HNSC 3162 Biological Concepts in Public Health (Cai)

Learning Objectives:

By the end of this section, you will be able to:

• Describe how our ancestors improved food with the use of invisible microbes
• Describe key historical events associated with the birth of microbiology

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Content:

• Microorganisms (or microbes) are living organisms that are generally too small to be seen without a microscope.
• Throughout history, humans have used microbes to make fermented foods such as beer, bread, cheese, and wine.

Fermented Foods and Beverages

People across the world have enjoyed fermented foods and beverages like beer, wine, bread, yogurt, cheese, and pickled vegetables for all of recorded history. Discoveries from several archeological sites suggest that even prehistoric people took advantage of fermentation to preserve and enhance the taste of food. Archaeologists studying pottery jars from a Neolithic village in China found that people were making a fermented beverage from rice, honey, and fruit as early as 7000 BC.³

Production of these foods and beverages requires microbial fermentation, a process that uses bacteria, mold, or yeast to convert sugars (carbohydrates) to alcohol, gases, and organic acids. While it is likely that people first learned about fermentation by accident—perhaps by drinking old milk that had curdled or old grape juice that had fermented—they later learned to harness the power of fermentation to make products like bread, cheese, and wine.

• Long before the invention of the microscope, some people theorized that infection and disease were spread by living things that were too small to be seen. They also correctly intuited certain principles regarding the spread of disease and immunity.
• Antonie van Leeuwenhoek, using a microscope, was the first to actually describe observations of bacteria, in 1675.
• During the Golden Age of Microbiology (1857–1914), microbiologists, including Louis Pasteur and Robert Koch, discovered many new connections between the fields of microbiology and medicine.

The Birth of Microbiology

While the ancients may have suspected the existence of invisible “minute creatures,” it wasn’t until the invention of the microscope that their existence was definitively confirmed. While it is unclear who exactly invented the microscope, a Dutch cloth merchant named Antonie van Leeuwenhoek (1632–1723) was the first to develop a lens powerful enough to view microbes. In 1675, using a simple but powerful microscope, Leeuwenhoek was able to observe single-celled organisms, which he described as “animalcules” or “wee little beasties,” swimming in a drop of rain water. From his drawings of these little organisms, we now know he was looking at bacteria and protists. (We will explore Leeuwenhoek’s contributions to microscopy further in How We See the Invisible World.)

Nearly 200 years after van Leeuwenhoek got his first glimpse of microbes, the “Golden Age of Microbiology” spawned a host of new discoveries between 1857 and 1914. Two famous microbiologists, Louis Pasteur and Robert Koch, were especially active in advancing our understanding of the unseen world of microbes (Figure 1.6 ). Pasteur, a French chemist, showed that individual microbial strains had unique properties and demonstrated that fermentation is caused by microorganisms. He also invented pasteurization, a process used to kill microorganisms responsible for spoilage, and developed vaccines for the treatment of diseases, including rabies, in animals and humans. Koch, a German physician, was the first to demonstrate the connection between a single, isolated microbe and a known human disease. For example, he discovered the bacteria that cause anthrax (Bacillus anthracis), cholera (Vibrio cholera), and tuberculosis (Mycobacterium tuberculosis).¹⁰

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Knowledge Check:

Learning Objectives:

By the end of this section, you will be able to:

• List the various types of microorganisms and describe their defining characteristics.
• Convert between units of length commonly used in microbiology.

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Content:

Most microbes are unicellular and small enough that they require artificial magnification to be seen. However, there are some unicellular microbes that are visible to the naked eye, and some multicellular organisms that are microscopic. An object must measure about 100 micrometers (µm) to be visible without a microscope, but most microorganisms are many times smaller than that. For some perspective, consider that a typical animal cell measures roughly 10 µm across but is still microscopic. Bacterial cells are typically about 1 µm, and viruses can be 10 times smaller than bacteria (Figure 1.12). See Table 1.1 for units of length used in microbiology.

Microorganisms differ from each other not only in size, but also in structure, habitat, metabolism, and many other characteristics. While we typically think of microorganisms as being unicellular, there are also many multicellular organisms that are too small to be seen without a microscope. Some microbes, such as viruses, are even acellular (not composed of cells).

Microorganisms are found in each of the three domains of life: Archaea, Bacteria, and Eukarya. Microbes within the domains Bacteria and Archaea are all prokaryotes (their cells lack a nucleus), whereas microbes in the domain Eukarya are eukaryotes (their cells have a nucleus). Some microorganisms, such as viruses, do not fall within any of the three domains of life. In this section, we will briefly introduce each of the broad groups of microbes.  

• Microorganisms are very diverse and are found in all three domains of life: Archaea, Bacteria, and Eukarya.
• Archaea and bacteria are classified as prokaryotes because they lack a cellular nucleus. Archaea differ from bacteria in evolutionary history, genetics, metabolic pathways, and cell wall and membrane composition.
• Archaea inhabit nearly every environment on earth, but no archaea have been identified as human pathogens.
• Eukaryotes studied in microbiology include algae, protozoa, fungi, and helminths.
  • Algae are plant-like organisms that can be either unicellular or multicellular, and derive energy via photosynthesis.
  • Protozoa are unicellular organisms with complex cell structures; most are motile.
  • Microscopic fungi include molds and also yeasts.
  • Helminths are multicellular parasitic worms. They are included in the field of microbiology because their eggs and larvae are often microscopic.
• Viruses are acellular microorganisms that require a host to reproduce.
• The field of microbiology is extremely broad. Microbiologists typically specialize in one of many subfields, but all health professionals need a solid foundation in clinical microbiology.

