Biochemistry
While rye and wheat are genetically similar enough to interbreed (resulting in hybrids known as triticale), their biochemistries sufficiently differ to affect the breadmaking process. The key issue is differing amylases, the enzyme which breaks starch down into sugar. While wheat amylases are generally not heat-stable and thus do not affect stronger wheat gluten that gives wheat bread its structure, rye amylase remains active at substantially higher temperatures. Since rye gluten is not particularly strong, rye dough structure is based on complex polysaccharides, including rye starch and pentosans. As a result, amylases in rye flour can break down dough structure, inhibiting it from rising.
There are two common solutions: The traditional manner, developed where obtaining wheat was traditionally impractical because of marginal growing conditions or supply difficulties, uses dough acidification to impede the function of rye amylases. Lowering dough pH, however, compromises the use of relatively acid-intolerant Saccharomyces cerevisiae-based "baker's yeast". Instead, addition of naturally acidic Lactobacillus "sourdough" cultures lowers bread pH, provides an acid-tolerant yeast strain, and helps gelatinize starches in the dough matrix. The byproduct of this approach is lighter breads.
In areas where high-gluten hard wheat is readily available the need for a complex polyculture of bacteria and yeast can often be reduced or removed by adding a large proportion of hard wheat flour to the rye flour. Its added gluten compensates for amylase activity on the starch in the dough, allowing the bread to retain its structure as it bakes. The "deli rye" tradition in the United States is based upon this mixing of grains. Use of high-gluten wheat flour also makes possible multigrain breads, such as the "rye and Indian" bread of the American colonies, which combined rye and wheat with cornmeal in one loaf.
Rye bread contains phenolic acids and ferulic acid dehydrodimers.
Read more about this topic: Rye Bread