OK, good! The diagram should look like your new drawing.
......E1
..........E2
..........E3
.........E4
A-------->B-------->C--------D--------F
...............................\
................................\ E5
.................................\
...................................------>G
Lainey wrote:I figured if you shut down E2, everything after it wouldn't be formed. I would like to point out, Juliod, that I did figure that one out myself, and just needed clarification.
Hee hee. Juliod has a good point, as always. Clarification can come somewhat close to being told the answer. In any event, your new diagram makes it pretty clear. Knock out E2, and you've got this:
......E1
.............X
...........E3
.........E4
A-------->B
-------->C--------D--------F
...............................\
................................\ E5
.................................\
...................................------>G
You can make B just fine, but if you can't make C, then you can't make anything that uses C as a starting material. Since G is made from C, you can't make G. Without something for the enzymes to work on, they can't do anything, even if the enzymes are there.
Lainey wrote: Y'see, it's like when there's science involved, a wall goes up in my brain. I know the answer's out there somewhere, but I have to get over the wall first. ... That's a lot of stuff to digest. I looked at your animations, and they helped, but I do pretty much understand the idea of substrates and how enzymes work on them. It's just the chain reactions I have trouble with. So from what you and Juliod said, it actually looks like it's pretty easy. I think I was making it harder in my head than it has to be. There's that brick wall again. ](*,)
There's a lot of societal indoctrination that goes on, that leads certain flavors of people to expect to be able to do things easily or with difficulty. Math and science are subjects that women "aren't supposed to be good at" so we learn from an early age to think that's why we might have gotten stuck on some problem or other. There are similar societal expectations for various minority groups--some expected to be good at this, poor at that, and other groups being expected to be good at something else. It's all bunk, but the expectations alone are enough to create these brick walls. Here's an interesting experiment: give girls a math test--the computer-graded kind. Have some of 'em identify their gender at the beginning, by filling in the circle labeled "female." Have the other half fill in the same circle
after they've finished the test. The ones who identify themselves as female
after the test get better scores than the ones who identifiy their sex
before the test. It's like that one little circle makes 'em think "uh-oh. I'm not supposed to be able to do this, so I'll get all the brick walls in place."
Brick walls are weird things. My wife describes them as windows that she can see through, but just when the picture is starting to get clear, they shut. In any event, if you hang in there, you'll find a way around the wall.
Lainey wrote:Still a little confused on this point. So, it would be you have to add just D? Or D and F? Or D and F and G? I guess if you added D, It would be like unplugging the hole in the chartreuse bucket, right? (I like the bucket analogy). So the reactions that came after it would still happen automatically, as long as D was put in. So you only need to add D? You said "D or F." But if you skipped D, wouldn't that miss something? Don't you still need to add D? Do you even need to add F at all?
(Reminder: we knock out E3, and can't make D, so we can't make F. By th bucket analogy, adding D would be like walking in and pouring Dark-red stuff (D) into the appropriate bucket that has the E4 hole in it. Then, the Dark-red stuff can be worked on by the E4 hole, and turned into F, the Flourescent, day-glow color that the whole A-B-C-D-F pathway is supposed to make.
You could, of course, add F directly--and the critters would get their F. They can make it from D if you give them D, or they can use F if you give them F. The way the diagram is presented, it
looks like it implies that the important things for the critters are F and G--the end products of this set of reactions. If they can make G, but can't make F, then you've gotta give 'em F or something to make F from (i.e. D). Giving them more C wouldn't help, because they can't convert C to D because the enzyme that does so has been knocked out.
This is kinda what we do with Vitamin A. Mom always tells us to eat our carrots, so we can see better at night. The beta-carotene in 'em is used to produce retinal, the photopigment in our eyes. it's also the precursor to
real vitamin A, retinoic acid. Think of the stuff in carrots (or other red and orange things) as the "D" in one of these pathways. We eat the "D" and our enzymes convert it into the active "F." It doesn't do us any good to eat, say, pyruvate, because we lack one or more of the enzymes to convert pyruvate to beta-carotene.