Eukaryotic Cell:

Eukaryotic organisms include protozoans, algae, fungi, plants, and animals. Some eukaryotic cells are independent, single-celled microorganisms, whereas others are part of multicellular organisms. The cells of eukaryotic organisms have several distinguishing characteristics. Above all, eukaryotic cells are defined by the presence of a nucleus surrounded by a complex nuclear membrane. Also, eukaryotic cells are characterized by the presence of membrane-bound organelles in the cytoplasm. Organelles such as mitochondria, the endoplasmic reticulum (ER), Golgi apparatus, lysosomes, and peroxisomes are held in place by the cytoskeleton, an internal network that supports transport of intracellular components and helps maintain cell shape (Figure 3.35). The genome of eukaryotic cells is packaged in multiple, rod-shaped chromosomes as opposed to the single, circular-shaped chromosome that characterizes most prokaryotic cells.

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Knowledge Check:

Learning Objectives:

By the end of this section, you will be able to:

• Explain the distinguishing characteristics that differentiate between prokaryotic and eukaryotic cells.
• Describe common cell morphologies and cellular arrangements typical of prokaryotic cells.
• Explain how prokaryotic cells maintain their morphology.
• Identify and describe structures and organelles unique to eukaryotic cells.
• Describe the plasma membrane eukaryotic and prokaryotic cells.

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Content:

Life takes many forms, from giant redwood trees towering hundreds of feet in the air to the tiniest known microbes, which measure only a few billionths of a meter. Humans have long pondered life’s origins and debated the defining characteristics of life, but our understanding of these concepts has changed radically since the invention of the microscope. In the 17th century, observations of microscopic life led to the development of the cell theory: the idea that the fundamental unit of life is the cell, that all organisms contain at least one cell, and that cells only come from other cells.

Despite sharing certain characteristics, cells may vary significantly. The two main types of cells are prokaryotic cells (lacking a nucleus) and eukaryotic cells (containing a well-organized, membrane-bound nucleus). Each type of cell exhibits remarkable variety in structure, function, and metabolic activity

Cell theory states that the cell is the fundamental unit of life. However, cells vary significantly in size, shape, structure, and function. At the simplest level of construction, all cells possess a few fundamental components. These include cytoplasm (a gel-like substance composed of water and dissolved chemicals needed for growth), which is contained within a plasma membrane (also called a cell membrane or cytoplasmic membrane); one or more chromosomes, which contain the genetic blueprints of the cell; and ribosomes, organelles used for the production of proteins.

Unique Characteristics of prokaryotic and eukaryotic cells:

Beyond these basic components, cells can vary greatly between organisms, and even within the same multicellular organism. The two largest categories of cells—prokaryotic cells and eukaryotic cells—are defined by major differences in several cell structures. Prokaryotic cells lack a nucleus surrounded by a complex nuclear membrane and generally have a single, circular chromosome located in a nucleoid. Eukaryotic cells have a nucleus surrounded by a complex nuclear membrane that contains multiple, rod-shaped chromosomes.¹⁶

All plant cells and animal cells are eukaryotic. Some microorganisms are composed of prokaryotic cells, whereas others are composed of eukaryotic cells. Prokaryotic microorganisms are classified within the domains Archaea and Bacteria, whereas eukaryotic organisms are classified within the domain Eukarya.

Prokaryotic Cells

The structures inside a cell are analogous to the organs inside a human body, with unique structures suited to specific functions. Some of the structures found in prokaryotic cells are similar to those found in some eukaryotic cells; others are unique to prokaryotes. Although there are some exceptions, eukaryotic cells tend to be larger than prokaryotic cells. The comparatively larger size of eukaryotic cells dictates the need to compartmentalize various chemical processes within different areas of the cell, using complex membrane-bound organelles. In contrast, prokaryotic cells generally lack membrane-bound organelles; however, they often contain inclusions that compartmentalize their cytoplasm. Figure 3.12 illustrates structures typically associated with prokaryotic cells.

• Prokaryotic cells differ from eukaryotic cells in that their genetic material is contained in a nucleoid rather than a membrane-bound nucleus. In addition, prokaryotic cells generally lack membrane-bound organelles.
• Prokaryotic cells of the same species typically share a similar cell morphology (cell shape), and cellular arrangement.
• Most prokaryotic cells have a cell wall that helps the organism maintain cellular morphology and protects it against changes in osmotic pressure. (Figure 3.15 & 16)

• Outside of the nucleoid, prokaryotic cells may contain extrachromosomal DNA in plasmids.
• Prokaryotic ribosomes that are found in the cytoplasm.
• Some prokaryotic cells have inclusions that store nutrients or chemicals for other uses.
• Some prokaryotic cells are able to form endospores through sporulation to survive in a dormant state when conditions are unfavorable. Endospores can germinate, transforming back into vegetative cells when conditions improve.
• Bacterial membranes are composed of phospholipids with integral or peripheral proteins. The fatty acid components of these phospholipids are ester-linked and are often used to identify specific types of bacteria. The proteins serve a variety of functions, including transport, cell-to-cell communication, and sensing environmental conditions.

Eukaryotic Cell:

Eukaryotic organisms include protozoans, algae, fungi, plants, and animals. Some eukaryotic cells are independent, single-celled microorganisms, whereas others are part of multicellular organisms. The cells of eukaryotic organisms have several distinguishing characteristics. Above all, eukaryotic cells are defined by the presence of a nucleus surrounded by a complex nuclear membrane. Also, eukaryotic cells are characterized by the presence of membrane-bound organelles in the cytoplasm. Organelles such as mitochondria, the endoplasmic reticulum (ER), Golgi apparatus, lysosomes, and peroxisomes are held in place by the cytoskeleton, an internal network that supports transport of intracellular components and helps maintain cell shape (Figure 3.35). The genome of eukaryotic cells is packaged in multiple, rod-shaped chromosomes as opposed to the single, circular-shaped chromosome that characterizes most prokaryotic cells.

