The assertion that “life only comes from life” was stated by Louis Pasteur in regard to his experiments that definitively refuted the theory of ___________.

22.

John Snow is known as the Father of _____________.

23.

The ____________ theory states that disease may originate from proximity to decomposing matter and is not due to person-to-person contact.

24.

The scientist who first described cells was _____________.

25.

Prokaryotic cells that are rod-shaped are called _____________.

26.

The type of inclusion containing polymerized inorganic phosphate is called _____________.

27.

Peroxisomes typically produce _____________, a harsh chemical that helps break down molecules.

28.

Microfilaments are composed of _____________ monomers.

Short Answer

29.

Explain in your own words Pasteur’s swan-neck flask experiment.

30.

Explain why the experiments of Needham and Spallanzani yielded in different results even though they used similar methodologies.

31.

How did the explanation of Virchow and Remak for the origin of cells differ from that of Schleiden and Schwann?

32.

What evidence exists that supports the endosymbiotic theory?

33.

What were the differences in mortality rates due to puerperal fever that Ignaz Semmelweis observed? How did he propose to reduce the occurrence of puerperal fever? Did it work?

34.

What is the direction of water flow for a bacterial cell living in a hypotonic environment? How do cell walls help bacteria living in such environments?

35.

How do bacterial flagella respond to a chemical gradient of an attractant to move toward a higher concentration of the chemical?

36.

Label the parts of the prokaryotic cell.

A diagram of a bacterial cell. The thick outer structure of the cell is not lableled. The next layer in (a thinner structure) is labeled E. A much thinner structure inside of that is labeled F. Inside of F is the main body of the cell. Small dots are labeled B. A long line forming a loop is labeled C. On the outside of the cell, short projectsions are labeled A and a long projection is labeled D.

37.

What existing evidence supports the theory that mitochondria are of prokaryotic origin?

38.

Why do eukaryotic cells require an endomembrane system?

39.

Name at least two ways that prokaryotic flagella are different from eukaryotic flagella.

40.

What would the results of Pasteur’s swan-neck flask experiment have looked like if they supported the theory of spontaneous generation?

41.

Why are mitochondria and chloroplasts unable to multiply outside of a host cell?

42.

Why was the work of Snow so important in supporting the germ theory?

43.

Which of the following slides is a good example of staphylococci?

A) A micrograph of rods in a cluster. B) a micrograph of individual rods. C) A micrograph of spheres in a chain. D) a micrograph of spheres in a cluster.

Figure 3.58 (credit a: modification of work by U.S. Department of Agriculture; credit b: modification of work by Centers for Disease Control and Prevention; credit c: modification of work by NIAID)

44.

Provide some examples of bacterial structures that might be used as antibiotic targets and explain why.

45.

The causative agent of botulism, a deadly form of food poisoning, is an endospore-forming bacterium called Clostridium botulinim. Why might it be difficult to kill this bacterium in contaminated food?

46.

Label the lettered parts of this eukaryotic cell.

4.1 Prokaryote Habitats, Relationships, and Microbiomes

Prokaryotes are unicellular microorganisms whose cells have no nucleus.
Prokaryotes can be found everywhere on our planet, even in the most extreme environments.
Prokaryotes are very flexible metabolically, so they are able to adjust their feeding to the available natural resources.
Prokaryotes live in communities that interact among themselves and with large organisms that they use as hosts (including humans).
The totality of forms of prokaryotes (particularly bacteria) living on the human body is called the human microbiome, which varies between regions of the body and individuals, and changes over time.
The totality of forms of prokaryotes (particularly bacteria) living in a certain region of the human body (e.g., mouth, throat, gut, eye, vagina) is called the microbiota of this region.
Prokaryotes are classified into domains Archaea and Bacteria.
In recent years, the traditional approaches to classification of prokaryotes have been supplemented by approaches based on molecular genetics.

4.2 Proteobacteria

Proteobacteria is a phylum of gram-negative bacteria discovered by Carl Woese in the 1980s based on nucleotide sequence homology.
Proteobacteria are further classified into the classes alpha-, beta-, gamma-, delta- and epsilonproteobacteria, each class having separate orders, families, genera, and species.
Alphaproteobacteria include several obligate and facultative intracellular pathogens, including the rickettsias. Some Alphaproteobacteria can convert atmospheric nitrogen to nitrites, making nitrogen usable for other forms of life.
Betaproteobacteria are a diverse group of bacteria that include human pathogens of the genus Neisseria and the species Bordetella pertussis.
Gammaproteobacteria are the largest and the most diverse group of Proteobacteria. Many are human pathogens that are aerobes or facultative anaerobes. Some Gammaproteobacteria are enteric bacteria that may be coliform or noncoliform. Escherichia coli, a member of Gammaproteobacteria, is perhaps the most studied bacterium.
Deltaproteobacteria make up a small group able to reduce sulfate or elemental sulfur. Some are scavengers and form myxospores, with multicellular fruiting bodies.
Epsilonproteobacteria make up the smallest group of Proteobacteria. The genera Campylobacter and Helicobacter are human pathogens.

4.3 Nonproteobacteria Gram-Negative Bacteria and Phototrophic Bacteria

Gram-negative nonproteobacteria include the taxa spirochetes; the Chlamydia, Cytophaga, Fusobacterium, Bacteroides group; Planctomycetes; and many representatives of phototrophic bacteria.
Spirochetes are motile, spiral bacteria with a long, narrow body; they are difficult or impossible to culture.
Several genera of spirochetes contain human pathogens that cause such diseases as syphilis and Lyme disease.
Cytophaga, Fusobacterium, and Bacteroides are classified together as a phylum called the CFB group. They are rod-shaped anaerobic organoheterotrophs and avid fermenters. Cytophaga are aquatic bacteria with the gliding motility. Fusobacteria inhabit the human mouth and may cause severe infectious diseases. Bacteroides are present in vast numbers in the human gut, most of them being mutualistic but some are pathogenic.
Planctomycetes are aquatic bacteria that reproduce by budding; they may form large colonies, and develop a holdfast.
Phototrophic bacteria are not a taxon but, rather, a group categorized by their ability to use the energy of sunlight. They include Proteobacteria and nonproteobacteria, as well as sulfur and nonsulfur bacteria colored purple or green.
Sulfur bacteria perform anoxygenic photosynthesis, using sulfur compounds as donors of electrons, whereas nonsulfur bacteria use organic compounds (succinate, malate) as donors of electrons.
Some phototrophic bacteria are able to fix nitrogen, providing the usable forms of nitrogen to other organisms.
Cyanobacteria are oxygen-producing bacteria thought to have played a critical role in the forming of the earth’s atmosphere.

