Introduction and Goals
Life is composed of a myriad of biomolecules (molecules found in living organisms). With all of life's diversity, however, there is a ubiquitous presence of carbon, oxygen, and hydrogen. Carbon plays a particularly important role in these molecules by virtue of its unique chemical properties. In this tutorial you will learn why some biomolecules readily interact with water, and why some do not. We will examine how relatively simple subunits, known as monomers, can be hooked together by chemical bonds to make much larger complex macromolecules, known as polymers.
By the end of this tutorial you should be able to:
- describe the structure of a water molecule, and its interactions with other water molecules
- explain the basic properties of water, and the importance of these properties to organisms
- explain why biological macromolecules are carbon-based
- define and give examples of anabolic and catabolic reactions
- describe the basic structure of the monomer(s) and polymer(s), and the functions of each of the major groups of molecules in cells and organisms
The Properties of Water
Water (H2O) is fundamental to the existence of life as we know it. Indeed, it is so familiar to us that we take its properties for granted. What makes water so important? What is the relationship between water and other biomolecules? In order to answer these questions we need to take a close look at water and at some of the properties of its electrons, which have a profound influence on its character.
As you probably learned in elementary school, a single molecule of water consists of two hydrogen atoms covalently bound to one oxygen atom. This arrangement does not sound very exciting; however, a closer examination of the bonds within the water molecule reveals something unique. Specifically, water is a polar molecule, meaning that it has different electrical properties on opposite ends; specifically, it has two partial positive charges in association with the two H-atoms, and two partial negative charges associated with the oxygen atom.
Figure 1. The polar nature of a water molecule and hydrogen bonds between water molecules. (Click to enlarge)
To understand these properties, you need to know that not all covalent bonds (those bonds that involve the sharing of electrons) are equal. Specifically, oxygen is highly electronegative and tends to pull electrons close to it when forming covalent bonds with hydrogen. This creates an unequal distribution around each O-H bond; therefore, the hydrogen has a partial positive charge (and conversely, the oxygen has a slightly negative character). Importantly, the partial negative charges on one water molecule can interact with the partial positive charges on another water molecule to form a hydrogen bond (as shown in Figure 1 with dotted lines). Hydrogen bonds contribute to many of the unique features of water.
More About Water
Figure 2. Surface tension of water. A stonefly stands on water. (Click to enlarge)
The state in which liquid water molecules are stuck together, via H-bonding, gives water a physical property termed cohesion. Due to cohesion, water has a high surface tension (resistance to disruption at the surface). This property is exploited by many insects (e.g., the stone fly in Figure 2) and some vertebrates (e.g., basilisk lizards), which can actually stand or run on water without breaking the surface and falling through.
Water is a repository for heat due to its high specific heat. This means that it takes a relatively large amount of energy to raise the temperature of water. Therefore, water absorbs (and stores) heat energy more efficiently than many other substances. Biologically, this is extremely important because large bodies of water tend to have relatively stable temperatures, whereas the air around them may fluctuate. The moderate temperatures in oceans and large lakes make them suitable year-round for an abundance of aquatic life. Water also has a relatively high heat of vaporization, therefore, water is relatively resistant to phase changes. (It takes a relatively large amount of energy to break all of the H-bonds in water to produce water vapor or steam.) This property allows some organisms to use water, in the form of sweat, to cool down.
Water expands during freezing (Figure 3). When water molecules slow down and ice forms (below freezing), the hydrogen bonds keep water molecules at a distance from each other in a characteristic, 3-dimensional crystal that is relatively spacious. The distinction between ice and liquid water is illustrated in this figure, which also depicts how this arrangement makes ice less dense than water, thereby allowing ice to float on water.
Figure 3. The structure of ice compared with the structure of water. (Click to enlarge)
Water is an excellent solvent, capable of dissolving many compounds. The polar character of water means that anything with a charge can dissolve in water. NaCl is table salt, and when added to water its sodium and chloride atoms disassociate. These ions have a charge. Both the positively charged sodium ions (Na+) and negatively charged chloride ions (Cl-) can readily bond to the polar water molecules and in doing so they dissolve. Compounds that dissolve readily in water are hydrophilic. Compounds that do not interact with water are hydrophobic.
There is an important class of molecules that have the unique ability to be both hydrophobic and hydrophilic, a property termed amphipathic. An amphipathic molecule has one end with some charge character, and the other end lacking charge. Phospholipid macromolecules (see Figure 8 below) are amphipathic. We will see the importance of these molecules in the discussion of phospholipids below.
In conclusion, water has many important properties that are important to life. The cells of terrestrial organisms (including ours) contain greater than 70% water, and most cells are surrounded by water. This means that a large percentage of biomolecules operate in an aqueous compartment. It should not surprise you to learn that water plays an important role in the functioning of biochemicals. In the next few sections you will learn about four classes of biomolecules and about how their unique characteristics (and synthesis) involve water.
