Catalysts and Basics of Biochemistry

An organism’s metabolism is the set of chemical reactions that must occur inside of the organism’s cells to stay alive. These chemical reactions enable an organism to grow, reproduce, and respond to its environment. One set of metabolic processes involves breaking down large molecules into smaller molecules. When you eat food, you are taking in animal and plant matter. Most of that matter consists of very large and complex molecules that our cells cannot use directly. In order to reuse the atoms in those molecules, we need to break them down into smaller molecules first. And once those large molecules have been broken down, a second set of metabolic processes take those smaller molecules and use them as components to build the large molecules that our cells specifically need.

Catalysts and enzymes

Chemical reactions inside of a cell are a little problematic. The combustion of hydrogen gas in oxygen begins with the collision between a H2 molecule and an O2 molecule.

water synthesis transition

This collision must be forceful enough to break a chemical bond. In general, the activation energy needed to get this reaction started comes from heating (speeding) up the molecules involved. Heating up molecules is really not a good option inside of a cell. Especially not to the kind of temperatures we would need to pull extremely stable molecules like CO2 and H2O apart.

The other problem is the creation of intermediate products. The reaction mechanism for the combustion of H2 produces H atoms, and OH and HO2 fragments. These atoms and fragments are called “free radicals.” They are highly unstable and will often react with the most stable of molecules. Once these free radicals have formed, there is no telling what kinds of chemical reactions will occur. For example, the hydroxyl radical (OH) can be extremely damaging to virtually all types of organic molecules. If it happens to run into a random organic molecule, it can convert that molecule into a potentially toxic hydroperoxide by removing one of its hydrogen atoms.

water synthesis step 3
The OH radical is supposed to run into a hydrogen atom, forming a water molecule and completing the reaction. But what happens if it runs into some other molecule instead?
water synthesis side reaction
This OH radical runs into a water molecule, producing a hydrogen atom and a hydrogen peroxide (H2O2) molecule.

Chemical reactions rarely produce a single product. Most reactions produce other by-products. To minimize the need for heat to activate chemical reactions and the possibility of undesirable side reactions, our cells use catalysts called enzymes to initiate and control desired reactions.

Catalysts work by providing a site for a reaction to occur… changing the reaction mechanism and lowering the activation energy. All molecules have specific shapes. Many molecules also have polar covalent bonds and dipole charges. A catalyst will lock onto the reactants for a specific chemical reaction, and enable the breaking and formation of chemical bonds.

The shape and dipole charges of the catalyst match the shape and dipole charges of the reactants.
The first reactant gets pulled into place by intermolecular attraction.
The second reactant is also pulled in by intermolecular attraction.
When both reactants are in place on the catalyst, the configuration places a strain on certain chemical bonds.
Existing chemical bonds break and new chemical bonds form. A water molecule is produced.
The newly created molecule is released from the catalyst and the catalyst is ready for a new set of reactants.

This catalyst enables a very specific reaction because only specific reactants are able to lock onto the catalyst, and only specific chemical bonds are affected by the catalyst’s configuration. This also reduces the reaction’s activation energy, the amount of energy needed to break the necessary chemical bonds.

catalyzed reaction energy

An enzyme catalyzes almost every chemical reaction that occurs in a cell. Without enzymes, cells would not be able to perform their metabolic functions and living organisms could not survive.

Proteins and amino acids

Enzymes are proteins, and proteins are made up of smaller molecular components called amino acids. There are twenty-two amino acids, and they all have the same basic structure.

amino acid
generic amino acid

Amino acids consist of a side-chain (“R”) chemically bonded to an amine (NH2) and a carboxylic acid (COOH) group. The specific type and behavior of the amino acid is determined by its side-chain. The amine and carboxylic acid groups enable amino acids to be linked together into long chains. These long chains are called proteins, and they can easily be 500 amino acids long. (The longest proteins, located in muscle cells, are over 25,000 amino acids long.)

protein synthesis

Enzymes inside the cell catalyze the linking of the amine group from one amino acid to the carboxylic acid group of another amino acid, forming a chemical bond between the two amino acids and releasing a water molecule. You can think of amino acids as letters linked together to form words (proteins). Depending on the sequence of amino acids, proteins will fold into unique three-dimensional structures called conformations. And because proteins are flexible molecules, they can also shift between different conformations, changing their shapes.

Besides catalyzing chemical reactions, proteins can also send signals, act as receptors for other molecules, provide structural support in cartilage and fingernails, and contract as muscles.

