Klug, Old Activity 14.1 Mutation at the DNA Level
Klug, NEW Activity 15.1 Mutation at the DNA Level
* In its revised format include old parts 14.1.1 through 14.1.10. Old Chapter 14 is now
Chapter 15. Segments should be separated from the original tutorial then combined to
form this new tutorial, Activity 15.1. 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 15.1, Mutation at the DNA Level
Introduction (New 15.1.1)
- This will not be part of the Flash animation but will be an html page
- Use the extant images of the three boxes following from the Cat Saw the Dog
box. Keep the same title “Mutations”.
- In the text window, only put the first paragraph (3 sentences) beginning
“Genetic mutations arise….” and delete all other text.
- This is the end of the segment.
- This is just the first part of old 14.1.1.., the rest put into another segment
below.
Animation (New 15.1.2) Types of Mutation
- This segment is a continuation of old 14.1.1 but is retitled.
- Use the same image as in the Introduction of the three boxes following from
the Cat Saw the Dog box.
- Put the title “Types of Mutation” in the graphics window
- Scroll the modified text of old 14.1.1.1, 14.1.1.2, and 14.1.1.3 as one unit of
text, with paragraph breaks which should specifically say:
“The illustration at the left depicts two categories of base mutations, base
substitutions and frameshift mutations. After examining these we will
look at some of the molecular mechanisms that may cause these types of
mutations.
Base mutations (also called point mutations) involve the replacement
during replication mismatch repair of one base for another. If the
replacement is of a pyrimidine for a pyrimidine or a purine for a purine,
the base mutation is called a transition. If the replacement involves a
purine for a pyrimidine (or the other way around), the mutation is called a
transversion. Recall that because of the redundancy of the genetic code, a
base substitution in a protein coding gene may not result in a change in the
translated protein.
Frameshift mutations always result in a change in the genetic
transcript…etc.” but DELETE the last line “To see changes indicated,
click the “Play” button”.
When the bottom line of text clears the bottom of the text window, freeze
the text and pause 4 seconds, then start the animation.
- The animation of new 15.1.2.2 shows changes in the lettering and
sentence structure of THE CAT SAW THE DOG in the graphics window.
Shortenup the pause between subsequences, especially the pause after the
first box changes and the letter “C” appears in the second box.
- This is the end of the segment
- Set scroll flags: “Mutations illustrated” at the start of 15.1.2.2.
Animation (New 15.1.3) Rare Tautomeric Shifts
- Start with the same image as in old 14.1.2.1 of the 6 part ring and the title
“Thymine”.
- Remove all hard stops between animation sequences.
- Scroll the text “Like most biological molecules, nucleotide bases….” from
the bottom of the text window to the top until the top line reaches the top.
Then pause 3 seconds and start the animation of 15.1.3.2.
- Run the animation of 15.1.3.2 that shows one structure sliding left and the
appearance of a second structure at right. Pause 4 seconds when this
concludes and dissolve directly to the next text and image sequence,
15.1.3.3.
- Bring up the title of “Guanine” and the structure associated with it.
- Scroll the text of 15.1.3.3 (“The most stable tautomers of thymine and
guanine….”) from the bottom to the top until the top line reaches the top.
Pause 4 seconds and start the animation of 15.1.3.4.
- In 15.1.3.4, the guanine structure slides left and a new structure appears to
the right. Pause 4 seconds when this concludes and dissolve directly to the
next text and image sequence, 15.1.3.5.
- In 15.1.3.5 the title “Cytosine” comes up with associated image.
- Scroll the text of 15.1.3.5 (“The most stable tautomers of cytosine…”)
from the bottom to the top until the top line reaches the top. Pause 4
seconds and start the animation of 15.1.3.6.
- In 15.1.3.6, the cytosine structure slides left and a new structure appears to
the right. Pause 4 seconds when this concludes and dissolve directly to the
next text and image sequence, 15.1.3.7.
- Scroll the text of 15.1.3.7 (“The low frequency and transient enol…”)
from the bottom to the top until the top line reaches the top. Pause 4
seconds and start the animation of 15.1.3.8.
- In 15.1.3.8, the adenine structure slides left and a new structure appears to
the right.
- This is the end of the segment.
- Set scroll flags at each sequence start: “T tautomers” at 15.1.3.2, “Keto
forms” at 15.1.3.3, “G tautomers” at 15.1.3.4, “Amino forms” at 15.1.3.5,
“C tautomers” at 15.1.3.6, “Mutation frequency” at 15.1.3.7, and “A
tautomers” at 15.1.3.8.