Figure 4. Organic compounds contain carbon. (Click to enlarge)
The world is comprised of organic and inorganic compounds. Inorganic compounds include water and mineral rocks. An inorganic compound does not contain carbon (with the exception of CO2 and several other C-containing molecules which are classified as inorganic molecules). In contrast, organic compounds contain carbon and are prevalent in living systems. They provide us with colors, tastes, and odors, along with the abilities to perceive and respond to our environment. In other words, carbon compounds are essential to our existence. What is it about carbon that makes it so fundamental to life on Earth? Carbon has four electrons (a negatively charged part of an atom) in its outermost orbital. This valence of four allows each carbon atom to form stable associations with up to four other atoms, including other carbon atoms. Carbon can form single, double, or triple bonds. That is, it can share one, two, or three of its valence electrons with another atom. By convention, a single, double, or triple line is used to denote these different types of bonds. A single carbon atom bound to another carbon atom is the building block for a seemingly endless variety of chain- and ring-structured molecules. The two figures on this page represent a small portion of the thousands of organic compounds that exist.
In this tutorial we will address four classes of large organic compounds (macromolecules): carbohydrates, lipids, proteins, and nucleic acids. Note that three of these (carbohydrates, proteins, and nucleic acids) are actually formed through the synthesis of many similar or identical building blocks. These building blocks (monomers) are linked to form polymers. The general process of joining monomers to form a polymer is termed anabolism, which can involve many steps. Conversely, a polymer can be broken down into its monomers by catabolism, which also can involve multiple steps.
Figure 5. Organic compounds occur in a variety of configurations. (Click to enlarge)
Hydrolysis and Condensation
There are thousands of different types of biochemical reactions. Although they may involve the joining or breaking down of a myriad of molecules, most use the same basic chemical reaction. Anabolic reactions typically involve the joining of monomers by the removal of a water molecule. In this case a hydroxide (OH) is removed from one molecule and a hydrogen (H) is removed from the adjacent combining molecule. This type of reaction, termed condensation synthesis (or dehydration synthesis), is illustrated in the animation shown here. Select condensation, and hit play.
This animation also depicts a hydrolysis reaction (a type of catabolism whereby a polymer is broken down by the addition of water). Hit the "home" icon to return to the beginning; select condensation and hit play.
Carbohydrate biomolecules generally have a basic structural formula that is written as C(H2O)n. For example, glucose has the structural formula C6H12O6. The carbohydrates have many functions in cells. They can be used for energy storage (e.g., starch) and as structural molecules (e.g., cellulose). And as we will see, they also play a role in information storage in nucleic acids (organic compounds that make up RNA and DNA).
The basic monomeric units of carbohydrates are the simple sugars (monosaccharides). Monosaccharides include glucose (also known as dextrose), fructose, ribose, galactose, and ribulose. Note, the -ose suffix is used by chemists to describe all carbohydrates.
A disaccharide is a sugar formed by a condensation reaction between two monosaccharides. Condensation synthesis of maltose (glucose + glucose), a common disaccharide, is illustrated in the following animation. Other disaccharides include sucrose (glucose + fructose) and lactose (glucose + galactose); sucrose is common table sugar, and lactose is milk sugar.
This animation shows the formation of disaccharides
More complex forms of carbohydrates can be synthesized by cells via additional condensation reactions. Polysaccharide polymers can consist of up to several thousand monomers of simple sugars. The type of polysaccharide is determined by the number, type, and arrangement of its monomers. Starch is a polymer of glucose monomers. It is used by plants to store surplus sugar and when we and other animals eat a starchy plant (such as a potato) we use the starch for energy and nutrients. Animals store surplus sugar in their livers in the form of a molecule known as glycogen.
Cellulose, another polymer of glucose, is an important component of plant cell walls; it is also the most abundant polymer on the planet. Although humans cannot digest cellulose, it is a valuable part of our diet because this "fiber" helps to maintain a healthy digestive tract. Some animals, such as the crab shown here, and fungi use another polysaccharide, chitin, for structural purposes.
Figure 6. Exoskeleton made of chitin. (Click to enlarge) The exoskeletons of arthropods, like this fiddler crab, are made of the polysaccharide chitin.
Figure 7. Triacylglycerols. (Click to enlarge) Fats and oils have three fatty acid molecules (only one strand is shown here) and one glycerol molecule (not shown). Double bonds determine whether a fat is saturated or unsaturated.
Lipids are an assortment of molecules so diverse that it may seem odd to group them together. However, they do share one common trait; they are all (to some extent) hydrophobic. Also, in contrast to the other groups of macromolecules, the lipids are not polymers. The lipids main biological functions include energy storage (e.g., fats), main structural components of cell membranes (e.g., phospholipids and cholesterol), and hormones and other cell signaling molecules (e.g., estrogen and testosterone). The lipids include dietary fats (also known as triacylglycerols), phospholipids (which are an important component of cell membranes), and steroids (e.g., cholesterol, estrogen and testosterone).