• Eukaryotic cells are defined by the presence of a nucleus containing the DNA genome and bound by a nuclear membrane (or nuclear envelope) composed of two lipid bilayers that regulate transport of materials into and out of the nucleus through nuclear pores.
• The nucleolus, located in the nucleus of eukaryotic cells, is the site of ribosomal synthesis and the first stages of ribosome assembly.
• Eukaryotic cells contain ribosomes in the rough endoplasmic reticulum (membrane bound-ribosomes) and cytoplasm (free ribosomes).
• Eukaryotic cells have evolved an endomembrane system, containing membrane-bound organelles involved in transport. These include vesicles, the endoplasmic reticulum, and the Golgi apparatus.
  • The smooth endoplasmic reticulum plays a role in lipid biosynthesis, carbohydrate metabolism, and detoxification of toxic compounds. The rough endoplasmic reticulum contains membrane-bound 80S ribosomes that synthesize proteins destined for the cell membrane
  • The Golgi apparatus processes proteins and lipids, typically through the addition of sugar molecules, producing glycoproteins or glycolipids, components of the plasma membrane that are used in cell-to-cell communication.
• Lysosomes contain digestive enzymes that break down small particles ingested by endocytosis, large particles or cells ingested by phagocytosis, and damaged intracellular components.
• Mitochondria are the site of cellular respiration. They have two membranes: an outer membrane and an inner membrane with cristae. The mitochondrial matrix, within the inner membrane, contains the mitochondrial DNA, 70S ribosomes, and metabolic enzymes.
• The plasma membrane of eukaryotic cells is similar in structure to the prokaryotic plasma membrane in that it is composed mainly of phospholipids forming a bilayer with embedded peripheral and integral proteins (Figure 3.54). These membrane components move within the plane of the membrane according to the fluid mosaic model. However, unlike the prokaryotic membrane, eukaryotic membranes contain sterols, including cholesterol, that alter membrane fluidity. Additionally, many eukaryotic cells contain some specialized lipids, including sphingolipids, which are thought to play a role in maintaining membrane stability as well as being involved in signal transduction pathways and cell-to-cell communication.

• Cells of fungi, algae, plants, and some protists have a cell wall, whereas cells of animals and some protozoans have a sticky extracellular matrix that provides structural support and mediates cellular signaling.

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Knowledge Check:

Learning Objectives:

By the end of this section, you will be able to:

• give examples of monosaccharides, disaccharides and polysaccharides.
• list main categories of lipids.
• compare triglycerides and phospholipids in their structure and function.
• describe how phospholipids are used to construct biological membranes.
• describe the chemical structures of proteins.
• summarize the functions of proteins.

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Content:

• The most abundant elements in cells are hydrogen, carbon, oxygen, nitrogen, phosphorus, and sulfur.
• Life is carbon based. Each carbon atom can bind to another one producing a carbon skeleton that can be straight, branched, or ring shaped.
• Macromolecules are polymers assembled from individual units, monomers, which bind together like building blocks. Many biologically significant macromolecules are formed by dehydration synthesis, a process in which monomers bind together by combining their functional groups and generating water molecules as byproducts.

7.2 Carbohydrates

• Carbohydrates, the most abundant biomolecules on earth, are widely used by organisms for structural and energy-storage purposes.
• Simple sugar, individual sugar molecules (monosaccharides), are the building blocks for the synthesis of polymers or complex carbohydrates. Common monosaccharides include glucose, fructose and galactose.
• Disaccharides such as sucrose, lactose, and maltose are molecules composed of two monosaccharides linked together by a glycosidic bond.
• Polysaccharides, or glycans, are polymers composed of hundreds of monosaccharide monomers linked together by glycosidic bonds. The energy-storage polymers starch and glycogen are examples of polysaccharides and are all composed of branched chains of glucose molecules.
• The polysaccharide cellulose is a common structural component of the cell walls of organisms.

7.3 Lipids

• Lipids are composed mainly of carbon and hydrogen, but they can also contain oxygen, nitrogen, sulfur, and phosphorous. They provide nutrients for organisms, store carbon and energy, play structural roles in membranes, and function as hormones, pharmaceuticals, fragrances, and pigments.
• Fatty acids are long-chain hydrocarbons with a carboxylic acid functional group. Their relatively long nonpolar hydrocarbon chains make them hydrophobic (“water fearing”). Fatty acids with no double bonds between carbon atoms are saturated; those with double bonds between carbon atoms are unsaturated.
• The primary classes of lipids include triglycerides, phospholipids and steroids.
• Fatty acids chemically bond to glycerol to form structurally essential lipids such as triglycerides (Figure 7.12) and phospholipids (Figure 7.13). 

Triglycerides comprise three fatty acids bonded to glycerol, yielding a hydrophobic molecule. Triglycerides are the primary components of adipose tissue (body fat) and are major constituents of sebum (skin oils). They play an important metabolic role, serving as efficient energy-storage molecules that can provide more than double the caloric content of both carbohydrates and proteins.

Phospholipids contain both hydrophobic hydrocarbon chains and polar head groups, making them amphipathic. Because the phosphate is charged, it is capable of strong attraction to water molecules and thus is hydrophilic, or “water loving.” and capable of forming uniquely functional large-scale structures. A molecule presenting a hydrophobic portion and a hydrophilic moiety is said to be amphipathic. The amphipathic nature of phospholipids enables them to form uniquely functional structures in aqueous environments.

Biological membranes are large-scale structures based on phospholipid bilayers that provide hydrophilic exterior and interior surfaces suitable for aqueous environments, separated by an intervening hydrophobic layer. These bilayers are the structural basis for cell membranes in most organisms, as well as subcellular components such as vesicles.

• Another type of lipids are steroids, complex, ringed structures that are found in cell membranes; some function as hormones. The most common types of steroids are sterols, and the most common sterol found in animal tissues is cholesterol.