Animation (New 15.1.4) Anomalous Base Pairing
-
Begin with the same graphic, title, and text as in the old 14.1.4 but scroll
the text “At left are depicted anomalous…” from the bottom of the text
window to the top until the top line reaches the top. Pause 3 seconds and
dissolve to the next image and text.
- In 15.1.4.2, the same graphic of anomalous base-pairs appears, slightly
shifted upwards in the graphic window – which is OK. Join together, with
paragraph break, the first and second pages of text beginning with “At left
are depicted anomalous…” followed by the paragraph beginning “Enol
thymine and imino cytosine..”. Scroll this joined text of New 15.1.4.2
upwards from the bottom of the text window until the last line clears the
bottom of the window.
- This is the end of the segment.
- Set Scroll flags at the beginning of each of the following segments:
”Anomalous pairs” at 15.1.4.2.
Animation (15.1.5) Transition Mutation
- Begin with the same graphic od the 4 unit short DNA molecule at the top
of the screen from old 14.1.5.
- Delete the extant text on this and the subsequent screen and replace it
with:
“The animation at the left will illustrate how a tautomeric shift in a
nitrogenous base can result in a base pair change (point mutation). We
begin with the semiconservative replication of this short strand of DNA.
-
A taugomeric shift from the amino form of adenine to the imino form
results in its pariing with cytosine instead of the thymine that is
complementary to the amino form.
A tautomeric shift from the unstable adenine (imino) to the more stable
amino form in the next round of replication restores the standard A-T
configuration in the molecule on the right but an A-T to G-C transition
mutation has occurred in the molecule on the left.”
Scroll these words from the bottom to the top of the text window, stopping
when the last line just clears the bottom of the text window. Try to get it
all in one window if possible. Pause 3 seconds and start the animation
(15.1.5.2)
- In the animation of 15.1.5.2, the original DNA molecule is shown to split
in a sequence of building images until the graphics reach the bottom of the
window.
- This is the end of the segment.
- Set Scroll flags at the beginning of each of the following segments:
”Replication” at 15.1.5.2.
Animation (New 15.1.6) 5-bromouracil
- This is a conversion of old 14.1.6.
- Begin with the extant “Similarity of 5-bromoruracil….” title with the three
chemical structures in the graphics window.
-
Scroll the text of 15.1.6.1 (“Molecules that may substitute for purines…”
from the bottom to the top of the text window until the top line reaches
the top. Then pause 3 seconds and dissolve to the new image and text.
- In 15.1.6.2, two rows of structures appear in the graphics window.
- Scroll the text of 15.1.6.2 (“The keto form of 5-bromouracil is an….”)
from the bottom to the top of the text window until the top line reaches
the top. Then pause 3 seconds and dissolve to the new image and text,
15.1.6.3.
- In 15.1.6.3, both the keto and enol forms of 5-bromouracil appear in the
graphics window. Scroll the text of 15.1.6.3 (“Note the two tautomers of
5-bromouracil….”)from the bottom to the top of the text window until the
top line reaches the top. Then pause 3 seconds and dissolve to the new
image and text of 15.1.6.4.
- In 15.1.6.4, Two rows of “5-BU” pairs appear in the graphics window.
Scroll the text of 15.1.6.4 (“The tautomeric shift of the thymine
analog….” from the bottom to the top of the text window until the top line
reaches the top. Then freeze the scrolling.
- This is the end of the segment.
- Place scroll flags at the start of the following segments and by the
following names: “Keto form” at 15.1.6.2, “2 Tautomers” at 15.1.6.3, and
“Abnormal pairing” at 15.1.6.4
Animation (New 15.1.7) Guanine Conversion
- This is a conversion of 14.1.7 of the same name.
- Delete any hard stops in the animation and previous start cues.
- Begin with the image of guanine and the title “Conversion of Guanine….”
- Scroll the text of 15.1.7.1 (“Another source of transition mutations…”)
from the bottom to the top of the text window until the top line reaches
the top. Then pause 3 seconds and dissolve to the new text of 15.1.6.2.
- In 15.1.6.2, two rows of structures appear in the graphics window.
