Biology literally means "the study of life". Biology is such a broad field, covering the minute workings of chemical machines inside our cells, to broad scale concepts of ecosystems and global climate change. Biologists study intimate details of the human brain, the composition of our genes, and even the functioning of our reproductive system. Biologists recently all but completed the deciphering of the human genome, the sequence of deoxyribonucleic acid (DNA) bases that may determine much of our innate capabilities and predispositions to certain forms of behavior and illnesses. DNA sequences have played major roles in criminal cases (O.J. Simpson, as well as the reversal of death penalties for many wrongfully convicted individuals), as well as the impeachment of President Clinton (the stain at least did not lie). We are bombarded with headlines about possible health risks from favorite foods (Chinese, Mexican, hamburgers, etc.) as well as the potential benefits of eating other foods such as cooked tomatoes. Informercials tout the benefits of metabolism-adjusting drugs for weight loss. Many Americans are turning to herbal remedies to ease arthritis pain, improve memory, as well as improve our moods.

Can a biology book give you the answers to these questions? No, but it will enable you learn how to sift through the biases of investigators, the press, and others in a quest to critically evaluate the question. To be honest, five years after you are through with this class it is doubtful you would remember all the details of meatbolism. However, you will know where to look and maybe a little about the process of science that will allow you to make an informed decision. Will you be a scientist? Yes, in a way. You may not be formally trained as a science major, but you can think critically, solve problems, and have some idea about what science can and cannoit do. I hope you will be able to tell the shoe from the shinola.

Science is an objective, logical, and repeatable attempt to understand the principles and forces operating in the natural universe. Science is from the Latin word, scientia, to know. Good science is not dogmatic, but should be viewed as an ongoing process of testing and evaluation. One of the hoped-for benefits of students taking a biology course is that they will become more familiar with the process of science.

Humans seem innately interested in the world we live in. Young children drive their parents batty with constant "why" questions. Science is a means to get some of those whys answered. When we shop for groceries, we are conducting a kind of scientific experiment. If you like Brand X of soup, and Brand Y is on sale, perhaps you try Brand Y. If you like it you may buy it again, even when it is not on sale. If you did not like Brand Y, then no sale will get you to try it again.

In order to conduct science, one must know the rules of the game (imagine playing Monopoly and having to discover the rules as you play! Which is precisely what one does with some computer or videogames (before buying the cheatbook). The scientific method is to be used as a guide that can be modified. In some sciences, such as taxonomy and certain types of geology, laboratory experiments are not necessarily performed. Instead, after formulating a hypothesis, additional observations and/or collections are made from different localities.

After a hypothesis has been repeatedly tested, a hierarchy of scientific thought develops. Hypothesis is the most common, with the lowest level of certainty. A theory is a hypothesis that has been repeatedly tested with little modification, e.g. The Theory of Evolution. A Law is one of the fundamental underlying principles of how the Universe is organized, e.g. The Laws of Thermodynamics, Newton's Law of Gravity. Science uses the word theory differently than it is used in the general population. Theory to most people, in general nonscientific use, is an untested idea. Scientists call this a hypothesis.

Scientific experiments are also concerned with isolating the variables. A good science experiment does not simultaneously test several variables, but rather a single variable that can be measured against a control. Scientific controlled experiments are situations where all factors are the same between two test subjects, except for the single experimental variable.

Consider a commonly conducted science fair experiment. Sandy wants to test the effect of gangsta rap music on pea plant growth. She plays loud rap music 24 hours a day to a series of pea plants grown under light, and watered every day. At the end of her experiment she concludes gangsta rap is conducive to plant growth. Her teacher grades her project very low, citing the lack of a control group for the experiment. Sandy returns to her experiment, but this time she has a separate group of plants under the same conditions as the rapping plants, but with soothing Led Zeppelin songs playing. She comes to the same conclusion as before, but now has a basis for comparison. Her teacher gives her project a better grade. 

