Lesson 2: The Chemistry of Life (Printer Friendly Format)

All organisms are composed of biological macromolecules. These are carbon-based compounds, which means that they have a fundamental structure composed of carbon atoms. Why carbon? Because carbon has only four electrons in its outer shell, it can form covalent bonds with four other atoms. Thus, it is able to form very stable bonds with other carbon molecules, enabling the formation of long carbon chains. Figure 2.7 shows methane,CH₄, a simple carbon compound formed by these covalent bonds.

Biological macromolecules generally are polymers, (poly = many; mer = unit), formed by joining monomers, or single molecules, together in a long chain. They are formed by the process of polymerization. In this process, dehydration synthesis, or the removal of a water molecule, joins two monomers together (Figure 2.8). When cells produce polypeptides, chains of amino acids, during protein synthesis, the reaction that joins these amino acids together is a dehydration reaction (also called a condensation reaction).

Water molecules can be inserted between monomers to break down a polymer in a reaction called hydrolysis (Figure 2.8). This happens during digestion. For example, when you eat a cracker, enzymes in your mouth catalyze a chemical reaction, hydrolyzing the starch (a polymer) in the cracker and breaking it down into more simple sugars. This is why a cracker begins to taste sweet after you chew it.

There are four major classes of biological macromolecules (Figure 2.9). The carbohydrates have two primary functions, to provide energy for cells and to provide structure.

Proteins play many roles in a cell, from enzymes which catalyze chemical reactions such as the amylase secreted by your salivary glands, to providing structure, the role of the keratin in your skin. Some proteins, such as insulin, function as hormones.

Lipids also have a diversity of functions, including energy storage as well as forming the primary structure of cell membranes.

Nucleic acids are information storage molecules, and play a role in converting this information into polypeptides.

These biological macromolecules can be very large. For example, the chemical formula of bovine growth hormone is C₉₉₉H₁₅₂₉N₂₆₃O₂₉₉S₇!

Proteins have many diverse functions within organisms. See Table 3.4 in your textbook. Proteins are polymers of amino acids. Organisms use about 20 different amino acids to make proteins, and this means that the possible sequences of amino acids within proteins are almost infinite. There are structural proteins, such as the keratin that gives support to your skin or to a bird's feather.

Enzymes are proteins that catalyze chemical reactions within a cell, such as amylase which breaks starch into disaccharides and DNA polymerase which joins together DNA monomers. Some proteins transport substances across cell membranes, or through the body. For example, hemoglobin transports oxygen through your circulatory system.

There are even some proteins that function as hormones, including insulin, which regulates the level of glucose in your blood.

All proteins have the same basic structure. Amino acids are the monomers of proteins (Figure 2.12). They consist of a central carbon atom, which is bonded to a carboxyl group (COOH) at one end and an amino group (NHH) at the other. The carboxyl group allows the molecule to act as an acid, donating H+, while the amino group allows it to act like a base, accepting H+ ions.

The central carbon is covalently bonded to a side chain, the functional or “R group”. This R group is different for each of the 20 common amino acids and determines the property of the amino acids. R groups range from a single hydrogen atom to complex ring structures. Amino acids are joined together by dehydration synthesis to form a molecule called a polypeptide. When two amino acids are covalently bonded together, the bond is called a peptide bond, hence the name polypeptide (Figure 2.12).

Most proteins do not function as a simple linear polypeptide chain.[, which is their primary structure]  In order to perform a specific task, they must be folded into a specific shape (Figure 2.13). There are four levels of protein structure. The first level, their primary structure, is the sequence of the amino acids.

Figure 2.13. Levels of Protein Structure (1)
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Tertiary structure involves folding of the molecules across longer distances (Figure 2.14), often through disulfide bridges, which are bonds between two amino acids that contain a sulfur atom. These bridges occur in the proteins in hair. If you go the the hairdresser and get a permanent, the tertiary structure is denatured chemically. Sulfur atoms are released, resulting in the characteristic odor. The hair is then treated with other chemicals that reform the bonds when the hair is on rollers, giving it a different shape, curly versus straight.