- Scroll the text of 15.1.6.2 (“Ethylmethane sulfonate is one compound….”)
from the bottom to the top of the text window until the top line reaches
the top. Then pause 3 seconds and start the animation of new15.1.6.3 that
shows guanine sliding left and “EMS” creating 6-Ethylguanine and
Thymine.
- This is the end of the segment.
- Place scroll flags at the start of the following segments and by the
following names: “EMS” at 15.1.7.2, “EMS yields” at 15.1.7.3
Animation (New 15.1.8) Deaminations
- This is a conversion of 14.1.8 of the same name.
- Delete any hard stops in the animation and previous start cues.
- Begin with the image of cytosine and the cytosine-guanine pair below it
and the title “Deamination of Cytosine….”
- Scroll the text of 15.1.8.1 (“Another class of mutagens cause
mutations…”) from the bottom to the top of the text window until the top
line reaches the top. Then pause 3 seconds and dissolve to the new text of
15.1.8.2.
-
In 15.1.8.2, two rows of structures (Cytosine and Uracil, Uracil and
Adenine) appear in the graphics window.
- Scroll the text of 15.1.8.2 (“Nitrous oxide demainates amimo group….”)
from the bottom to the top of the text window until the top line reaches
the top. Then pause 3 seconds and dissolve to the new image and text of
15.1.8.3.
- In 15.1.8.3, Adenine, Hypoxanthine and a pair of Hypox.- Cytosine
appears in the graphics window.
- Scroll the text of 15.1.8.3 (“Deamination of adenine, depicted in the
panel….”) from the bottom to the top of the text window until the top line
reaches the top. Then freeze the scroll.
- This is the end of the segment.
- Place scroll flags at the start of the following segments and by the
following names: “Nitrous oxide” at 15.1.8.2, “Adenine deamination” at
15.1.7.3
Animation (New 15.1.9) Proflavin and Acridine Orange
- This is a conversion of 14.1.9 of the same name.
- In the 4e version the title of this segment is cut off in the header bar –
watch this when you convert to the new format.
- Delete any hard stops in the animation and previous start cues.
- Begin with the image of proflavin, acridine orange, and cytosine-guanine
and the same title “Causes of Frameshift Mutations”.
- Scroll the combined text of the two text pages in New 15.1.9.1 (“Other
types of mutagens are known to cause frameshift…”) coupled with “The
frameshift mutations is generated through the addition or deletion of one
or more bases to correct for the slippage.” from the bottom to the top of
the text window until the top line reaches the top. Then freeze the
scrolling.
- This is the end of the segment.
- No scroll flags.
Summary (New 15.1.10)
- This will be converted to an html page and will not be part of the Flash
animation.
Post-quiz (New 15.1.11)
-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 10/20/03
-- I reviewed the version posted on this date even though a note on the website said
“Done but not posted” as it looked done to me.
1. For the Introductory Page, I’d like to see us narrow the text and expand the
graphic showing “The Cat Saw the Dog” permutations; it’s pretty squished and
hard to read right now. Let’s enlarge the graphic and narrow the text.
[Andy 10/23: Please make this change.]
2. None of the segments in this tutorial start playing by default when the user arrives
with a click of the NEXT button. We need these animations to begin playing
when the user arrives, instead of requiring the user to start it.
[Andy 10/23: Please make this change.]
3. In 15.1.2.1, Types of Mutation, please add a comma to the text in the first
sentence. Add the comma after the words “base substitutions” so it reads “….two
categories of base mutations, base substitutions, and frameshift mutations.”
[Andy 10/23: Please make this change.]
[Andy 10/23: Add a scroll flag to the start of every animation file. The scroll flag
should be titled to match the title of the animation. The title for 15.1.2 should be
“Types of Mutations” in this format.]
4. In 15.1.3., the text of all the subsequences scroll a bit too fast. Can we slow this
down.
[Andy 10/23: Please slow the scroll speed.]
5. In other tutorials we adopted a standard of putting a scroll flag at the head of each
segment which contained the title of that segment. This tutorial is missing these
scroll flags. For consistency, I think we should put them in.
[Andy 10/23: Please make this change.]
6. In 15.1.4 (Anomalous Bair Pairing) at the scroll flag transition named Anomalous
Pairs, let’s keep the graphic onscreen and only change the title and text. It looks
weird to fade out and fade in the same graphic. Also, there is a flash frame in this
transition where the molecular structures have been moved lower and to the left.
Cut out this flash frame.
[Andy 10/23: Please make this change.]
