Unit 6. Enzymes and Metabolism

BIOCHEMISTRY FOR CITIZENS

Lysozyme: small enzyme with a big job


The action of many enzymes can be described by a relatively simple and general model:

E + S ---->  ES ---->  EP ----> E + P

In words, this chemical equation says that an enzyme E attaches itself to a substrate S, chemically alters it to make product P, and then releases P, with the enzyme unchanged and ready to repeat the process. A substance that promotes a reaction but emerges unchanged, ready to do it again, is called a catalyst. Enzymes are biological catalysts. Most enzymes are proteins, but some are RNA or protein-RNA combinations.

As an example, at the end of the process by which muscle uses the sugar glucose as a fuel, the enzyme lactate dehydrogenase catalyzes the conversion of pyruvate to lactate, as shown here:

This reaction, the addition of two hydrogen atoms (white) to the pyruvate (the substrate), is responsible for the lactate (product) that builds up during intense muscle exercise, such as during a sprint. One of the hydrogens comes from a form of the vitamin nicotinic acid, also known as niacin or vitamin B3, one of the many functions that makes niacin an indispensable part of your diet. The other hydrogen is a hydrogen ion (H+), taken from the surrounding solution. This reaction thus reduces the number of hydrogen ions produced from muscle action, and partially ward off the cramping that comes from excessive exercise. (It is a common misconception that muscle action produces "lactic acid". It produces acidity [hydrogen ions], and produces lactate ions in a process that consumes some of those hydrogen ions, thus reducing the acidity.)

The enzyme lysozyme is a first line of defense against infection in the eyes and nose.
(Enzyme, green ribbon; active-site side chains, B&S; carbohydrate product of the cutting reaction, SF).

Another enzyme whose action is described by the simple chemical model above is lysozyme (green ribbon model), which is found in tears and mucus secretions. This enzyme protects us from bacteria that might infect the eyes and nostrils. Lysozyme provides this protection by cutting cell-wall carbohydrates (SF model), causing the bacterium’s protective wall to rupture and the bacterium to die. The substrate S for this reaction is a carbohydrate molecule that is an essential part of the bacterial cell wall structure. The image above is a model of EP, the Enzyme holding on to the already-cut Product of the reaction (note the gap in the middle of the SF model). The active site building blocks (B&S) are the cutters. Other side chains of lysozyme (not shown) recognize and grip the cell-wall molecules with such precision that lysozyme acts only on these molecules and does not damage other carbohydrates, even very similar ones.

The rate of cell-wall cutting by lysozyme is a simple function of the amount of substrate present (called the concentration of S, and symbolized by [S]), as follows:

Rate = Vmax [S)/(Km + [S]

in which Vmax and Km are numerical values that are different for every enzyme. This equation can be derived from the model of enzyme action above.

A graph of the rate versus the quantity of S, shows that the more S present, the faster that reaction will occur, but that the rate of enzyme action is limited when the level of substrate is very high, because all enzyme molecules are kept busy; that is, there is no time delay between the release of product P and an encounter with another molecule of substrate S.

The rate of an enzymatic reaction increases when there is more substrate
present, up to the point that each enzyme molecule is always busy.

Enzymes make possible the hundreds to thousands of chemical reactions that make a living organism living. Rates of all chemical reactions depend on temperature (reactions are faster when hotter), concentration of substrates (reactions are faster when more substrate is present, as shown in the graph above), and the presence of catalysts. The molecules of life—carbohydrates, fats, proteins, and nucleic acids— are stable only at modest temperatures (below 100° F, or 37C), so high temperatures are not an option for making reactions faster. Catalysts are essential.

Most of the reactions on which life depends would proceed too slowly without the catalytic action of enzymes. For example, nerve action depends on many reactions that must proceed rapidly if nerves are to drive quick recognition, quick decisions, and sudden movements. The enzyme acetylcholinesterase, which cleans up after a nerve impulse to prepare for the next one, is among the fastest enzymes known. In fact, theoretical studies suggest that it is as fast as an enzyme can possibly be. So don’t expect people of the future to have significantly faster reflexes than people of today.

