Chemistry I: atom and molecule

Atoms

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, summarized in Table 1. 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).

Table 1. Subatomic particles of use in biology.

Name	Charge	Location	Mass
Proton	+1	atomic nucleus	1.6726 X 10-27 kg
Neutron	0	atomic nucleus	1.6750 X 10-27 kg
Electron	-1	electron orbital	9.1095 X 10-31 kg

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, shown in Figure 1 and Figure 2, 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.

Figure 1. Note that each of these isotopes of hydrogen has only one proton. Isotopes differ from each other in the number of neutrons, not in the number of protons. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Some isotopes are radioisotopes, which spontaneously decay, releasing radioactivity. Other isotopes are stable. Examples of radioisotopes are Carbon-14 (symbol ¹⁴C), and deuterium (also known as Hydrogen-2; ²H). Stable isotopes are ¹²C and ¹H.

Figure 2. Carbon has three isotopes, of which carbon-12 and carbon-14 are the most well known. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

The Periodic Table of the Elements, a version of which is shown in Figure 3, provides a great deal of information about various elements. An on-line Periodic Table is available by clicking here,

Figure 3. 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. Image from James K. Hardy's chemistry site at the University of Akron.

Electrons and energy

Electrons, because they move so fast (approximately at the speed of light), seem to straddle the fence separating energy from matter. Albert Einstein developed his famous E=mc² equation relating matter and energy over a century ago. Because of his (and others) work, 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, as shown in Figure 4.

Figure 4. Excitation of an electron by energy, causing the electron to "jump" to another electron (energy) level known as the excited state. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

An orbital is also an area of space in which an electron will be found 90% of the time. Orbitals have a variety of shapes. Each orbital has a characteristic energy state and a characteristic shape. The s orbital is spherical. Since each orbital can hold a maximum of two electrons, atomic numbers above 2 must fill the other orbitals. The p_x, p_y, and p_z orbitals are dumbbell shaped, along the x, y, and z axes respectively. These orbital shapes are shown in Figure 5.

Energy levels (also referred to as electron shells) are located a certain "distance" from the nucleus. The major energy levels into which electrons fit, are (from the nucleus outward) K, L, M, and N. Sometimes these are numbered, with electron configurations being: 1s²2s²2p¹, (where the first shell K is indicated with the number 1, the second shell L with the number 2, etc.). This nomenclature tells us that for the atom mentioned in this paragraph, the first energy level (shell) has two electrons in its s orbital (the only orbital it can have), and second energy level has a maximum of two electrons in its s orbital, plus one electron in its p orbital.

Figure 5. Geometry of orbitals. S-orbitals are spherical, p-orbitals are shaped like a dumbbell or figure 8. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Chemical Bonding

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 two or eight 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. Atomic diagrams for several atoms are shown in Figure 6.

Figure 6. Atomic diagrams illustrating the filling of the outer electron shells. Images from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

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 (see Figure 6). 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 the chloride ion) and Na⁺ (the symbol for the sodium ion, using the Greek word natrium) form an ionic bond, becoming the molecule sodium chloride, shown in Figure 7. 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.

Figure 7. TOP: Formation of a crystal of sodium chloride. Each positively charged sodium ion is surropunded by six negatively charged chloride ions; likewise each negatively charged chloride ion is surrounded by six positively charged sodium ions. The overall effect is electrical neutrality. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission. BOTTOM: Table Salt Crystal (SEM x625). This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.

Covalent bonds form when atoms share electrons. Since electrons move very fast they can be shared, effectively filling or emptying the outer shells of the atoms involved in the bond. Such bonds are referred to as electron-sharing bonds. An analogy can be made to child custody: the children are like electrons, and tend to spend some time with one parent and the rest of their time with the other parent. In a covalent bond, the electron clouds surrounding the atomic nuclei overlap, as shown in Figure 8.

Figure 8. Formation of a covalent bond between two Hydrogen atoims. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Carbon (C) is in Group IVa, meaning it has four electrons in its outer shell. Thus to become a "happy atom", Carbon can either gain or lose four electrons. By sharing the electrons with other atoms, Carbon can become a happy atom,. alternately filling and emptying its outer shell, as with the four hydrogens shown in Figure 9.

Figure 9. Formation of covalent bonds in methane. Carbon needs to share four electrons, in effect it has four slots. Each hydrogen provides an electron to each of these slots. At the same time each hydrogen needs to fill one slot, which is done by sharing an electron with the carbon. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

The molecule methane (chemical formula CH₄) has four covalent bonds, one between Carbon and each of the four Hydrogens. Carbon contributes an electron, and Hydrogen contributes an electron. The sharing of a single electron pair is termed a single bond. When two pairs of electrons are shared, a double bond results, as in carbon dioxide. Triple bonds are known, wherein three pairs (six electrons total) are shared as in acetylene gas or nitrogen gas. The types of covalent bonds are shown in Figure 10.

Figure 10. Ways of representing covalent bonds. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Sometimes electrons tend to spend more time with one atom in the bond than with the other. In such cases a polar covalent bond develops. Water (H₂O) is an example. Since the electrons spend so much time with the oxygen (oxygen having a greater electronegativity, or electron affinity) that end of the molecule acquires a slightly negative charge. Conversely, the loss of the electrons from the hydrogen end leaves a slightly positive charge. The water molecule is thus polar, having positive and negative sides.

Hydrogen bonds, as shown in Figure 11, result from the weak electrical attraction between the positive end of one molecule and the negative end of another. Individually these bonds are very weak, although taken in a large enough quantity, the result is strong enough to hold molecules together or in a three-dimensional shape.