Nucleic acids

Nucleic acids are DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) molecules. DNA molecules encode the instructions for putting together proteins from amino acids. When you pass down your DNA to your offspring, you are passing down the set of instructions your offspring’s cells will need to produce their own proteins. And those proteins control how a cell grows and behaves. You can think of DNA as the master copy of those instructions stored securely in a cell’s nucleus. If a cell’s DNA ever gets damaged, then the cell (and sometimes even the organism) is in trouble. RNA is the disposable copy of the master copy that gets sent to the workers (proteins) down on the factory (ribosome) floor.

Nucleic acids are made up of smaller molecular components called nucleotides. Like amino acids, nucleotides have standard “connectors” that enable them to be linked together into long DNA and RNA molecules.

nucleic acid synthesis

In this reaction, a cytosine (C) nucleotide is chemically bonding with a thymine (T) nucleotide, releasing a water molecule in the process. Each sequence of three nucleotides represents a specific amino acid in a protein. For example, TTC is the DNA code for a phenylalanine amino acid, and CAG is the DNA code for a glutamine amino acid. By reading the RNA instructions sent from the cell’s nucleus, the proteins in the ribosome are able to catalyze a specific protein with a specific sequence of amino acids.

Carbohydrates and respiration

The average human adult burns about 2000 kcal per day. Just keeping the human body running, even without any physical activity, requires over 1200 kcal per day. This is because a cell must perform over a million chemical reactions each second, and many of those chemical reactions take energy.

The primary energy source for a cell is the glucose molecule. Glucose is a simple sugar. It is burned in a cell for energy in a process called respiration. You can think of respiration as a controlled form of combustion where energy is released as chemical energy instead of heat. Transforming one glucose molecule into carbon dioxide and water molecules releases 4.8 × 10-18 J of energy. This means that a human adult will burn about 1.75 × 1024 molecules of glucose a day, or about 520 g (1.15 lb) of sugar.

C6H12O6 + 6O2 → 6CO2 + 6H2O + energy

You should notice that the reactants in respiration are glucose and oxygen molecules. Oxygen is breathed in by your lungs and transported to individual cells through the blood stream. The products of the chemical reaction are carbon dioxide and water. Carbon dioxide is transported away from individual cells through the blood stream and breathed out by your lungs.

The reaction mechanism for respiration is extremely complex. There are over twenty individual chemical reactions involved in breaking down one molecule of glucose in oxygen. There is no way that this complex reaction could proceed efficiently without enzymes to catalyze each step.

VReaction Mechanism for Aerobic Respiration

When a glucose molecule is not needed for energy right away, it can be stored as a carbohydrate. Carbohydrate molecules are sugar molecules (monosaccharides) chemically bonded together. Glucose is a monosaccharide. Fructose, the sugar in fruit, is another monosaccharide. Sucrose (table sugar) and lactose (the sugar in milk) are both disaccharides. (Sucrose is a glucose molecule chemically bonded to a fructose molecule.) Larger and more complex carbohydrates include starch. A starch molecule is basically long chains of glucose molecules chemically bonded together. Although our bodies burn over one pound of sugar a day in respiration, it does not mean that we are eating that much sugar. Just as cells have enzymes to chemically bond sugars together, they also have enzymes to take carbohydrates apart when needed. So when you eat starch in the form of pasta, your cells will store the starch until they need energy. Then they will use enzymes to break the starch down to individual glucose molecules, burning the glucose for energy in respiration.

Besides storing energy, carbohydrates can also be used as structural elements in cells. The cell walls in plant cells are made of a carbohydrate called cellulose. These cell walls are what give a plant its rigidity. While cellulose could be a source of glucose molecules (a cellulose molecule consists of hundreds or thousands of glucose molecules chemically bonded together), human cells lack the enzymes needed to break down (digest) cellulose molecules. This is why cows and sheep can obtain much more nutrition from chewing on grass than you or I can. Lobster and crab shells are made of another kind of carbohydrate called chitin.


The other major type of molecule found in cells and living organisms are lipids. Lipids form cell membranes and are also used to store energy. While lipids include a wide range of molecules (including wax, cholesterol, and vitamin A), many people think of lipids as fats. Fats are actually a specific type of lipid called a triglyceride. A triglyceride molecule consists of a glycerol chemically bonded to three fatty acids.

You will learn much more about lipids and cell membranes later in this unit when we investigate the solubility of polar and nonpolar molecules.