Finally, quaternary structure is the association of multiple polypeptides (Figure 2.14). For example, the protein hemoglobin consists of four polypeptides joined together.

Lipids have a number of different functions within cells. They are energy storage molecules, they are a major component of the plasma membrane, and they also function as hormones. So, how can lipids carry out these different functions? They are not polymers in the sense that we have discussed for proteins and carbohydrates. The fundamental structure of a lipid is comprised of fatty acids and a glycerol molecule. Fatty acids are a type of hydrocarbon, long chains of carbon atoms bonded to hydrogens. Because electrons usually are distributed evenly around these molecules, they are nonpolar, or hydrophobic (water-fearing), and therefore not water soluble. We will discuss the major groups of lipids and how this structure is modified to perform different functions.

Fats are used to store energy within their chemical bonds. They also serve as insulation in organisms that maintain a constant body temperature, such as mammals and birds. The building blocks of fats are triacylglycerol molecules. These molecules are composed of one glycerol and three fatty acids. The fatty acids are bonded to the glycerol molecule through three dehydration synthesis reactions, forming a triacylglycerol (Figure 2.15).

Fatty acids determine the type of fat molecule, and can differ in the number of carbon atoms and the number of carbon to carbon double bonds. Steric acid is an example of a saturated fatty acid. It has no double bonds within its hydrocarbon chain; each carbon has the maximum number of hydrogens covalently bonded, it is “saturated”. Because of this, the chains lie flat (Figure 2.16). Saturated fats are usually solid at room temperature and usually come from animal sources.

Linoleic acid is an example of an unsaturated fatty acid. There are double bonds between some of the carbons within the hydrocarbon chain. These [some] carbons are not bound to the maximum number of hydrogens possible, or are unsaturated. Because of this, the chains tend to bend and flex (Figure 2.16). Therefore, unsaturated fats are usually liquid at room temperature. and These usually come from plant sources, such as corn, olives, and soybeans. Studies have shown that a diet high in saturated fats can raise the level of LDL cholesterol in the blood. Read "The Facts on Fats" on the Discovery Health Web site for more information on fats in the diet.

Fats are used for energy storage in both plants and animals. The average human has about 36 pounds of fat distributed throughout their body. Fat is also used for insulation. This is especially important in marine animals, because body heat is easily lost to the water (hypothermia). Therefore, mammals such as whales and dolphins have a thick layer of blubber, which insulates their bodies and greatly reduces heat loss.

Phospholipids are the molecules that comprise the basic structure of all plasma membranes. We will go into much more detail about these membranes in lesson 3. In this lesson, we will concentrate on how the structure of these molecules leads to their function within the membrane.

Phospholipids have the same basic structures as triacylglycerols. However a phosphate group is present instead of the third fatty acid (Figure 2.17). This phosphate group has a negative charge. Because of this, the two ends of the molecule have different properties. The fatty acid end, with its long hydrocarbon tail, is nonpolar, and therefore insoluble in water. However, the end with the phosphate group is polar, therefore it is water soluble.

When these molecules interact to form a membrane, they form two layers, with the nonpolar fatty acid tails of each layer on the inside of the membrane and the polar phosphate groups on the outside. We will leave the discussion of the complexity of the membrane until lesson 3.

Steroids are the group of lipids that includes many hormones. These molecules are secreted from glands that are part of the endocrine system and are used for long-range communication within the body. We will discuss the action of hormones when we cover human reproduction in lesson 10. Testosterone and estrogen are steroid hormones. These molecules generally have more complex ring structures, as shown in Figure 2.18.

Another type of steroid is cholesterol. Although excess levels of LDL cholesterol have been associated with coronary disease in human, this molecule is an integral part of the plasma membrane in most animal cells. Pigments are another important group of steroids. We will discuss the pigment chlorophyll in lesson 4.