Robert Hooke (1635-1703), one of the first scientists to use a microscope to examine pond water, cork and other things, referred to the cavities he saw in cork as "cells", Latin for chambers. Mattias Schleiden (in 1838) concluded all plant tissues consisted of cells. In 1839, Theodore Schwann came to a similar conclusion for animal tissues. Rudolf Virchow, in 1858, combined the two ideas and added that all cells come from pre-existing cells, formulating the Cell Theory. Thus there is a chain-of-existence extending from your cells back to the earliest cells, over 3.5 billion years ago. The cell theory states that all organisms are composed of one or more cells, and that those cells have arisen from pre-existing cells.

James Watson (L) and Francis Crick (R), and the model they built of the structure of DNA. Image from the Internet.

In 1953, James Watson and Francis Crick developed the model for deoxyribonucleic acid (DNA), a chemical that had (then) recently been deduced to be the physical carrier of inheritance. Crick hypothesized the mechanism for DNA replication and further linked DNA to proteins, an idea since referred to as the central dogma. Information from DNA "language" is converted into RNA (ribonucleic acid) "language" and then to the "language" of proteins. The central dogma explains the influence of heredity (DNA) on the organism (proteins).

Homeostasis is the maintainence of a dynamic range of conditions within which the organism can function. Temperature, pH, and energy are major components of this concept. Theromodynamics is a field of study that covers the laws governing energy transfers, and thus the basis for life on earth. Two major laws are known: the conservation of matter and energy, and entropy. These will be discussed in more detail in a later chapter. The universe is composed of two things: matter (atoms, etc.) and energy.

These first three theories are very accepted by scientists and the general public. The theory of evolution is well accepted by scientists and most of the general public. However, it remains a lightening rod for school boards, politicians, and television preachers. Much of this confusion results from what the theory says and what it does not say. 

Modern biology is based on several unifying themes, such as the cell theory, genetics and inheritance, Francis Crick's central dogma of information flow, and Darwin and Wallace's theory of evolution by natural selection. In this first unit we will examine these themes and the nature of science.

The Ancient Greek philosopher Anaxiamander (611-547 B.C.) and the Roman philosopher Lucretius (99-55 B.C.) coined the concept that all living things were related and that they had changed over time. The classical science of their time was observational rather than experimental. Another ancient Greek philosopher, Aristotle developed his Scala Naturae, or Ladder of Life, to explain his concept of the advancement of living things from inanimate matter to plants, then animals and finally man. This concept of man as the "crown of creation" still plagues modern evolutionary biologists (See Gould, 1989, for a more detailed discussion).

Post-Aristotlean "scientists" were constrained by the prevailing thought patterns of the Middle Ages -- the inerrancy of the biblical book of Genesis and the special creation of the world in a literal six days of the 24-hour variety. Archbishop James Ussher of Ireland, in the late 1600's calculated the age of the earth based on the geneologies from Adam and Eve listed in the biblical book of Genesis (note to the no-longer young: Phil Collins and Peter Grabriel were not in this Genesis). According to Ussher's calculations, the earth was formed on October 22, 4004 B.C. These calculations were part of Ussher's book, History of the World. The chronology he developed was taken as factual, and was even printed in the front pages of bibles. Ussher's ideas were readily accepted, in part because they posed no threat to the social order of the times; comfortable ideas that would not upset the linked applecarts of church and state.

Archbishop James Ussher. Image from the Internet.

Often new ideas must "come out of left field", appearing as wild notions, but in many cases prompting investigation which may later reveal the "truth". Ussher's ideas were comfortable, the Bible was viewed as correct, therefore the earth must be only 5000 years old.