7. The weird flash frame happens again at the very end of 15.1.4 where the
molecules inexplicably dissolve to the offset image and back again to the standard
image. This should be fixed.
[Andy 10/23: Please make this change.]
8. In 15.1.5.1 (Transition Mutation) there is a typo in the first sentence. We need to
change the word “nitrogenos” to “nitrogenous” to read “…..shift in a nitrogenous
base can result in….”
[Andy 10/23: Please make this change.]
9. The scroll bar in 15.1.5 doesn’t control the animation sequence – I can’t access
intermediate points in the sequence with it.
[Andy 10/23: Don’t embed movies in movies. The reader must have control of the
animation through the scroll bar control panel. This is a universal “must have.”]
10. There is a flash frame in the animation of 15.1.5 just after the spread DNA
molecule moves to a third image below that has two double stranded DNA
molecules (Semiconservative replication label). What happens is the image of the
two double stranded DNAs moves slightly rightwards when it is supposed to stay
static. Align the positioning of this third image so it stays put.
[Andy 10/23: Please make this change.]
11. The text scrolling in 15.1.6 is on cocaine! Slow it down please!
[Andy 10/23: Please make this change.]
12. The transition in 15.1.6 at the scroll flag called “Tautomers” is some kind of
sequenced dissolve where the image partly disappears and then comes back.
Make this transition smoother.
[Andy 10/23: Please make this change.]
13. In 15.1.6.3 the text has a typo. This text unit begins “Note the two tautomers of
5-bromouracil…..” The error is in the last sentence, in the term “by5bromouracil”. It should be change to read “5-bromouracil”.
[Andy 10/23: Please make this change.]
14. The text scrolling in 15.1.7 and 15.1.8 is too fast. Slow it down.
[Andy 10/23: Please make this change.]
15. In 15.1.9, the text scrolling speed is about right. Use this as a standard to set the
speed for the previous segments.
[Andy 10/23: It’s always good to have an example.]
Second Pass Comments from 10/30/03
1. The scroll bar slider doesn’t control the animation fully in 15.1.2 in the last part of
the segment. I can’t reverse or slide through the animation sequentially with the
scroll bar.
[Andy 10/31: Make this change. The action must be under the user’s control.]
[Andy 11/7: Corrected.]
2. The first scroll flag in 15.1.3 hangs offscreen to the left.
[Andy 10/31: Make this change.]
[Andy 11/7: Corrected.]
3. Let’s enlarge the words under the molecules in 15.1.4.
[Andy 10/31: Make this change. In nearly all cases, the labels are too small and need
to be enlarged. See “Standard Base-pairing Arrangements” as an example of labels
that are too small. The labels are nicely sized in the .swf that is labeled “Thymine.”
Also, some of the labels are black and some are brown. They should all be the same
color.]
[Andy 11/7: Increase the font size for the labels on the following animations:
Standard Base-pairing Arrangements
Transition Mutations
Similarity of 5-bromoruracil Structure to Thymine
Conversion of Guanine to 6-ethylguanine
Deaminations of Cytosine caused by HNO2
Cause of Frameshift Mutations.]
[Andy 11/7: Also, please make sure that the titles for these segments are all the
same font size and treatment. I noticed that the title for Conversion of Guanine to
6-ethylguanine is different than the others. Pleas correct.]
[Andy 11/10: Change was made]
4. In 15.1.5 a second set of smaller arrows appear in the Replication scroll flag
sequence just after the lower DNA sequences appear under the first splitting DNA
molecule. These extra arrows are confusing and I think should be deleted.
[Andy 10/31: Make this change. This is the set that begins at the top.]
[Andy 10/31: Also, this segment begins with a 4 base-pair DNA image that is too
small for the screen. Please begin with an image sized for the screen then as it
transitions, reduce the size. And, the transition from one 4 base-pair set to two 4
base-pair sets is now well positioned. This graphic should occupy the center of the
screen UNTIL it transitions and needs more space. DON’T leave big white spaces.]
[Andy 11/7: This transition is required.]
[Andy 11/10: Change was made]
5. As I arrive at 15.1.9 with the click of the NEXT button, the animation doesn’t
begin playing by default, when it should. Please also enlarge the words under the
molecules.
[Andy 10/31: Make this change.]
[Andy 11/10: Change was made]
Third Pass Review by Andy 11/10/03
* This is ready for copyediting.