Klug, Old Activity 15.1 Regulation of Gene Expression: Prokaryotes
Klug, NEW Activity 16.1 Regulation of Gene Expression: Prokaryotes
* In its revised format include old parts 15.1.1 through 15.1.12. Segments should be
separated from the original tutorial then combined to form this new tutorial, Activity
16.1. 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 16.1, Regulation in Prokaryotes
Introduction (New 16.1)
- This will need to be a flash animation.
- Use the extant image of the two boxes showing proteins with curly sections.
- In the text window, combine the two paragraphs on the old text pages 1 and 2
into a single text element, with paragraph break: “Glucose is the main food
source used by a bacterium…” and “This is one of the best-understood
examples…”. Scroll the text from the bottom to the top of the text window,
stopping when the last line clears the bottom of the text window. Pause 5
seconds after the end of the scroll and dissolve to the new image and text of
16.1.1.2.
- In 16.1.1.2, the image is of a chain of boxes with blue and orange blobs with
the title “Negative Control”.
- Scroll the text of 16.1.1.2 (“In response to environmental signals,
regulatory…”) [please add the “s” to the end of the word “signals”] from the
bottom to the top of the text window, stopping when the top line reaches the
top the text window. Pause 4 seconds after the end of the scroll and dissolve
to the new image 16.1.1.3.
- In 16.1.1.3, the title changes to “Positive Control” and a long purple DNA bar
shows CAP and polymerase coming to the DNA. Pause 5 seconds after
revealing this and dissolve to the new text and image of 16.1.1.4.
- In 16.1.1.4, the title changes to “Cis-trans Dominance” and the image is a
chain of segments labeled I, P, O, Lac Z, Lac Y, etc.
- Scroll the text of 16.1.1.4 (“Genes have the ability to affect other genes…”)
from the bottom to the top of the text window, stopping when the top line
reaches the top the text window. Pause 3 seconds after the end of the scroll
and dissolve the scrolling of the second page of text, 16.1.1.5.
- Scroll 16.1.1.5 (“Regulatory sites are genes that control…”) from the bottom
to the top of the text window, stopping when the top line reaches the top the
text window.
- This is the end of the segment.
- Set Scroll flags at the start of the following sequences: “Negative Control” at
the start of 16.1.1.2, “Positive Control” at 16.1.1.3, “Cis-trans” at 16.1.1.4,
and“Regulatory sites” at 16.1.1.5.
Exercise (New 16.1.2) Lactose Gene Cluster
- This segment is a revision of old 15.1.2 by the same name.
-
Use the same screen showing the text at upper left and the genes I, P, O, etc
across the center of the screen. Delete the last line of text that says “Click on
each part of the diagram….”
- To the Interaction Instructions box add: “Click on each part of the diagram to
view a the function of each DNA sequence.”
- Use the same interactivity as in the extant segment.
- This is the end of the segment.
Animation (New 16.1.3) Conversion of Lactose
- Bring up the extant image of the lactose molecule in the graphics box.
- Scroll the text “To break down the lactose molecule…” from the bottom to
the top of the text window, stopping when the top line reaches the top the
text window. Pause 1 second and start the animation of 16.1.3.2.
- Run 16.1.3.2 showing the splitting of lactose into galactose and glucose.
- This is the end of the segment.
- Set scroll flags at each sequence start: “Lactose hydrolysis” at 16.1.3.1.”
Animation (New 16.1.4) The Operon Model
- This animation will combine old 15.1.4, 15.1.5, and 15.1.6
- Remove all stops between animations in these three sequences.
- The first image is of a chain of DNA rectangles labeled Repressor gene,
etc. as in extant 15.1.4.1.
- Add a title over the graphic which says “The Operon Model”.
- Scroll the text “This diagram is the operon model” from the bottom to the
top of the text window, stopping when the top line reaches the top the text
window. Pause 3 seconds and dissolve to the new text and image of
16.1.4.2.
- 16.1.4.2 is the first screen of the old Repression (15.1.5) sequence. The
new title is “Lactose Absent” with the DNA bar below it.
- Scroll the text of New 16.1.4.2 (“When lactose is not present…”) from
the bottom to the top of the text window, stopping when the top line
reaches the top the text window. DELETE the last line which says “Press
Play…..” Pause 3 seconds after the text stops and start the animation of
16.1.3.3.