Geologists had for some time doubted the "truth" of a 5,000 year old earth. Leonardo da Vinci (painter of the Last Supper, and the Mona Lisa, architect and engineer) calculated the sedimentation rates in the Po River of Italy. Da Vinci concluded it took 200,000 years to form some nearby rock deposits. Galileo, convicted heretic for his contention that the Earth was not the center of the Universe, studied fossils (evidence of past life) and concluded that they were real and not inanimate artifacts. James Hutton, regarded as the Father of modern Geology, developed the Theory of Uniformitarianism, the basis of modern geology and paleontology. According to Hutton's work, certain geological processes operated in the past in much the same fashion as they do today, with minor exceptions of rates, etc. Thus many geological structures and processes cannot be explained if the earth is only 5000 years old.

Radiometric age assignments based on the rates of decay of radioactive isotopes, not discovered until the late 19th century, suggest the earth is over 4.5 billion years old. The Earth is thought older than 4.5 billion years, with the oldest known rocks being 3.96 billion years old. Geologic time divides into eons, eroas, and smaller units. An overview of geologic time may be obtained at http://www.ucmp.berkeley.edu/help/timeform.html.

Erasmus Darwin (1731-1802; grandfather of Charles Darwin) a British physician and poet in the late 1700's, proposed that life had changed over time, although he did not present a mechanism. Georges-Louis Leclerc, Comte de Buffon (pronounced Bu-fone; 1707-1788) in the middle to late 1700's proposed that species could change. This was a major break from earlier concepts that species were created by a perfect creator and therefore could not change because they were perfect, etc.

Swedish botanist Carl Linne (more popularly known as Linneus, after the common practice of the day which was to latinize names of learned men), attempted to pigeon-hole all known species of his time (1753) into immutable categories. Many of these categories are still used in biology, although the underlying thought concept is now evolution and not immutability of species. Linnean hierarchical classification was based on the premise that the species was the smallest unit, and that each species (or taxon) belonged to a higher category.

 Linneus also developed the concept of binomial nomenclature, whereby scientists speaking and writing different languages could communicate clearly. For example Man in English is Hombre  in Spanish, Mensch in German, and Homo  in Latin. Linneus settled on Latin, which was the language of learned men at that time. If a scientist refers today to Homo, all scientists know what he or she means.

William "Strata" Smith (1769-1839), employed by the English coal mining industry, developed the first accurate geologic map of England. He also, from his extensive travels, developed the Principle of Biological Succession. This idea states that each period of Earth history has its own unique assemblages of fossils. In essence Smith fathered the science of stratigraphy, the correlation of rock layers based on (among other things) their fossil contents. He also developed an idea that life had changed over time, but did not overtly state that.

Abraham Gottlob Werner and Baron Georges Cuvier (1769-1832) were among the foremost proponents of catastrophism, the theory that the earth and geological events had formed suddenly, as a result of some great catastrophe (such as Noah's flood). This view was a comfortable one for the times and thus was widely accepted. Cuvier eventually proposed that there had been several creations that occurred after catastrophies. Louis Agassiz (1807-1873) proposed 50-80 catastrophies and creations.

Jean Baptiste de Lamarck (1744-1829) developed one of the first theories on how species changed. He proposed the inheritance of acquired characteristics to explain, among other things, the length of the giraffe neck. The Lamarckian view is that modern giraffe's have long necks because their ancestors progressively gained longer necks due to stretching to reach food higher and higher in trees. According to the 19th century concept of use and disuse the stretching of necks resulted in their development, which was somehow passed on to their progeny. Today we realize that only bacteria are able to incorporate non-genetic (nonheritable) traits. Lamarck's work was a theory that plainly stated that life had changed over time and provided (albeit an erroneous) mechanism of change.

Charles Darwin, former divinity student and former medical student, secured (through the intercession of his geology professor) an unpaid position as ship's naturalist on the British exploratory vessel H.M.S. Beagle. The voyage would provide Darwin a unique opportunity to study adaptation and gather a great deal of proof he would later incorporate into his theory of evolution. On his return to England in 1836, Darwin began (with the assistance of numerous specialists) to catalog his collections and ponder the seeming "fit" of organisms to their mode of existence. 

