WATER AND ORGANIC MOLECULES

1. Structure of Water

It can be quite correctly argued that life exists on Earth because of the abundant liquid water. Other planets have water, but they either have it as a gas (Venus) or ice (Mars). This relationship is shown in Figure 1. Recent studies of Mars reveal the presence sometime in the past of running fluid, possibly water. The chemical nature of water is thus one we must examine as it permeates living systems: water is a universal solvent, and can be too much of a good thing for some cells to deal with.

Figure 1. Water can exist in all three states of matter on Earth, while only in one state on our two nearest neighboring planets. 

Water is polar covalently bonded within the molecule. This unequal sharing of the electrons results in a slightly positive and a slightly negative side of the molecule. Other molecules, such as Ethane, are nonpolar, having neither a positive nor a negative side, as shown in Figure 2.

Figure 2. The difference between a polar (water) and nonpolar (ethane) molecule is due to the unequal sharing of electrons within the polar molecule. Nonpolar molecules have electrons equally shared within their covalent bonds. 

These link up by the hydrogen bond discussed earlier. Consequently, water has a great interconnectivity of individual molecules, which is caused by the individually weak hydrogen bonds, shown in Figure 3, that can be quite strong when taken by the billions.

Figure 3. Formation of a hydrogen bond between the hydrogen side of one water molecule and the oxygen side of another water molecule.

Water has been referred to as the universal solvent. Living things are composed of atoms and molecules within aqueous solutions (solutions that have materials dissolved in water). Solutions are uniform mixtures of the molecules of two or more substances. The solvent is usually the substance present in the greatest amount (and is usually also a liquid). The substances of lesser amounts are the solutes.

The solubility of many molecules is determined by their molecular structure. You are familiar with the phrase "mixing like oil and water." The biochemical basis for this phrase is that the organic macromolecules known as lipids (of which fats are an important, although often troublesome, group) have areas that lack polar covalent bonds. The polar covalently bonded water molecules act to exclude nonpolar molecules, causing the fats to clump together. The structure of many molecules can greatly influence their solubility. Sugars, such as glucose, have many hydroxyl (OH) groups, which tend to increase the solubility of the molecule. This aspect of water is illustrated in Figure 4.

 Figure 4. Dissolution of an ionically bonded compound, sodium chloride, by water molecules. 

used with permission.

Water tends to disassociate into H⁺ and OH^- ions. In this disassociation, the oxygen retains the electrons and only one of the hydrogens, becoming a negatively charged ion known as hydroxide. Pure water has the same number (or concentration) of H⁺ as OH^- ions. Acidic solutions have more H⁺ ions than OH^- ions. Basic solutions have the opposite.The pH of several common solutions is shown in Figure 5. An acid causes an increase in the numbers of H⁺ ions and a base causes an increase in the numbers of OH^- ions.

Figure 5. pH of some common items. 

The pH scale is a logarithmic Figure 5. pH of some common items. scale representing the concentration of H⁺ ions in a solution. Remember that as the H⁺concentration increases the OH^- concentration decreases and vice versa . If we have a solution with one in every ten molecules being H⁺, we refer to the concentration of H⁺ ions as 1/10. Remember from algebra that we can write a fraction as a negative exponent, thus 1/10 becomes 10^-1. Conversely 1/100 becomes 10^-2 , 1/1000 becomes 10^-3, etc. Logarithms are exponents to which a number (usually 10) has been raised. For example log 10 (pronounced "the log of 10") = 1 (since 10 may be written as 10¹). The log 1/10 (or 10^-1) = -1. pH, a measure of the concentration of H⁺ ions, is the negative log of the H⁺ ion concentration. If the pH of water is 7, then the concentration of H⁺ ions is 10^-7, or 1/10,000,000. In the case of strong acids, such as hydrochloric acid (HCl), an acid secreted by the lining of your stomach, [H⁺] (the concentration of H⁺ ions, written in a chemical shorthand) is 10^-1; therefore the pH is 1.