7.4 Proteins

• Amino acids are small molecules essential to all life. Each has an α carbon to which a hydrogen atom, carboxyl group, and amine group are bonded. The fourth bonded group, represented by R, varies in chemical composition, size, polarity, and charge among different amino acids, providing variation in properties. A few examples illustrating these possibilities are provided in Figure 7.17.

• Proteins are polymers formed by the linkage of a very large number of amino acids. They perform many important functions in a cell, serving as nutrients and enzymes; storage molecules for carbon, nitrogen, and energy; and structural components.
• The structure of a protein is a critical determinant of its function and is described by a graduated classification: primary, secondary, tertiary, and quaternary. The native structure of a protein may be disrupted by denaturation, resulting in loss of its higher-order structure and its biological function.
• Some proteins are formed by several separate protein subunits, the interaction of these subunits composing the quaternary structure of the protein complex.

• Proteins can function as structural components of cells and subcellular entities, as sources of nutrients, as atom- and energy-storage reservoirs, and as functional species such as hormones, enzymes, receptors, and transport molecules.

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Knowledge Check:

Learning Objectives:

By the end of this section, you will be able to:

• name the 6 essential nutrients for humans.
• Identify examples in each category of essential nutrients.
• Summarize the functions of each.

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Content:

Nutrition can be defined as the science of food, beverages, and their components in biological systems. A nutrient is a compound that provides a needed function in the body. Nutrients can be further classified based on the amount needed in the body.

Essential Nutrients

The six Essential Nutrients are the nutrients that our bodies need in order to survive. They can be broken into two categories: macronutrients and micronutrients. Throughout this class we will go into more detail about each of the essential nutrients.

Macronutrients are nutrients needed in larger amounts.  There are four macronutrients which include:

• carbohydrates
• lipids
• protein
• water

Micronutrients are nutrients needed in smaller amounts, but they are still considered essential. There are two groups of micronutrients which are:

• vitamins
• minerals

Carbohydrates

Carbohydrates are the primary form of energy. The name carbohydrate means “hydrated carbon” or carbon with water. Thus, it isn’t a surprise that carbohydrates are made up of carbon, hydrogen, and oxygen. Sucrose (table sugar) is an example of a commonly consumed carbohydrate. Some dietary examples of carbohydrates are whole-wheat bread, oatmeal, rice, sugary snacks/drinks, and pasta.

Grains, such as those in this whole wheat bread, are carbohydrates.

 

Lipids (Fats)

Lipids consist of fatty acids, triglycerides, phospholipids, and sterols (i.e. cholesterol). Lipids are also composed of carbon, hydrogen, and oxygen. Some dietary sources of lipids include oils, butter, and egg yolks.

Butter is a food source of lipids.

Proteins

Proteins are also made up of carbon, hydrogen, and oxygen, but they also contain nitrogen. Several dietary sources of proteins include nuts, beans/legumes, skim milk, egg whites, and meat.

Eggs are a source of protein.

Water

Water is made up of hydrogen and oxygen (H2O) and is the only macronutrient that doesn’t provide energy.

Thirsty? There is a reason

Vitamins

Vitamins are compounds that are essential for normal physiologic processes in the body.

Oranges are a food source for Vitamin C.

Minerals

Minerals are elements (think periodic table) that are essential for normal physiologic processes in the body.

Table salt is a food source for sodium, a mineral.

Importance of Food Groups

The organic molecules required for building cellular material and tissues must come from food. During digestion, digestible carbohydrates are ultimately broken down into glucose and used to provide energy within the cells of the body. Complex carbohydrates, including polysaccharides, can be broken down into glucose through biochemical modification; however, humans do not produce the enzyme necessary to digest cellulose (fiber). The intestinal flora in the human gut are able to extract some nutrition from these plant fibers. These plant fibers are known as dietary fiber and are an important component of the diet. The excess sugars in the body are converted into glycogen and stored for later use in the liver and muscle tissue. Glycogen stores are used to fuel prolonged exertions, such as long-distance running, and to provide energy during food shortage. Fats are stored under the skin of mammals for insulation and energy reserves.

Proteins in food are broken down during digestion and the resulting amino acids are absorbed. All the proteins in the body must be formed from these amino-acid constituents; no proteins are obtained directly from food.

Fats add flavor to food and promote a sense of satiety or fullness. Fatty foods are also significant sources of energy, and fatty acids are required for the construction of lipid membranes. Fats are also required in the diet to aid the absorption of fat-soluble vitamins and the production of fat-soluble hormones.

While the animal body can synthesize many of the molecules required for function from precursors, there are some nutrients that must be obtained from food. These nutrients are termed essential nutrients, meaning they must be eaten, because the body cannot produce them.

The fatty acids omega-3 alpha-linolenic acid and omega-6 linoleic acid are essential fatty acids needed to make some membrane phospholipids. Vitamins are another class of essential organic molecules that are required in small quantities. Many of these assist enzymes in their function and, for this reason, are called coenzymes. Absence or low levels of vitamins can have a dramatic effect on health. Minerals are another set of inorganic essential nutrients that must be obtained from food. Minerals perform many functions, from muscle and nerve function, to acting as enzyme cofactors. Certain amino acids also must be procured from food and cannot be synthesized by the body. These amino acids are the “essential” amino acids. The human body can synthesize only 11 of the 20 required amino acids; the rest must be obtained from food.

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Knowledge Check:

Learning Objectives:

By the end of this section, you will be able to:

• define metabolism, anabolism, and catabolism, exergonic and the endergonic reactions.
• compare autotrophs and heterotrophs.
• describe the importance of oxidation-reduction reactions in metabolism.
• describe why ATP, FAD, NAD+, and NADP+ are important in a cell.
• explain why the phosphate bonds in ATP are called high energy phosphate bonds.