Unlike the upper-class Darwin, Alfred Russel Wallace (1823-1913) came from a different social class. Wallace spent many years in South America, publishing salvaged notes in Travels on the Amazon and Rio Negro in 1853. In 1854, Wallace left England to study the natural history of Indonesia, where he contracted malaria. During a fever Wallace managed to write down his ideas on natural selection.

In 1858, Darwin received a letter from Wallace, in which Darwin's as-yet-unpublished theory of evolution and adaptation was precisely detailed. Darwin arranged for Wallace's letter to be read at a scientific meeting, along with a synopsis of his own ideas. To be correct, we need to mention that both Darwin and Wallace developed the theory, although Darwin's major work was not published until 1859 (On the Origin of Species by Means of Natural Selection). While there have been some changes to the theory since 1859, most notably the incorporation of genetics and DNA into what is termed the "Modern Synthesis" during the 1940's, most scientists today accept evolution as the guiding theory on which modern biology is based.

Recent revisions of biology curricula stressed the need for underlying themes. Evolution serves as such a universal theme. An excellent site devoted to Darwin's thoughts and work is available by clicking here. At that same site is a timeline showing many of the events mentioned above in their historical contexts. 

Evolutionary theory and the cell theory provide us with a basis for the interrelation of all living things. We also utilize Linneus' hierarchical classification system, adopting (generally) five kingdoms of living organisms. Viruses, as discussed later, are not considered living. Click here for a table summarizing the five kingdoms. Recent studies suggest that there might be a sixth Kingdom, the Archaea.

Monera, the most primitive kingdom, contain living organisms remarkably similar to ancient fossils. Organisms in this group lack membrane-bound organelles associated with higher forms of life. Such organisms are known as prokaryotes. Bacteria (technically the Eubacteria) and blue-green bacteria (sometimes called blue-green algae, or cyanobacteria) are the major forms of life in this kingdom. The most primitive group, the archaebacteria, are today restricted to marginal habitats such as hot springs or areas of low oxygen concentration.

Fungi are almost entirely multicellular (with yeast, Saccharomyces cerviseae, being a prominent unicellular fungus), heterotrophic (deriving their energy from another organism, whether alive or dead), and usually having some cells with two nuclei (multinucleate, as opposed to the more common one, or uninucleate) per cell. Ecologically this kingdom is important (along with certain bacteria) as decomposers and recyclers of nutrients. Economically, the Fungi provide us with food (mushrooms; Bleu cheese/Roquefort cheese; baking and brewing), antibiotics (the first of the wonder drugs, Penicillin, was isolated from a fungus Penicillium), and crop parasites (doing several billion dollars per year of damage).

Plantae (click here for more information about the Plantae) include multicelled organisms that are all autotrophic (capable of making their own food by the process of photosynthesis, the conversion of sunlight energy into chemical energy). Ecologically, this kingdom is generally (along with photosynthetic organisms in Monera and Protista) termed the producers, and rest at the base of all food webs. A food web is an ecological concept to trace energy flow through an ecosystem. Economically, this kingdom is unparalleled, with agriculture providing billions of dollars to the economy (as well as the foundation of "civilization"). Food, building materials, paper, drugs (both legal and illegal), and roses, are plants or plant-derived products.

Animalia consists entirely of multicelluar heterotrophs that are all capable (at some point during their life history) of mobility. Ecologically, this kingdom occupies the level of consumers, which can be subdivided into herbivore (eaters of plants) and carnivores (eaters of other animals). Humans, along with some other organisms, are omnivores (capable of functioning as herbivores or carnivores). Economically, animals provide meat, hides, beasts of burden, pleasure (pets), transportation, and scents (as used in some perfumes).