4.4 Gram-Positive Bacteria

Gram-positive bacteria are a very large and diverse group of microorganisms. Understanding their taxonomy and knowing their unique features is important for diagnostics and treatment of infectious diseases.
Gram-positive bacteria are classified into high G+C gram-positive and low G+C gram-positive bacteria, based on the prevalence of guanine and cytosine nucleotides in their genome
Actinobacteria is the taxonomic name of the class of high G+C gram-positive bacteria. This class includes the genera Actinomyces, Arthrobacter, Corynebacterium, Frankia, Gardnerella, Micrococcus, Mycobacterium, Nocardia, Cutibacterium, Rhodococcus, and Streptomyces. Some representatives of these genera are used in industry; others are human or animal pathogens.
Examples of high G+C gram-positive bacteria that are human pathogens include Mycobacterium tuberculosis, which causes tuberculosis; M. leprae, which causes leprosy (Hansen’s disease); and Corynebacterium diphtheriae, which causes diphtheria.
Clostridia spp. are low G+C gram-positive bacteria that are generally obligate anaerobes and can form endospores. Pathogens in this genus include C. perfringens (gas gangrene), C. tetani (tetanus), and C. botulinum (botulism).
Lactobacillales include the genera Enterococcus, Lactobacillus, Leuconostoc, and Streptococcus. Streptococcus is responsible for many human diseases, including pharyngitis (strep throat), scarlet fever, rheumatic fever, glomerulonephritis, pneumonia, and other respiratory infections.
Bacilli is a taxonomic class of low G+C gram-positive bacteria that include rod-shaped and coccus-shaped species, including the genera Bacillus and Staphylococcus. B. anthracis causes anthrax, B. cereus may cause opportunistic infections of the gastrointestinal tract, and S. aureus strains can cause a wide range of infections and diseases, many of which are highly resistant to antibiotics.
Mycoplasma spp. are very small, pleomorphic low G+C gram-positive bacteria that lack cell walls. M. pneumoniae causes atypical pneumonia.

4.5 Deeply Branching Bacteria

Deeply branching bacteria are phylogenetically the most ancient forms of life, being the closest to the last universal common ancestor.
Deeply branching bacteria include many species that thrive in extreme environments that are thought to resemble conditions on earth billions of years ago
Deeply branching bacteria are important for our understanding of evolution; some of them are used in industry

4.6 Archaea

Archaea are unicellular, prokaryotic microorganisms that differ from bacteria in their genetics, biochemistry, and ecology.
Some archaea are extremophiles, living in environments with extremely high or low temperatures, or extreme salinity.
Only archaea are known to produce methane. Methane-producing archaea are called methanogens.
Halophilic archaea prefer a concentration of salt close to saturation and perform photosynthesis using bacteriorhodopsin.
Some archaea, based on fossil evidence, are among the oldest organisms on earth.
Archaea do not live in great numbers in human microbiomes and are not known to cause disease.

Image of a cell. the outside line is labeled A. A long projection to the outside is labeled H. A large sphere in the cell has an outer line labeled B. A smaller sphere in the larger sphere is labeled C. Outside of this sphere but still inside the cell are folds of membranes with dots labeled F. Another set of folded membranes in a stack is labeld G; smaller spheres are coming off of these stacks. An oval structure with lines inside is labeld D and two small tubes are labeled E.

47.

How are peroxisomes more like mitochondria than like the membrane-bound organelles of the endomembrane system? How do they differ from mitochondria?

48.

Why must the functions of both lysosomes and peroxisomes be compartmentalized?

Multiple Choice

The term prokaryotes refers to which of the following?

very small organisms
unicellular organisms that have no nucleus
multicellular organisms
cells that resemble animal cells more than plant cells

The term microbiota refers to which of the following?

all microorganisms of the same species
all of the microorganisms involved in a symbiotic relationship
all microorganisms in a certain region of the human body
all microorganisms in a certain geographic region

Which of the following refers to the type of interaction between two prokaryotic populations in which one population benefits and the other is not affected?

mutualism
commensalism
parasitism
neutralism

Which of the following describes Proteobacteria in domain Bacteria?

phylum
class
species
genus

Which of the following Alphaproteobacteria is the cause of Rocky Mountain spotted fever and typhus?

Bartonella
Coxiella
Rickettsia
Ehrlichia
Brucella

Class Betaproteobacteria includes all but which of the following genera?

Neisseria.
Bordetella.
Leptothrix.
Campylobacter.

Haemophilus influenzae is a common cause of which of the following?

influenza
dysentery
upper respiratory tract infections
hemophilia

Which of the following is the organelle that spirochetes use to propel themselves?

plasma membrane
axial filament
pilum
fimbria

Which of the following bacteria are the most prevalent in the human gut?

cyanobacteria
staphylococci
Borrelia
Bacteroides

10.

Which of the following refers to photosynthesis performed by bacteria with the use of water as the donor of electrons?

oxygenic
anoxygenic
heterotrophic
phototrophic

11.

Which of the following bacterial species is classified as high G+C gram-positive?

Corynebacterium diphtheriae
Staphylococcus aureus
Bacillus anthracis
Streptococcus pneumonia

12.

The term “deeply branching” refers to which of the following?

the cellular shape of deeply branching bacteria
the position in the evolutionary tree of deeply branching bacteria
the ability of deeply branching bacteria to live in deep ocean waters
the pattern of growth in culture of deeply branching bacteria

13.

Which of these deeply branching bacteria is considered a polyextremophile?

Aquifex pyrophilus
Deinococcus radiodurans
Staphylococcus aureus
Mycobacterium tuberculosis

14.

Archaea and Bacteria are most similar in terms of their ________.

genetics
cell wall structure
ecology
unicellular structure

15.

Which of the following is true of archaea that produce methane?

They reduce carbon dioxide in the presence of nitrogen.
They live in the most extreme environments.
They are always anaerobes.
They have been discovered on Mars.

5.1 Unicellular Eukaryotic Parasites

Protists are a diverse, polyphyletic group of eukaryotic organisms.
Protists may be unicellular or multicellular. They vary in how they get their nutrition, morphology, method of locomotion, and mode of reproduction.
Important structures of protists include contractile vacuoles, cilia, flagella, pellicles, and pseudopodia; some lack organelles such as mitochondria.
Taxonomy of protists is changing rapidly as relationships are reassessed using newer techniques.
The protists include important pathogens and parasites.

5.2 Parasitic Helminths

Helminth parasites are included within the study of microbiology because they are often identified by looking for microscopic eggs and larvae.
The two major groups of helminth parasites are the roundworms (Nematoda) and the flatworms (Platyhelminthes).
Nematodes are common intestinal parasites often transmitted through undercooked foods, although they are also found in other environments.
Platyhelminths include tapeworms and flukes, which are often transmitted through undercooked meat.

5.3 Fungi

The fungi include diverse saprotrophic eukaryotic organisms with chitin cell walls
Fungi can be unicellular or multicellular; some (like yeast) and fungal spores are microscopic, whereas some are large and conspicuous
Reproductive types are important in distinguishing fungal groups
Medically important species exist in the four fungal groups Zygomycota, Ascomycota, Basidiomycota, and Microsporidia
Members of Zygomycota, Ascomycota, and Basidiomycota produce deadly toxins
Important differences in fungal cells, such as ergosterols in fungal membranes, can be targets for antifungal medications, but similarities between human and fungal cells make it difficult to find targets for medications and these medications often have toxic adverse effects

5.4 Algae

Algae are a diverse group of photosynthetic eukaryotic protists
Algae may be unicellular or multicellular
Large, multicellular algae are called seaweeds but are not plants and lack plant-like tissues and organs
Although algae have little pathogenicity, they may be associated with toxic algal blooms that can and aquatic wildlife and contaminate seafood with toxins that cause paralysis
Algae are important for producing agar, which is used as a solidifying agent in microbiological media, and carrageenan, which is used as a solidifying agent

5.5 Lichens

Lichens are a symbiotic association between a fungus and an algae or a cyanobacterium
The symbiotic association found in lichens is currently considered to be a controlled parasitism, in which the fungus benefits and the algae or cyanobacterium is harmed
Lichens are slow growing and can live for centuries in a variety of habitats
Lichens are environmentally important, helping to create soil, providing food, and acting as indicators of air pollution

Which genus includes the causative agent for malaria?