Speaking of pyruvate and enzyme pathways, check out
Page 7 of my animations. There are a couple of glycolysis animations--one of which shows
all the gory details of the chemicals involved, and the other attempts to
illustrate the idea that the enzymes work on their substrates because they happen to fit the shapes of the enzymes. In this one, you move the enzymes around and try to make the reactions go--which they won't if the enzyme doesn't fit the substrate. This animation also tries to get at the idea that lots and lots and lots of reactions are going on all at once, and we
can't describe anything at all without hiding most of what's there. If you go from page 7 to the interactive mitochondria animation, you'll see an oxygen molecule "suddenly appear" when it is needed. My students often say "and than oxygen appears" when they should, instead, see it as "oxygen is always there (if you're breathing), dissolved in the water of the cell, and when the appropriate enzyme grabs it, the enzyme uses it...but we can't show everything at once, so we'll only draw it in when it comes into play." Think of it as an ant colony, and we've gotta hide all of the ants except for the one we're watching, or else it's too messy to tell what's going on.
Here's another cute bit you should know: Enzymes don't waste time doing stuff they don't need to do. In our example of E1,2,3,4, and 5 making B,C,D,F, and G out of A, it wouldn't be at all surprising if the enzyme E1 has a pocket on it that compound F would fit into--and in doing so,
slow down the reaction. E1 might have a second pocket that G can fit into, that would also slow E1 down. Usually, the first enzyme in a pathway is regulated this way--by the end product slowing it down. We'd draw it this way (using another arrow that means something completely different than any of the other arrows):
.........._____________________
........./
..........................................\
.......V
.............................................\
......E1
..........E2
..........E3
.........E4
.....\
A-------->B-------->C-------->D-------->F
...............................\
................................\ E5
.................................\
...................................------>G
I don't know if this looks right...it should be an arrow going back from F and pointing at E1. Another concept, another arrow! It would probably look better without the E5 and G in there, since most enzymes that are regulated this way are the first one in a pathway that makes only one product. Here, E1 is in a pathway that makes both F and G...but such things are not unknown.
t's just the chain reactions I have trouble with.
How about another analogy? To make a car, ya gotta have a bunch of steps, from the starting material to the finished product. Each step needs a worker (or machine) to do that step. That worker/machine is the analog of an enzyme in a multi-step pathway.
Digestion and metabolism of food might be another good example. You eat a potato. The starch molecules have to be broken down to glucose molecules before your digestive system can take them up. There's step one. Then there's transport into cells, using an appropriate transport enzyme. There's step 2. Then there's a bunch of reactions that happen, breaking the glucose down further--steps 3 through 13. At the end of this, you've got pyruvate.
Yippee!
Well, don't look at me that way! Pyruvate
matters. You want bread? The yeast eat the sugar, make pyruvate, and then ferment it to CO2 and ethanol. The CO2 makes the bread rise. You want wine? Again, you use yeast, and it makes pyruvate, then ferments it to CO2 and ethanol. You leet the CO2 bubble away (unless you want beer or champagne, in which case you save some of the CO2 for carbonation). But, don't get any bacteria into the fermentation vat, 'cause they ferment pyruvate to lactic acid, and make the stuff taste bad. That is, after all, what happens when milk goes sour--bacteria eat the milk sugar, run it through glycolysis to pyruvate, then ferment it to lactic acid--sour milk. They do this because there's no air in bread dough, milk cartons, or fermentation vats--so they can't metabolize the pyruvate the way we do, using our mitochondria. In any event, you can get pretty far in the kitchen if you keep track of the pyruvate.
Of course, the goal is not to make pyruvate, but to destroy the glucose and extract the energy that's in it--by capturing it in the formation of ATP. But we can talk about
that later...
I hope you don't lecture me because I don't understand this part! Y'see, it's like when there's science involved, a wall goes up in my brain. I know the answer's out there somewhere, but I have to get over the wall first. ](*,) 
:censored: 