2. Organic molecules

Organic molecules are those that: 1) formed by the actions of living things; and/or 2) have a carbon backbone. Methane (CH₄) is an example of this. If we remove the H from one of the methane units below, and begin linking them up, while removing other H units, we begin to form an organic molecule. (NOTE: Not all methane is organically derived, methane is a major component of the atmosphere of Jupiter, which we think is devoid of life). When two methanes are combined, the resultant molecule is Ethane, which has a chemical formula C₂H₆. Molecules made up of H and C are known as hydrocarbons. The formulas and structural representations of several simple organic molecules are shown in Figure 6.

Figure 6. Types of hydrocarbon compounds and their structure. 

Scientists eventually realized that specific chemical properties were a result of the presence of particular functional groups. Functional groups are clusters of atoms with characteristic structure and functions. Polar molecules (with +/- charges) are attracted to water molecules and are hydrophilic. Nonpolar molecules are repelled by water and do not dissolve in water; are hydrophobic. Hydrocarbon is hydrophobic except when it has an attached ionized functional group such as carboxyl (acid) (COOH), then molecule is hydrophilic. Since cells are 70-90% water, the degree to which organic molecules interact with water affects their function. One of the most common groups is the -OH (hydroxyl) group. Its presence will enable a molecule to be water soluble. Isomers are molecules with identical molecular formulas but differ in arrangement of their atoms (e.g., glyceraldehyde and dihydroxyacetone). Selected functional groups and related data are shown in Figure 7.

Figure 7. Functional groups in organic molecules. 

Carbon has four electrons in outer shell, and can bond with up to four other atoms (usually H, O, N, or another C). Since carbon can make covalent bonds with another carbon atom, carbon chains and rings that serve as the backbones of organic molecules are possible.

Chemical bonds store energy. The C-C covalent bond has 83.1 Kcal (kilocalories) per mole, while the C=C double covalent bond has 147 Kcal/mole. Energy is in two forms: kinetic, or energy in use/motion; and potential, or energy at rest or in storage. Chemical bonds are potential energy, until they are converted into another form of energy, kinetic energy (according to the two laws of thermodynamics).

Each organic molecule group has small molecules (monomers) that are linked to form a larger organic molecule (macromolecule). Monomers can be jouined together to form polymers that are the large macromolecules made of three to millions of monomer subunits.

Macromolecules are constructed by covalently bonding monomers by condensation reactions where water is removed from functional groups on the monomers. Cellular enzymes carry out condensation (and the reversal of the reaction, hydrolysis of polymers). Condensation involves a dehydration synthesis because a water is removed (dehydration) and a bond is made (synthesis). When two monomers join, a hydroxyl (OH) group is removed from one monomer and a hydrogen (H) is removed from the other. This produces the water given off during a condensation reaction. Hydrolysis (hydration) reactions break down polymers in reverse of condensation; a hydroxyl (OH) group from water attaches to one monomer and hydrogen (H) attaches to the other.

There are four classes of macromolecules (polysaccharides, triglycerides, polypeptides, nucleic acids). These classes perform a variety of functions in cells.

2.1 Carbohydrates have the general formula [CH₂O]_n where n is a number between 3 and 6. Note the different CH₂O units in Figure 8. Carbohydrates function in short-term energy storage (such as sugar); as intermediate-term energy storage (starch for plants and glycogen for animals); and as structural components in cells (cellulose in the cell walls of plants and many protists), and chitin in the exoskeleton of insects and other arthropods.

Sugars are structurally the simplest carbohydrates. They are the structural unit which makes up the other types of carbohydrates. Monosaccharides are single (mono=one) sugars. Important monosaccharides include ribose (C₅H₁₀O₅), glucose (C₆H₁₂O₆), and fructose (same formula but different structure than glucose).