Euglena
Paramecium
Plasmodium
Trypanosoma

Which protist is a concern because of its ability to contaminate water supplies and cause diarrheal illness?

Plasmodium vivax
Toxoplasma gondii
Giardia lamblia
Trichomonas vaginalis

A fluke is classified within which of the following?

Nematoda
Rotifera
Platyhelminthes
Annelida

A nonsegmented worm is found during a routine colonoscopy of an individual who reported having abdominal cramps, nausea, and vomiting. This worm is likely which of the following?

nematode
fluke
trematode
annelid

A segmented worm has male and female reproductive organs in each segment. Some use hooks to attach to the intestinal wall. Which type of worm is this?

fluke
nematode
cestode
annelid

Mushrooms are a type of which of the following?

conidia
ascus
polar tubule
basidiocarp

Which of the following is the most common cause of human yeast infections?

Candida albicans
Blastomyces dermatitidis
Cryptococcus neoformans
Aspergillus fumigatus

Which of the following is an ascomycete fungus associated with bat droppings that can cause a respiratory infection if inhaled?

Candida albicans
Histoplasma capsulatum
Rhizopus stolonifera
Trichophyton rubrum

Which polysaccharide found in red algal cell walls is a useful solidifying agent?

chitin
cellulose
phycoerythrin
agar

10.

Which is the term for the hard outer covering of some dinoflagellates?

theca
thallus
mycelium
shell

11.

Which protists are associated with red tides?

red algae
brown algae
dinoflagellates
green algae

12.

You encounter a lichen with leafy structures. Which term describes this lichen?

crustose
foliose
fruticose
agarose

13.

Which of the following is the term for the outer layer of a lichen?

the cortex
the medulla
the thallus
the theca

14.

The fungus in a lichen is which of the following?

a basidiomycete
an ascomycete
a zygomycete
an apicomplexan

6.1 Viruses

Viruses are generally ultramicroscopic, typically from 20 nm to 900 nm in length. Some large viruses have been found.
Virions are acellular and consist of a nucleic acid, DNA or RNA, but not both, surrounded by a protein capsid. There may also be a phospholipid membrane surrounding the capsid.
Viruses are obligate intracellular parasites.
Viruses are known to infect various types of cells found in plants, animals, fungi, protists, bacteria, and archaea. Viruses typically have limited host ranges and infect specific cell types.
Viruses may have helical, polyhedral, or complex shapes.
Classification of viruses is based on morphology, type of nucleic acid, host range, cell specificity, and enzymes carried within the virion.
Like other diseases, viral diseases are classified using ICD codes.

6.2 The Viral Life Cycle

Many viruses target specific hosts or tissues. Some may have more than one host.
Many viruses follow several stages to infect host cells. These stages include attachment, penetration, uncoating, biosynthesis, maturation, and release.
Bacteriophages have a lytic or lysogenic cycle. The lytic cycle leads to the death of the host, whereas the lysogenic cycle leads to integration of phage into the host genome.
Bacteriophages inject DNA into the host cell, whereas animal viruses enter by endocytosis or membrane fusion.
Animal viruses can undergo latency, similar to lysogeny for a bacteriophage.
The majority of plant viruses are positive-strand ssRNA and can undergo latency, chronic, or lytic infection, as observed for animal viruses.
The growth curve of bacteriophage populations is a one-step multiplication curve and not a sigmoidal curve, as compared to the bacterial growth curve.
Bacteriophages transfer genetic information between hosts using either generalized or specialized transduction.

6.3 Isolation, Culture, and Identification of Viruses

Viral cultivation requires the presence of some form of host cell (whole organism, embryo, or cell culture).
Viruses can be isolated from samples by filtration.
Viral filtrate is a rich source of released virions.
Bacteriophages are detected by presence of clear plaques on bacterial lawn.
Animal and plant viruses are detected by cytopathic effects, molecular techniques (PCR, RT-PCR), enzyme immunoassays, and serological assays (hemagglutination assay, hemagglutination inhibition assay).

6.4 Viroids, Virusoids, and Prions

Other acellular agents such as viroids, virusoids, and prions also cause diseases. Viroids consist of small, naked ssRNAs that cause diseases in plants. Virusoids are ssRNAs that require other helper viruses to establish an infection. Prions are proteinaceous infectious particles that cause transmissible spongiform encephalopathies.
Prions are extremely resistant to chemicals, heat, and radiation.
There are no treatments for prion infection.

7.1 Organic Molecules

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.
The same numbers and types of atoms may bond together in different ways to yield different molecules called isomers. Isomers may differ in the bonding sequence of their atoms (structural isomers) or in the spatial arrangement of atoms whose bonding sequences are the same (stereoisomers), and their physical and chemical properties may vary slightly or drastically.
Functional groups confer specific chemical properties to molecules bearing them. Common functional groups in biomolecules are hydroxyl, methyl, carbonyl, carboxyl, amino, phosphate, and sulfhydryl.
Macromolecules are polymers assembled from individual units, the 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.
Carbohydrates include individual sugar molecules (monosaccharides) as well as two or more molecules chemically linked by glycosidic bonds. Monosaccharides are classified based on the number of carbons the molecule as trioses (3 C), tetroses (4 C), pentoses (5 C), and hexoses (6 C). They are the building blocks for the synthesis of polymers or complex carbohydrates.
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. Other structural polysaccharides, such as N-acetyl glucosamine (NAG) and N-acetyl muramic acid (NAM), incorporate modified glucose molecules and are used in the construction of peptidoglycan or chitin.

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. Fatty acids with no double bonds are saturated; those with double bonds are unsaturated.
Fatty acids chemically bond to glycerol to form structurally essential lipids such as triglycerides and phospholipids. Triglycerides comprise three fatty acids bonded to glycerol, yielding a hydrophobic molecule. Phospholipids contain both hydrophobic hydrocarbon chains and polar head groups, making them amphipathic and capable of forming uniquely functional large scale structures.
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.
Isoprenoids are lipids derived from isoprene molecules that have many physiological roles and a variety of commercial applications.
A wax is a long-chain isoprenoid that is typically water resistant; an example of a wax-containing substance is sebum, produced by sebaceous glands in the skin. Steroids are lipids with complex, ringed structures that function as structural components of cell membranes and as hormones. Sterols are a subclass of steroids containing a hydroxyl group at a specific location on one of the molecule’s rings; one example is cholesterol.
Bacteria produce hopanoids, structurally similar to cholesterol, to strengthen bacterial membranes. Fungi and protozoa produce a strengthening agent called ergosterol.

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.
Peptides are polymers formed by the linkage of amino acids via dehydration synthesis. The bonds between the linked amino acids are called peptide bonds. The number of amino acids linked together may vary from a few to many.
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.
Conjugated proteins have a nonpolypeptide portion that can be a carbohydrate (forming a glycoprotein) or a lipid fraction (forming a lipoprotein). These proteins are important components of membranes.