Figure 11. TOP: Formation of a hydrogen bond between the hydrogen side of one water molecule and the oxygen side of another water molecule. BOTTOM: The presence of polar areas in the amino acids that makeup a protein allows for hydrogen bonds to form, giving the molecule a three-dimensional shape that is often vital to that protein's proper functioning. Images from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Chemical reactions and molecules

Molecules are compounds in which the elements are in definite, fixed ratios, as seen in Figure 12. Those atoms are held together usually by one of the three types of chemical bonds discussed above. For example: water, glucose, ATP. Mixtures are compounds with variable formulas/ratios of their components. For example: soil. Molecular formulas are an expression in the simplest whole-number terms of the composition of a substance. For example, the sugar glucose has 6 Carbons, 12 hydrogens, and 6 oxygens per repeating structural unit. The formula is written C₆H₁₂O₆.

Figure 12. Determination of molecular weights by addition of the weights of the atoms that make up the molecule. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Chemical reactions occur in nature, and some also can be performed in a laboratory setting. One such reaction is diagrammed in Figure 13. Chemical equations are linear representations of how these reactions occur. Combination reactions occur when two separate reactants are bonded together, e.g. A + B -----> AB. Disassociation reactions occur when a compound is broken into two products, e.g. AB -----> A + B.

Figure 13. Diagram of a chemical reaction: the combustion of propane with oxygen, resulting in carbon dioxide, water, and energy (as heat and light). This chemical reaction takes place in a camping stove as well as in certain welding torches. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Biological systems, while unique to each species, are based on the chemical bonding properties of carbon. Major organic chemicals (those associated with or formed by the actions of living things) usually include some ratios of the following elements: C, H, N, O, P, S.

READ MORE - Chemistry I: atom and molecule

Cellular Organization

Life exhibits varying degrees of organization. Atoms are organized into molecules, molecules into organelles, and organelles into cells, and so on. According to the Cell Theory, all living things are composed of one or more cells, and the functions of a multicellular organism are a consequence of the types of cells it has. Cells fall into two broad groups: prokaryotes and eukaryotes. Prokaryotic cells are smaller (as a general rule) and lack much of the internal compartmentalization and complexity of eukaryotic cells. No matter which type of cell we are considering, all cells have certain features in common, such as a cell membrane, DNA and RNA, cytoplasm, and ribosomes. Eukaryotic cells have a great variety of organelles and structures.

Cell Size and Shape 

The shapes of cells are quite varied with some, such as neurons, being longer than they are wide and others, such as parenchyma (a common type of plant cell) and erythrocytes (red blood cells) being equidimensional. Some cells are encased in a rigid wall, which constrains their shape, while others have a flexible cell membrane (and no rigid cell wall).

The size of cells is also related to their functions. Eggs (or to use the latin word, ova) are very large, often being the largest cells an organism produces. The large size of many eggs is related to the process of development that occurs after the egg is fertilized, when the contents of the egg (now termed a zygote) are used in a rapid series of cellular divisions, each requiring tremendous amounts of energy that is available in the zygote cells. Later in life the energy must be acquired, but at first a sort of inheritance/trust fund of energy is used.

Cells range in size from small bacteria to large, unfertilized eggs laid by birds and dinosaurs. The realtive size ranges of biological things is shown in Figure 1. In science we use the metric system for measuring. Here are some measurements and convesrions that will aid your understanding of biology.

1 meter = 100 cm = 1,000 mm = 1,000,000 µm = 1,000,000,000 nm

1 centimenter (cm) = 1/100 meter = 10 mm

1 millimeter (mm) = 1/1000 meter = 1/10 cm

1 micrometer (µm) = 1/1,000,000 meter = 1/10,000 cm

1 nanometer (nm) = 1/1,000,000,000 meter = 1/10,000,000 cm

Figure 1. Sizes of viruses, cells, and organisms. Images from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

The Cell Membrane

The cell membrane functions as a semi-permeable barrier, allowing a very few molecules across it while fencing the majority of organically produced chemicals inside the cell. Electron microscopic examinations of cell membranes have led to the development of the lipid bilayer model (also referred to as the fluid-mosaic model). The most common molecule in the model is the phospholipid, which has a polar (hydrophilic) head and two nonpolar (hydrophobic) tails. These phospholipids are aligned tail to tail so the nonpolar areas form a hydrophobic region between the hydrophilic heads on the inner and outer surfaces of the membrane. This layering is termed a bilayer since an electron microscopic technique known as freeze-fracturing is able to split the bilayer, shown in Figure 2.

Figure 2. Cell Membranes from Opposing Neurons (TEM x436,740). This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.

Cholesterol is another important component of cell membranes embedded in the hydrophobic areas of the inner (tail-tail) region. Most bacterial cell membranes do not contain cholesterol. Cholesterol aids in the flexibility of a cell membrane.

Proteins, shown in Figure 2, are suspended in the inner layer, although the more hydrophilic areas of these proteins "stick out" into the cells interior as well as outside the cell. These proteins function as gateways that will allow certain molecules to cross into and out of the cell by moving through open areas of the protein channel. These integral proteins are sometimes known as gateway proteins. The outer surface of the membrane will tend to be rich in glycolipids, which have their hydrophobic tails embedded in the hydrophobic region of the membrane and their heads exposed outside the cell. These, along with carbohydrates attached to the integral proteins, are thought to function in the recognition of self, a sort of cellular identification system.

The contents (both chemical and organelles) of the cell are termed protoplasm, and are further subdivided into cytoplasm (all of the protoplasm except the contents of the nucleus) and nucleoplasm (all of the material, plasma and DNA etc., within the nucleus).

