So my understanding of the digestive side of things is that the sugar compounds that are difficult to break down during digestion are the products that contribute to buildup of flatulence. The compounds make it to the large intestine and the bacteria living there get a feast. When the bacteria are breaking down these complex sugar compounds they release waste materials including gasses that we have to get rid of somehow and when enough of them build up . . well, it has to go somewhere.
OK, so that's why we get gas but why do eating some plants cause gas while others don't?
When plants are in sunlight they are harvesting the sun's energy, but they need to convert that energy into something stable that they can transport to parts of the plant that aren't able to do photosynthesis (roots, seeds, new leaves) and to save it for a rainy day. They harvest the energy by fixing and reducing carbon dioxide (CO2) – they take in CO2, add sunlight and make sugars (which is why destruction of rainforests can have a huge effect on global warming- not only does burning trees release all the CO2 they have fixed for years back into the atmosphere at once, it also reduces the number of plants that can take the CO2 already in the atmosphere back out).
Plants put the carbon from CO2 into sugars. They can't keep all the sugars just as simple glucose molecules (because the osmotic pressure would rupture the cells) so they put them into long chains.
One long chain that is used by many plants for storage of sugars is starch. Starch is made by not only sticking the sugars together end to end to form a long chain (amylose), but sugars are also stuck on so they branch out into chains (amylopectin).
Amylose, the one that forms long strings of sugars, can pack tightly together and therefore enzymes in our digestive track have a hard time getting in there and breaking it down. Therefore amylose makes it into the large intestine where those gas producing bacteria get a chance to work on it. Amylopectin, with its branches, can't pack down as tightly, and has many ends for our enzymes to get started on- so we can break it down easier before it reaches the gassy bacteria. How much sugar goes into each type of starch depends on the type of plant. Most cereals, especially rice have a high amylopectin content and are therefore easily digested without much gas production. Tubers and legumes tend to have more amylose. I can not find the amylose content of peppers, but my guess is that if this is a factor it has to do with cooking. Cooking your food will help break down the starch- it will separate out the strands of amylose and amylopectin and water molecules will get trapped inside. This opening up of the starch also makes it easier for enzymes to get in there and digest it. So one possibility is that you are eating your peppers raw, or lightly cooked, if this is the case, you can cook them a bit longer and this might help.
An interesting side note . . .
When starch grains are heated in water they attach to the water, absorbing it into the chains, when they cool the water is locked into the chains and you get a thick gooey mess- if you add sugar and flavoring during the process this would be called pudding.
Now, if you stick pudding in the freezer (or refrigerator for a long time) the starch will pack up again forming crystals and become a pretty gross sight, but you can fix this by reheating the pudding. A similar thing happens to bread. The starches absorb water during baking, but when the bread cools, the starch molecules form tighter and tighter crystals over time, and thus the bread becomes hard and stale. However, if you reheat the bread in the presence of a bit of water it will regain its flexibility and taste fresh again.
Plants also can use sugars as a protectant against water loss. For example, when some plants are exposed to drought or low temperatures they increase the amount of raffinose (a combination of three sugar molecules) in their tissue. Raffinose helps to hold on the the water molecules that are in the plant and keep them from being lost to the outside of the plant. Raffinose is notoriously hard to digest it requires an enzyme called alpha galactosides which we don't produce. However, the bugs in our gut do- and they love raffinose- it is a good source of energy for them so they get very active (and gas producing) when it is available. Raffinose is present in high levels in beans, brussel sprouts (gross- who'd eat those nasty things anyway), and broccoli. The sweet taste from peppers also comes from raffinose so this could also be the source of your er “air.” I don't know the total level of raffinose in peppers, but it is interesting that peppers are fairly drought resistant- just a thought - but one possibility is that they accumulate more raffinose and this is why- I wonder if anyone has looked into that. . . .
I don't know any way to avoid gas caused by raffinose. “Bean-no” the product you take to avoid gas is the enzyme alpha galactosidase but in looking up this I read several times that it isn't more effective than a placebo. . . does someone else know if there is any effectiveness in taking this?
One more rant that is close to but not exactly on the topic. . .
Depending on the type of plant, about a third of the sugar pool goes into making cell walls. For example, cellulose is a major component of cell walls. Cellulose is basically glucose molecules linked together to make a long chain. However, they are linked in such a way that we don't have the enzymes in our bodies to break them apart. Even the bacteria in our gut can't digest cellulose, so it goes through us in long chains. Only termites have the bacteria that can digest cellulose. Cellulose and similar long chains that we can't break apart form the fiber we need in our diet to help keep things ummm- running smoothly. Fiber that is composed mostly of cellulose is considered insoluble and goes right through without producing much gas. However there are insoluble fibers which are composed of other cell wall components, and these the little fellas in the gut can work on and these produce a lot of gas- again, beans have a large amount of insoluble fiber.
And a final rant completely off topic . .
Cellulose is actually the biggest component of biomass on the earth. And therefore it is often talked about as an important source for biofuels. The idea being that if we can use cellulose efficiently for fuel we could harvest crops that take the carbon dioxide out of the air and put it into cellulose, use the cellulose for fuel, putting the carbon dioxide back into the air and regrow the crops the next year taking the carbon dioxide back out. As opposed to what we do now by burning fossil fuels- which is put the carbon dioxide in the air that was taken out millions of years ago. It would be a good step in the right direction if it works.