Figure 8. The chain (left) and ring (center and right) method of representing carbohydrates. We classify monosaccharides by the number of carbon atoms and the types of functional groups present in the sugar. For example, glucose and fructose, illustrated in Figure 9, have the same chemical formula (C₆H₁₂O₆), but a different structure: glucose having an aldehyde (internal hydroxyl shown as: -OH) and fructose having a keto group (internal double-bond O, shown as: =O). This functional group difference, as small as it seems, accounts for the greater sweetness of fructose as compared to glucose.

Figure 9. Models of glucose and fructose.

In an aqueous solution, glucose tends to have two structures, a (alpha) and b (beta), with an intermediate straight-chain form (shown in Figure 10). The a form and b form differ in the location of one -OH group, as shown in Figure 9. Glucose is a common hexose, six carbon sugar, in plants. The products of photosynthesis are assembled to form glucose. Energy from sunlight is converted into and stored as C-C covalent bond energy. This energy is released in living organisms in such a way that not enough heat is generated at once to incinerate the organisms. One mole of glucose yields 673 Kcal of energy. (A calorie is the amount of heat needed to raise one gram of water one degree C. A Kcal has 1000 times as much energy as a cal.). Glucose is also the form of sugar measured in the human bloodstream.

Figure 10. D-Glucose in various views (stick and space-filling). 

Disaccharides are formed when two monosaccharides are chemically bonded together. Sucrose, a common plant disaccharide is composed of the monosaccharides glucose and fructose. Lactose, milk sugar, is a disaccharide composed of glucose and the monosaccharide galactose. The maltose that flavors a malted milkshake (and other items) is also a disaccharide made of two glose molecules bonded together as shown in Figure 11.

Figure 11. Formation of a disaccharide (top) by condensation and structure of two common disaccharides. 

Polysaccharides are large molecules composed of individual monosaccharide units. A common plant polysaccharide is starch (shown in Figure 12), which is made up of many glucoses (in a polypeptide these are referred to as glucans). Two forms of polysaccharide, amylose and amylopectin makeup what we commonly call starch. The formation of the ester bond by condensation (the removal of water from a molecule) allows the linking of monosaccharides into disaccharides and polysaccharides. Glycogen (see Figure 12) is an animal storage product that accumulates in the vertebrate liver.

Figure 12. Images of starch (top), glycogen (middle), and cellulose (bottom). 

Cellulose, illustrated in Figure 13 and 14, is a polysaccharide found in plant cell walls. Cellulose forms the fibrous part of the plant cell wall. In terms of human diets, cellulose is indigestible, and thus forms an important, easily obtained part of dietary fiber. As compared to starch and glycogen, which are each made up of mixtures of a and b glucoses, cellulose (and the animal structural polysaccharide chitin) are made up of only b glucoses. The three-dimensional structure of these polysaccharides is thus constrained into straight microfibrils by the uniform nature of the glucoses, which resist the actions ofenzymes (such as amylase) that breakdown storage polysaccharides (such a starch).

Figure 13. Structure of cellulose as it occurs in a plant cell wall. 

Figure 14. Cellulose Fibers from Print Paper (SEM x1,080). 

2.2 Lipids are involved mainly with long-term energy storage. They are generally insoluble in polar substances such as water. Secondary functions of lipids include structural components (as in the case of phospholipids that are the major building block in cell membranes) and "messengers" (hormones) that play roles in communications within and between cells. Lipids are composed of three fatty acids (usually) covalently bonded to a 3-carbon glycerol. The fatty acids are composed of CH₂ units, and are hydrophobic/not water soluble. Some examples of fatty acids are shown in Figure 15.

Fatty acids can be saturated (meaning they have as many hydrogens bonded to their carbons as possible) or unsaturated (with one or more double bonds connecting their carbons, hence fewer hydrogens). A fat is solid at room temperature, while an oil is a liquid under the same conditions. The fatty acids in oils are mostly unsaturated, while those in fats are mostly saturated.

Figure 15. Saturated (top and middle) and unsaturated (bottom) fatty acids. The term staurated refers to the "saturation" of the molecule by hydrogen atoms. The presence of a double C=C covalent bond reduces the number of hydrogens that can bond to the carbon chain, hence the application of therm "unsaturated". 