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1. Introduction Content:

The term used to describe all of the chemical reactions inside a cell is metabolism (Figure 8.2). Cellular processes such as the building or breaking down of complex molecules occur through series of stepwise, interconnected chemical reactions called metabolic pathways. Reactions that are spontaneous and release energy are exergonic reactions, whereas endergonic reactions require energy to proceed. The term anabolism refers to those endergonic metabolic pathways involved in biosynthesis, converting simple molecular building blocks into more complex molecules, and fueled by the use of cellular energy. Conversely, the term catabolism refers to exergonic pathways that break down complex molecules into simpler ones. Molecular energy stored in the bonds of complex molecules is released in catabolic pathways and harvested in such a way that it can be used to produce high-energy molecules, which are used to drive anabolic pathways. Thus, in terms of energy and molecules, cells are continually balancing catabolism with anabolism.

Organisms Classification by Carbon and Energy Source

Organisms can be identified according to the source of carbon they use for metabolism as well as their energy source. The prefixes auto- (“self”) and hetero- (“other”) refer to the origins of the carbon sources various organisms can use. Organisms that convert inorganic carbon dioxide (CO2) into organic carbon compounds are autotrophs. Plants and cyanobacteria are well-known examples of autotrophs. Conversely, heterotrophs rely on more complex organic carbon compounds as nutrients; these are provided to them initially by autotrophs. Many organisms, ranging from humans to many prokaryotes, including the well-studied Escherichia coli, are heterotrophic.

Oxidation and Reduction in Metabolism

The transfer of electrons between molecules is important because most of the energy stored in atoms and used to fuel cell functions is in the form of high-energy electrons. The transfer of energy in the form of electrons allows the cell to transfer and use energy incrementally; that is, in small packages rather than a single, destructive burst. Reactions that remove electrons from donor molecules, leaving them oxidized, are oxidation reactions; those that add electrons to acceptor molecules, leaving them reduced, are reduction reactions. Because electrons can move from one molecule to another, oxidation and reduction occur in tandem. These pairs of reactions are called oxidation-reduction reactions, or redox reactions.

Energy Carriers: NAD+, NADP+, FAD, and ATP

The energy released from the breakdown of the chemical bonds within nutrients can be stored either through the reduction of electron carriers or in the bonds of adenosine triphosphate (ATP). In living systems, a small class of compounds functions as mobile electron carriers, molecules that bind to and shuttle high-energy electrons between compounds in pathways. The principal electron carriers we will consider originate from the B vitamin group and are derivatives of nucleotides; they are nicotinamide adenine dinucleotide (NAD+), nicotine adenine dinucleotide phosphate (NADP+), and flavin adenine dinucleotide (FAD). These compounds can be easily reduced or oxidized and have the ability to donate electrons to various chemical reactions.

A living cell must be able to handle the energy released during catabolism in a way that enables the cell to store energy safely and release it for use only as needed. Living cells accomplish this by using the compound adenosine triphosphate (ATP). ATP is often called the “energy currency” of the cell, and, like currency, this versatile compound can be used to fill any energy need of the cell. At the heart of ATP is a molecule of adenosine monophosphate (AMP), which is composed of an adenine molecule bonded to a ribose molecule and a single phosphate group. Ribose is a five-carbon sugar found in RNA, and AMP is one of the nucleotides in RNA. The addition of a second phosphate group to this core molecule results in the formation of adenosine diphosphate (ADP); the addition of a third phosphate group forms ATP (Figure 8.3). Adding a phosphate group to a molecule, a process called phosphorylation, requires energy. Thus, the bonds between phosphate groups (one in ADP and two in ATP) are called high-energy phosphate bonds. When these high-energy bonds are broken to release one phosphate or two connected phosphate groups from ATP through a process called dephosphorylation, energy is released to drive endergonic reactions (Figure 8.4).

Similarly, the exergonic reaction of ATP dephosphorylation is coupled to the endergonic reaction of polysaccharide formation, an example of anabolism.

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Knowledge Check:

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Learning Objectives:

By the end of this section, you will be able to:

• By the end of this section, you will be able to:
• List the product resulting from glycolysis.
• Explain how the three-carbon pyruvate molecules are funneled into the Krebs cycle.
• List the products resulting from the Krebs cycle.

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2. Catabolism of Carbohydrate Content:

Extensive enzyme pathways exist for breaking down carbohydrates to capture energy in ATP bonds. In addition, many catabolic pathways produce intermediate molecules that are also used as building blocks for anabolism.

For bacteria, eukaryotes, and most archaea, glycolysis is the most common pathway for the catabolism of glucose; it produces energy, reduced electron carriers, and precursor molecules for cellular metabolism. Every living organism carries out some form of glycolysis, suggesting this mechanism is an ancient universal metabolic process. The process itself does not use oxygen; however, glycolysis can be coupled with additional metabolic processes that are either aerobic or anaerobic. Glycolysis takes place in the cytoplasm of prokaryotic and eukaryotic cells. It begins with a single six-carbon glucose molecule and ends with two molecules of a three-carbon sugar called pyruvate. Pyruvate may be broken down further after glycolysis to harness more energy through aerobic or anaerobic respiration, but many organisms, including many microbes, may be unable to respire; for these organisms, glycolysis may be their only source of generating ATP.

The type of glycolysis found in animals and that is most common in microbes is the Embden-Meyerhof-Parnas (EMP) pathway, named after Gustav Embden (1874–1933), Otto Meyerhof (1884–1951), and Jakub Parnas (1884–1949). Glycolysis using the EMP pathway consists of two distinct phases (Figure 8.10)

Overall, in this process of glycolysis, the net gain from the breakdown of a single glucose molecule is:

• two ATP molecules
• two NADH molecule, and
• two pyruvate molecules.

