The Molecules of Life
The elements involved in life processes can, and do, form millions of different compounds. Thankfully, these millions of compounds fall into four major groups: carbohydrates, proteins, lipids, and nucleic acids. Though all of these groups are organized around carbon, each group has its own special structure and function.
Carbohydrates
Carbohydrates are compounds that have carbon, hydrogen, and oxygen atoms in a ratio of about 1:2:1. If you’re stuck on an SAT II Biology question about whether a compound is a carbohydrate, just count up the atoms and see if they fit this ratio. Carbohydrates are often sugars, which provide energy for cellular processes.
Like all of the biologically important classes of compounds, carbohydrates can be monomers, dimers, or polymers. The names of most carbohydrates end in “-ose”: glucose, fructose, sucrose, and maltose are some common examples.
Monosaccharides
Carbohydrate monomers are known as monosaccharides. This group includes glucose, C6H12O6, which is a key substance in biochemistry. Sugars that an animal eats are converted into glucose, which is then converted into energy to fuel the animal’s activities by respiration (see Cell Processes).
Glucose has a cousin called fructose with the same chemical formula. But these two compounds have different structures:
Glucose and fructose differ in one important way: glucose has a double-bonded oxygen on the top carbon, while fructose has its double-bonded carbon on the second carbon. This difference is most apparent when the two monosaccharides are in their ring forms. Glucose generally forms a hexagonal ring (six sided), while fructose forms a pentagonal ring (five sided). Whereas fructose is the sugar most often found in fruits, glucose is most often used as the major source of energy for cellular activities.
Disaccharides
Disaccharides are carbohydrate dimers. These dimers are formed from two monomers by dehydration synthesis. Any two monosaccharides can form a disaccharide. For example, maltose is formed by the dehydration synthesis of two glucose molecules. Sucrose, common table sugar, comes from the linkage of one molecule of glucose and one of fructose.
Polysaccharides
Polysaccharides can consist of as few as three and as many as several thousand monosaccharides. Depending on their structure and the monosaccharides they contain, polysaccharides can function as a means of storing excess energy or provide structural support.
When cells ingest more carbohydrates than they need for fuel, they link the sugars together to form polysaccharides. The structure of these polysaccharides is different in plants and animals: in plants, polysaccharides take the form of starch, whereas in animals, they are linked in a structure called glycogen.
Polysaccharides can also have structural roles in plants and animals. Cellulose, which forms the cell walls of plant cells, is a structural polysaccharide. In animals, the polysaccharide chitin forms the hard outer armor of insects, crabs, spiders, and other arthropods. Many fungi also use chitin as a structural carbohydrate.
Proteins
More than half of the organic compounds in cells are proteins, which play an important function in almost every cellular process. Proteins, for example, provide structural support to the cell in the cytoskeleton and make up many of the hormones that send messages around the body. Enzymes, which regulate chemical reactions in the cell, are also proteins.
Amino Acids
Proteins are made up of monomers called amino acids. The names of many, but not all, amino acids end in -ine: methionine, lysine, serine, etc. Each amino acid consists of a central carbon atom attached to a set of three designated groups: an atom of hydrogen (–H), an amino group (–NH2), and a carboxyl group (–COOH). The final group, designated (–R) in the diagram below, varies between different amino acids.
It is possible to make an infinite number of amino acids by attaching different compounds to the R position of the central carbon. However, only 20 types of R groups exist in nature, so there are only 20 naturally occurring amino acids.
Polypeptides
All proteins are made of chains of some or all of these 20 amino acids. The bond formed between two amino acids by dehydration synthesis is known as a peptide bond.
A particular protein has a specific sequence of amino acids, which is known as its primary structure. Every protein also winds, coils, and folds in three-dimensional space in specific and predetermined ways, taking on a unique secondary (initial winding and coiling) and tertiary structure (overall folding). In harsh conditions, such as high temperature or extreme pH, proteins can lose their normal tertiary shape and cease to function properly. When a protein unfolds in harsh conditions, it has been “denatured.”