The Cell Wall

Not all living things have cell walls, most notably animals and many of the more animal-like protistans. Bacteria have cell walls containing the chemical peptidoglycan. Plant cells, shown in Figures 3 and 4, have a variety of chemicals incorporated in their cell walls. Cellulose, a nondigestible (to humans anyway) polysaccharide is the most common chemical in the plant primary cell wall. Some plant cells also have lignin and other chemicals embedded in their secondary walls.

The cell wall is located outside the plasma membrane. Plasmodesmata are connections through which cells communicate chemically with each other through their thick walls. Fungi and many protists have cell walls although they do not contain cellulose, rather a variety of chemicals (chitin for fungi).

Animal cells, shown in Figure 5, lack a cell wall, and must instead rely on their cell membrane to maintain the integrity of the cell. Many protistans also lack cell walls, using variously modified cell membranes o act as a boundary to the inside of the cell.

Figure 3. Structure of a typical plant cell. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Figure 4. Lily Parenchyma Cell (cross-section) (TEM x7,210). Note the large nucleus and nucleolus in the center of the cell, mitochondria and plastids in the cytoplasm. This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.

Figure 5. Liver Cell (TEM x9,400). This image is copyright Dennis Kunkel. This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.

The nucleus

The nucleus, shown in Figures 6 and 7, occurs only in eukaryotic cells. It is the location for most of the nucleic acids a cell makes, such as DNA and RNA. Danish biologist Joachim Hammerling carried out an important experiment in 1943. His work (click here for a diagram) showed the role of the nucleus in controlling the shape and features of the cell. Deoxyribonucleic acid, DNA, is the physical carrier of inheritance and with the exception of plastid DNA (cpDNA and mDNA, found in the chloroplast and mitochondrion respectively) all DNA is restricted to the nucleus. Ribonucleic acid, RNA, is formed in the nucleus using the DNA base sequence as a template. RNA moves out into the cytoplasm where it functions in the assembly of proteins. The nucleolus is an area of the nucleus (usually two nucleoli per nucleus) where ribosomes are constructed.

Figure 6. Structure of the nucleus. Note the chromatin, uncoiled DNA that occupies the space within the nuclear envelope. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Figure 7. Liver cell nucleus and nucleolus (TEM x20,740). Cytoplasm, mitochondria, endoplasmic reticulum, and ribosomes also shown.This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.

The nuclear envelope, shown in Figure 8, is a double-membrane structure. Numerous pores occur in the envelope, allowing RNA and other chemicals to pass, but the DNA not to pass.

Figure 8. Structure of the nuclear envelope and nuclear pores. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Figure 9. Nucleus with Nuclear Pores (TEM x73,200). The cytoplasm also contains numerous ribosomes. This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.

Cytoplasm

The cytoplasm was defined earlier as the material between the plasma membrane (cell membrane) and the nuclear envelope. Fibrous proteins that occur in the cytoplasm, referred to as the cytoskeleton maintain the shape of the cell as well as anchoring organelles, moving the cell and controlling internal movement of structures. Elements that comprose the cytoskeleton are shown in Figure 10. Microtubules function in cell division and serve as a "temporary scaffolding" for other organelles. Actin filaments are thin threads that function in cell division and cell motility. Intermediate filaments are between the size of the microtubules and the actin filaments.

Figure 10. Actin and tubulin components of the cytoskeleton. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Vacuoles and vesicles

Vacuoles are single-membrane organelles that are essentially part of the outside that is located within the cell. The single membrane is known in plant cells as a tonoplast. Many organisms will use vacuoles as storage areas. Vesicles are much smaller than vacuoles and function in transporting materials both within and to the outside of the cell.

Ribosomes

Ribosomes are the sites of protein synthesis. They are not membrane-bound and thus occur in both prokaryotes and eukaryotes. Eukaryotic ribosomes are slightly larger than prokaryotic ones. Structurally, the ribosome consists of a small and larger subunit, as shown in Figure 11. . Biochemically, the ribosome consists of ribosomal RNA (rRNA) and some 50 structural proteins. Often ribosomes cluster on the endoplasmic reticulum, in which case they resemble a series of factories adjoining a railroad line. Figure 12 illustrates the many ribosomes attached to the endoplasmic reticulum. Click here for Ribosomes (More than you ever wanted to know about ribosomes!)

Figure 11. Structure of the ribosome. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Figure 12. Ribosomes and Polyribosomes - liver cell (TEM x173,400). This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.

Endoplasmic reticulum

Endoplasmic reticulum, shown in Figure 13 and 14, is a mesh of interconnected membranes that serve a function involving protein synthesis and transport. Rough endoplasmic reticulum (Rough ER) is so-named because of its rough appearance due to the numerous ribosomes that occur along the ER. Rough ER connects to the nuclear envelope through which the messenger RNA (mRNA) that is the blueprint for proteins travels to the ribosomes. Smooth ER; lacks the ribosomes characteristic of Rough ER and is thought to be involved in transport and a variety of other functions.

Figure 13. The endoplasmic reticulum. Rough endoplasmic reticulum is on the left, smooth endoplasmic reticulum is on the right. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Figure 14. Rough Endoplasmic Reticulum with Ribosomes (TEM x61,560). This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.

Golgi Apparatus and Dictyosomes

Golgi Complexes, shown in Figure 15 and 16, are flattened stacks of membrane-bound sacs. Italian biologist Camillo Golgi discovered these structures in the late 1890s, although their precise role in the cell was not deciphered until the mid-1900s . Golgi function as a packaging plant, modifying vesicles produced by the rough endoplasmic reticulum. New membrane material is assembled in various cisternae (layers) of the golgi.

Figure 15. Structure of the Golgi apparatus and its functioning in vesicle-mediated transport. Images from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Figure 16. Golgi Apparatus in a plant parenchyma cell from Sauromatum guttatum (TEM x145,700). Note the numerous vesicles near the Golgi. This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.

