scroll flag. Adjust its position so that it is all
on screen. Also, add “Polynucleotides” as the screen title at the opening of this
.swf segment.]
8. Make the transition from the image of 10.1.6.1 (two nucleotides with 4 orange
ball blobs at left) to 10.1.6.2 (chain of orange P balls and sticks) a softer one by
dissolving, rather than cutting abruptly between them.
[Andy 10/7: Yes, use a softer transition.]
9. The text of 10.1.7.1 (Watson and Crick Model) has a grammatical error in the
fourth sentence of the text. The line “The C-5’ to C-3’ orientation of each chain
run in the opposite directions” should be changed to read “The C-5’ to C-3’
orientation of each chain runs in the opposite direction.”
[Andy 10/7: Please make this correction. ]
10. Delete the scroll flag at the head of 10.1.7.1 (Schematic Structure of DNA) which
doesn’t fit anyway and is redundant.
[Andy 10/7: No, I like the opening scroll flag. Adjust its position so that it is all
on screen. ]
11. The emperor has no clothes! Someone forgot to write a conclusion to this
tutorial, or it isn’t done yet (10/5/03).
[Andy 10/7: No one forgot to write a Conclusion. It’s in the old tutorial on the
website. This is the “Module Summary” text. It needs to be rendered as an
HTML page then linked to the review site. ]
Second Pass Comments from Eric Stavney 10/30/03
1. Change the title of the Conclusions page to simply “Conclusion”.
[Andy 10/31: Make this change.]
[Andy 10/31: In the exercises, the instruction box should open automatically then
close automatically after 4-5 seconds.]
[Andy 10/31: The Intro graphic is too big and too busy. Instead, use the lead graphic
on the “Base Paring” segment of “Schematic Structure of DNA”. This is the DNA
without any letters or labels. It will look much better on the Intro.]