7.5 Using Biochemistry to Identify Microorganisms

Accurate identification of bacteria is essential in a clinical laboratory for diagnostic and management of epidemics, pandemics, and food poisoning caused by bacterial outbreaks.
The phenotypic identification of microorganisms involves using observable traits, including profiles of structural components such as lipids, biosynthetic products such as sugars or amino acids, or storage compounds such as poly-β-hydroxybutyrate.
An unknown microbe may be identified from the unique mass spectrum produced when it is analyzed by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF).
Microbes can be identified by determining their lipid compositions, using fatty acid methyl esters (FAME) or phospholipid-derived fatty acids (PLFA) analysis.
Proteomic analysis, the study of all accumulated proteins of an organism; can also be used for bacterial identification.
Glycoproteins in the plasma membrane or cell wall structures can bind to lectins or antibodies and can be used for identification.

8.1 Energy, Matter, and Enzymes

Metabolism includes chemical reactions that break down complex molecules (catabolism) and those that build complex molecules (anabolism).
Organisms may be classified according to their source of carbon. Autotrophs convert inorganic carbon dioxide into organic carbon; heterotrophs use fixed organic carbon compounds.
Organisms may also be classified according to their energy source. Phototrophs obtain their energy from light. Chemotrophs get their energy from chemical compounds. Organotrophs use organic molecules, and lithotrophs use inorganic chemicals.
Cellular electron carriers accept high-energy electrons from foods and later serve as electron donors in subsequent redox reactions. FAD/FADH₂, NAD⁺/NADH, and NADP⁺/NADPH are important electron carriers.
Adenosine triphosphate (ATP) serves as the energy currency of the cell, safely storing chemical energy in its two high-energy phosphate bonds for later use to drive processes requiring energy.
Enzymes are biological catalysts that increase the rate of chemical reactions inside cells by lowering the activation energy required for the reaction to proceed.
In nature, exergonic reactions do not require energy beyond activation energy to proceed, and they release energy. They may proceed without enzymes, but at a slow rate. Conversely, endergonic reactions require energy beyond activation energy to occur. In cells, endergonic reactions are coupled to exergonic reactions, making the combination energetically favorable.
Substrates bind to the enzyme’s active site. This process typically alters the structures of both the active site and the substrate, favoring transition-state formation; this is known as induced fit.
Cofactors are inorganic ions that stabilize enzyme conformation and function. Coenzymes are organic molecules required for proper enzyme function and are often derived from vitamins. An enzyme lacking a cofactor or coenzyme is an apoenzyme; an enzyme with a bound cofactor or coenzyme is a holoenzyme.
Competitive inhibitors regulate enzymes by binding to an enzyme’s active site, preventing substrate binding. Noncompetitive (allosteric) inhibitors bind to allosteric sites, inducing a conformational change in the enzyme that prevents it from functioning. Feedback inhibition occurs when the product of a metabolic pathway noncompetitively binds to an enzyme early on in the pathway, ultimately preventing the synthesis of the product.

8.2 Catabolism of Carbohydrates

Glycolysis is the first step in the breakdown of glucose, resulting in the formation of ATP, which is produced by substrate-level phosphorylation; NADH; and two pyruvate molecules. Glycolysis does not use oxygen and is not oxygen dependent.
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.
After the transition step, coenzyme A transports the two-carbon acetyl to the Krebs cycle, where the two carbons enter the cycle. Per turn of the cycle, one 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.
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.

8.3 Cellular Respiration

Most ATP generated during the cellular respiration of glucose is made by oxidative phosphorylation.
An electron transport system (ETS) 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.
Each ETS complex has a different redox potential, and electrons move from electron carriers with more negative redox potential to those with more positive redox potential.
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.
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.
As electrons are passed from NADH and FADH₂ through an ETS, the electron loses energy. This energy is stored through the pumping of H⁺ across the membrane, generating a proton motive force.
The energy of this proton motive force can be harnessed by allowing hydrogen ions to diffuse back through the membrane by chemiosmosis using ATP synthase. As hydrogen ions diffuse through down their electrochemical gradient, components of ATP synthase spin, making ATP from ADP and P_i by oxidative phosphorylation.
Aerobic respiration forms more ATP (a maximum of 34 ATP molecules) during oxidative phosphorylation than does anaerobic respiration (between one and 32 ATP molecules).

8.4 Fermentation

Fermentation uses an organic molecule as a final electron acceptor to regenerate NAD⁺ from NADH so that glycolysis can continue.
Fermentation does not involve an electron transport system, and no ATP is made by the fermentation process directly. Fermenters make very little ATP—only two ATP molecules per glucose molecule during glycolysis.
Microbial fermentation processes have been used for the production of foods and pharmaceuticals, and for the identification of microbes.
During lactic acid fermentation, pyruvate accepts electrons from NADH and is reduced to lactic acid. Microbes performing homolactic fermentation produce only lactic acid as the fermentation product; microbes performing heterolactic fermentation produce a mixture of lactic acid, ethanol and/or acetic acid, and CO₂.
Lactic acid production by the normal microbiota prevents growth of pathogens in certain body regions and is important for the health of the gastrointestinal tract.
During ethanol fermentation, pyruvate is first decarboxylated (releasing CO₂) to acetaldehyde, which then accepts electrons from NADH, reducing acetaldehyde to ethanol. Ethanol fermentation is used for the production of alcoholic beverages, for making bread products rise, and for biofuel production.
Fermentation products of pathways (e.g., propionic acid fermentation) provide distinctive flavors to food products. Fermentation is used to produce chemical solvents (acetone-butanol-ethanol fermentation) and pharmaceuticals (mixed acid fermentation).
Specific types of microbes may be distinguished by their fermentation pathways and products. Microbes may also be differentiated according to the substrates they are able to ferment.

8.5 Catabolism of Lipids and Proteins

Collectively, microbes have the ability to degrade a wide variety of carbon sources besides carbohydrates, including lipids and proteins. The catabolic pathways for all of these molecules eventually connect into glycolysis and the Krebs cycle.
Several types of lipids can be microbially degraded. Triglycerides are degraded by extracellular lipases, releasing fatty acids from the glycerol backbone. Phospholipids are degraded by phospholipases, releasing fatty acids and the phosphorylated head group from the glycerol backbone. Lipases and phospholipases act as virulence factors for certain pathogenic microbes.
Fatty acids can be further degraded inside the cell through β-oxidation, which sequentially removes two-carbon acetyl groups from the ends of fatty acid chains.
Protein degradation involves extracellular proteases that degrade large proteins into smaller peptides. Detection of the extracellular proteases gelatinase and caseinase can be used to differentiate clinically relevant bacteria.

8.6 Photosynthesis

Heterotrophs depend on the carbohydrates produced by autotrophs, many of which are photosynthetic, converting solar energy into chemical energy.
Different photosynthetic organisms use different mixtures of photosynthetic pigments, which increase the range of the wavelengths of light an organism can absorb.
Photosystems (PSI and PSII) each contain a light-harvesting complex, composed of multiple proteins and associated pigments that absorb light energy. The light-dependent reactions of photosynthesis convert solar energy into chemical energy, producing ATP and NADPH or NADH to temporarily store this energy.
In oxygenic photosynthesis, H₂O serves as the electron donor to replace the reaction center electron, and oxygen is formed as a byproduct. In anoxygenic photosynthesis, other reduced molecules like H₂S or thiosulfate may be used as the electron donor; as such, oxygen is not formed as a byproduct.
Noncyclic photophosphorylation is used in oxygenic photosynthesis when there is a need for both ATP and NADPH production. If a cell’s needs for ATP outweigh its needs for NADPH, then it may carry out cyclic photophosphorylation instead, producing only ATP.
The light-independent reactions of photosynthesis use the ATP and NADPH from the light-dependent reactions to fix CO₂ into organic sugar molecules.