Fats and oils function in long-term energy storage. Animals convert excess sugars (beyond their glycogen storage capacities) into fats. Most plants store excess sugars as starch, although some seeds and fruits have energy stored as oils (e.g. corn oil, peanut oil, palm oil, canola oil, and sunflower oil). Fats yield 9.3 Kcal/gm, while carbohydrates yield 3.79 Kcal/gm. Fats thus store six times as much energy as glycogen.

Diets are attempts to reduce the amount of fats present in specialized cells known as adipose cells that accumulate in certain areas of the human body. By restricting the intakes of carbohydrates and fats, the body is forced to draw on its own stores to makeup the energy debt. The body responds to this by lowering its metabolic rate, often resulting in a drop of "energy level." Successful diets usually involve three things: decreasing the amounts of carbohydrates and fats; exercise; and behavior modification.

Another use of fats is as insulators and cushions. The human body naturally accumulates some fats in the "posterior" area. Subdermal ("under the skin") fat plays a role in insulation.

Phospholipids and glycolipids are important structural components of cell membranes. Phospholipids, shown in Figure 16, are modified so that a phosphate group (PO₄^-) is added to one of the fatty acids. The addition of this group makes a polar "head" and two nonpolar "tails". Waxes are an important structural component for many organisms, such as the cuticle, a waxy layer covering the leaves and stems of many land plants; and protective coverings on skin and fur of animals.

Figure 16. Structure of a phospholipid, space-filling model (left) and chain model (right). 

Cholesterol and steroids: Most mention of these two types of lipids in the news is usually negative. Cholesterol, illustrated in Figure 17, has many biological uses, it occurs in cell membranes, and its forms the sheath of some types of nerve cells. However, excess cholesterol in the blood has been linked to atherosclerosis, hardening of the arteries. Recent studies suggest a link between arterial plaque deposits of cholesterol, antibodies to the pneumonia-causing form of Chlamydia, and heart attacks. The plaque increases blood pressure, much the way blockages in plumbing cause burst pipes in old houses.

Figure 17. Structure of four steroids. Image from Purves et al.

2.3 Proteins are very important in biological systems as control and structural elements. Control functions of proteins are carried out by enzymes and proteinaceous hormones. Enzymes are chemicals that act as organic catalysts (a catalyst is a chemical that promotes but is not changed by a chemical reaction). Click here for an illustrated page about enzymes. Structural proteins function in the cell membrane, muscle tissue, etc.

The building block of any protein is the amino acid, which has an amino end (NH₂) and a carboxyl end (COOH). The struucture of a generalized aminio acid as well as the specific structures of the 20 biological amino acids are shown in Figure 18 and 19 respectively. The R indicates the variable component (R-group) of each amino acid. Alanine and Valine, for example, are both nonpolar amino acids, but they differ, as do all amino acids, by the composition of their R-groups. All living things (and even viruses) use various combinations of the same twenty amino acids. A very powerful bit of evidence for the phylogenetic connection of all living things.

Figure 18. Structure of an amino acid.

Figure 19. Structures in the R-groups of the twenty amino acids found in all living things.

Amino acids are linked together by joining the amino end of one molecule to the carboxyl end of another. Removal of water allows formation of a type of covalent bond known as a peptide bond. This process is illustrated in Figure 20.

Figure 20. Formation of a peptide bond between two amino acids by the condensation (dehydration) of the amino end of one amino acid and the acid end of the other amino acid. 

Amino acids are linked together into a polypeptide, the primary structure in the organization of proteins. The primary structure of a protein is the sequence of amino acids, which is directly related to the sequence of information in the RNA molecule, which in turn is a copy of the information in the DNA molecule. Changes in the primary structure can alter the proper functioning of the protein. Protein function is usually tied to their three-dimensional structure. The primary structure is the sequence of amino acids in a polypeptide..

