Klug, Old Activity 12.1 Transcription
Klug, NEW Activity 13.1 Transcription
* In its revised format include parts 12.1.1 through 12.1.19. These parts should be separated from the original tutorial then combined to form this new tutorial, Activity 13.1. 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 13.1, Transcription
Introduction (New 13.1.1) – OLD “OVERVIEW”
-This will need to be Flash animation.
-Use the final frame of the animation (full build) from old 12.1.1 showing “The Flow of Genetic Information” from the “Gene” all the way tot he string of orange balls at the bottom. Make this a static graphic.
-Unite the text from old pages 1 and 2 in 12.1.1 (“For most genes… “) and (“In this process, each three-base…” together, with a paragraph break between them. Scroll this text from the bottom of the window to the top until the first line of the second text unit (“In this process, each three-bases DNA…”) reaches the top of the text window. Freeze the scrolling at this point and dissolve the image and text to 12.1.1.2.
-The graphic of 12.1.1.2 is the boxes diagram of “Transfer RNAs”. Bring up the text of 12.1.1.2 (“Transfer RNAs (tRNAs) also play…”) as a static element just as in the extant animation.
-This is the end of the introductory segment.
- Set a Scroll flag at the dissolve to 12.1.1.2 and call it “tRNAs”.
Animation (New 13.1.2) The Genetic Code
- Begin with the same image entitled “mRNA and Triplet Code Words as in old 12.2.2.1.
- Delete any hard stops between animation segments to come.
- Scroll the text of old 12.2.2.1 (“The genetic code provides…”) 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 4 seconds, and dissolve to the next paired unit of text and graphics.
- In 12.2.2.2 the image shows “Degeneracy of the Code” and the text, which should scroll from the bottom of the text window until the top line reaches the top, continues the previous list “4. The code is degenerate meaning…”. Freeze the scrolling at this point, and dissolve the image to the “Start and Stop Codes” graphic of 12.2.2.3
- Bring up 11.2.2.3 with the same text, now static, from the previous sequence.
- This is the end of the segment.
- Set Scroll Flags called “Degeneracy” at 11.2.2.2, and “Start/Stop Codes” at 12.2.2.3.
DELETE OLD 12.1.3 Genetic Code Quiz – these will be added to the final post-quiz.
Animation (New 13.1.3) Triplet Nature of the Code (Changed from old
“Experimental Studies”
- Begin with the same original graphic showing the gray box with A, G, U, and C followed by “20 amino acids” below. Keep the same title “Triplet Nature…” onscreen. This is 12.1.3.1.
- Unite the two “pages” /paragraphs of text “In 1961, Jacob and Monod” and “Crick induced mutations…” together onto one page. Scroll if necessary (if it doesn’t all fit) from the bottom to the top until the last line clears the bottom of the text box – then freeze. Pause for 3 seconds.
- Dissolve the graphic to the beginning of the animation of 12.1.3.2 showing the Phage T4 B gene sequentially revealing two green “E.coli K12” ovals and other stuff.
- This is the end of the segment.
- Set up one scroll flag called “ T4 B Expt” at the beginning of 12.1.3.2.
Animation (New 13.1.4) Frameshift Mutations
- In 12.1.4.1, the title “Effect of Frameshift Mutations” comes up with the blue line graphic. The 4 paragraphs of the two text pages should be one unit text, with a paragraph breaks between extant paragraphs-- “Crick used the mutagen proflavin” and the two paragraphs beginning with “Note that here, 3 bases…” and should scroll from the bottom to the top of the text window until the “Note that here, 3 bases are shown as…” reaches the top of the window. Freeze the scrolling at this point, pause 3 seconds, and advance the animation in the graphics window.
- The animation in the graphics window (12.1.4.2) reveals the “Original Sequence” and blue DNA bar above the other bar onscreen. A “G” inserts into the DNA and then up comes the bracketed names under the blue bars “Met, Val, Leu, Ser, Gln”. Run this animation to the end of the sequence, pause 3 seconds, and dissolve to the next image.
- 12.1.4.3 shows the same illustration but with colors changed to gold. Hold this image for only 3 seconds, and dissolve to the next animation sequence.
- In 12.1.4.4, a red GAG inserts itself into the blue DNA molecule.
- This is the end of the segment.
- Set up scroll flags at the following places and with the following names: “Insertion” at the start of 12.1.4.2, “Frameshift sequence” at 12.1.4.3, and “Triplet insertion” at 12.1.4.4.
Animation (New 13.1.5) Deciphering the Code
- Use the same diagram “pro --->Proline, etc” with the same title “The Code’s Triplet Nature” in the graphics window.
- Scroll the text “Once the code was shown to be triplet” from the bottom of the text window to the top, stopping when the top line reaches the top. Pause for 4 seconds and dissolve both image and text to the next sequence.
- Remove all hard stops between animation sequences.
- In 12.1.5.2, the “Degradation of RNA” title appears and RNA and Inorganic phosphate are shown. Scroll the next text “The ability to synthesize artificial mRNAs…” from the bottom to the top of the text window, stopping then the top line hits the top. Freeze the scroll, pause 4 seconds, and start the animation of 12.1.5.3.
- Run the animation of 12.1.5.3 showing the appearance of three Ribonucleoside diphosphates at the bottom of the screen with accompanying graphics window text. Pause for 4 seconds and move to the next animation, 12.1.5.4
- In 12.1.5.4, the title changes to “Synthesis of RNA” and a three part RNA molecule forms in the graphics window. The text stays the same.
- This is the end of the segment.
- Set up scroll flags: “RNA Degredation” at the start of 12.1.5.2, “Catalysis” at the start of 12.1.5.3, and “RNA Synthesis” at the start of 12.1.5.4.
Animation (New 13.1.6) Working out the mRNA Codons -- this is a fusion of old 12.1.7-
12.1.10, incorporating old Phenylalanine, A Mix of Bases, Triplet Binding Assay,
and Repeating Copolymers.
- Begin with the diagram of the blue DNA line with the same title “Radioactive Phenylalanine in the graphics window.
- Scroll the text “The first mRNAs to by synthesized” from the bottom of the text window to the top, stopping when the top line reaches the top. Pause for 4 seconds and dissolve both image and text to the next sequence.
- Remove all hard stops between animation sequences.
- In 12.1.6.2, the “Mixed Copolymer Experiment” title appears and a table is shown. Scroll the next text “Attention was now turned to a mix…” from the bottom to the top of the text window, stopping then the top line hits the top. Freeze the scroll, pause 4 seconds, and start the animation of 12.1.6.3.
- Run the animation of 12.1.6.3 showing the appearance of another DNA strand and another table at the bottom of the screen with accompanying graphics window text. Pause for 5 seconds and dissolve to the new text and graphic of 12.1.6.4
- In 12.1.6.4, the title changes to “UUU Triplet…” and a picture of a blue ribosome. The text “More advanced techniques were developed….” Should scroll from bottom to top, stopping as the top line reaches the top. Pause 4 seconds and proceed directly to the animation of 12.1.6.5.
- Run 12.1.6.5 showing the blue and gold pieces of the tRNA inserting into the ribosome. Pause for 5 seconds and move to the text and image of 12.1.6.6
- In 12.1.6.6, the image is a large unfilled table with the title “Conversion of di-, tri-, and tetranucelotides”. The text “The remaining codes were determined….” should be scrolled from bottom to top until the top line reaches the top of the text window. At this point, freeze the scrolling, pause 3 seconds, and start the animation in the graphics window (12.1.6.7).
- Run the animation showing the sequential filling of the table (12.1.6.7).
- This is the end of the segment.
- Set up scroll flags: “Copolymer Expt” at the start of 12.1.6.2, “Copolymer Results” at the start of 12.1.6.3, and “UUU Triplet” at the start of 12.1.6.4, “AAA tRNA” at the start of 12.1.6.5, “Other codons” at the start of 12.16.6, and “Expt results” at the start of 12.1.6.7.
Exercise (New 13.1.7) The Coding Dictionary
- Begin with the colorful table of codes and the same title “The Genetic Coding Dictionary” in the graphics window.
- Use the text “The coding dictionary is shown…” (static) but delete the second paragraph of instructions: “Press the Instructions button….
- Delete the Instructions button in the graphics window.
- To the Interaction Instructions box add “Click on each amino acid to view it’s chemical structure in a new window. When you’re finished, press Close Window, and click on a new amino acid.”