Lysosomes

Lysosomes, shown in Figure 17, are relatively large vesicles formed by the Golgi. They contain hydrolytic enzymes that could destroy the cell. Lysosome contents function in the extracellular breakdown of materials.

Figure 17. Role of the Golgi in forming lysosomes. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Mitochondria

Mitochondria contain their own DNA (termed mDNA) and are thought to represent bacteria-like organisms incorporated into eukaryotic cells over 700 million years ago (perhaps even as far back as 1.5 billion years ago). They function as the sites of energy release (following glycolysis in the cytoplasm) and ATP formation (by chemiosmosis). The mitochondrion has been termed the powerhouse of the cell. Mitochondria are bounded by two membranes. The inner membrane folds into a series of cristae, which are the surfaces on which adenosine triphosphate (ATP) is generated. The matrix is the area of the mitochondrion surrounded by the inner mitochondrial membrane. Ribosomes and mitochondrial DNA are found in the matrix. The significance of these features will be discussed below. The structure of mitochondria is shown in Figure 18 and 19.

Figure 18. Structure of a mitochondrion. Note the various infoldings of the mitochondrial inner membrane that produce the cristae. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Figure 19. Muscle Cell Mitochondrion (TEM x190,920). This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.

Mitochondria and endosymbiosis

During the 1980s, Lynn Margulis proposed the theory of endosymbiosis to explain the origin of mitochondria and chloroplasts from permanent resident prokaryotes. According to this idea, a larger prokaryote (or perhaps early eukaryote) engulfed or surrounded a smaller prokaryote some 1.5 billion to 700 million years ago. Steps in this sequence are illustrated in Figure 20.

Figure 20. The basic events in endosymbiosis. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Instead of digesting the smaller organisms the large one and the smaller one entered into a type of symbiosis known as mutualism, wherein both organisms benefit and neither is harmed. The larger organism gained excess ATP provided by the "protomitochondrion" and excess sugar provided by the "protochloroplast", while providing a stable environment and the raw materials the endosymbionts required. This is so strong that now eukaryotic cells cannot survive without mitochondria (likewise photosynthetic eukaryotes cannot survive without chloroplasts), and the endosymbionts can not survive outside their hosts. Nearly all eukaryotes have mitochondria. Mitochondrial division is remarkably similar to the prokaryotic methods that will be studied later in this course. A summary of the theory is available by clicking here.

Plastids

Plastids are also membrane-bound organelles that only occur in plants and photosynthetic eukaryotes. Leucoplasts, also known as amyloplasts (and shown in Figure 21) store starch, as well as sometimes protein or oils. Chromoplasts store pigments associated with the bright colors of flowers and/or fruits.

Figure 21. Starch grains ina fresh-cut potato tuber. Image from http://images.botany.org/set-13/13-008v.jpg.

Chloroplasts, illustrated in Figures 22 and 23, are the sites of photosynthesis in eukaryotes. They contain chlorophyll, the green pigment necessary for photosynthesis to occur, and associated accessory pigments (carotenes and xanthophylls) in photosystems embedded in membranous sacs, thylakoids (collectively a stack of thylakoids are a granum [plural = grana]) floating in a fluid termed the stroma. Chloroplasts contain many different types of accessory pigments, depending on the taxonomic group of the organism being observed.

Figure 22. Structure of the chloroplast. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Figure 23. Chloroplast from red alga (Griffthsia spp.). x5,755--(Based on an image size of 1 inch in the narrow dimension). This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.

Chloroplasts and endosymbiosis

Like mitochondria, chloroplasts have their own DNA, termed cpDNA. Chloroplasts of Green Algae (Protista) and Plants (descendants of some of the Green Algae) are thought to have originated by endosymbiosis of a prokaryotic alga similar to living Prochloron (the sole genus present in the Prochlorobacteria, shown in Figure 24). Chloroplasts of Red Algae (Protista) are very similar biochemically to cyanobacteria (also known as blue-green bacteria [algae to chronologically enhanced folks like myself :)]). Endosymbiosis is also invoked for this similarity, perhaps indicating more than one endosymbiotic event occurred.

Figure 24. Prochloron, a photosynthetic bacteria, reveals the presence of numerous thylakoids in the transmission electron micrograph on the left. Prochloron occurs in long filaments, as shown by the light micrograph on the right below. Image from http://www.cas.muohio.edu/~wilsonkg/bot191/mouseth/m19p32.jpg.

Cell Movement

Cell movement; is both internal, referred to as cytoplasmic streaming, and external, referred to as motility. Internal movements of organelles are governed by actin filaments and other components of the cytoskeleton. These filaments make an area in which organelles such as chloroplasts can move. Internal movement is known as cytoplasmic streaming. External movement of cells is determined by special organelles for locomotion.

The cytoskeleton is a network of connected filaments and tubules. It extends from the nucleus to the plasma membrane. Electron microscopic studies showed the presence of an organized cytoplasm. Immunofluorescence microscopy identifies protein fibers as a major part of this cellular feature. The cytoskeleton components maintain cell shape and allow the cell and its organelles to move.

Actin filaments, shown in Figure 25, are long, thin fibers approximately seven nm in diameter. These filaments occur in bundles or meshlike networks. These filaments are polar, meaning there are differences between the ends of the strand. An actin filament consists of two chains of globular actin monomers twisted to form a helix. Actin filaments play a structural role, forming a dense complex web just under the plasma membrane. Actin filaments in microvilli of intestinal cells act to shorten the cell and thus to pull it out of the intestinal lumen. Likewise, the filaments can extend the cell into intestine when food is to be absorbed. In plant cells, actin filaments form tracts along which chloroplasts circulate.