The secondary structure is the tendency of the polypeptide to coil or pleat due to H-bonding between R-groups. The tertiary structure is controlled by bonding (or in some cases repulsion) between R-groups. Tertiary structure of an HIV protein and its similarity to gamma interferon are shown in Figure 22. Many proteins, such as hemoglobin, are formed from one or more polypeptides. Such structure is termed quaternary structure. Structural proteins, such as collagen, have regular repeated primary structures. Like the structural carbohydrates, the components determine the final shape and ultimately function. Collagens have a variety of functions in living things, such as the tendons, hide, and corneas of a cow. Keratin is another structural protein. It is found in fingernails, feathers, hair, and rhinoceros horns. Microtubules, important in cell division and structures of flagella and cilia (among other things), are composed of globular structural proteins.

Figure 21. HIV p17 protein and similarities of its structure to gamma interferon. 

2.4 Nucleic acids are polymers composed of monomer units known as nucleotides. There are a very few different types of nucleotides. The main functions of nucleotides are information storage (DNA), protein synthesis (RNA), and energy transfers (ATP and NAD). Nucleotides, shown in Figure 22, consist of a sugar, a nitrogenous base, and a phosphate. The sugars are either ribose or deoxyribose. They differ by the lack of one oxygen in deoxyribose. Both are pentoses usually in a ring form. There are five nitrogenous bases. Purines (Adenine and Guanine) are double-ring structures, while pyrimidines (Cytosine, Thymine and Uracil) are single-ringed.

Figure 22. Structure of two types of nucleotide. 

Deoxyribonucleic acid (better known as DNA) is the physical carrier of inheritance for 99% of living organisms. The bases in DNA are C, G, A and T, as shown in Figure 23. We will learn more about the DNA structure and function later in the course (click here for a quick look [actually take all the time you want!] ;)).

Figure 23. Structure of a segment of a DNA double helix. 

DNA functions in information storage. Figure 23. Structure of a segment of a DNA double helix. The English alphabet has 26 letters that can be variously combined to form over 50,000 words. DNA has four letters (C, G, A, and T, the nitrogenous bases) that code for twenty words (the twenty amino acids found in all living things) that can make an infinite variety of sentences (polypeptides). Changes in the sequences of these basesinformation can alter the meaning of a sentence.

For example take the sentence: I saw Elvis. This implies certain knowledge (that I've been out in the sun too long without a hat, etc.).

If we alter the sentence by inverting the middle word, we get: I was Elvis (thank you, thank you very much). Now we have greatly altered the information.

A third alteration will change the meaning: I was Levis. Clearly the original sentence's meaning is now greatly changed.

Changes in DNA information will be translated into changes in the primary structure of a polypeptide, and from there to thesecondary and tertiary structures. A mutation is any change in the DNA base sequence. Most mutations are harmful, few are neutral, and a very few are beneficial and contribute the organism's reproductive success. Mutations are the wellspring of variation, variation is central to Darwin and Wallace's theory of evolution by natural selection.

Ribonucleic acid (RNA), shown in Figure 24 was discovered after DNA. DNA, with exceptions in chloroplasts and mitochondria, is restricted to the nucleus (in eukaryotes, the nucleoid region in prokaryotes). RNA occurs in the nucleus as well as in the cytoplasm (also remember that it occurs as part of the ribosomes that line the rough endoplasmic reticulum). There are three types of RNA:

Messenger RNA (mRNA) is the blueprint for construction of a protein.

Ribosomal RNA (rRNA) is the construction site where the protein is made.

Transfer RNA (tRNA) is the truck delivering the proper amino acid to the site at the right time.

Details of RNA and its role in protein synthesis are available by clicking here.

Figure 24. Structure of the RNA molecule. 

Adenosine triphosphate, better known as ATP (Figure 25), the energy currency or coin of the cell, transfers energy from chemical bonds to endergonic (energy absorbing) reactions within the cell. Structurally, ATP consists of the adenine nucleotide (ribose sugar, adenine base, and phosphate group, PO₄^-2) plus two other phosphate groups.

Energy is stored in the covalent bonds between phosphates, with the greatest amount of energy (approximately 7 kcal/mole) in the bond between the second and third phosphate groups. This covalent bond is known as a pyrophosphate bond.

