What is the effect of adding alkaline or acidic substances to wheat flour?
I can think of adding alkali or acid substances mainly as means of changing the ph of the dough. And adding can be understood as in the dough, or on its surface.

Alkali/basic additives or ingredients


Gluten only works if PH is between 3 and 11. Outside those values it loses its stength.

Before reaching PH>11  it will make flour have a higher absorption.
It's a way to relax the dough, as the technic used to stretch noodles as it has previously been cited in this question (see @TFD and @Chad's answers), and also in this question. To make that kind of noodles, you add the alkali to the flour, resulting it to be in the dough.
Another way basic substances are used in dough is giving them a bath in caustic soda, as  Germans do with their Laugengebäck (the most known ones outside Germany probably are the Brezels/Pretzels). The lye makes them have their characteristic crust: brown, and hard and thin, like a good sausage.


Acidic additives or ingredients

Acids can also weaken the gluten, but in bread making is not so strange to add certain acids, or wanting an acidic dough.


One of the reasons on wanting an acidic final loaf is it will help increasing the shelf life, as it will act as a preservative.
Besides that, there is a very common acid used in doughs: Citric acid / Ascorbic acid / E-300. It helps the dough to rise more and faster, and be more manageable and have a crumb that resembles like cotton candy. You can read more on Ascorbic acid at the page of the Real Bread Campaign, and in this YouTube video you can see its effect in dough. 
Another reason for wanting a low PH dough is to avoid starch degradation. Flours have enzymes (amylase) that end up degrading it. But that enzymatic activity is stopped with a PH&lt;4.5. This is well known with 100% rye breads:


  I know the question states wheat flour, but this example is clarifier. Rye flour has low gluten, and it has a somehow "low quality" (if compared with "normal" wheat flour). Some recipes call for strong high gluten wheat flour to retain gas bubbles from the leavening that won't get trapped by rye's gluten. But in 100% rye breads gas can also be trapped. That is why usually rye breads are made with sourdough, which has acetic and lactic acids. They give the dough the right PH, and the starches in rye will get gelatinized and catch the gasses in a similar (although less effective way) than gluten. Sometimes, instead of sourdough, yeasts and acid are added as ingredients.


That was an specific example with rye, but wheat flour also has starches, and they can also be gelatinized, giving a distinctive sourdough touch to to 100% wheat breads.


Acidic and basic at the same time

(Thanks @ChrisSteinbach for reminding me it)


When mixing an acid and a base, a chemical reaction happens, neutralizing both and releasing CO2 gas: 

NaHCO3 + H+ → Na+ + CO2 + H2O

That gas is employed to leaven the dough, as in a chemical leavener. I.E. in Irish bread or typical cakes. 


Stuff that is not acidic nor basic... yet


As a chemical leaveners improvement, one would like the reaction wouldn't start as soon as acid, base and water are mixed, but a bit later. This woud let some more time to work on the dough. Some salts have the characteristic of degrading at high temperatures into acid, helping (usually in the oven) for a second rise.