Fats and oils are triacylglycerols, which are formed when three fatty acid molecules and one glycerol molecule join via condensation synthesis. This animation depicts the synthesis of a triacylglycerol molecule.
This animation shows synthesis of a fat:
Fats can be saturated or unsaturated. Saturated fats do not have double bonds in their hydrocarbon chains because their carbon is bound to two other carbons and two hydrogens. Unsaturated fats have double bonds along their lengths (monounsaturated = one double bond, polyunsaturated = more than one double bond). Saturated fats have straight chains that organize into more tightly packed arrangements. In contrast, unsaturated fats have kinks caused by the double bonds, which do not permit tight packing. Thus, saturated fats tend to be solids at room temperature, whereas unsaturated fats are usually liquid. A liquid unsaturated fat can be converted to a solid saturated fat by a process called hydrogenation (e.g., margarine).
Fats are used in energy storage, protection, and insulation. Aquatic and polar mammals counteract heat loss by having extra fat for insulation. Compare the Arctic polar bear and subtropical gazelle. Clearly, they don't have a similar need for extra insulation.
In contrast to the fats, phospholipids are amphipathic molecules that have only two fatty acids molecules, and a glycerol joined to a phosphate group. This figure depicts this arrangement of two hydrophobic "tails" attached to a hydrophilic "head" (the phosphate group is charged, allowing it to dissolve in water). This unique structure forms the basis for the phospholipid bilayer of cell membranes (a topic to be discussed in future tutorials).
Figure 8. Phospholipids. (Click to enlarge)
Phospholipids have two fatty acid molecules, and a glycerol molecule joined to a phosphate group.
Figure 9. Steroids. (Click to enlarge)
Steroids are four-fused ring structures. Cholesterol is a steroid.
Another group of lipids, the steroids, is characterized by a four-fused ring structure (Figure 9). The steroids include cholesterol, and certain hormones (e.g., estrogen and testosterone) produced from cholesterol. Cholesterol is an important component of cell membranes and the vertebrate animal sex hormones estrogen and testosterone are synthesized from cholesterol.
Proteins are polymers that are functionally and structurally diverse. The digestive enzymes that break apart your food are proteins. The pigment that affects skin color, melanin, is a protein. Silk is a protein. Proteins move your muscles, attack invading bacteria and viruses, and transport oxygen to all of the cells in your body. The main biological functions of proteins include structural and mechanical roles (e.g, actin and myosin in muscle cells), and their roles as enzymes (e.g., amylase – a digestive enzyme).
Figure 10. The general formula for amino acids. (Click to enlarge)
The basic monomer of proteins is the amino acid. The general structure of an amino acid is shown here. Note, this basic structure contains an "R" group that is variable in chemical composition. Typically there are twenty different R-groups, and hence the same number of commonly seen amino acids.
This figure depicts the chemical diversity of the twenty amino acids that make up proteins. Note the "R-group" can be classified as nonpolar, polar, or charged.
Figure 11. The twenty amino acids that make up proteins. (Click to enlarge)
The R-groups are found in the shaded boxes.
Polypeptides are a polymer (chain) of amino acids. Proteins consist of one or more polypeptide chains arranged in a specific conformation. The order of amino acids in a particular polypeptide chain is determined by the specific gene for that chain. In other words, every polypeptide chain has a corresponding gene.
The animation shown here illustrates the formation of a polypeptide. Do not simply think of proteins as linear strings of amino acids. In reality, they fold into a three-dimensional structure and take on complex shapes (basic protein structure is discussed in the case study below).
The nucleic acids include deoxyribonucleic acid (DNA) and ribonucleic acid(RNA). DNA and RNA work together to affect the synthesis of proteins. Nucleic acid molecules are polymers of nucleotides, which are simple structures that consist of a sugar, a phosphate, and a nitrogenous base. Nitrogenous bases are ringed structures consisting of nitrogen, carbon, and hydrogen (depicted at right).
Figure 12. The structure of nucleic acids. (Click to enlarge) DNA and RNA consist of a sugar, a phosphate group, and a nitrogenous base.
Figure 13. DNA nucleotide components.(Click to enlarge)
Specifically, RNA nucleotides have ribose as their sugar and any one of the following nitrogenous bases: adenine, guanine, cytosine, and uracil. DNA nucleotides have deoxyribose as their sugar and any one of the following nitrogenous bases: adenine, guanine, cytosine, and thymine (shown at left).
This figure illustrates how nucleotide monomers are joined to make a nucleic acid polymer; in this case a DNA double helix.