Figure 25. A cartoon and space-filling view of ATP. 

3. Learning Objectives 

• Dissolved substances are called solutes; a fluid in which one or more substances can dissolve is called a solvent. Describe several solutions that you use everyday in terms of what is the solvent and what is the solute.
• Define acid and base and be able to cite an example of each.
• The concentration of free hydrogen ions in solutions is measured by the pH scale..
• Nearly all large biological molecules have theor organization influenced by interactions with water. Describe this interaction as it exists with carbohydrate molecules.
• Be able to list the three most abundant elements in living things.
• Each carbon atom can form as many as four covalent bonds with other carbon atoms as well as with other elements. Be able to explain why this is so.
• Be able to list the four main groups of organic molecules and their functions in living things.
• Enzymes are a special class of proteins that speed up chemical reactions in cells. What about the structure of proteins allows for the reaction specificity that occurs with most enzymes.
• Condensation reactions result in the formation of covalent bonds between small molecules to form larger organic molecules. Be able to describe a condensation reaction in words.
• Be able to describe what occurs during a hydrolysis reaction.
• Be able to define carbohydrates and list their functions.
• The simplest carbohydrates are sugar monomers, the monosaccharides. Be able to give examples and their functions.
• A polysaccharide is a straight or branched chain of hundreds or thousands of sugar monomers, of the same or different kinds. Be able to give common examples and their functions.
• Be able to define lipids and to list their functions.
• Distinguish betwen a saturated fat and an unsaturated fat. Why is such a distinction a life and death matter for many people?
• A phospholipid has two fatty acid tails attached to a glycerol backbone. What is the importance of these molecules.
• Define steroids and describe their chemical structure. Be able to discuss the importance of the steroids known as cholesterol and hormones.
• Be able to describe proteins and cite their general functions.
• Be prepared to make a sketch and name the three parts of every amino acid.
• Describe the complex structure of a protein through its primary, secondary, tertiary, and quaternary structure. How does this relate to the three-dimensional structure of proteins?
• Describe the three parts of every nucleotide..
• Be able to give the general functions of DNA and RNA molecules.

Questions 

1.   The chemical reaction where water is removed during the formation of a covalent bond linking two monomers is known as ___. a) dehydration; b) hydrolysis; c) photosynthesis; d) protein synthesis

2.   The monomer that makes up polysaccharides is ____. a) amino acids; b) glucose; c) fatty acids; d) nucleotides; e) glycerol

3.   Proteins are composed of which of these monomers? a) amino acids; b) glucose; c) fatty acids; d) nucleotides; e) glycerol

4.   Which of these is not a function of lipids? a) long term energy storage; b) structures in cells; c) hormones; d) enzymes; e) sex hormones

5.   All living things use the same ___ amino acids. a) 4; b) 20; c) 100; d) 64

6.   The sequence of ___ bases determines the ___ structure of a protein. a) RNA, secondary; b) DNA, quaternary; c) DNA, primary; d) RNA, primary

7.   Which of these is not a nucleotide base found in DNA? a) uracil; b) adenine; c) guanine; d) thymine; e) cytosine

8.   Which of these carbohydrates constitutes the bulk of dietary fiber? a) starch; b) cellulose; c) glucose; d) fructose; e) chitin

9.   A diet high in _____ is considered unhealthy, since this type of material is largely found in animal tissues. a) saturated fats; b) testosterone; c) unsaturated fats; d) plant oils

10.                The form of RNA that delivers information from DNA to be used in making a protein is ____. a) messenger RNA; b) ribosomal RNA; c) transfer RNA; d) heterogeneous nuclear RNA

11.                The energy locked inside an organic molecule is most readily accessible in a ___ molecule. a) fat; b) DNA; c) glucose; d) chitin; e) enzyme

12.                Phospholipids are important components in ____. a) cell walls; b) cytoplasm; c) DNA; d) cell membranes; e) cholesterol