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.
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.
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.
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.
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.
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.
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 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.)
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 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.
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.
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.
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.
Aerobic respiration is when glucose is burned in oxygen. To completely break down one molecule of glucose into carbon dioxide and water molecules, you need six molecules of oxygen (O2). (If your body cannot get enough oxygen to your cells, then the cells will burn glucose without oxygen. This process, called ”anaerobic“ respiration, releases much less energy than aerobic respiration. One by-product of anaerobic respiration is lactic acid. The build up of lactic acid is what causes your muscles to burn during strenuous exercise.)
The first step in aerobic respiration is to split the glucose (C6H12O6) molecule into two pyruvic acid (CH3COCOOH) molecules with the assistance of phosphoric acid (H3PO4).
Pyruvate (CH3COCOO-) ions from the pyruvic acid release a carbon dioxide (CO2) molecule and bond with an enzyme.
The acetyl group (C2H3O) from the enzyme chemically bonds with an oxaloacetic acid (C4H4O5) molecule to form a citric acid (C6H8O7) molecule.
Over a sequence of ten steps called the citric acid (or Krebs) cycle, the citric acid molecule reacts with two oxygen (O2) molecules, producing two carbon dioxide (CO2) molecules, two water (H2O) molecules, and an oxaloacetic (C4H4O5) acid molecule. The oxaloacetic acid molecule is then ready to chemically bond with another acetyl group, starting the cycle over again.
Carbon dioxide and water molecules are both much more stable than a glucose molecule. So when the chemical bonds in a glucose molecule are broken, and the carbon, hydrogen, and oxygen atoms enter more stable configurations as carbon dioxide and water molecules, energy is released. This is why combustion almost always involves the breaking of C-H and C-C bonds and the production of carbon dioxide and water.
Once carbon, hydrogen, and oxygen atoms are in stable configurations as carbon dioxide and water molecules, they have essentially reached the bottom of the “energy well.” You cannot get energy out of carbon dioxide and water because you cannot transform them into more stable molecules. This is why carbon dioxide and water will not burn.
Plants use a process called photosynthesis to build new glucose molecules out of carbon dioxide and water molecules. Oxygen molecules are a by-product of this reaction. (When organisms first started using photosynthesis, the oxygen produced was toxic to most living organisms. Most early organisms were anaerobic and did not breathe oxygen. There was a mass extinction event called the Great Oxygenation Event about 2.4 billion years ago as the Earth’s atmosphere filled with oxygen. It took millions of years for organisms to evolve defenses, such as hemoglobin, against oxygen.)
Because respiration is an exothermic reaction, photosynthesis is an endothermic reaction. Not only does it take energy to get this reaction going, but it also requires energy throughout the reaction to build glucose molecules; the same amount of energy, in fact, that we get by breaking down glucose molecules.
Plant cells use energy from the sun to drive photosynthesis. This makes the reaction mechanism for photosynthesis both longer and more complex than the reaction mechanism for respiration. Not only do the carbon dioxide and water molecules need to be reassembled into glucose, but energy also needs to be captured from the sun.
Plant cells capture sunlight with a substance called chlorophyll (it is the pigment that gives plants their green color). When a chlorophyll molecule absorbs a photon of light, it loses an electron. This electron gets passed through a series of molecules called an electron transport chain. As more and more electrons get transported from one part of the cell to another, an electrochemical gradient is created. There is a build up of positive charge inside the chloroplast (where chlorophyll is stored) and a build up of negative charge outside of the chloroplast. This literally creates a battery inside of the cell, and the energy from this battery is used to activate the other chemical reactions in photosynthesis.
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.