The final group of biologial macromolecules are the nucleic acids, which function to store genetic information and to express that information in the production of polypeptides. The monomer of nucleic acids is the nucleotide. This monomer consists of three parts (Figure 2.19). The first is a five-carbon sugar molecule, either ribose or deoxyribose. The nucleic acid DNA has deoxyribose as its sugar, and the nucleic acid RNA has ribose (Figure 2.20). This sugar is joined to a phosphate group. These phosphates and sugars alternate to form the backbone of the nucleic acid. The third component, the nitrogenous base, is also bonded to the sugar, and is approximately perpedicular to the sugar/phosphate backbone. There are four types of nucleotides in DNA and RNA. Both include the nucleotides adenine (A), cytosine (C) and guanine (G). DNA includes the nucleotide thymine (T), which is replaced by uracil (U) in RNA (Figure 2.20).

Figure 2.19. The Structure of a Nucleotide
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Figure 2.20. DNA and RNA Comparison
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RNA molecules are a single strand of nucleotides, whereas DNA is composed of two nucleotide strands that twist around each other. The structure of DNA is called a double helix (Figure 2.21). The two strands are held together by the hydrogren bonding of the nitrogenous bases. If you untwist the DNA and think of the sugar/phosphate backbone as the sides of the ladder, then the nitrogenous bases would be the rungs. The base adenine, which has a double ring structure, pairs with thymine, a single ring, while guanine, a double ring, pairs with cytosine, a single ring. This keeps the same spacing between the sides, thus insuring that the double helix has a constant width. We will discuss nucleic acids in much more detail in lesson 7.

The origin of life is one of the most interesting questions in biology. However, it also is one of the most difficult to address. There was no one there to witness the process, therefore we must deduce what happened through other means of inquiry. To address how life originated, we can perform experiments and examine organisms that live today. To address where this may have happened, we can examine existing organisms and perform experiments. Finally, to address when life first arose, we can look to the fossil record, as well as use the information from molecular clocks.

The universe formed about 10-15 billion years ago in a process known as The Big Bang. Earth formed 4.5 billion years ago. How do we know this date so precisely? There are no rocks on earth that are this old; the oldest rocks date to about 4 billion years ago (Figure 2.22). However, there are moon rocks, collected on manned missions to the moon, that have been dated to 4.5 billion years. Because it is assumed that the Earth and the moon formed at approximately the same time, these rocks provide information on the age of the Earth.

A Single Origin of Life

At some point between 4 billion and 3.5 billion years ago, Earth was transformed from a non-living system to a living system. This time is constrained by the cooling of the Earth's crust. There was probably no constant surface water before about 4 billion years. The fossil record indicates that by 3.5 billion years there were prokaryotes on Earth. The evidence suggests that all life today had a single common ancestor, or a single origin. The most compelling argument for this is that all organisms use the same triplets of nucleotides to code for amino acids. This universality of the genetic code across all known organisms indicates a single common ancestor.

Early Conditions on Earth

The early Earth was very different from the planet we a familiar with. The surface would have been a chaotic place, with strong volcanic activity. Volcanoes today produce large amounts of water vapor and carbon dioxide, and it is assumed that the same would have been true early in Earth's history. Earth also would have experienced heavy bombardment by bolides, extraterrestrial objects such as asteroids and meteorites. While those impact craters are no longer apparent today, we only have to look at the surface of the moon to see evidence that bolide impacts were common in the early solar system. The atmosphere of early Earth also would have been very different. It would have been composed primarily of nitrogen, water vapor, carbon dioxide, with trace amounts of carbon monoxide, hydrogen and methane. Perhaps most importantly, there would have been little or no free oxygen. Therefore, the earliest forms of life were most likely anaerobic, that is they did not require oxygen for their cellular metabolism. Energy sources on the early earth would have been lightning, which is produced during volcanic eruptions, and sunlight. While the sun was weaker at that time, there was no protective ozone layer in the atmosphere; therefore more ultraviolet (UV) radiation would have struck Earth's surface.

The Miller-Urey Experiments

In 1953, Stanley Miller, then a graduate student, and Harold Urey, devised an experiment that would cast new light on the origin of life. They set up an apparatus that simulated the atmosphere of early Earth. They then applied energy, in the form of an electric spark, and collected the chemicals that resulted from this reaction. They were able to synthesize a number of organic molecules from inorganic components, including some amino acids. Their experiments have come under scrutiny in recent years because the "atmosphere" that they used was more H rich than the early Earth's atmosphere is now believed to be. But, if this experiment is run using a less reducing atmosphere, biological molecules or their precursors are synthesized. Formaldehyde (H₂CO) is produced, and sugars can be derived from this molecule. Nucleotide bases can be synthesized from HCN, which is derived from methane. Finally, some molecules, such as phosphate, could come from the weathering of rock. But, it is clear that these experiments have shown that biotic compounds can be synthesized from abiotic compounds.