8.7 Biogeochemical Cycles

The recycling of inorganic matter between living organisms and their nonliving environment is called a biogeochemical cycle. Microbes play significant roles in these cycles.
In the carbon cycle, heterotrophs degrade reduced organic molecule to produce carbon dioxide, whereas autotrophs fix carbon dioxide to produce organics. Methanogens typically form methane by using CO₂ as a final electron acceptor during anaerobic respiration; methanotrophs oxidize the methane, using it as their carbon source.
In the nitrogen cycle, nitrogen-fixing bacteria convert atmospheric nitrogen into ammonia (ammonification). The ammonia can then be oxidized to nitrite and nitrate (nitrification). Nitrates can then be assimilated by plants. Soil bacteria convert nitrate back to nitrogen gas (denitrification).
In sulfur cycling, many anoxygenic photosynthesizers and chemoautotrophs use hydrogen sulfide as an electron donor, producing elemental sulfur and then sulfate; sulfate-reducing bacteria and archaea then use sulfate as a final electron acceptor in anaerobic respiration, converting it back to hydrogen sulfide.
Human activities that introduce excessive amounts of naturally limited nutrients (like iron, nitrogen, or phosphorus) to aquatic systems may lead to eutrophication.
Microbial bioremediation is the use of microbial metabolism to remove or degrade xenobiotics and other environmental contaminants and pollutants. Enhanced bioremediation techniques may involve the introduction of non-native microbes specifically chosen or engineered for their ability to degrade contaminants.

9.1 How Microbes Grow

Most bacterial cells divide by binary fission. Generation time in bacterial growth is defined as the doubling time of the population.
Cells in a closed system follow a pattern of growth with four phases: lag, logarithmic (exponential), stationary, and death.
Cells can be counted by direct viable cell count. The pour plate and spread plate methods are used to plate serial dilutions into or onto, respectively, agar to allow counting of viable cells that give rise to colony-forming units. Membrane filtration is used to count live cells in dilute solutions. The most probable cell number (MPN) method allows estimation of cell numbers in cultures without using solid media.
Indirect methods can be used to estimate culture density by measuring turbidity of a culture or live cell density by measuring metabolic activity.
Other patterns of cell division include multiple nucleoid formation in cells; asymmetric division, as in budding; and the formation of hyphae and terminal spores.
Biofilms are communities of microorganisms enmeshed in a matrix of extracellular polymeric substance. The formation of a biofilm occurs when planktonic cells attach to a substrate and become sessile. Cells in biofilms coordinate their activity by communicating through quorum sensing.
Biofilms are commonly found on surfaces in nature and in the human body, where they may be beneficial or cause severe infections. Pathogens associated with biofilms are often more resistant to antibiotics and disinfectants.

9.2 Oxygen Requirements for Microbial Growth

Aerobic and anaerobic environments can be found in diverse niches throughout nature, including different sites within and on the human body.
Microorganisms vary in their requirements for molecular oxygen. Obligate aerobes depend on aerobic respiration and use oxygen as a terminal electron acceptor. They cannot grow without oxygen.
Obligate anaerobes cannot grow in the presence of oxygen. They depend on fermentation and anaerobic respiration using a final electron acceptor other than oxygen.
Facultative anaerobes show better growth in the presence of oxygen but will also grow without it.
Although aerotolerant anaerobes do not perform aerobic respiration, they can grow in the presence of oxygen. Most aerotolerant anaerobes test negative for the enzyme catalase.
Microaerophiles need oxygen to grow, albeit at a lower concentration than 21% oxygen in air.
Optimum oxygen concentration for an organism is the oxygen level that promotes the fastest growth rate. The minimum permissive oxygen concentration and the maximum permissive oxygen concentration are, respectively, the lowest and the highest oxygen levels that the organism will tolerate.
Peroxidase, superoxide dismutase, and catalase are the main enzymes involved in the detoxification of the reactive oxygen species. Superoxide dismutase is usually present in a cell that can tolerate oxygen. All three enzymes are usually detectable in cells that perform aerobic respiration and produce more ROS.
A capnophile is an organism that requires a higher than atmospheric concentration of CO₂ to grow.

9.3 The Effects of pH on Microbial Growth

Bacteria are generally neutrophiles. They grow best at neutral pH close to 7.0.
Acidophiles grow optimally at a pH near 3.0. Alkaliphiles are organisms that grow optimally between a pH of 8 and 10.5. Extreme acidophiles and alkaliphiles grow slowly or not at all near neutral pH.
Microorganisms grow best at their optimum growth pH. Growth occurs slowly or not at all below the minimum growth pH and above the maximum growth pH.

9.4 Temperature and Microbial Growth

Microorganisms thrive at a wide range of temperatures; they have colonized different natural environments and have adapted to extreme temperatures. Both extreme cold and hot temperatures require evolutionary adjustments to macromolecules and biological processes.
Psychrophiles grow best in the temperature range of 0–15 °C whereas psychrotrophs thrive between 4°C and 25 °C.
Mesophiles grow best at moderate temperatures in the range of 20 °C to about 45 °C. Pathogens are usually mesophiles.
Thermophiles and hyperthemophiles are adapted to life at temperatures above 50 °C.
Adaptations to cold and hot temperatures require changes in the composition of membrane lipids and proteins.

9.5 Other Environmental Conditions that Affect Growth

Halophiles require high salt concentration in the medium, whereas halotolerant organisms can grow and multiply in the presence of high salt but do not require it for growth.
Halotolerant pathogens are an important source of foodborne illnesses because they contaminate foods preserved in salt.
Photosynthetic bacteria depend on visible light for energy.
Most bacteria, with few exceptions, require high moisture to grow.

9.6 Media Used for Bacterial Growth

Chemically defined media contain only chemically known components.
Selective media favor the growth of some microorganisms while inhibiting others.
Enriched media contain added essential nutrients a specific organism needs to grow
Differential media help distinguish bacteria by the color of the colonies or the change in the medium.

10.1 Using Microbiology to Discover the Secrets of Life

DNA was discovered and characterized long before its role in heredity was understood. Microbiologists played significant roles in demonstrating that DNA is the hereditary information found within cells.
In the 1850s and 1860s, Gregor Mendel experimented with true-breeding garden peas to demonstrate the heritability of specific observable traits.
In 1869, Friedrich Miescher isolated and purified a compound rich in phosphorus from the nuclei of white blood cells; he named the compound nuclein. Miescher’s student Richard Altmann discovered its acidic nature, renaming it nucleic acid. Albrecht Kossell characterized the nucleotide bases found within nucleic acids.
Although Walter Sutton and Theodor Boveri proposed the Chromosomal Theory of Inheritance in 1902, it was not scientifically demonstrated until the 1915 publication of the work of Thomas Hunt Morgan and his colleagues.
Using Acetabularia, a large algal cell, as his model system, Joachim Hämmerling demonstrated in the 1930s and 1940s that the nucleus was the location of hereditary information in these cells.
In the 1940s, George Beadle and Edward Tatum used the mold Neurospora crassa to show that each protein’s production was under the control of a single gene, demonstrating the “one gene–one enzyme” hypothesis.
In 1928, Frederick Griffith showed that dead encapsulated bacteria could pass genetic information to live nonencapsulated bacteria and transform them into harmful strains. In 1944, Oswald Avery, Colin McLeod, and Maclyn McCarty identified the compound as DNA.
The nature of DNA as the molecule that stores genetic information was unequivocally demonstrated in the experiment of Alfred Hershey and Martha Chase published in 1952. Labeled DNA from bacterial viruses entered and infected bacterial cells, giving rise to more viral particles. The labeled protein coats did not participate in the transmission of genetic information.

10.2 Structure and Function of DNA

Nucleic acids are composed of nucleotides, each of which contains a pentose sugar, a phosphate group, and a nitrogenous base. Deoxyribonucleotides within DNA contain deoxyribose as the pentose sugar.
DNA contains the pyrimidines cytosine and thymine, and the purines adenine and guanine.
Nucleotides are linked together by phosphodiester bonds between the 5ʹ phosphate group of one nucleotide and the 3ʹ hydroxyl group of another. A nucleic acid strand has a free phosphate group at the 5ʹ end and a free hydroxyl group at the 3ʹ end.
Chargaff discovered that the amount of adenine is approximately equal to the amount of thymine in DNA, and that the amount of the guanine is approximately equal to cytosine. These relationships were later determined to be due to complementary base pairing.
Watson and Crick, building on the work of Chargaff, Franklin and Gosling, and Wilkins, proposed the double helix model and base pairing for DNA structure.
DNA is composed of two complementary strands oriented antiparallel to each other with the phosphodiester backbones on the exterior of the molecule. The nitrogenous bases of each strand face each other and complementary bases hydrogen bond to each other, stabilizing the double helix.
Heat or chemicals can break the hydrogen bonds between complementary bases, denaturing DNA. Cooling or removing chemicals can lead to renaturation or reannealing of DNA by allowing hydrogen bonds to reform between complementary bases.
DNA stores the instructions needed to build and control the cell. This information is transmitted from parent to offspring through vertical gene transfer.

10.3 Structure and Function of RNA

Ribonucleic acid (RNA) is typically single stranded and contains ribose as its pentose sugar and the pyrimidine uracil instead of thymine. An RNA strand can undergo significant intramolecular base pairing to take on a three-dimensional structure.
There are three main types of RNA, all involved in protein synthesis.
Messenger RNA (mRNA) serves as the intermediary between DNA and the synthesis of protein products during translation.
Ribosomal RNA (rRNA) is a type of stable RNA that is a major constituent of ribosomes. It ensures the proper alignment of the mRNA and the ribosomes during protein synthesis and catalyzes the formation of the peptide bonds between two aligned amino acids during protein synthesis.
Transfer RNA (tRNA) is a small type of stable RNA that carries an amino acid to the corresponding site of protein synthesis in the ribosome. It is the base pairing between the tRNA and mRNA that allows for the correct amino acid to be inserted in the polypeptide chain being synthesized.
Although RNA is not used for long-term genetic information in cells, many viruses do use RNA as their genetic material.

10.4 Structure and Function of Cellular Genomes

The entire genetic content of a cell is its genome.
Genes code for proteins, or stable RNA molecules, each of which carries out a specific function in the cell.
Although the genotype that a cell possesses remains constant, expression of genes is dependent on environmental conditions.
A phenotype is the observable characteristics of a cell (or organism) at a given point in time and results from the complement of genes currently being used.
The majority of genetic material is organized into chromosomes that contain the DNA that controls cellular activities.
Prokaryotes are typically haploid, usually having a single circular chromosome found in the nucleoid. Eukaryotes are diploid; DNA is organized into multiple linear chromosomes found in the nucleus.
Supercoiling and DNA packaging using DNA binding proteins allows lengthy molecules to fit inside a cell. Eukaryotes and archaea use histone proteins, and bacteria use different proteins with similar function.
Prokaryotic and eukaryotic genomes both contain noncoding DNA, the function of which is not well understood. Some noncoding DNA appears to participate in the formation of small noncoding RNA molecules that influence gene expression; some appears to play a role in maintaining chromosomal structure and in DNA packaging.
Extrachromosomal DNA in eukaryotes includes the chromosomes found within organelles of prokaryotic origin (mitochondria and chloroplasts) that evolved by endosymbiosis. Some viruses may also maintain themselves extrachromosomally.
Extrachromosomal DNA in prokaryotes is commonly maintained as plasmids that encode a few nonessential genes that may be helpful under specific conditions. Plasmids can be spread through a bacterial community by horizontal gene transfer.
Viral genomes show extensive variation and may be composed of either RNA or DNA, and may be either double or single stranded.

11.1 The Functions of Genetic Material

DNA serves two important cellular functions: It is the genetic material passed from parent to offspring and it serves as the information to direct and regulate the construction of the proteins necessary for the cell to perform all of its functions.
The central dogma states that DNA organized into genes specifies the sequences of messenger RNA (mRNA), which, in turn, specifies the amino acid sequence of proteins.
The genotype of a cell is the full collection of genes a cell contains. Not all genes are used to make proteins simultaneously. The phenotype is a cell’s observable characteristics resulting from the proteins it is producing at a given time under specific environmental conditions.

11.2 DNA Replication

The DNA replication process is semiconservative, which results in two DNA molecules, each having one parental strand of DNA and one newly synthesized strand.
In bacteria, the initiation of replication occurs at the origin of replication, where supercoiled DNA is unwound by DNA gyrase, made single-stranded by helicase, and bound by single-stranded binding protein to maintain its single-stranded state. Primase synthesizes a short RNA primer, providing a free 3’-OH group to which DNA polymerase III can add DNA nucleotides.
During elongation, the leading strand of DNA is synthesized continuously from a single primer. The lagging strand is synthesized discontinuously in short Okazaki fragments, each requiring its own primer. The RNA primers are removed and replaced with DNA nucleotides by bacterial DNA polymerase I, and DNA ligase seals the gaps between these fragments.
Termination of replication in bacteria involves the resolution of circular DNA concatemers by topoisomerase IV to release the two copies of the circular chromosome.
Eukaryotes typically have multiple linear chromosomes, each with multiple origins of replication. Overall, replication in eukaryotes is similar to that in prokaryotes.
The linear nature of eukaryotic chromosomes necessitates telomeres to protect genes near the end of the chromosomes. Telomerase extends telomeres, preventing their degradation, in some cell types.
Rolling circle replication is a type of rapid unidirectional DNA synthesis of a circular DNA molecule used for the replication of some plasmids.

11.3 RNA Transcription

During transcription, the information encoded in DNA is used to make RNA.
RNA polymerase synthesizes RNA, using the antisense strand of the DNA as template by adding complementary RNA nucleotides to the 3’ end of the growing strand.
RNA polymerase binds to DNA at a sequence called a promoter during the initiation of transcription.
Genes encoding proteins of related functions are frequently transcribed under the control of a single promoter in prokaryotes, resulting in the formation of a polycistronic mRNA molecule that encodes multiple polypeptides.
Unlike DNA polymerase, RNA polymerase does not require a 3’-OH group to add nucleotides, so a primer is not needed during initiation.
Termination of transcription in bacteria occurs when the RNA polymerase encounters specific DNA sequences that lead to stalling of the polymerase. This results in release of RNA polymerase from the DNA template strand, freeing the RNA transcript.
Eukaryotes have three different RNA polymerases. Eukaryotes also have monocistronic mRNA, each encoding only a single polypeptide.
Eukaryotic primary transcripts are processed in several ways, including the addition of a 5’ cap and a 3′-poly-A tail, as well as splicing, to generate a mature mRNA molecule that can be transported out of the nucleus and that is protected from degradation.

11.4 Protein Synthesis (Translation)

In 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.
Prokaryotic (70S) and cytoplasmic eukaryotic (80S) ribosomes are each composed of a large subunit and a small subunit of differing sizes between the two groups. Each subunit is composed of rRNA and protein. Organelle ribosomes in eukaryotic cells resemble prokaryotic ribosomes.
Some 60 to 90 species of tRNA exist in bacteria. Each tRNA has a three-nucleotide anticodon as well as a binding site for a cognate amino acid. All tRNAs with a specific anticodon will carry the same amino acid.
Initiation of translation occurs when the small ribosomal subunit binds with initiation factors and an initiator tRNA at the start codon of an mRNA, followed by the binding to the initiation complex of the large ribosomal subunit.
In prokaryotic cells, the start codon codes for N-formyl-methionine carried by a special initiator tRNA. In eukaryotic cells, the start codon codes for methionine carried by a special initiator tRNA. In addition, whereas ribosomal binding of the mRNA in prokaryotes is facilitated by the Shine-Dalgarno sequence within the mRNA, eukaryotic ribosomes bind to the 5’ cap of the mRNA.
During the elongation stage of translation, a charged tRNA binds to mRNA in the A site of the ribosome; a peptide bond is catalyzed between the two adjacent amino acids, breaking the bond between the first amino acid and its tRNA; the ribosome moves one codon along the mRNA; and the first tRNA is moved from the P site of the ribosome to the E site and leaves the ribosomal complex.
Termination of translation occurs when the ribosome encounters a stop codon, which does not code for a tRNA. Release factors cause the polypeptide to be released, and the ribosomal complex dissociates.
In prokaryotes, transcription and translation may be coupled, with translation of an mRNA molecule beginning as soon as transcription allows enough mRNA exposure for the binding of a ribosome, prior to transcription termination. Transcription and translation are not coupled in eukaryotes because transcription occurs in the nucleus, whereas translation occurs in the cytoplasm or in association with the rough endoplasmic reticulum.
Polypeptides often require one or more post-translational modifications to become biologically active.

11.5 Mutations

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 point mutation affects a single base pair. A point mutation may cause a silent mutation if the mRNA codon codes for the same amino acid, a missense mutation if the mRNA codon codes for a different amino acid, or a nonsense mutation if the mRNA codon becomes a stop codon.
Missense mutations may retain function, depending on the chemistry of the new amino acid and its location in the protein. Nonsense mutations produce truncated and frequently nonfunctional proteins.
A frameshift mutation results from an insertion or deletion of a number of nucleotides that is not a multiple of three. The change in reading frame alters every amino acid after the point of the mutation and results in a nonfunctional protein.
Spontaneous mutations occur through DNA replication errors, whereas induced mutations occur through exposure to a mutagen.
Mutagenic agents are frequently carcinogenic but not always. However, nearly all carcinogens are mutagenic.
Chemical mutagens include base analogs and chemicals that modify existing bases. In both cases, mutations are introduced after several rounds of DNA replication.
Ionizing radiation, such as X-rays and γ-rays, leads to breakage of the phosphodiester backbone of DNA and can also chemically modify bases to alter their base-pairing rules.
Nonionizing radiation like ultraviolet light may introduce pyrimidine (thymine) dimers, which, during DNA replication and transcription, may introduce frameshift or point mutations.
Cells have mechanisms to repair naturally occurring mutations. DNA polymerase has proofreading activity. Mismatch repair is a process to repair incorrectly incorporated bases after DNA replication has been completed.
Pyrimidine dimers can also be repaired. In nucleotide excision repair (dark repair), enzymes recognize the distortion introduced by the pyrimidine dimer and replace the damaged strand with the correct bases, using the undamaged DNA strand as a template. Bacteria and other organisms may also use direct repair, in which the photolyase enzyme, in the presence of visible light, breaks apart the pyrimidines.
Through comparison of growth on the complete plate and lack of growth on media lacking specific nutrients, specific loss-of-function mutants called auxotrophs can be identified.
The Ames test is an inexpensive method that uses auxotrophic bacteria to measure mutagenicity of a chemical compound. Mutagenicity is an indicator of carcinogenic potential.

11.6 How Asexual Prokaryotes Achieve Genetic Diversity

Horizontal gene transfer is an important way for asexually reproducing organisms like prokaryotes to acquire new traits.
There are three mechanisms of horizontal gene transfer typically used by bacteria: transformation, transduction, and conjugation.
Transformation allows for competent cells to take up naked DNA, released from other cells on their death, into their cytoplasm, where it may recombine with the host genome.
In generalized transduction, any piece of chromosomal DNA may be transferred by accidental packaging of the degraded host chromosome into a phage head. In specialized transduction, only chromosomal DNA adjacent to the integration site of a lysogenic phage may be transferred as a result of imprecise excision of the prophage.
Conjugation is mediated by the F plasmid, which encodes a conjugation pilus that brings an F plasmid-containing F⁺ cell into contact with an F^- cell.
The rare integration of the F plasmid into the bacterial chromosome, generating an Hfr cell, allows for transfer of chromosomal DNA from the donor to the recipient. Additionally, imprecise excision of the F plasmid from the chromosome may generate an F’ plasmid that may be transferred to a recipient by conjugation.
Conjugation transfer of R plasmids is an important mechanism for the spread of antibiotic resistance in bacterial communities.
Transposons are molecules of DNA with inverted repeats at their ends that also encode the enzyme transposase, allowing for their movement from one location in DNA to another. Although found in both prokaryotes and eukaryotes, transposons are clinically relevant in bacterial pathogens for the movement of virulence factors, including antibiotic resistance genes.