Metabolism: enzyme-driven assembly lines

Paths by which nutrients are broken down, one aspect of metabolism.

We run our muscles and nerves, just as we do most of our automobiles, on energy from oxidation—one type of which is the reaction of fuels with oxygen to produce carbon dioxide and water (sometimes called combustion). In our bodies, the main fuels are the building blocks of the complex foods we eat. The process of extracting energy begins in digestion, which dismantles complex foods into simpler building blocks: carbohydrates like starch (polysaccharides) into sugars (monosaccharides), fats (a type of lipid) into fatty acids, proteins into amino acids. nucleic acids into sugars and bases (not shown above). This dismantling, involving enzymes like the serine proteases described earlier, entails using water to break links between the building blocks, a process called hydrolysis (cutting with water).

Next, these fuels enter the bloodstream and are absorbed by cells, which convert the many building blocks into a small number of simple fuels (such as acetylCoA in the figure). These fuels enter the mitochondria, where they finally encounter oxygen, and all of their carbons are rendered as carbon dioxide.

These final reactions release the most energy, and much of the energy is conserved in the form of the chemical agent ATP, the mitochondrion’s main contribution to the cell. ATP provides the energy to build the complex molecules of the cell, to drive muscle movement, to power nerve action. Biochemists refer to these processes collectively as metabolism. This term encompasses the breakdown of nutrients (catabolism), the conservation of energy from that breakdown in the form of ATP and other energy-rich molecules, and the use of these energy sources to drive the non-spontaneous synthesis of complex molecules such as membrane lipids, complex carbohydrates, and proteins (all called biosynthesis).

ATP, a source of chemical energy that drives muscle action and many reactions in biosynthesis.
The blue, red, and white portion is adenosine, the A of DNA and RNA. The red and yellow portion
is a triphosphate, a reactive group that can drive many chemical reactions to completion.

A typical metabolic pathway is a series of chemical reactions, each catalyzed by an different, highly specific enzyme. For example, in active muscle, glucose—a sugar and a favorite fuel of many cells—can be broken down to lactate by a series of nine or ten reactions, each catalyzed by a different enzyme. This process consumes no oxygen, and thus can drive fast movement even after muscle has exhausted its oxygen supply, as happens during an extended sprint. The lactate can be exported for conversion back into glucose by the liver, or can be further broken down to carbon dioxide and water when rapid energy consumption is over.

When an athlete sprints, muscles draws first on ATP that is already present; next, on ATP made using creatine phosphate, a fast back-up energy provider; and finally, on ATP produced by production of lactate from glucose released from muscle starch. After the sprint, muscle cells at rest can oxidize lactate to carbon dioxide, resupplying their ATP and creatine phosphate, and making ready for the next sudden energy demands. Excess lactate can be exported to the liver, converted back into glucose, returned to muscle, and stored as starch.

A leg up

Bacteriorhodopsin and sunrise, Back Cove, Portland, Maine

Bacteria are important links in food chains that support the abundant and varied life in bodies of water like Back Cove, Portland, Maine. During daylight hours, proteins like the one depicted here are hard at work for common types of photosynthetic bacteria in the Cove's surface waters. Bacteriorhodopsins of archaebacteria and their more-recently discovered marine bacterial relatives, proteorhodopsins, transform light energy into chemical energy, using absorbed light (photons) to pump hydrogen ions (protons) across cell membranes. The resulting disparity between the quantities of protons inside and outside the bacterial membrane, called a concentration gradient, is a fundamental and versatile source of chemical energy (that ever-present ATP again) that bacteria use for maintenance, propulsion, and reproduction. In many ways, a gradient is like the disparity in height between water above and below the water wheel that turns one stone against another to grind grain to flour.

In mitochondria, the chemical energy of oxidation, rather than light energy, produces concentration gradients that are used to make ATP. The ATP-making machinery is very similar in mitochondria, in photosynthetic bacteria, and in plants, showing how deep the molecular relationships run among all living organisms.