2. Elements of general biology

Outline: Autotrophs and Heterotrophs. How the Organisms Take In Energy. Photosynthesis: Using Energy for Making Food. Light and Dark Reactions. Glycolysis and Fermentation. The Role of Pigments. Respiration in the Cell: Aerobic and Anaerobic. Genetics is the Study of Heredity. Mendel and His Experiments. Punnett Square. The Chromosome Theory. Heredity and Regularity of Variability. The Role of Environment in Development and Manifestation of Traits. Twins. Sex-Linked Traits. Genetic Disorders. Blood Groups. The Beginnings of Selection and Breeding. Genetic Engineering. Growth as a Basic Life Process. DNA. Mitosis. Asexual and Sexual Reproduction. Parthenogenesis and Embryogenesis. Classification and identification. Different methods of classification. Naming organisms. Five kingdoms and their subdivisions. Tool for identification.

2.1. Introduction to Cell Biology

Charles Darwin faced a dilemma. In his great book On the Origin of Species, published in 1859, he proposed the theory of natural selection to explain the gradual appearance and disappearance of different forms of animals and plants over long periods of time. But he realized that the fossil record, on which he based his theory, was incomplete, especially for the beginning of life. The oldest fossils that had been found in Darwin’s time were complex organisms in rocks dated at about 550 million years ago (the Cambrian period). Where were the missing Precambrian fossils? These would surely provide a link to the origin of life. Conditions on Earth were probably suitable for the emergence of life by 4 billion years ago, about 600 million years after Earth began to form. But until recently there was no evidence for life older than the Cambrian. By the turn of the twentieth century, there was evidence for fossilized clumps of algae (simple aquatic photosynthetic organisms) in rocks at the base of the Grand Canyon that were close to 1 billion years old. It took nearly another century to push the clock of life back nearer to its origins. In 1993, geologist J. William Schopf found fossilized chains of cylindrical objects, quite similar in size and shape to contemporary cyanobacteria (“blue-green algae”), in rocks in Western Australia that he dated an astonishing 3.5 billion years old. He then used a chemical analysis method called laser Raman spectroscopy to show that these objects apparently contain carbon deposits that are chemical signatures of life. Rounded or cylindrical objects in the Earth’s rocks or in a meteorite from Mars get scientists excited because they realize that life is not just a bunch of macromolecules. Rather, life is macromolecules that can perform unique functions because they are enclosed in a structural compartment that is separate from the external environment. This separation allows living things to maintain a constant internal environment (homeostasis). The water-insoluble phospholipid structure that defines and contains cells is called the plasma membrane. It and its functions are so important. Subsequent pages will be devoted to the chemical activities that take place inside all cells.

2.1.1. Cells: The Basic Units of Life

Just as atoms are the units of chemistry, cells are the building blocks of life. Three statements constitute the cell theory:

Cells are the fundamental units of life.

All organisms are composed of cells.

All cells come from preexisting cells.

Cells are composed of water molecules and the small and large molecules. Each cell contains at least 10,000 different types of molecules, most of them present in many copies. Cells use these molecules to transform matter and energy, to respond to their environment, and to reproduce themselves. The cell theory has three important implications. First, it means that studying cell biology is in some sense the same as studying life. The principles that underlie the functions of the single cell in a bacterium are similar to those governing the 60 trillion cells of your body. Second, it means that life is continuous. All those cells in your body came from a single cell, the fertilized egg, which came from the fusion of two cells, a sperm and an egg from your parents, whose cells came from their fertilized eggs, and so on. Finally, it means that the origin of life on Earth was marked by the origin of the first cells.

Cells may have come from stable bubbles

Isolation from the general environment can be achieved in the laboratory within aggregates produced from molecules made in prebiotic synthesis experiments. Called protobionts, these aggregates cannot reproduce, but they can maintain internal chemical environments that differ from their surroundings. Under the microscope, they look a lot like tiny cells. In the 1920s, Alexander Oparin mixed a large protein and a polysaccharide in solution. When he agitated this mixture, bubbles formed. He could also do this with other polymers. The interiors of these bubbles had much higher concentrations of the macromolecules than their surroundings. Moreover, they catalyzed chemical reactions, and they had some control over what left them and crossed the boundary into the environment. In other words, they were protobionts. Later, other researchers showed that if lipids are mixed in an aqueous environment, they spontaneously arrange themselves into droplets surrounded by a bilayer. Taken together with the prebiotic chemistry models and RNAworld hypothesis, these experiments suggest a bubble theory for the origin of cells.

Cell size is limited by the surface area-to-volume ratio

Most cells are tiny. The volume of cells ranges from 1 to 1,000 m3. The eggs of some birds are enormous exceptions, to be sure, and individual cells of several types of algae and bacteria are large enough to be viewed with the unaided eye. And although neurons (nerve cells) have a volume that is within the “normal” cell range, they often have fine projections that may extend for meters, carrying signals from one part of a large animal to another. But by and large, cells are minuscule. The reason for this relates to the change in the surface area-to-volume ratio (SA/V) of any object as it increases in size. As a cell increases in volume, its surface area also increases, but not to the same extent. This phenomenon has great biological significance for two reasons: The volume of a cell determines the amount of chemical activity it carries out per unit of time. The surface area of a cell determines the amount of substances the cell can take in from the outside environment and the amount of waste products it can release to the environment. As a living cell grows larger, its rate of waste production and its need for resources increase faster than its surface area. This explains why large organisms must consist of many small cells: cells are small in volume in order to maintain a large surface area-to-volume ratio. In a multicellular organism, the large surface area represented by the multitude of small cells that make up the organism enables it to carry out the multitude of functions required for survival. Special structures transport food, oxygen and waste materials to and from the small cells that are distant from the external surface of the organism.