Actin filaments move by interacting with myosin, The myosin combines with and splits ATP, thus binding to actin and changing the configuration to pull the actin filament forward. Similar action accounts for pinching off cells during cell division and for amoeboid movement.

Figure 25. Skeletal muscle fiber with exposed intracellular actin myosin filaments. The muscle fiber was cut perpendicular to its length to expose the intracellular actin myosin filaments. SEM X220. This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.

Intermediate filaments are between eight and eleven nm in diameter. They are between actin filaments and microtubules in size. The intermediate fibers are rope-like assemblies of fibrous polypeptides. Some of them support the nuclear envelope, while others support the plasma membrane, form cell-to-cell junctions.

Microtubules are small hollow cylinders (25 nm in diameter and from 200 nm-25 µm in length). These microtubules are composed of a globular protein tubulin. Assembly brings the two types of tubulin (alpha and beta) together as dimers, which arrange themselves in rows.

In animal cells and most protists, a structure known as a centrosome occurs. The centrosome contains two centrioles lying at right angles to each other. Centrioles are short cylinders with a 9 + 0 pattern of microtubule triplets. Centrioles serve as basal bodies for cilia and flagella. Plant and fungal cells have a structure equivalent to a centrosome, although it does not contain centrioles.

Cilia are short, usually numerous, hairlike projections that can move in an undulating fashion (e.g., the protzoan Paramecium, the cells lining the human upper respiratory tract). Flagella are longer, usually fewer in number, projections that move in whip-like fashion (e.g., sperm cells). Cilia and flagella are similar except for length, cilia being much shorter. They both have the characteristic 9 + 2 arrangement of microtubules shown in figures 26.

Figure 26. Cilia from an epithelial cell in cross section (TEM x199,500). Note the 9 + 2 arrangement of cilia. This image is copyright Dennis Kunkel at www.DennisKunkel.com, used with permission.

Cilia and flagella move when the microtubules slide past one another. Both oif these locomotion structures have a basal body at base with thesame arrangement of microtubule triples as centrioles. Cilia and flagella grow by the addition of tubulin dimers to their tips.

Flagella work as whips pulling (as in Chlamydomonas or Halosphaera) or pushing (dinoflagellates, a group of single-celled Protista) the organism through the water. Cilia work like oars on a viking longship (Paramecium has 17,000 such oars covering its outer surface). The movement of these structures is shown in Figure 27.

Figure 27. Movement of cilia and flagella. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

Not all cells use cilia or flagella for movement. Some, such as Amoeba, Chaos (Pelomyxa) and human leukocytes (white blood cells), employ pseudopodia to move the cell. Unlike cilia and flagella, pseudopodia are not structures, but rather are associated with actin near the moving edge of the cell. The formation of a pseudopod is shown in Figure 28.

Figure 28. Formation and functioning of a pseudopod by an amoeboid cell. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

READ MORE - Cellular Organization

The Origin of Cells

Origin of the Earth and Life

Scientific estimates place the origin of the Universe at between 10 and 20 billion years ago. The theory currently with the most acceptance is the Big Bang Theory, the idea that all matter in the Universe existed in a cosmic egg (smaller than the size of a modern hydrogen atom) that exploded, forming the Universe. Recent discoveries from the Space Telescope and other devices suggest this theory smay need some modification. Evidence for the Big Bang includes:

1) The Red Shift: when stars/galaxies are moving away from us the energy they emit is shifted to the red side of the visible-light spectrum. Those moving towards us are shifted to the violet side. This shift is an example of the Doppler effect. Similar effects are observed when listening to a train whistle-- it will sound higher (shorter wavelengths) approaching and lower (longer wavelengths) as it moves away. Likewise red wavelengths are longer than violet ones. Most galaxies appear to be moving away from ours. 2) Background radiation: two Bell Labs scientists discovered that in interstellar space there is a slight background radiation, thought to be the residual afterblast remnant of the Big Bang. Click here for additional information from sites dealing with the Big Bang, or here for a Powerpoint slideshow about the Big Bang.

Soon after the Big Bang the major forces (such as gravity, weak nuclear force, strong nuclear force, etc.) differentiated. While in the cosmic egg, scientists think that matter and energy as we understand them did not exist, but rather they formed soon after the bang. After 10 million to 1 billion years the universe became clumpy, with matter beginning to accumulate into solar systems. One of those solar systems, ours, began to form approximately 5 billion years ago, with a large "protostar" (that became our sun) in the center. The planets were in orbits some distance from the star, their increasing gravitational fields sweeping stray debris into larger and larger planetesimals that eventually formed planets.

The processes of radioactive decay and heat generated by the impact of planetesimals heated the Earth, which then began to differentiate into a "cooled" outer cooled crust (of silicon, oxygen and other relatively light elements) and increasingly hotter inner areas (composed of the heavier and denser elements such as iron and nickel). Impact (asteroid, comet, planetismals) and the beginnings of volcanism released water vapor, carbon dioxide, methane, ammonia and other gases into a developing atmosphere. Sometime "soon" after this, life on Earth began.

Where did life originate and how?

Extra-terrestrial: In 1969, a meteorite (left-over bits from the origin of the solar system) landed near Allende, Mexico. The Allende Meteorite (and others of its sort) have been analyzed and found to contain amino acids, the building blocks of proteins, one of the four organic molecule groups basic to all life. The idea of panspermia hypothesized that life originated out in space and came to Earth inside a meteorite. Recently, this idea has been revived as Cosmic Ancestry. The amino acids recovered from meteorites are in a group known as exotics: they do not occur in the chemical systems of living things. The ET theory is now not considered by most scientists to be correct, although the August 1996 discovery of the Martian meteorite and its possible fossils have revived thought of life elsewhere in the Solar System.

Supernatural: Since science is an attempt to measure and study the natural world, this theory is outside science (at least our current understanding of science). Science classes deal with science, and this idea is in the category of not-science. 

Organic Chemical Evolution: Until the mid-1800's scientists thought organic chemicals (those with a C-C skeleton) could only form by the actions of living things. A French scientist heated crystals of a mineral (a mineral is by definition inorganic), and discovered that they formed urea (an organic chemical) when they cooled. Russian scientist and academecian A.I. Oparin, in 1922, hypothesized that cellular life was preceeded by a period of chemical evolution. These chemicals, he argued, must have arisen spontaneously under conditions exisitng billions of years ago (and quite unlike current conditions).

Figure 1. Ingredients used in Miller's experiments, simple molecules thought at the time to have existed on the Earth billions of years ago. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

In 1950, then-graduate student Stanley Miller designed an experimental test for Oparin's hypothesis. Oparin's original hypothesis called for : 1) little or no free oxygen (oxygen not bonded to other elements); and 2) C H O and N in abundance. Studies of modern volcanic eruptions support inference of the existence of such an atmosphere. Miller discharged an electric spark into a mixture thought to resemble the primordial composition of the atmosphere. Miller's atmosphere contents are shown in Figure 1. From the water receptacle, designed to model an ancient ocean, Miller recovered amino acids. Subsequent modifications of the atmosphere have produced representatives or precursors of all four organic macromolecular classes. His experimental apparatus is shown in Figure 2. 

Figure 2. A diagrammatic representation of Miller's experimental apparatus. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

The primordial Earth was a very different place than today, with greater amounts of energy, stronger storms, etc. The oceans were a "soup" of organic compounds that formed by inorganic processes (although this soup would not taste umm ummm good). Miller's (and subsequent) experiments have not proven life originated in this way, only that conditions thought to have existed over 3 billion years ago were such that the spontaneous (inorganic) formation of organic macromolecules could have taken place. The simple inorganic molecules that Miller placed into his apparatus, produced a variety of complex molecules, shown below in Figure 3.

Figure 3. Molecules recovered from Miller's and similar experiments. Images from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

The interactions of these molecules would have increased as their concentrations increased. Reactions would have led to the building of larger, more complex molecules. A pre-cellular life would have began with the formation of nucleic acids. Chemicals made by these nucleic acids would have remained in proximity to the nucleic acids. Eventually the pre-cells would have been enclosed in a lipid-protein membrane, which would have resulted in the first cells.

Biochemically, living systems are separated from other chemical systems by three things.

1. The capacity for replication from one generation to another. Most organisms today use DNA as the hereditary material, although recent evidence (ribozymes) suggests that RNA may have been the first nucleic acid system to have formed. Nobel laureate Walter Gilbert refers to this as the RNA world. Recent studies suggest a molecular
2. The presence of enzymes and other complex molecules essential to the processes needed by living systems. Miller's experiment showed how these could possibly form.
3. A membrane that separates the internal chemicals from the external chemical environment. This also delimits the cell from not-cell areas. The work of Sidney W. Fox has produced proteinoid spheres, which while not cells, suggest a possible route from chemical to cellular life.

Fossil evidence supports the origins of life on Earth earlier than 3.5 billion years ago. The North Pole microfossils from Australia, illustrated in Figure 4, are complex enough that more primitive cells must have existed earlier. From rocks of the Ishua Super Group in Greenland come possibly the earliest cells, as much as 3.8 billion years old. The oldest known rocks on Earth are 3.96 billion years old and are from Arctic Canada. Thus, life appears to have begun soon after the cooling of the Earth and formation of the atmosphere and oceans. 

Figure 4. Microfossils from the Apex Chert, North Pole, Australia. These organisms are Archean in age, approximately 3.465 billion years old, and resemble filamentous cyanobacteria. Image from http://www.astrobiology.ucla.edu/ESS116/L15/1515%20Apex%20Chert.jpg.

These ancient fossils occur in marine rocks, such as limestones and sandstones, that formed in ancient oceans. The organisms living today that are most similar to ancient life forms are the archaebacteria. This group is today restricted to marginal environments. Recent discoveries of bacteria at mid-ocean ridges add yet another possible origin for life: at these mid-ocean ridges where heat and molten rock rise to the Earth's surface.

Archaea and Eubacteria are similar in size and shape. When we do recover "bacteria" as fossils those are the two features we will usually see: size and shape. How can we distinguish between the two groups: the use of molecular fossils that will point to either (but not both) groups. Such a chemical fossil has been found and its presence in the Ishua rocks of Greenland (3.8 billion years old) suggests that the archeans were present at that time.

Is there life on Mars, Venus, anywhere else?

The proximity of the Earth to the sun, the make-up of the Earth's crust (silicate mixtures, presence of water, etc.) and the size of the Earth suggest we may be unique in our own solar system, at least. Mars is smaller, farther from the sun, has a lower gravitational field (which would keep the atmosphere from escaping into space) and does show evidence of running water sometime in its past. If life did start on Mars, however, there appears to be no life (as we know it) today. Venus, the second planet, is closer to the sun, and appears similar to Earth in many respects. Carbon dioxide build-up has resulted in a "greenhouse planet" with strong storms and strongly acidic rain. Of all planets in the solar system, Venus is most likely to have some form of carbon-based life. The outer planets are as yet too poorly understood, although it seems unlikely that Jupiter or Saturn harbor life as we know it. Like Goldilocks would say "Venus is too hot, Mars is too cold, the Earth is just right!"

Mars: In August 1996, evidence of life on Mars (or at least the chemistry of life), was announced. Click here to view that article and related ones. The results of years of study are inconclusive at best. The purported bacteria are much smaller than any known bacteria on Earth, were not hollow, and most could possibly have been mineral in origin. However, many scientists consider that the chemistry of life appears to have been established on Mars. Search for martian life (or its remains) continues.

Terms applied to cells

Heterotroph (other-feeder): an organism that obtains its energy from another organism. Animals, fungi, bacteria, and mant protistans are heterotrophs.

Autotroph (self-feeder): an organism that makes its own food, it converts energy from an inorganic source in one of two ways. Photosynthesis is the conversion of sunlight energy into C-C covalent bonds of a carbohydrate, the process by which the vast majority of autotrophs obtain their energy. Chemosynthesis is the capture of energy released by certain inorganic chemical reactions. This is common in certain groups of likely that chemosynthesis predates photosynthesis. At mid-ocean ridges, scientists have discovered black smokers, vents that release chemicals into the water. These chemical reactions could have powered early ecosystems prior to the development of an ozone layer that would have permitted life to occupy the shallower parts of the ocean. Evidence of the antiquity of photosynthesis includes: a) biochemical precursors to photosynthesis chemicals have been synthesized in experiments; and b) when placed in light, these chemicals undergo chemical reactions similar to some that occur in primitive photosynthetic bacteria.

Prokaryotes are among the most primitive forms of life on Earth. Remember that primitive does not necessarily equate to outdated and unworkable in an evolutionary sense, since primitive bacteria seem little changed, and thus may be viewed as well adapted, for over 3.5 Ga. Prokaryote (pro=before, karyo=nucleus): these organisms lack membrane-bound organelles, as seen in Figures 5 and 6. Some internal membrane organization is observable in a few prokaryotic autotrophs, such as the photosynthetic membranes associated with the photosynthetic chemicals in the photosynthetic bacterium Prochloron. (click here to view Prochloron and other cyanobacteria at the Tree of Life Page). A transmission electron micrograph of Prochloron is shown in Figure 5. 

Figure 5 Prochloron, an extant prokaryote thought related to the ancestors of some eukarypote chloroplasts. Image fom http://tidepool.st.usm.edu/pix/prochloron.gif.

Figure 6. The main features of a generalized prokaryote cell. Image from Purves et al., Life: The Science of Biology, 4th Edition, by Sinauer Associates (www.sinauer.com) and WH Freeman (www.whfreeman.com), used with permission.

The Cell Theory is one of the foundations of modern biology. Its major tenets are:

• All living things are composed of one or more cells;
• The chemical reactions of living cells take place within cells;
• All cells originate from pre-existing cells; and
• Cells contain hereditary information, which is passed from one generation to another.

Components of Cells

Cell Membrane (also known as plasma membrane or plasmalemma) is surrounds all cells. It: 1) separates the inner parts of the cell from the outer environment; and 2) acts as a selectively permeable barrier to allow certain chemicals, namely water, to pass and others to not pass. In multicellular organisms certain chemicals on the membrane surface act in the recognition of self. Antigens are substances located on the outside of cells, viruses and in some cases other chemicals. Antibodies are chemicals (Y-shaped) produced by an animal in response to a specific antigen. This is the basis of immunity and vaccination.

Hereditary material (both DNA and RNA) is needed for a cell to be able to replicate and/or reproduce. Most organisms use DNA. Viruses and viroids sometimes employ RNA as their hereditary material. Retroviruses include HIV (Human Immunodefficiency Virus, the causative agent of AIDS) and Feline Leukemia Virus (the only retrovirus for which a successful vaccine has been developed). Viroids are naked pieces of RNA that lack cytoplasm, membranes, etc. They are parasites of some plants and also as possible glimpses of the functioning of pre-cellular life forms. Prokaryotic DNA is organized as a circular chromosome contained in an area known as a nucleoid. Eukaryotic DNA is organized in linear structures, the eukaryotic chromosomes, which are associations of DNA and histone proteins contained within a double membrane nuclear envelope, an area known as the cell nucleus.

Organelles are formed bodies within the cytoplasm that perform certain functions. Some organelles are surrounded by membranes, we call these membrane-bound organelles.

Ribosomes are the tiny structures where proteins synthesis occurs. They are not membrane-bound and occur in all cells, although there are differences between the size of subunits in eukaryotic and prokaryotic ribosomes.

The Cell Wall is a structure surrounding the plasma membrane. Prokaryote and eukaryote (if they have one) cell walls differ in their structure and chemical composition. Plant cells have cellulose in their cell walls, other organisims have different materials cpmprising their walls. Animals are distinct as a group in their lack of a cell wall.

Membrane-bound organelles occur only in eukaryotic cells. They will be discussed in detail later. Eukaryotic cells are generally larger than prokaryotic cells. Internal complexity is usually greater in eukaryotes, with their compartmentalized membrane-bound organelles, than in prokaryotes. Some prokaryotes, such as Anabaena azollae, and Prochloron, have internal membranes associated with photosynthetic pigments.

The Origins of Multicellularity

The oldest accepted prokaryote fossils date to 3.5 billion years; Eukaryotic fossils to between 750 million years and possibly as old as 1.2-1.5 billion years. Multicellular fossils, purportedly of animals, have been recovered from 750Ma rocks in various parts of the world. The first eukaryotes were undoubtedly Protistans, a group that is thought to have given rise to the other eukaryotic kingdoms. Multicellularity allows specialization of function, for example muscle fibers are specialized for contraction, neuron cells for transmission of nerve messages.