- Run 16.1.4.3 showing the orange blob bouncing off the DNA. Pause 4
seconds after this concludes and dissolve directly to the new text and
image of the old 15.1.6 (Induction).
- Bring up the image of the DNA and the repressor, lactose, and RNA
polymerase under it with the title “Lactose Present” from old 15.1.6.1.
This sequence is New 16.1.4.4.
- Scroll the text of 16.1.4.4 (“When lactose is present, enzymes are
needed…”) from the bottom to the top of the text window, stopping when
the top line reaches the top the text window. DELETE the last line which
says “Press Play…..” Pause 3 seconds after the text stops and start the
animation of 16.1.4.5.
- Run 16.1.4.5 showing the binding of the orange blob, the blob sliding
rightwards, and transcription and translation ensuing.
- This is the end of the segment.
Set scroll flags at the start of the following sequences: “Repression” at
16.1.4.2, “Events of Repression” at 16.1.4.3, “Induction” at 16.1.4.4,
and“Events of Induction” at 16.1.4.5.
Animation (New 16.1.5) Mutant Repressor
- This is a revision of old 15.1.7 by the same name
- Remove all stops between animations.
- The first image is of a chain of DNA rectangles with the “Mutant gene
LacI” at far left and the title “Mutant Repressor Protein”.
- Scroll the text “This mutation of the LacI gene…” from the bottom to the
top of the text window, stopping when the top line reaches the top the text
window. DELETE the last line of the text saying “Press Play…” Pause 3
seconds when the scrolling stops and start the animation of 16.1.5.2.
- Run 16.1.5.2 showing the orange blob binding and sliding on the DNA,
yielding transcription and translation.
- This is the end of the segment.
- Set scroll flags at the start of the following sequence: “Constitutive
transcription” at 16.1.5.2.
Animation (New 16.1.6) Mutant Operator
- This is a revision of old 15.1.8 by the same name
- Remove all stops between animations.
- The first image is of a chain of DNA rectangles with the “Mutant
operator” in the middle and the title “Mutant Operator Gene”.
- Scroll the text “In this case, the operator gene is the mutant…” from the
bottom to the top of the text window, stopping when the top line reaches
the top the text window. DELETE the last line of the text saying “Press
Play…” Pause 3 seconds when the scrolling stops and start the animation
of 16.1.6.2.
- Run 16.1.6.2 showing the orange blob binding and sliding on the DNA,
yielding transcription and translation.
- This is the end of the segment.
- Set scroll flags at the start of the following sequence: “Constitutive
transcription” at 16.1.6.2.
Exercise (16.1.7) Understanding the Lac Operon
- This a revision of the old Interactive Quiz from 15.1.9
- Go straight to the first question page of old 15.1.9.2 showing Question 1;
delete 15.1.9.1 showing just the operon diagram and text instructions.
- Redo the title in the graphics window so the permanent title
Understanding the Lac Operon is at the top, and subsequent subtitles for
each question (i.e. Lactose Present) come up just underneath it.
- Delete any text on old 15.1.9.2 that says “After pressing play….” and
perhaps enlarge the graphics to encompass the old text window area.
- Into the Interaction Instructions box, write “ Answer the questions by
selecting on the correct answer and clicking on the Submit button.”
- Allow the same interactivity as in the extant segment. However, when the
user clicks on an answer, a feedback box appears – change these boxes to
our new format (Correct and Incorrect boxes I think). When the correct
-
answer is selected, run the animation and bring up the positive feedback
text for that question, but DELETE the line in the feedback that says
“Press PLAY to continue”. Pause 6 seconds after the animation finishes
comes up, and dissolve to the next question.
- Do the same thing for all six questions, and delete the “Press Play to
continue” after the “You’re finished” feedback at the very end.
- This is the end of the segment.
Exercise (New 16.1.8) Gene Activity
- This is a revision of old 15.1.10 by the same name
- Remove all stops between animations.
- The image is of a table showing ß Galactosidase Activity and the title
“Comparison of Gene Activity….”