Figure 14. The structure of a DNA molecule. (Click to enlarge)
DNA usually exists as paired strands, with the two sides held together by hydrogen bonds between the nitrogenous bases (shown in more detail at right). Specifically, cytosine will bind to guanine, and thymine to adenine. However, RNA is typically a single-stranded molecule.The roles of DNA and RNA will be discussed in more detail in future tutorials.
Figure 15. Base pairing in a molecule of DNA. (Click to enlarge)
This tutorial focused on basic biochemistry. Many of life's chemical processes involve the synthesis of larger molecules from smaller building blocks, in an event that is generally termed anabolism. These larger molecules can then be broken down in a process that is termed catabolism. Later in the course we will examine some specific anabolic events and how they contribute to the life of a growing organism. We will also examine how catabolic events can be used to convert energy that is necessary to sustain life. To understand these biochemical events, it is important to know some basic chemistry.
Our bodies are comprised of over 70% water. All life on the planet depends on this molecule, and you should be aware of the polar character of this molecule and how polarity affects the ability of one water molecule to interact with another water molecule, as well as with other polar molecules. Water is an excellent solvent and is capable of dissolving a variety of polar molecules. A molecule that can readily interact with water is a hydrophilic molecule, and one that does not interact with water is a hydrophobic molecule. Not all molecules have a strictly hydrophilic/hydrophobic character; some have both and are termed amphipathic.
Carbon is a very important element for life. Due to its chemical versatility, it is found in thousands of compounds within living organisms. To understand biochemistry, you need to have a fundamental understanding of the major classes of molecules that are composed of carbon. Additionally, it is important to understand the relationship between these carbon-containing molecules and water.
Lipids are a class of carbon-containing molecules that have a hydrophobic character. They either totally lack any polar characteristics or their polar character is limited to a small area of the molecule. Be sure that you understand how the polar character of a molecule influences its ability to interact with water. Fats are lipids that are solid at room temperature and that do not readily interact with water. On the other hand, oils are lipids that are liquid at room and that do not readily interact with water. Phospholipids are a class of lipids that have amphipathic properties, and they are a major component of cellular membranes.
Carbohydrates are another class of carbon-bearing molecules, and they are used by the cell for energy storage and as structural molecules. Later in the course you will learn how energy is extracted from monosaccharides in the processes of glycolysis and cellular respiration. Carbohydrates are also found as polysaccharides, which are involved in energy storage and in building various cellular components.
Proteins are composed of amino acids (there are twenty naturally occurring amino acids), and these subunits are linked together (via peptide bonds) to form polypeptide chains. A protein may be comprised of a single polypeptide chain (which is encoded by a single gene), or it may be comprised of two or more polypeptides (each polypeptide chain may be encoded for by a separate gene). Proteins play a variety of roles within the living organism. They can catalyze various chemical reactions (catabolic and anabolic), and they can form structural elements. Additionally, some proteins can convert chemical energy into mechanical energy; such proteins are involved in various motor activities within organisms.
This tutorial used the following terms that you should be able to define:
Case Study for Carbon and Life
A recurring theme in biology is that structure is related to function. This theme is particularly important in understanding proteins. Humans have tens of thousands of different proteins and each has a specific structure and function. Despite the diversity of proteins, they are all constructed from the same 20 amino acids. Different proteins have different sequences of these 20 amino acids.
The sequence of amino acids in a protein is referred to as its primary structure. The secondary structure of a protein refers to regions of the molecule that are coiled or folded (α helices or β pleated sheets). Tertiary structure refers to the overall shape of the protein due to interactions between the side chains (R groups) of the amino acids. Some proteins are made of more than one polypeptide chain – the aggregation of these polypeptide chains refers to a protein’s quaternary structure. A change in a protein’s primary structure results in a change in the overall structure of the protein.
Sickle-cell is a genetic disease that results in the abnormal production of the protein hemoglobin which causes misshapen red blood cells. The abnormality is in the 6th position of the β subunit of the molecule. Normal hemoglobin has a glutamic acid while sickle-cell hemoglobin has a valine in the 6th position. The presence of the valine causes hemoglobin molecules to aggregate together into rod formations. These rods of hemoglobin are not effective at carrying oxygen. People with sickle-cell anemia suffer episodes of “sickle-cell crises” which are painful and, left untreated, can lead to death.
- Refer to Figure 11 in this tutorial and use your understanding of the chemical behavior of the R groups to predict what would happen if the glutamic acid in the 6th position of the β subunit was replaced with an aspartic acid (instead of valine). Would this cause more or less disruption to the function of the resulting hemoglobin?
Now that you have read this tutorial and worked through the case study, go to ANGEL and complete the tutorial quiz to test your understanding (the due dates for the tutorial quizzes are posted on ANGEL). Questions? Either send your instructor a message through ANGEL or attend a weekly review session (the times and places are posted on ANGEL).