Homeostasis is the maintenance of a constant (yet also dynamic) internal environment in terms of temperature, pH, water concentrations, etc. Much of our own metabolic energy goes toward keeping within our own homeostatic limits. If you run a high fever for long enough, the increased temperature will damage certain organs and impair your proper functioning. Swallowing of common household chemicals, many of which are outside the pH  (acid/base) levels we can tolerate, will likewise negatively impact the human body's homeostatic regime. Muscular activity generates heat as a waste product. This heat is removed from our bodies by sweating. Some of this heat is used by warm-blooded animals, mammals and birds, to maintain their internal temperatures.

Since all cells come from existing cells, they must have some way of reproducing, whether that involves asexual  (no recombination of genetic material) or sexual  (recombination of genetic material). Most living things use the chemical DNA (deoxyribonucleic acid) as the physical carrier of inheritance and the genetic information. Some organisms, such as retroviruses  (of which HIV  is a member), use RNA (ribonucleic acid) as the carrier. The variation that Darwin and Wallace recognized as the wellspring of evolution and adaptation, is greatly increased by sexual reproduction.

Most of the Universe consists of matter and energy. Energy is the capacity to do work. Matter has mass and occupies space. All matter is composed of basic elements that cannot be broken down to substances with different chemical or physical properties. Elements are substances consisting of one type of atom, for example Carbon atoms make up diamond, and also graphite. Pure (24K) gold is composed of only one type of atom, gold atoms. Atoms are the smallest particle into which an element can be divided. The ancient Greek philosophers developed the concept of the atom, although they considered it the fundamental particle that could not be broken down. Since the work of Enrico Fermi and his colleagues, we now know that the atom is divisible, often releasing tremendous energies as in nuclear explosions or (in a controlled fashion in) thermonuclear power plants.

Subatomic particles were discovered during the 1800s. For our purposes we will concentrate only on three of them. The proton is located in the center (or nucleus) of an atom, each atom has at least one proton. Protons have a charge of +1, and a mass of approximately 1 atomic mass unit (amu). Elements differ from each other in the number of protons they have, e.g. Hydrogen has 1 proton; Helium has 2.

The neutron also is located in the atomic nucleus (except in Hydrogen). The neutron has no charge, and a mass of slightly over 1 amu. Some scientists propose the neutron is made up of a proton and electron-like particle.

The electron is a very small particle located outside the nucleus. Because they move at speeds near the speed of light the precise location of electrons is hard to pin down. Electrons occupy orbitals, or areas where they have a high statistical probability of occurring. The charge on an electron is -1. Its mass is negligible (approximately 1800 electrons are needed to equal the mass of one proton).

The atomic number is the number of protons an atom has. It is characteristic and unique for each element. The atomic mass (also referred to as the atomic weight) is the number of protons and neutrons in an atom. Atoms of an element that have differing numbers of neutrons (but a constant atomic number) are termed isotopes. Isotopes can be used to determine the diet of ancient peoples by determining proportions of isotopes in mummified or fossilized human tissues. Biochemical pathways can be deciphered by using isotopic tracers. The age of fossils and artifacts can be determined by using radioactive isotopes, either directly on the fossil (if it is young enough) or on the rocks that surround the fossil for older fossils like dinosaurs). Isotopes are also the source of radiation used in medical diagnostic and treatment procedures.

The Periodic Table of the Elements. Each Roman numeraled column on the label (at least the ones ending in A) tells us how many electrons are in the outer shell of the atom. Each numbered row on the table tells us how many electron shells an atom has. Thus, Hydrogen, in column IA, row 1 has one electron in one shell. Phosphorous in column VA, row 3 has 5 electrons in its outer shell, and has three shells in total.

Electrons, because they move so fast (approximately at the speed of light), seem to straddle the fence separating energy from matter. Because of this, we think of electrons both as particles of matter (having mass is a property of matter) and as units (or quanta) of energy. When subjected to energy, electrons will acquire some of that energy.