• After glycolysis, a three-carbon pyruvate is decarboxylated to form a two-carbon acetyl group, coupled with the formation of NADH. The acetyl group is attached to a large carrier compound called coenzyme A, forming acetyl Co A. (Figure 8.13).
• After the transition step, the Krebs cycle, where the acetyl group derived from glycolysis is further oxidized, producing three NADH molecules, one FADH2, and one ATP by substrate-level phosphorylation, and releasing two CO2 molecules. In substrate-level phosphorylation, a phosphate group is removed from an organic molecule and is directly transferred to an available ADP molecule, producing ATP. The ATP molecules produced during the energy payoff phase of glycolysis are also formed by substrate-level phosphorylation.
• The Krebs cycle may be used for other purposes. Many of the intermediates are used to synthesize important cellular molecules, including amino acids, chlorophylls, fatty acids, and nucleotides.

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Knowledge Check:

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Learning Objectives:

By the end of this section, you will be able to:

• Compare and contrast the electron transport system location and function in a prokaryotic cell and a eukaryotic cell.
• Compare the differences between substrate-level and oxidative phosphorylation

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3. Cellular Respiration Content:

We have just discussed two pathways in glucose catabolism—glycolysis and the Krebs cycle—that generate ATP by substrate-level phosphorylation. Most ATP, however, is generated during a separate process called oxidative phosphorylation, which occurs during cellular respiration. Cellular respiration begins when electrons are transferred from NADH and FADH2—made in glycolysis, the transition reaction, and the Krebs cycle—through a series of chemical reactions to a final inorganic electron acceptor (either oxygen in aerobic respiration or non-oxygen inorganic molecules in anaerobic respiration). These electron transfers take place on the inner part of the cell membrane of prokaryotic cells or in specialized protein complexes in the inner membrane of the mitochondria of eukaryotic cells. The energy of the electrons is harvested to generate an electrochemical gradient across the membrane, which is used to make ATP by oxidative phosphorylation.

• An electron transport system (ETS) (Figure 8.15) is composed of a series of membrane-associated protein complexes and associated mobile accessory electron carriers. The ETS is embedded in the cytoplasmic membrane of prokaryotes and the inner mitochondrial membrane of eukaryotes.
• In aerobic respiration, the final electron acceptor (i.e., the one having the most positive redox potential) at the end of the ETS is an oxygen molecule (O2) that becomes reduced to water (H2O) by the final ETS carrier.
• Organisms performing anaerobic respiration use alternative electron transport system carriers for the ultimate transfer of electrons to the final non-oxygen electron acceptors.
• Microbes show great variation in the composition of their electron transport systems, which can be used for diagnostic purposes to help identify certain pathogens.
• To carry out aerobic respiration, a cell requires oxygen as the final electron acceptor. A cell also needs a complete Krebs cycle, an appropriate cytochrome oxidase, and oxygen detoxification enzymes to prevent the harmful effects of oxygen radicals produced during aerobic respiration.
• Aerobic respiration forms more ATP during oxidative phosphorylation than does anaerobic respiration.

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Knowledge Check:

Learning Objectives:

By the end of this section, you will be able to:

• Define binary fission.
• describe generation time for both prokaryotic and eukaryotic cells.
• Describe 4 phases of the growth curve, and their significance in the medical management of an infection.

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Content:

The bacterial cell cycle involves the formation of new cells through the replication of DNA and partitioning of cellular components into two daughter cells. In prokaryotes, reproduction is always asexual, although extensive genetic recombination in the form of horizontal gene transfer takes place.

Binary Fission:

The most common mechanism of cell replication in bacteria is a process called binary fission, which is depicted in Figure 9.2. Before dividing, the cell grows and increases its number of cellular components. Next, the replication of DNA starts at a location on the circular chromosome called the origin of replication, where the chromosome is attached to the inner cell membrane. Replication continues in opposite directions along the chromosome until the terminus is reached.

Generation Time

In eukaryotic organisms, the generation time is the time between the same points of the life cycle in two successive generations. For example, the typical generation time for the human population is 25 years. This definition is not practical for bacteria, which may reproduce rapidly or remain dormant for thousands of years. In prokaryotes (Bacteria and Archaea), the generation time is also called the doubling time and is defined as the time it takes for the population to double through one round of binary fission. Bacterial doubling times vary enormously. Whereas Escherichia coli can double in as little as 20 minutes under optimal growth conditions in the laboratory, bacteria of the same species may need several days to double in especially harsh environments. Most pathogens grow rapidly, like E. coli, but there are exceptions. For example, Mycobacterium tuberculosis, the causative agent of tuberculosis, has a generation time of between 15 and 20 hours. On the other hand, M. leprae, which causes Hansen’s disease (leprosy), grows much more slowly, with a doubling time of 14 days.

The Growth Curve

Microorganisms grown in closed culture (also known as a batch culture), in which no nutrients are added and most waste is not removed, follow a reproducible growth pattern referred to as the growth curve. An example of a batch culture in nature is a pond in which a small number of cells grow in a closed environment. The culture density is defined as the number of cells per unit volume. In a closed environment, the culture density is also a measure of the number of cells in the population. Infections of the body do not always follow the growth curve, but correlations can exist depending upon the site and type of infection. When the number of live cells is plotted against time, distinct phases can be observed in the curve (Figure 9.5).

The Lag Phase

The beginning of the growth curve represents a small number of cells, referred to as an inoculum, that are added to a fresh culture medium, a nutritional broth that supports growth. The initial phase of the growth curve is called the lag phase, during which cells are gearing up for the next phase of growth. The number of cells does not change during the lag phase; however, cells grow larger and are metabolically active, synthesizing proteins needed to grow within the medium. If any cells were damaged or shocked during the transfer to the new medium, repair takes place during the lag phase. The duration of the lag phase is determined by many factors, including the species and genetic make-up of the cells, the composition of the medium, and the size of the original inoculum.