Most cells are invisible to the human eye. The smallest object a person can typically discern is about 0.2 mm size. We refer to this measure as resolution, the distance apart two objects must be in order for them to be distinguished as separate; if they are closer together, they appear as a single blur. Many cells are much smaller than 0, 2 mm Microscopes are instruments used to improve resolution so that cells and their internal structures can be seen. There are two basic types of microscopes: light microscopes and electron microscopes. The light microscope (LM) uses glass lenses and visible light to form a magnified image of an object. It has a resolving power of about 0. 2 nano-m, which is 1,000 times that of the human eye. It allows visualization of cell sizes and shapes and some internal cell structures. The latter are hard to see under ordinary light, so cells are often killed and stained with various dyes to make certain structures stand out.

An electron microscope (EM) uses magnets to focus an electron beam, much as a light microscope uses glass lenses to focus a beam of light. Since we cannot see electrons, the electron microscope directs them at a fluorescent screen or photographic film to create a visible image. The resolving power of electron microscopes is about 0.5 nm, which is 400,000 times that of the human eye. This resolving power permits the details of many subcellular structures to be distinguished. Many techniques have been developed to enhance the views of cells we see under the light and electron microscopes.

Cells are surrounded by a plasma membrane

As we have noted, a plasma membrane separates each cell from its environment, creating a segregated (but not isolated) compartment. The plasma membrane is composed of a phospholipids bilayer, with the hydrophilic “heads” of the lipids facing the cell’s aqueous interior on one side of the membrane and the extracellular environment on the other. Proteins are embedded in the lipids. In many cases, these proteins protrude into the cytoplasm and into the extracellular environment. The plasma membrane allows the cell to maintain a more or less constant internal environment. A self-maintaining, constant internal environment is a key characteristic of life.

The plasma membrane acts as a selectively permeable barrier, preventing some substances from crossing while permitting other substances to enter and leave the cell. As the cell’s boundary with the outside environment, the plasma membrane is important in communicating with adjacent cells and receiving extracellular signals. The plasma membrane often has molecules protruding from it that are responsible for binding and adhering to adjacent cells.

Cells show two organizational patterns

Prokaryotic cell organization is characteristic of the domains Bacteria and Archaea. Organisms in these domains are called prokaryotes. Their cells do not have membrane-enclosed internal compartments. The first cells ever to form were undoubtedly similar in organization to modern prokaryotes.

Eukaryotic cell organization is found in the domain Eukarya, which includes the protists, plants, fungi, and animals.

The genetic material (DNA) of eukaryotic cells is contained in a special membrane-enclosed compartment called the nucleus. Eukaryotic cells also contain other membrane-enclosed compartments in which specific chemical reactions take place. Organisms with this type of cell organization are known as eukaryotes. Both prokaryotes and eukaryotes have prospered for many hundreds of millions of years of evolution and both are great success stories.

Prokaryotic Cells

Prokaryotes can live off more different and diverse energy sources than any other living creatures and they inhabit greater environmental extremes, such as very hot springs and very salty water. Prokaryotic cells are generally smaller than eukaryotic cells. Each prokaryote is a single cell, but many types of prokaryotes are usually seen in chains, small clusters, or even clusters containing hundreds of individuals. In this section, we will first consider the features that cells in the domains Bacteria and Archaea have in common. Then we will examine structural features that are found in some but not all prokaryotes.

Prokaryotic cells share certain features

All prokaryotic cells have the same basic structure:

The plasma membrane encloses the cell regulating the traffic of materials into and out of the cell and separating it from its environment.

A region called the nucleoid contains the hereditary material (DNA) of the cell.

The rest of the material enclosed in the plasma membrane is called the cytoplasm. The cytoplasm is composed of two parts: the liquid cytosol, and insoluble suspended particles including ribosomes.

The cytosol consists mostly of water that contains dissolved ions, small molecules, and soluble macromolecules such as proteins.

Ribosomes are granules about 25 nm in diameter that are sites of protein synthesis. The cytoplasm is not a static region. Rather, the substances in this aqueous environment are in constant motion. For example, a typical protein moves around the entire cell within a minute, and encounters many molecules along the way. Although structurally less complicated than eukaryotic cells, prokaryotic cells are functionally complex, carrying out thousands of biochemical transformations.

Some prokaryotic cells have specialized features

As they evolved, some prokaryotes developed specialized structures that gave a selective advantage to those cells that had them. These structures include a protective cell wall, an internal membrane for compartmentalization of chemical reactions and flagella for cell movement through the watery environment.

Cell walls

Most prokaryotes have a cell wall located outside the plasma membrane. The rigidity of the cell wall supports the cell and determines its shape. The cell walls of most bacteria, but not archaea, contain peptidoglycan, a polymer of amino sugars, cross-linked by covalent bonds to form a single giant molecule around the entire cell. In some bacteria, another layer—the outer membrane (a polysaccharide- rich phospholipid membrane)—encloses the peptidoglycan layer. Unlike the plasma membrane, this outer membrane is not a major permeability barrier, and some of its polysaccharides are disease-causing toxins. Enclosing the cell wall in some bacteria is a layer of slime composed mostly of polysaccharides and referred to as a capsule. The capsules of some bacteria may protect them from attack by white blood cells in the animals they infect. The capsule helps keep the cell from drying out, and sometimes it helps the bacterium attach to other cells. Many prokaryotes produce no capsule, and those that do have capsules can survive even if they lose them, so the capsule is not essential to cell life. As you will see later in this chapter, eukaryotic plant cells also have a cell wall, but it differs in composition and structure from the cell walls of prokaryotes.