An orbital is also an area of space in which an electron will be found 90% of the time. Orbitals are of different shapes. Each orbital has a characteristic energy state and a characteristic shape. The s orbital is spherical, and located closest to the nucleus. Since each orbital can hold a maximum of two electrons, atomic numbers above 2 must fill the other orbitals. The px, py, and pz orbitals are dumbbell shaped, along the x, y, and z axes respectively. The major energy levels (also known as shells) into which electrons fit, are (from the nucleus outward) K, L, M, and N. Sometimes these are numbered, with electron configurations being: 1s22s22p1, etc. This nomenclature tells us the 1st energy level (shell) has 2 electrons in the s orbital, and 2nd energy level has 2 electrons in its s orbital, plus one electron in its p orbital.

During the nineteenth century, chemists arranged the then-known elements according to chemical bonding, recognizing that one group (the furthermost right column on the Periodic Table, referred to as the Inert Gases or Noble Gases) tended to occur in elemental form (in other words, not in a molecule with other elements). It was later determined that this group had outer electron shells containing two (as in the case of Helium) or eight (Neon, Xenon, Radon, Krypton, etc.) electrons.

As a general rule, for the atoms we are likely to encounter in biological systems, atoms tend to gain or lose their outer electrons to achieve a Noble Gas outer electron shell configuration of 2 or 8 electrons. The number of electrons that are gained or lost is characteristic for each element, and ultimately determines the number and types of chemical bonds atoms of that element can form.

Ionic bonds are formed when atoms become ions by gaining or losing electrons. Chlorine is in a group of elements having seven electrons in their outer shells. Members of this group tend to gain one electron, acquiring a charge of -1. Sodium is in another group with elements having one electron in their outer shells. Members of this group tend to lose that outer electron, acquiring a charge of +1. Oppositely charged ions are attracted to each other, thus Cl- (the symbolic representation of chlorine) and Na+ (the symbol for sodium, using the Greek word natrium) form an ionic bond, becoming the molecule sodium chloride. Ionic bonds generally form between elements in Group I (having one electron in their outer shell) and Group VIIa (having seven electrons in their outer shell). Such bonds are relatively weak, and tend to disassociate in water, producing solutions that have both Na and Cl ions.

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). 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.

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.

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.

Carbohydrates have the general formula [CH2O]n where n is a number between 3 and 6. Note the different CH2O units on the diagram below. 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).

Classification of monosaccharides is done by the number of carbon atoms and the types of functional groups. For example, glucose and fructose have the same chemical formula, but different structure: glucose having an aldehyde (internal hydroxyl shown as: -OH) and fructose having a keto group (internal double-bond O, shown as: =O).

In aqueous solution, glucose tends to have two structures, a and b, with an intermediate straight-chain form. The a form and b form differ in the location of one -OH group. Glucose is a common hexose in plants. The products of photosynthesis are assembled to make a glucose. Energy from sunlight is converted into the 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.)

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.

Polysaccharides are large molecules composed of individual monosaccharide units. A common plant polysaccharide is starch, 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 is an animal storage product that accumulates in the vertebrate liver.

Cellulose 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 the structural polysaccharides is thus constrained into straight microfibrils by the uniform nature of the glucoses, which resist the actions of enzymes (such as amylase) that breakdown storage polysaccharides (such a starch).

Lipids are involved mainly with long-term energy storage. They are generally insoluble in polar substances such as water. Secondary functions of lipids are as structural components (as in the case of phospholipids that are the major building block in cell membranes) and as "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.

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".

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.

Fats and oils function for in 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 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 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.

Most mention of these two in the news is usually negative. Cholesterol has many biological uses, such as its occurrence in the cell membranes, and its role in forming the sheath of some neurons. 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.

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 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. 

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.

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. 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.

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 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.

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. 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!] ;)). DNA functions in information storage. The English alphabet has 26 letters and over 50,000 words. DNA has 4 letters (C, G, A, and T) and 20 words (the 20 amino acids) that can make an infinite variety of sentences (polypeptides).

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 the secondary 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) 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.