Lipids
Lipids are carbon compounds that do not dissolve in water. They are distinguished from other macromolecules by characteristic hydrocarbon chains—long strings of carbon molecules with hydrogens attached. Such chains do not dissolve well in water because they are nonpolar.
Triglycerides
Triglycerides consist of three long hydrocarbon chains known as fatty acids attached to each other by a molecule called glycerol.
Because they include three fatty acids, fats and oils are also known as triglycerides. As you might expect by this point, glycerol and each fatty acid chain are joined to each other by dehydration synthesis.
Some fats are saturated, while others are unsaturated. These terms refer to the presence or absence of double bonds in the fatty acids of fats. Saturated fats have no double bonds, whereas unsaturated fats contain one or more such bonds. In general, plant fats are unsaturated and animal fats are saturated. Saturated fats are generally solid at room temperature, while unsaturated fats are typically liquid.
Phospholipids
Phospholipids, which are important components of cell membranes, consist of a glycerol molecule attached to two fatty acid chains and one phosphate group (PO4–2):
Like all fats, the hydrocarbon tails of phospholipids do not dissolve in water. However, phosphate groups do dissolve in water because they are polar. The different solubilities of the two ends of phospholipid molecules allow them to form the bilayers that make up the cell membrane.
Steroids
Steroids are the primary structure in hormones, substances that play important signaling roles in the body. Structurally, steroids are made up of four fused carbon rings attached to a hydrocarbon chain.
The linked rings indicate that each carbon atom is attached to other carbon atoms that form multiple loops. Cholesterol, the steroid in the image above, is the central steroid from which other steroids, such as the sex hormones, are synthesized. Cholesterol is only found in animal cells.
Nucleic Acids
Cells use a class of compounds called nucleic acids to store and use hereditary information. Individual nucleic acid monomers, known as nucleotides, consist of three main units: a nitrogenous base (a compound made with nitrogen), a phosphate group, and a sugar:
There are two main types of nucleotides, differentiated by their sugars: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). DNA nucleotides have one less oxygen than RNA nucleotides. The “deoxy” in deoxyribonucleic acid refers to the missing oxygen molecule. In terms of function, DNA molecules store genetic information for the cell, while RNA molecules carry genetic messages from the DNA in the nucleus to the cytoplasm for use in protein synthesis and other processes.
Within both DNA and RNA, there are further subdivisions of nucleotides by nitrogenous bases. For DNA, there are four kinds of nitrogenous bases:
- adenine (A)
- guanine (G)
- cytosine (C)
- thymine (T)
The nitrogenous base of a nucleotide provides it with its chemical identity, so the nucleotides are called by the name of their nitrogenous base. RNA also has four nitrogenous bases. Three—adenine, guanine, and cytosine—are identical to those found in DNA. The fourth, uracil, replaces thymine.
DNA and RNA
In 1953, James Watson and Francis Crick published the discovery of the three-dimensional structure of DNA. Watson and Crick hypothesized that DNA nucleotides are organized into a polymer that looks like a ladder twisted into a coil. They called this structure the double helix.
Two separate DNA polymers make up each side of the ladder. The sugar and phosphate molecules of the DNA form the vertical supports, while the nitrogenous bases stick out to form the rungs. The rungs attach to each other by hydrogen bonding.
The nitrogen bases attach to each other according to two simple rules: adenine (A) pairs with thymine (T), and guanine (G) pairs with cytosine (C). The exclusivity of the attachments between nitrogen bases is known as base pairing.
The rules of base pairing are frequently tested on the SAT II Biology. A test question might ask, “What is the complementary DNA strand to ‘CAT’?” Following the rules of DNA base pairing, you can deduce that the answer is “CAT.” (“DOG” is the wrong answer, smart guy.)
RNA Structure
Unlike the double-stranded DNA, RNA is single stranded. It looks like a ladder cut down the middle. As you will see when we discuss protein synthesis in the chapter on Cell Processes, this structure of RNA is very important to its functions as a messenger from the DNA in the nucleus to the cytoplasm.
|
|
DNA |
RNA |
|
Bases |
Adenine, guanine, cytosine, thymine |
Adenine, guanine, cytosine, uracil |
|
Structure |
Double helix |
Single helix |
|
Function |
Stores genetic material and passes it from generation to generation |
Carries messages from the nucleus to the cytoplasm |
Summary of the Molecules of Life
|
|
Proteins |
Lipids |
Nucleic Acids |
Carbohydrates |
|
Function |
Structure, signaling, catalysis |
Energy storage, signaling, membrane constituents |
Store genetic material |
Energy source, energy storage, structural |
|
Monomer |
Amino acid |
|
Nucleotide |
Monosaccharide |
|
Polymer |
Polypeptide, protein |
|
RNA, DNA |
Polysaccharide |
|
Example |
Insulin, transcriptase (an enzyme) |
Corn oil |
A chromosome |
Glucose |
Enzymes
Some chemical reactions simply happen when the two reactants come into contact. For example, you may be familiar with the bubbly “volcano” that forms when baking soda and vinegar are placed together in a glass. This reaction is spontaneous because it does not require outside energy to force it to occur.
Most reactions, however, require energy. For example, the chemical reactions that produce a cake do not take place when baking soda, flour, and the other ingredients of a cake are simply left in a pan on the kitchen counter. Heat is required to break the existing chemical bonds in the ingredients so that they can undergo chemical reactions and combine with each other in new ways.
In the laboratory, chemists use heat to create the activation energy needed to get nonspontaneous reactions started. Animals, however, can’t rely on internal Bunsen burners to get their chemical reactions cooking. In order to perform chemical reactions at low temperatures, the body uses special proteins called enzymes, which lower the activation energy necessary for chemical reactions to achievable levels. Enzymes lower the activation energy by interacting with the substrates, the primary molecules or compounds involved in the reaction. If you think of the activation energy needed for a chemical reaction as a mountain that the reactants have to climb, think of an enzyme as opening up a tunnel through the mountain. Less energy is required to go through the tunnel than to climb all the way up the mountain.
Enzymes are not themselves altered when they help reactions along. Consequently, a single enzyme can be used repeatedly in many reactions. Because enzymes can be used over and over again and because they can act very quickly, a relatively small amount of enzyme is needed to facilitate reactions involving relatively large amounts of material.
Each enzyme is designed to fit only the substrates in the reaction that the enzyme is meant to control. The one-to-one correspondence between enzyme and substrate is referred to as specificity. An analogy to a lock and key is useful for understanding the specificity of enzymes. Each enzyme can be thought of as a lock that can interact only with the appropriate key, or substrate. The region of the enzyme that interacts with the substrate is known as the active site.
Enzymes help form bonds by holding two substrates near each other in the active site. Compounds can form bonds with each other more easily when they are adjacent than when they are floating around the cell randomly.
Often, enzymes are named for their substrate. The name of the enzyme is the name of the starting material followed by the “-ase.” For example, maltase is an enzyme that breaks down maltose, a common sugar. (Be careful not to confuse sugars, which end in “-ose,” with enzymes, which end in “-ase.”)
Factors Affecting Enzymes
Like all proteins, enzymes have a unique three-dimensional structure that changes under unusual environmental conditions. Enzymes do not function well when their structure is altered.
Temperature and pH
Depending on where it is normally located in the body, an enzyme will have different temperature and pH values at which its structure is most stable. As conditions deviate from this point, the enzyme’s ability to help along reactions decreases.
Most enzymes work best near a pH of 7, but some enzymes operate most effectively in a particularly acidic environment, such as the stomach; a neutral environment impairs their function. Likewise, the enzymes of creatures that live at high temperatures, such as bacteria that live in hot springs, do not function properly at human body temperature.
Cofactors and Inhibitors
In order to control enzyme activity more precisely, the body has developed a number of compounds that turn enzymes on or off and make them work faster or slower. Sometimes these compounds attach to the active site along with the substrate, and sometimes they bind to another site on the enzyme. Activators of enzymes are known as cofactors or coenzymes. Many vitamins are coenzymes. Molecules that prevent enzymes from functioning properly are known as inhibitors.
