Enzyme helpers, conditions, and ribozymes

An enzyme’s protein chain isn’t always enough on its own. Some enzymes need a nonprotein partner, most work well only within a narrow range of conditions, and some of the cell’s catalysts aren’t proteins at all.

Nonprotein helpers

Enzymes are proteins, but some need small nonprotein molecules or ions to do their job. These helpers come in three kinds:

The right temperature and pH

Enzymes are sensitive to their surroundings, especially temperature, pH, and the ions present. Most enzymes work best within a narrow range of temperature and pH, and their activity drops outside it.

Many human enzymes work best at 37 °C (98.6 °F), normal body temperature. If body temperature rises or falls several degrees, from an infection or from the environment, many enzymes slow down sharply. Very high temperatures can denature an enzyme: the protein unfolds and loses its three-dimensional shape, including the shape of its active site, so it stops working.

pH measures acidity: the lower the number, the more acidic, and pH 7 is neutral. Each enzyme has a pH at which it works best.

Pepsin, a protease (an enzyme that digests proteins) released into the stomach, works best near pH 2, which is extremely acidic. Many enzymes in the cytosol, the fluid inside cells, work best near pH 7.2, the normal pH of human cytosol. Well above or below that value, their activity falls.

Ribozymes: RNA that acts as a catalyst

For a long time, biologists thought every catalyst in a cell was a protein. In the 1980s, some RNA molecules turned out to catalyze reactions too. An RNA molecule that catalyzes a chemical reaction is a ribozyme.

A classic example is RNase P, which helps make tRNAs, the small RNA molecules that carry amino acids to the ribosome (the cell’s protein-building machine). Each tRNA is first made as a longer, unfinished version called a precursor tRNA (ptRNA). RNase P cuts one specific bond in the ptRNA, releasing a small fragment from one end (the 5′ end) and leaving a mature tRNA that can do its job in protein synthesis.

RNase P has two parts, an RNA subunit and a small protein subunit. To find out which part does the cutting, researchers purified each subunit separately. They then incubated ptRNA with the RNA subunit alone, with both subunits, or with neither, at low or high concentrations of magnesium ions (Mg²⁺):

• With no RNase P at all, the ptRNA stayed intact at either magnesium level, so magnesium alone doesn’t cut it.
• At low Mg²⁺, the RNA subunit alone did nothing, but the RNA and protein subunits together cut the ptRNA.
• At high Mg²⁺, the RNA subunit alone cut the ptRNA into a mature tRNA and the 5′ fragment.

That last result showed the RNA itself is the catalyst. High magnesium apparently holds the RNA in its active shape, a job the protein subunit probably does in a living cell. Later work confirmed that the RNA subunit is a true catalyst: it speeds up the reaction and isn’t permanently changed by it.

What ribozymes do

Ribozymes have since been found doing two general jobs in cells:

• Cutting RNA molecules. Besides RNase P, an RNA inside the spliceosome, a large RNA-and-protein complex in eukaryotic cells, cuts out introns, stretches that must be removed from a gene’s RNA copy before it’s used. Some introns in mitochondrial, chloroplast, and bacterial RNAs even cut themselves out, a process called self-splicing.
• Making polypeptides. An RNA in the ribosome catalyzes the covalent bonds that join neighboring amino acids as a protein is built.

Check yourselfA reaction in a cell extract keeps running when a protease is added, but it stops when an enzyme that destroys RNA is added instead. What kind of catalyst is most likely involved?

A ribozyme. Destroying proteins didn’t stop the reaction, so the catalyst isn’t a protein, but destroying RNA did, so the catalyst is most likely an RNA molecule. If the protease had stopped the reaction, that would point to a protein enzyme instead.