The Log Phase

In the logarithmic (log) growth phase, sometimes called exponential growth phase, the cells are actively dividing by binary fission and their number increases exponentially. For any given bacterial species, the generation time under specific growth conditions (nutrients, temperature, pH, and so forth) is genetically determined, and this generation time is called the intrinsic growth rate. During the log phase, the relationship between time and number of cells is not linear but exponential.

Cells in the log phase show constant growth rate and uniform metabolic activity. For this reason, cells in the log phase are preferentially used for industrial applications and research work. The log phase is also the stage where bacteria are the most susceptible to the action of disinfectants and common antibiotics that affect protein, DNA, and cell-wall synthesis.

Stationary Phase

As the number of cells increases through the log phase, several factors contribute to a slowing of the growth rate. Waste products accumulate and nutrients are gradually used up. In addition, gradual depletion of oxygen begins to limit aerobic cell growth. This combination of unfavorable conditions slows and finally stalls population growth. The total number of live cells reaches a plateau referred to as the stationary phase (Figure 9.5). In this phase, the number of new cells created by cell division is now equivalent to the number of cells dying; thus, the total population of living cells is relatively stagnant.

During the stationary phase, cells switch to a survival mode of metabolism. As growth slows, so too does the synthesis of peptidoglycans, proteins, and nucleic-acids; thus, stationary cultures are less susceptible to antibiotics that disrupt these processes. In bacteria capable of producing endospores, many cells undergo sporulation during the stationary phase. In certain pathogenic bacteria, the stationary phase is also associated with the expression of virulence factors, products that contribute to a microbe’s ability to survive, reproduce, and cause disease in a host organism.

The Death Phase

As a culture medium accumulates toxic waste and nutrients are exhausted, cells die in greater and greater numbers. Soon, the number of dying cells exceeds the number of dividing cells, leading to an exponential decrease in the number of cells (Figure 9.5). This is the aptly named death phase, sometimes called the decline phase. Many cells lyse and release nutrients into the medium, allowing surviving cells to maintain viability and form endospores. A few cells, the so-called persisters, are characterized by a slow metabolic rate. Persister cells are medically important because they are associated with certain chronic infections, such as tuberculosis, that do not respond to antibiotic treatment.

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Knowledge Check:

Learning Objectives:

By the end of this section, you will be able to:

• Describe the general characteristics of viruses as pathogens.
• Define viroids, virusoids, and prions

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Content:

Viruses

Today, we can see viruses using electron microscopes and we know much more about them. Viruses are distinct biological entities; however, their evolutionary origin is still a matter of speculation. In terms of taxonomy, they are not included in the tree of life because they are acellular (not consisting of cells). In order to survive and reproduce, viruses must infect a cellular host, making them obligate intracellular parasites. The genome of a virus enters a host cell and directs the production of the viral components, proteins and nucleic acids, needed to form new virus particles called virions. New virions are made in the host cell by assembly of viral components. The new virions transport the viral genome to another host cell to carry out another round of infection. Table 6.1 summarizes the properties of viruses.

Fermented Foods and Beverages

People across the world have enjoyed fermented foods and beverages like beer, wine, bread, yogurt, cheese, and pickled vegetables for all of recorded history. Discoveries from several archeological sites suggest that even prehistoric people took advantage of fermentation to preserve and enhance the taste of food. Archaeologists studying pottery jars from a Neolithic village in China found that people were making a fermented beverage from rice, honey, and fruit as early as 7000 BC.³

Production of these foods and beverages requires microbial fermentation, a process that uses bacteria, mold, or yeast to convert sugars (carbohydrates) to alcohol, gases, and organic acids. While it is likely that people first learned about fermentation by accident—perhaps by drinking old milk that had curdled or old grape juice that had fermented—they later learned to harness the power of fermentation to make products like bread, cheese, and wine.

• Long before the invention of the microscope, some people theorized that infection and disease were spread by living things that were too small to be seen. They also correctly intuited certain principles regarding the spread of disease and immunity.
• Antonie van Leeuwenhoek, using a microscope, was the first to actually describe observations of bacteria, in 1675.
• During the Golden Age of Microbiology (1857–1914), microbiologists, including Louis Pasteur and Robert Koch, discovered many new connections between the fields of microbiology and medicine.

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Knowledge Check:

Learning Objectives:

By the end of this section, you will be able to:

• explain the two functions of DNA.
• explain the meaning of the central dogma of molecular biology.
• explain mutation.
• differentiate between genotype and phenotype and explain what factors influence phenotype.
• explain how asexual gene transfer results in prokaryotic genetic diversity.
• describe three mechanisms of horizontal gene transfer.

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Content:

The Functions of Genetic Material:

DNA serves two essential functions that deal with cellular information. First, DNA is the genetic material responsible for inheritance and is passed from parent to offspring for all life on earth. To preserve the integrity of this genetic information, DNA must be replicated with great accuracy, with minimal errors that introduce changes to the DNA sequence. A genome contains the full complement of DNA within a cell and is organized into smaller, discrete units called genes that are arranged on chromosomes and plasmids. The second function of DNA is to direct and regulate the construction of the proteins necessary to a cell for growth and reproduction in a particular cellular environment.

A gene is composed of DNA that is “read” or transcribed to produce an RNA molecule during the process of transcription. One major type of RNA molecule, called messenger RNA (mRNA), provides the information for the ribosome to catalyze protein synthesis in a process called translation. The processes of transcription and translation are collectively referred to as gene expression. Gene expression is the synthesis of a specific protein with a sequence of amino acids that is encoded in the gene. The flow of genetic information from DNA to RNA to protein is described by the central dogma (Figure 11.2).  