- Scroll the text of just this page: “This chart compares the gene activity…”
from the bottom to the top of the text window, stopping when the top line
reaches the top the text window. Add to the bottom of this text the
following sentence as a new paragraph: “Study the information
containined in the chart. When you are ready, click on the Start button.”
- Place a Start button at the bottom right of the table to allow the user to
move to the interactive portion of the exercise, 15.2.8.2.
- Delete the second page of text in the opening sequence which begins “You
will now fill out two charts….”
- When the user presses Start, dissolve to the new table of seven rows of
radio buttons in 16.1.8.2.
- Change the text that comes up (“In these lac genotypes, predict….”) to
just the following:
“In these lac genotypes, predict whether the structural genes ZYA
are constitutive, repressed, or indicible in the presence of lactose.”
This text can be laid out in the text window about even with the line of
buttons that say Submit, Clear, etc. so that when the user gets feedback
from the exercise, the feedback boxes won’t obliterate the text that sits in
the upper right corner in the extant version. Currently the feedback boxes
extend rightwards from the table and cover up the text.
- To the Interaction Instructions box, put “ Click on the circle for each
genotype which indicates whether activity of the ZYA genes will be
constitutive, repressed, or indicible. When you are done filling in the
chart, click Submit. Change any of your answers by clicking on your new
answer and clicking Submit again. To move to the next set of questions,
click on Next Set.”
- Add another button to the line of buttons along the bottom of the table that
says Next Set. This could be accomplished by moving the existing three
buttons leftwards and adding the new button at the very far right of the
button row. It should fit.
- When the user clicks Next Set, move to 16.1.8.3 showing the table of 10
rows of radio buttons and the text “In these lac genotypes and
conditions…”
-
Change the text of 16.1.8.3 to ONLY say:
“In these lac genotypes and conditions, predict whether functional
enzymes are made, nonfunctional enzymes are made, or no
enzymes are made. It is possible for a genotype to make both
nonfunctional and functional enzymes at the same time.”
This text can be laid out at the very upper right of the text window and the
table can be dropped lower until the button row is right along the bottom
of the graphics window. The text, then, sits just to the right of the column
headers in the table. This will prevent obliteration of the text when the
feedback boxes appear during the interactivity.
- To the Interaction Instructions box, put “ Click on the circle for each
genotype which to indicate if an organism with that genotype could make
a functional enzyme, non-functional enzyme, or no enzyme at all. When
you are done filling in the chart, click Submit. Change any of your
answers by clicking on your new answer and clicking Submit again.”
- Use the same interactivity and feedback boxes as in the extant exercise.
- This is the end of the segment.
Animation (New 16.1.9) Catabolite Repression
- This is a revision of old 15.2.11 by the same name
- Remove all stops between animations.
- The first image is of a purple DNA segment, CAP, and associated proteins
and the title “Glucose Absent”.
- Scroll the combined text of pages 1 and 2: “Another form of repression
involves the promoter…”, with paragraph break, and “There is yet another
molecule…” from the bottom to the top of the text window, stopping
when the last line clears the bottom of the window. Pause 5 seconds when
the scrolling stops and start the animation of 16.1.9.2.
- In 16.1.9.2, the CAP protein binds to the DNA and the orange polymerase
binds and moves rightward. Pause 5 seconds after this concludes and
dissolve to the start of the next animation, 16.1.9.3.
- In 16.1.9.3, the new title “Glucose Present” should be modified with color
so the user won’t miss the change. Perhaps change the color of the word
“Present” to a dark red, or some other color so that when the dissolve
occurs from “Glucose Absent” to “Glucose Present”, the change will be
readily obvious.
- Pause 5 seconds after the dissolve to 16.1.9.3 showing the new
configuration and new title in the graphics window. Then start the
animation directly, a sequence we’ll call 16.1.9.4.
- In 16.1.9.4, the pink and orange blobs are seen to bounce off the DNA.
- This is the end of the segment.
- Set scroll flags at the start of the following sequences: “Glucose absent: at
16.1.9.2, “Glucose present” at 16.1.9.3.
Summary (New 16.1.10)
- This will be an html page and will not be part of the Flash animation.
Post-quiz (New 16.1.11)
-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 10/29/03
1. Please make the captions larger on the graphics on the Introductory Page. This
may be microbiology but the font doesn’t have to be micro-sized.
