The food industry is very interested in questions like this. All organisms have certain ranges where they do well, survive (but may not grow well or reproduce), or do not survive. Different bacteria have different pH zones that are optimal (best), survivable, or deadly. There are a lot of acidic foods, like pickles and yogurt, that are fermented by bacteria that do well in low pH (acidic) environments. Even with these bacteria, there’s a lower pH limit.

The reason is a bit complicated, so let’s look at what we mean by pH. Plain water has a pH of 7 (neutral) because it has an equal number of hydrogen ions (protons without electrons) and hydroxyls (OH). Hydrogen ions have a positive charge and OH groups have a negative charge. When there are equal numbers, they cancel each other out. When something has a low pH, it has a lot more hydrogen ions.

Normally, bacteria can keep their inside pH at a constant rate, even when the environmental pH changes. Maintaining a fairly constant environment is called “homeostasis.” It’s a characteristic of life. For example, our internal body temperature stays about the same whether it’s hot or cold out. But if you try to spend a day outside in the summer in Death Valley or without shelter in Antarctica, your body may not be able to maintain homeostasis.

Back to bacteria. The outer surface and inner membrane of some bacteria are good at keeping protons out, but there are limits. If bacteria that do fine in yogurt, for example, get exposed to an even lower pH, the hydrogen ions outside get into the inside of the cell and start to cause trouble.

Proteins are long chains of different amino acids. The functions of proteins usually depend on their shapes. A protein’s shape is determined by charges along the protein that folds up into a particular shape. Opposite charges attract each other. The shape is also determined by the environment of the protein as it folds because charges on the protein interact with water and charged particles like hydrogen ions. A change in pH can make proteins fold up wrong, so they don’t do their jobs. One critical category of protein is the enzymes, which catalyze biological reactions. In other words, they speed up the reactions that living things require. Enzymes have to be a particular shape or they don’t work. Low pH can also directly damage the DNA or the cell membrane. Again, the hydrogen ions can interfere with other charges, changing their shapes and function.

Why might a food company add acids to particular foods? Thanks for asking,

Low pH levels can change the structure and solubility of certain proteins, small molecules, or other substances that are essential to their survival. For instance, if low pH values change the structure of a protein, then the protein can no longer perform its intended function. If this protein is needed for starting a process that either makes more proteins or regulates bacterial metabolism, then the downstream effects can quickly become catastrophic. Sometimes, the changing of a protein's function can be as simple as taking away, or in the case of low pH, adding a proton onto the binding or active site of the protein, thus changing its efficacy for interacting with other molecules and catalyzing reactions. Furthermore, bacteria grow most optimally in certain ranges of pH gradients across their membranes, so overly acidic environments, especially in the cytoplasm of bacteria, disrupt the pH gradient and the regulated processes of energy transfer (in terms of the proton motive force) in the bacterial cell. Without the function of proteins and the maintenance of the pH gradient, bacterial cells will quickly succumb to cellular damage due to inhibited transcriptional, metabolic, and repair processes and die due to the accumulated damage.

Bacteria, like all living things, use enzymes, proteins that carry out essential functions that keep them alive. Proteins work in a set range of pH levels and get "denatured" - i.e. turned into another type of molecule - if placed in a solution with a pH outside of that range. Low pH levels will thus denature the enzymes of any bacterium that has not evolved to live in low-pH environments. Since these enzymes do essential things, denaturing them will kill the bacterium. It would kill you, too, to dump you into a big vat of acid, for the exact same reason, as it would denature your enzymes and other proteins.

Low pH levels are acid pH levels, and too much acid is toxic. pH levels lower than 7 are acidic, and lower pH levels are more acidic.