• The DNA replication process results in two DNA molecules, each having one parental strand of DNA and one newly synthesized strand.
• During transcription, the information encoded in DNA is used to make RNA.
• In protein synthesis (translation), polypeptides are synthesized using mRNA sequences and cellular machinery, including tRNAs that match mRNA codons to specific amino acids and ribosomes composed of RNA and proteins that catalyze the reaction.
• The genetic code is degenerate in that several mRNA codons code for the same amino acids. The genetic code is almost universal among living organisms.
• A mutation is a heritable change in DNA. A mutation may lead to a change in the amino-acid sequence of a protein, possibly affecting its function.

A cell’s genotype is the full collection of genes it contains, whereas its phenotype is the set of observable characteristics that result from those genes. The phenotype is the product of the array of proteins being produced by the cell at a given time, which is influenced by the cell’s genotype as well as interactions with the cell’s environment. Genes code for proteins that have functions in the cell. Production of a specific protein encoded by an individual gene often results in a distinct phenotype for the cell compared with the phenotype without that protein. For this reason, it is also common to refer to the genotype of an individual gene and its phenotype. Although a cell’s genotype remains constant, not all genes are used to direct the production of their proteins simultaneously. Cells carefully regulate expression of their genes, only using genes to make specific proteins when those proteins are needed (Figure 11.3).

There was obvious interest in applying Mendel's laws to agriculture. Mendel's ideas were also embraced by the eugenics movement, the goal of which was to improve the human species by better breeding. Eugenicists encouraged marriages between people of "good" genetic stock, and discouraged reproduction of the "genetically unfit."

Eugenicists wrongly used simple dominant/recessive schemes to explain complex behaviors and mental illnesses — which we now know involve many genes. They also failed to account for environmental effects on human development. In the United States, restrictive eugenics legislation reflected political and social prejudices, rather than genetic facts. The eugenic description of human life was finally discredited by the horrible consequences of the Nazi quest for racial purity.

How Asexual Prokaryotes Achieve Genetic Diversity

Typically, when we consider genetic transfer, we think of vertical gene transfer, the transmission of genetic information from generation to generation. Vertical gene transfer is by far the main mode of transmission of genetic information in all cells. In sexually reproducing organisms, crossing-over events and independent assortment of individual chromosomes during meiosis contribute to genetic diversity in the population. Genetic diversity is also introduced during sexual reproduction, when the genetic information from two parents, each with different complements of genetic information, are combined, producing new combinations of parental genotypes in the diploid offspring. The occurrence of mutations also contributes to genetic diversity in a population. Genetic diversity of offspring is useful in changing or inconsistent environments and may be one reason for the evolutionary success of sexual reproduction.

When prokaryotes and eukaryotes reproduce asexually, they transfer a nearly identical copy of their genetic material to their offspring through vertical gene transfer. Although asexual reproduction produces more offspring more quickly, any benefits of diversity among those offspring are lost. How then do organisms whose dominant reproductive mode is asexual create genetic diversity? In prokaryotes, horizontal gene transfer (HGT), the introduction of genetic material from one organism to another organism within the same generation, is an important way to introduce genetic diversity. HGT allows even distantly related species to share genes, influencing their phenotypes. It is thought that HGT is more prevalent in prokaryotes but that only a small fraction of the prokaryotic genome may be transferred by this type of transfer at any one time. As the phenomenon is investigated more thoroughly, it may be revealed to be even more common. Many scientists believe that HGT and mutation are significant sources of genetic variation, the raw material for the process of natural selection, in prokaryotes. Although HGT is more common among evolutionarily related organisms, it may occur between any two species that live together in a natural community.

HGT in prokaryotes is known to occur by the three primary mechanisms that are illustrated in Figure 11.26:

1. Transformation: naked DNA is taken up from the environment
2. Transduction: genes are transferred between cells in a virus (see The Viral Life Cycle)
3. Conjugation: use of a hollow tube called a conjugation pilus to transfer genes between cells

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Knowledge Check:

Learning Objectives:

By the end of this section, you will be able to:

• Explain the concept of drug resistance.

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Content:

Antimicrobial resistance is not a new phenomenon. In nature, microbes are constantly evolving in order to overcome the antimicrobial compounds produced by other microorganisms. Human development of antimicrobial drugs and their widespread clinical use has simply provided another selective pressure that promotes further evolution. Several important factors can accelerate the evolution of drug resistance. These include the overuse and misuse of antimicrobials, inappropriate use of antimicrobials, subtherapeutic dosing, and patient noncompliance with the recommended course of treatment.

Exposure of a pathogen to an antimicrobial compound can select for chromosomal mutations conferring resistance, which can be transferred vertically to subsequent microbial generations and eventually become predominant in a microbial population that is repeatedly exposed to the antimicrobial. Alternatively, many genes responsible for drug resistance are found on plasmids or in transposons that can be transferred easily between microbes through horizontal gene transfer (see How Asexual Prokaryotes Achieve Genetic Diversity). Transposons also have the ability to move resistance genes between plasmids and chromosomes to further promote the spread of resistance.

• Antimicrobial resistance is on the rise and is the result of selection of drug-resistant strains in clinical environments, the overuse and misuse of antibacterials, the use of subtherapeutic doses of antibacterial drugs, and poor patient compliance with antibacterial drug therapies.
• Drug resistance genes are often carried on plasmids or in transposons that can undergo vertical transfer easily and between microbes through horizontal gene transfer.
• Problematic microbial strains showing extensive antimicrobial resistance are emerging; many of these strains can reside as members of the normal microbiota in individuals but also can cause opportunistic infection. The transmission of many of these highly resistant microbial strains often occurs in clinical settings, but can also be community-acquired.

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Knowledge Check: