Thursday, October 29, 2009

Hi All, Since a lot of us are going to be working on the biology in the next little while I realized that I needed to publish the list of all the changes that I know about that need to be made from the layout versions of the animations. Here are the links to view the latest version of each layout animation and the current list of changes that we have for each one:

1. Beef up the thickness of the chromosomes starting at 00:30. They should be much more substantial that the microphillaments.
2. Where do the centriols come from at 00:31? should they be at the polls when we switch to UV light or migrate from one spot as shown?
3. Vary the lengths of the chromosomes.
4. Have the nuclear membrane fade in more gradually around the unraveling chromosomes between 00:50 - 00:58.
5. Pinch and flow the organelles when dividing the outer membrane at the end of division 00:58-01:01.

1. Beef up the thickness of the chromosomes starting at 00:30. They should be much more substantial that the microphillaments.
2. Where do the centriols come from at 00:31? should they be at the polls when we switch to UV light or migrate from one spot as shown?
3. At 00:42 have chromosomes pair up near each other like in image "Meiosis Part 2 Screen Shot #1.jpg"
4. At 00:53 have all of the spindle fibers growing or shrinking "Meiosis Part 2 Screen Shot #2.jpg"
5. Align first chromosome pull at 00:53 and cell division axis at 01:02 see "Meiosis Part 2 Screen Shot #3.jpg"
6. Don't unwind chromosomes at 00:59
7. Spindle fibers don't fade out and grow against each other to push cell a part and lead to division.
8. Centrosome couplets travel to polls at 01:10.
9. At 01:20-01:28 Follow the sperm maturation process.
10. Make a female end version with 3 of 4 eggs disappearing and one remaining 01:22-01:29.

DNA replication:
1. at 00:04 focus on single DNA strand and pan left to see opened strand at 00:08 (maybe make pan take longer)
2. at 00:13 The doughnut-shaped binding clamp binds to the DNA just after the RNA primer is added. The clamp then serves to recruit the polymerase.
3. at 00:22 The polymerase on the lagging strand not only polymerase DNA, but also forces the RNA primers off the existing DNA and cut the RNA primers off. Then the same polymerase adds DNA nucleotides in the place of the RNA primer. See "DNA Replication Screen Shot #2.jpg"
0:20 -0:22 DNA polymerase (the Green blob) will remove the RNA primer one residue at a time and replace the RNA with DNA one residues at a time. (the other protein – the grey smashed candy corn – should not be there).
4. At 00:24 and 00:31 These proteins are unnecessary because the original polymerase performs the duty of removing the RNA primer. See "DNA Replication Screen Shot #3.jpg"
5. at 00:40 leave shot with two diverging strands of DNA.

1. add in longer proteins strands in backgound
2. At 00:00 - 00:05 make ribosomes on the rough ER should be the same color and shape as the ribosomes in the cytoplasm. If possible, it would be great to see ribosomes come onto and off of the rough ER as the animation progresses
3. At 00:00 - 00:06 circularize the mRNA as shown in " Translation Screen Shot #2.jpg"
4. At 00:21 make the growing protein strand to ball up outside the ribosome as it is made. This is a natural folding process in which the protein binds to itself.
Have the emerging peptide chain fold up. If you don’t think there are enough residues to fold up properly, then either lengthen the movie or speed up the process to fit more residues in.

1. add in nuclear pore in background 00:42-00:52 and have mRNA strand head up toward pore like it will be going out of it.
0:21 What are the attacking molecules at 0:21
0:30 Can you stay zoomed out until the mRNA leaves the complex (about 0:32)?
The mRNA chain needs to move away from the DNA strand. You might add a peripheral Ribosome to the mRNA chain.

Photosynthesis -light reaction:
1. At 00:00 add a yellowish membrane to the inside wall of the green plant cell wall
2. At 00:00 Give the Golgi 5 pancake stacks with the two outermost stacks having many vesicles blebbing off.
3. At 00:00 Make the mitochondria about half the size, or less, than the chloroplasts.
4. At 00:00 Make the cell membranes of every organelle the same width
5. At 00:00 The smooth ER should be continuous with the rough AND they should be slightly different shades of the same color. Remember that the smooth ER is more tubular while the rough ER is stacked like pancakes.
6. At 00:04 Make the outermost membranes of the chloroplast translucent to light green--preferrably slightly different shades and very light compared to the grana (the stacks of discs inside the chloroplast, which should be rich green like they are)
7. At 00:05 Ideally, the entire surface of the thylakoid discs would be somewhat populated with the proteins of the photosynthesis electron chain.
8. At 00:07 Make the membrane containing our proteins completely horizontal.
9. At 00:07 Populate the membrane with phospholipids that slightly wiggle. (See Steve Herron's bioenergetics Membrane Animations in email)
10. At 00:10 Make the electrons bluish balls of energy (balls of light) and the photons yellowish balls of energy.
11. At 00:19 For the water molecule colors, oxygen should be red and hydrogen should be white (with a pearly sheen so that they have some texture).
12. At 00:34 Unite the 2 orange hydrogens to the first mobile electron carrier protein before it moves from the first complex to the next complex (while it is still located near the top sheet of the membrane).
13. At 00:37 Cause the electrons to follow each other through a U-shaped path up into the core of the complex that begins at the currently designated startpoint and ends at the currently designated transfer point.
14. At 00:39 Cause the second mobile electron carrier to remain in close contact with the membrane during its movement from the second comlex to the third complex.
15. At 00:57 Place the Ferrodoxin NADP Reductase (FNR) enzyme on the top surface of the membrane, not integrated into the membrane.
16. At 01:01 Once NADP is reduced by adding hydrogen allow it to dissociate from FNR and randomly move away from the membrane surface.
17. At 01:05 Be sure that hydrogens are on either side of the membrane, but not in the membrane space itself.
18. At 01:05 Make the ATP Synthase complex move from the time that it can be seen on screen.
19. At 01:08 Cause the freshly created ATP and cycled hydrogens to randomly dissociate away from the ATP synthase once emitted from the protein complex.
20. Let ATP rotary pump (01:06-01:10) cycle longer by adding another 6 seconds.

Lac Operon - Gene regulation:
1. At 00:03 - 00:11 Please include 3 or fewer lactose molecules until after the RNA Polymerase's first pass (the unsuccessful DNA-binding event). Then cause more lactose molecules to appear and bind the repressor.
2. At 00:03 - 00:11 The lac repressor actually binds a loop of DNA on either end. The Lac Operon Picture #1, depicts the bound DNA loop. The animation could show the unlooping after repressor deactivation then the subsequent binding of RNA polymerase.
3. Let regulator move off instead of using transition at 00:22.
4. At 00:30 - 00:47 See Screen Shots #2a and #2b--The ribosome subunits bind to the RNA separately. First the small subunit binds. Second, the first tRNA binds. Last, the large subunit binds. I imagine this portion of the animation be somewhat more similar to the already produced translation animation but simplified. Could we make simple tRNAs that simply enter the ribosome and others that exit the ribosome out the other side? This animation ties together other DNA-associated animations (transcription and translation), so I, personally, would like a couple of the main steps from those animations to reappear here.
5. At 01:09 - 01:16 After the repressor has re-bound to the DNA please animate 3 or fewer lactose molecules.
0;30-0:32 I think the Ribosome should attach to the mRNA earlier (around 0:30 not 0:32), first with the small subunit and then the large subunit (as mentioned in your notes).
The Ribosome should bind near the beginning of the mRNA molecule, but not at the end. There is an mRNA cap and associated proteins (to complex to add) that bind to the very beginning the ribosome typically binds several residues downstream of the cap.
Peptides should appear fairly quickly after the Ribosome starts down the chain. In this version of the animation you have the Ribosome binding at
0:32 and peptides first appear at 0:36 (too long).
The peptide should appear as a chain folded (as noted in your notes).
0:59 The blue lactate molecules in the cytosol need to be bigger or the lactate molecules on the Lac Repressor (the Gold tooth) need to get smaller as the molecules move towards β-galactosidase.
1:03 As the blue lactate get degraded by β-galactosidase, the glucose and galactose molecules should appear (two smaller gray molecules).

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