Where did life originate?

This question of where life originated is very difficult to address. Darwin spoke of a warm little pond as home for the first life forms. The support for this is that organic molecules can be synthesized from a simulated early atmosphere. It has been suggested that these compounds could rain down into pools, where further biochemical reactions would then occur. However, there are a number of arguments against this scenario. Remember, in our discussion of polymerization, that many of those reactions are a dehydration synthesis, with the loss of a water molecule.

Some biochemists argue that these reactions would have been unlikely to occur spontaneously in the water. Also, the surface of the early earth was most likely repeatedly sterilized by bolide impacts. As mentioned above, we can see impact craters on the surface of the moon. Some are very large. The Mare Imbrium crater was caused by a bolide about 70 miles in diameter.

Recently, some researchers have argued that life may have originated at deep-sea hydrothermal vents. Today, these vents house a diverse array of organisms whose ecosystem is based on chemosynthesis, rather than photosynthesis. Proponents of this theory point to DNA sequence information from organisms that live today. The data shows that many of the most divergent (oldest) lineages within the bacteria and archaea are thermophiles, species that live in very hot environments. However, this also could be the result of a selective event early in the history of life.

Finally, some researchers have suggested that earth was "seeded" by complex organic molecules from space. This theory is called panspermia. In 1969, a meteorite fell near Murchison, Australia. When that meteorite was examined, it was found to carry many organic chemicals, including amino acids, and in proportions similar to those generated by the Miller and Urey experiments. Most recently, it has been suggested that a Martian meteorite collected in Antarctica contains evidence that life existed on that planet. Obviously, this question will continue to be debated for many years to come.

How did the first macromolecules and cells form?

If polymerization in an aqueous environment does not seem likely, how did the first macromolecules form? It has been shown that polymers can be created in the laboratory without biological catalysts. In these experiments, dilute solutions of monomers, such as amino acids or nucleotides, are placed on a hot, mineral substrate, such as clay or sand. The water vaporizes and short polymers will form. It also has been shown that macromolecules will aggregate in solution. Microspheres, which are small droplets composed of protenoids (short polymers of amino acids), have been synthesized in the lab. These do show some properties of cells, including selective permeability.

How did early life transmit genetic information?

For many years, scientists were puzzled by a seeming paradox. DNA carries genetic information and the information is used to direct the synthesis of proteins within a cell. However, in order for this message to be transcribed from the DNA, or for the DNA to replicate, proteins are required. This leads to the question of which came first -- DNA or proteins?

In the 1980s, it was discovered that RNA, in addition to carrying genetic information, could, as "ribozymes", catalyze some basic reactions. This raised the possibility that perhaps the early earth was an RNA World, with RNA both carrying genetic information and catalyzing chemical reactions. This also is supported by the many functions of RNA within the cell; it is integral to all aspects of protein synthesis, including the formation of the peptide bond.

When did life originate?

The first prokaryotic fossils date to approximately 3.5 billion years ago. Many of these earliest fossils are microfossils, requiring a microscope to detect them. There are fossils of structures that look very much like present day stromatolites. These stromatolites are formed by mats of cyanobacteria, and are only found in very saline marine environments from which grazing animals are excluded. There are some chemical fossils dated to 3.8 billion years that suggest biological activity because they are enriched in the isotope of carbon, C12, that is used by living organisms. However, because there are relatively few rocks older than 3.5 billion years, fossils of the very earliest organisms may never be found. But, from the available evidence, it is likely that life originated and diversified within a 500 million year period; that earliest life was probably prokaryotic, and anaerobic. Aerobic respiration and the eukaryotic cell arose about 1 billion years later. In the next lesson, we turn our attention to cell structure, focusing on the eukaryotic cell.