- Use the same interactivity and popup boxes when the user clicks on an amino acid name in the table.
- This is the end of the segment
Animation (New 13.1.8) Anticodon-Codon Base-Pairing Rules
- Use the same graphic of the table and the title “Anticodon-Codon Base-Pairing Rules”.
- Add the last paragraph of text on page 2 of this segment (“Because of wobble pairing….”) onto the end of the first page of text, with a break, and scroll the whole text beginning with “Crick suggested that third base mRNA…” from the bottom of the text window to the top, stopping when the first line reaches the top.
- This is the end of the segment
- No scroll flags.
Animation (New 13.1.9) Altered Code
- Use the same graphic of the blue DNA line and the title “Methionine”.
- Scroll the text “The codon that initiates all proteins” from bottom to top until the top of the text reaches the top of the window. Freeze the scroll, pause 5 seconds, and dissolve to the next unit of text and graphic (12.1.9.2).
- In 12.1.9.2, the title changes to “Nonsense Mutations” and shows UAA, UAG, UGA with other words. Scroll the text “There are three termination codons…” from the bottom of the text window to the top until the first line meets the top. Freeze the scrolling, pause 4 seconds, and dissolve to the next combination of text and graphic, 12.1.9.3.
- In 12.1.9.3, the title changes to “Altered Codes….” and shows a table of “Triplet, Normal code, Altered Code”. Scroll the text “The genetic code is nearly universal…” from the bottom of the text window to the top until the first line meets the top. Freeze the scrolling at this point
- This is the end of the segment
- Set scroll flags at “Nonsense Mutations” at the start of 12.1.9.2, and “Altered Codes” at the start of 12.1.9.3.
DELETE THE QUIZ (Experimental and Coding Quiz) of old 12.1.9.14 -- this will be
moved to the post quiz.
Animation (New 13.1.10) Transcription in Prokaryotes
- Use the same graphic of the blue blob and red DNA molecule and the title “Early Stages of Transcription….”.
- Scroll the text “DNA is copies into RNA by an enzyme [called] RNA polymerase” – please insert the word “called” into this text --from bottom to top until the top of the text reaches the top of the window. Freeze the scroll, pause 3 seconds, and dissolve to the next unit of text (page 2 of old sequence).
- Scroll page 2 of the text (“There are two promoter regions…”),which will now be named 12.1.10.2, from bottom to top until the top of the text reaches the top of the window. Freeze the scroll, pause 3 seconds, and dissolve to the next unit of text (page 3 of old sequence).
- Scroll page 3 of the text (“Copying goes past the termination codon…”),which will now be named 12.1.10.3, from bottom to top until the top of the text reaches the top of the window. Freeze the scroll, pause 3 seconds, and start the animation of 12.1.10.4
- Delete any hard stops between animation sequences.
- In 12.1.10.4, the blue blob joins the DNA molecule. Keep the same text onscreen. Pause 3 seconds after the animation concludes and move to the next sequence, 12.1.10.5.
- In 12.1.10.5, the “Insertion of ribonucleotides” appears and the blue blob moves to the right. Pause 3 seconds after this animation concludes and move to the next sequence, 12.1.10.6
- In 12.1.10.7, the Sigma blob “dissociates” from the bigger blob.
- This is the end of the segment
- Set scroll flags at “Promotors” at the start of 12.1.10.2, “Copying” at the start of 12.1.10.3, “RNA Pol binds” at the start of 12.1.10.4, “Synthesis begins” at 12.1.10.5, and “Sigma dissociates” at the start of 12.1.10.6.
Animation (New 13.1.11) Transcription in Eukaryotes
- Use the same graphic of the Animal Cell and the title “Animal Cell”
- Scroll the text “Transcription in eukaryotes differs…” from bottom to top until the top of the text reaches the top of the window. Freeze the scroll, pause 3 seconds, and dissolve to the next unit of text and illustration, 12.1.11.2.
- In 12.1.11.2, show the green and black DNA line with the title “Eukaryotic Gene Structure”. Scroll the text “2. Upstream promoter areas are more…..” from bottom to top until the top of the text reaches the top of the window. Freeze the scroll, pause 3 seconds, and dissolve to the next unit of text and illustration, 12.1.11.3.