Microscopes

Microscopes are important tools for studying cellular structures. In this class we will use light microscopes for our laboratory observations. Your text will also show light photomicrographs (pictures taken with a light microscope) and electron micrographs (pictures taken with an electron microscope). There are many terms and concepts which will help you in maximizing your study of microscopy.

There are many different types of microscopes used in studying biology. These include the light microscopes (dissecting, compound brightfield, and compound phase-contrast), electron microscopes (transmission and scanning), and atomic force microscope.

The microscope is an important tool used by biologists to magnify small objects. There are several concepts fundamental to microscopy.

Magnification is the ratio of enlargement (or eduction) between the specimen and its image (either printed photograph or the virtual image seen through the eyepiece). To calculate magnification we multiply the power of each lens through which the light from the specimen passes, indicating that product as GGGX, where GGG is the product. For example: if the light passes through two,lenses (an objective lens and an ocular lens) we multiply the 10X ocular value by the value of the objective lens (say it is 4X): 10 X 4=40, or 40X magnification.

Resolution is the ability to distinguish between two objects (or points). The closer the two objects are, the easier it is to distinguish recognize the distance between them. What microscopes do is to bring small objects "closer" to the observer by increasing the magnification of the sample. Since the sample is the same distance from the viewer, a "virtual image" is formed as the light (or electron beam) passes through the magnifying lenses. Objects such as a human hair appear smooth (and feel smooth) when viewed with the unaided or naked) eye. However, put a hair under a microscope and it takes on a VERY different look!

Working distance is the distance between the specimen and the magnifying lens.

Depth of field is a measure of the amount of a specimen that can be in focus.

Magnification and resolution are terms used frequently in the study of cell biology, often without an accurate definition of their meanings. Magnification is a ratio of the enlargement (or reduction) of an image (drawing or photomicrograph), usually expressed as X1, X1/2, X430, X1000, etc. Resolution is the ability to distinguish between two points. Generally resolution increases with magnification, although there does come a point of diminishing returns where you increase magnification beyond added resolution gain.

Scientists employ the metric system to measure the size and volume of specimens. The basic unit of length is the meter (slightly over 1 yard). Prefixes are added to the "meter" to indicate multiple meters (kilometer) or fractional meters (millimeter). Below are the values of some of the prefixes used in the metric system.

kilo = one thousand of the basic unit

meter = basic unit of length

centi = one hundreth (1/100) of the basic unit

milli = one thousandth (1/1000) of the basic unit

micro = one millionth (1/1,000,000) of the basic unit

nano = one billionth (1/1,000,000,000) of the basic unit

The basic unit of length is the meter (m), and of volume it is the liter (l). The gram (g). Prefixes listed above can be applied to all of these basic units, abbreviated as km, kg, ml, mg, nm....etc. The Greek letter micron (µ) is applied to small measurements (thoud\sandths of a millimeter), producing the micrometer (symbolized as µm). Measurements in microscopy are usually expressed in the metric system. General units you will encounter in your continuing biology careers include micrometer (µm, 10^-6m), nanometer (nm, 10^-9m), and angstrom (Å, 10^-10m).

Light microscopes were the first to be developed, and still the most commonly used ones. The best resolution of light microscopes (LM) is 0.2 µm. Magnification of LMs is generally limited by the properties of the glass used to make microscope lenses and the physical properties of their light sources. The generally accepted maximum magnifications in biological uses are between 1000X and 1250X. Calculation of LM magnification is done by multiplying objective value by eyepiece value.

To view relatively large objects at lower magnifications we utilize the dissecting microscope (shown in Figure 7). Common uses of this microscope include examination of prepared microscope slides at low magnification, dissection (hence the name) of flowers or animal organs, and examinations of the surface of objects such as pennies and five dollar bills. Magnification on the dissecting microscope is calculated by multiplying the ocular (or eyepiece) value (usually 10X) by the value of the objective lens (a variable between 0.7 and 3X). The value of the objective lens is selected using a dial on the body tube of the microscope.

Figure 7. Parts of a Nikon dissecting microscope. Image courtesy of Nikon Co.

The compound light microscope, shown in Figure 8, uses two ground glass lenses to form the image. The lenses in this microscope, however, are aligned with the light source and specimen so that the light passes through the specimen, rather than reflects off the surface (as in the dissecting microscope shown in Figure 7). The compound microscope provides greater magnification (and resoultion), but only thin specimens (or thin slices of a specimen) can be viewed with this type of microscope.

Figure 8. Parts of a Nikon compound microscope. Image courtesy of Nikon Co.

Electron microscopes, two examples of which are shown in Fgure 9, are more rarely encountered by beginning biology students. However, the images gathered from these microscopes reveal a greater structure of the cell, so some familiarity with the strengths and weaknesses of each type is useful. Instead of using light as an imaging source, a high energy beam of electrons (between five thousand and one billion electron volts) is focused through electromagnetic lenses (instead of glass lenses used in the light microscope). The increased resolution results from the shorter wavelength of the electron beam, increasing resolution in the transmission electron microscope (TEM) to a theoretical limit of 0.2 nm. The magnifications reached by TEMs are commonly over 100,000X, depending on the nature of the sample and the operating condition of the TEM. The other type of electron microscope is the scanning electron microscope (SEM). It uses a different method of electron capture and displays images on high resolution television monitors. The resolution and magnification of the SEM are less than that of the TEM although still orders of magnitude above the LM.

Figure 9. Electron microcsopes. The above (left) image of a transmission electron microscope is from http://nsm.fullerton.edu/~skarl/EM/Equipment/TEM.html. The above right image of a scanning electron microscope is from http://nsm.fullerton.edu/~skarl/EM/Equipment/SEM.html.

READ MORE - The Origin of Cells