[Andy 10/29: Delete captions from the JPEG and render them as HTML so that they can
be read easily.]
2. It looks like we didn’t catch the animator before he/she made a segment the same
as the Introduction page. What I mean is that 16.1.2 has identical text to that on
the Introductory page. Let’s scrap the first sequence of 16.1.2 (the Introduction
scroll flag section) and let 16.1.2 start immediately with Negative Control. We
can call this new 16.1.2 something like Introduction to DNA Regulation if we
need another title.
[Andy 10/29: Please make this correction.]
3. In 16.1.2 the fourth scroll flag in the extant version says “Cis-trans donimance”
and should instead by “Cis-trans dominance”.
[Andy 10/29: Please make this correction.]
4. In 16.1.3 we need to change “b-galactosidase” in the first sentence of the text to
“ß-galactosidase”
[Andy 10/29: Please make this correction.]
5. In 16.1.5 the term “lacI-“ is used twice in the scrolling text. We need to make the
minus sign a superscript, to make it “lacI-“.
[Andy 10/29: Please make this correction.]
6. In 16.1.5 the term “lacOc” is use in the first sentence of the text. We need to
make the letter “c” a superscript, to make it “lacOc”, just as it shows in the
graphic over the green gene in the DNA.
[Andy 10/29: Please make this correction.]
[Andy 10/29: Add the title “Lac Operon” to the 1st exercise. This is the one with the
clickable chromosome. Also in this exercise, the first popup is missing a period in the
last sentence OR the rest of the sentence is missing. Please correct.]
7. In 16.1.8.3 the feedback text that comes up to the right of those phenotypes whose
radio buttons were incorrectly marked is truncated. Only 5-7 words of each of the
feedback statements show on screen after the submit button has been clicked. The
first of these statements is “With this mutant I gene, there is….” Can we fix it so
the user can see the whole feedback statement for each questions marked wrong?
[Andy 10/29: Please make this correction.]
8. In 16.1.9, right after the Glucose Absent scroll flag, the animation gets “hung” and
stops. I can restart the progression by clicking on the play button, however.
Remove this stop.
[Andy 10/29: Please make this correction.]
9. I’m also seeing a two programmed stops in 16.1.9 just before the Glucose Present
scroll flag that shouldn’t be there. I can play from Stop 1 to Stop 2 and then
further by clicking twice on the play button. Please remove these stops.
[Andy 10/29: Please make this correction.]
[Andy 10/29: Also, there should be a HARD transition between the Glucose Absent and
Glucose Present segments.]
10. On the Conclusion page, we need to make “lacI-“ in the fourth paragraph into
“lacI-“ [superscript] and reassociate the hanging comma on the following line
back with lacI. Then in the second sentence of the fourth paragraph, “lacOC”
needs to be changed to “lacOc”. Finally, in the fifth paragraph, first word, we
need to change “b-galactosidase” into “ß-galactosidase”
[Andy 10/29: Please make this correction.]
Second Pass Comments from Eric Stavney 11/1/03
1. The Flash animations are not scalable in this tutorial. I don’t know where we are
with our policy on this now, but it would be nice if they were scalable.
[Andy 11/4: Please make this change.]
2. Text scrolling in 16.1.4 is a tad too slow. Please speed this up.
[Andy 11/4: Please make this change.]
3. Text scrolling inn 16.1.5 is also a tad slow. Turn up the gas!
[Andy 11/4: Please make this change.]
4. Let’s just say that text scrolling is a bit slow in this whole tutorial.
[Andy 11/4: Please make this change.]
5. In 16.1.9, I believe we have an animation error. In the Glucose Absent scroll flag
sequence, the red “shell” of Camp is supposed to encircle or attach to the top of
the pink CAP molecule BEFORE the CAP binds to the binding site. It looks to
me like they currently move over together in parallel registration, but they need to
be tightly bound together before binding to the purple DNA.
[Andy 11/4: Please make this change.]
6. On the Conclusion page, fourth paragraph, it looks like you properly made the
superscript for “lacOc” except that the letter C appears to be in a different font
style than the rest of the text. Let’s fix this if possible because it stands out.
[Andy 11/4: Please make this change.]
[Andy 11/4: On the Intro graphic delete the labels, leader lines, and caption. Leave
only the art.]