11.7 Gene Regulation: Operon Theory

Gene expression is a tightly regulated process.
Gene expression in prokaryotes is largely regulated at the point of transcription. Gene expression in eukaryotes is additionally regulated post-transcriptionally.
Prokaryotic structural genes of related function are often organized into operons, all controlled by transcription from a single promoter. The regulatory region of an operon includes the promoter itself and the region surrounding the promoter to which transcription factors can bind to influence transcription.
Although some operons are constitutively expressed, most are subject to regulation through the use of transcription factors (repressors and activators). A repressor binds to an operator, a DNA sequence within the regulatory region between the RNA polymerase binding site in the promoter and first structural gene, thereby physically blocking transcription of these operons. An activator binds within the regulatory region of an operon, helping RNA polymerase bind to the promoter, thereby enhancing the transcription of this operon. An inducer influences transcription through interacting with a repressor or activator.
The trp operon is a classic example of a repressible operon. When tryptophan accumulates, tryptophan binds to a repressor, which then binds to the operator, preventing further transcription.
The lac operon is a classic example an inducible operon. When lactose is present in the cell, it is converted to allolactose. Allolactose acts as an inducer, binding to the repressor and preventing the repressor from binding to the operator. This allows transcription of the structural genes.
The lac operon is also subject to activation. When glucose levels are depleted, some cellular ATP is converted into cAMP, which binds to the catabolite activator protein (CAP). The cAMP-CAP complex activates transcription of the lac operon. When glucose levels are high, its presence prevents transcription of the lac operon and other operons by catabolite repression.
Small intracellular molecules called alarmones are made in response to various environmental stresses, allowing bacteria to control the transcription of a group of operons, called a regulon.
Bacteria have the ability to change which σ factor of RNA polymerase they use in response to environmental conditions to quickly and globally change which regulons are transcribed.
Prokaryotes have regulatory mechanisms, including attenuation and the use of riboswitches, to simultaneously control the completion of transcription and translation from that transcript. These mechanisms work through the formation of stem loops in the 5’ end of an mRNA molecule currently being synthesized.
There are additional points of regulation of gene expression in prokaryotes and eukaryotes. In eukaryotes, epigenetic regulation by chemical modification of DNA or histones, and regulation of RNA processing are two methods.

12.1 Microbes and the Tools of Genetic Engineering

Biotechology is the science of utilizing living systems to benefit humankind. In recent years, the ability to directly alter an organism’s genome through genetic engineering has been made possible due to advances in recombinant DNA technology, which allows researchers to create recombinant DNA molecules with new combinations of genetic material.
Molecular cloning involves methods used to construct recombinant DNA and facilitate their replication in host organisms. These methods include the use of restriction enzymes (to cut both foreign DNA and plasmid vectors), ligation (to paste fragments of DNA together), and the introduction of recombinant DNA into a host organism (often bacteria).
Blue-white screening allows selection of bacterial transformants that contain recombinant plasmids using the phenotype of a reporter gene that is disabled by insertion of the DNA fragment.
Genomic libraries can be made by cloning genomic fragments from one organism into plasmid vectors or into bacteriophage.
cDNA libraries can be generated to represent the mRNA molecules expressed in a cell at a given point.
Transfection of eukaryotic hosts can be achieved through various methods using electroporation, gene guns, microinjection, shuttle vectors, and viral vectors.

12.2 Visualizing and Characterizing DNA, RNA, and Protein

Finding a gene of interest within a sample requires the use of a single-stranded DNA probe labeled with a molecular beacon (typically radioactivity or fluorescence) that can hybridize with a complementary single-stranded nucleic acid in the sample.
Agarose gel electrophoresis allows for the separation of DNA molecules based on size.
Restriction fragment length polymorphism (RFLP) analysis allows for the visualization by agarose gel electrophoresis of distinct variants of a DNA sequence caused by differences in restriction sites.
Southern blot analysis allows researchers to find a particular DNA sequence within a sample whereas northern blot analysis allows researchers to detect a particular mRNA sequence expressed in a sample.
Microarray technology is a nucleic acid hybridization technique that allows for the examination of many thousands of genes at once to find differences in genes or gene expression patterns between two samples of genomic DNA or cDNA,
Polyacrylamide gel electrophoresis (PAGE) allows for the separation of proteins by size, especially if native protein charges are masked through pretreatment with SDS.
Polymerase chain reaction allows for the rapid amplification of a specific DNA sequence. Variations of PCR can be used to detect mRNA expression (reverse transcriptase PCR) or to quantify a particular sequence in the original sample (real-time PCR).
Although the development of Sanger DNA sequencing was revolutionary, advances in next generation sequencing allow for the rapid and inexpensive sequencing of the genomes of many organisms, accelerating the volume of new sequence data.

12.3 Whole Genome Methods and Pharmaceutical Applications of Genetic Engineering

The science of genomics allows researchers to study organisms on a holistic level and has many applications of medical relevance.
Transcriptomics and proteomics allow researchers to compare gene expression patterns between different cells and shows great promise in better understanding global responses to various conditions.
The various –omics technologies complement each other and together provide a more complete picture of an organism’s or microbial community’s (metagenomics) state.
The analysis required for large data sets produced through genomics, transcriptomics, and proteomics has led to the emergence of bioinformatics.
Reporter genes encoding easily observable characteristics are commonly used to track gene expression patterns of genes of unknown function.
The use of recombinant DNA technology has revolutionized the pharmaceutical industry, allowing for the rapid production of high-quality recombinant DNA pharmaceuticals used to treat a wide variety of human conditions.
RNA interference technology has great promise as a method of treating viral infections by silencing the expression of specific genes

12.4 Gene Therapy

While gene therapy shows great promise for the treatment of genetic diseases, there are also significant risks involved.
There is considerable federal and local regulation of the development of gene therapies by pharmaceutical companies for use in humans.
Before gene therapy use can increase dramatically, there are many ethical issues that need to be addressed by the medical and research communities, politicians, and society at large.

13.1 Controlling Microbial Growth

Inanimate items that may harbor microbes and aid in their transmission are called fomites. The level of cleanliness required for a fomite depends both on the item’s use and the infectious agent with which the item may be contaminated.
The CDC and the NIH have established four biological safety levels (BSLs) for laboratories performing research on infectious agents. Each level is designed to protect laboratory personnel and the community. These BSLs are determined by the agent’s infectivity, ease of transmission, and potential disease severity, as well as the type of work being performed with the agent.
Disinfection removes potential pathogens from a fomite, whereas antisepsis uses antimicrobial chemicals safe enough for tissues; in both cases, microbial load is reduced, but microbes may remain unless the chemical used is strong enough to be a sterilant.
The amount of cleanliness (sterilization versus high-level disinfection versus general cleanliness) required for items used clinically depends on whether the item will come into contact with sterile tissues (critical item), mucous membranes (semicritical item), or intact skin (noncritical item).
Medical procedures with a risk for contamination should be carried out in a sterile field maintained by proper aseptic technique to prevent sepsis.
Sterilization is necessary for some medical applications as well as in the food industry, where endospores of Clostridium botulinum are killed through commercial sterilization protocols.
Physical or chemical methods to control microbial growth that result in death of the microbe are indicated by the suffixes -cide or -cidal (e.g., as with bactericides, viricides, and fungicides), whereas those that inhibit microbial growth are indicated by the suffixes -stat or-static (e.g., bacteriostatic, fungistatic).
Microbial death curves display the logarithmic decline of living microbes exposed to a method of microbial control. The time it takes for a protocol to yield a 1-log (90%) reduction in the microbial population is the decimal reduction time, or D-value.
When choosing a microbial control protocol, factors to consider include the length of exposure time, the type of microbe targeted, its susceptibility to the protocol, the intensity of the treatment, the presence of organics that may interfere with the protocol, and the environmental conditions that may alter the effectiveness of the protocol.

13.2 Using Physical Methods to Control Microorganisms

Heat is a widely used and highly effective method for controlling microbial growth.
Dry-heat sterilization protocols are used commonly in aseptic techniques in the laboratory. However, moist-heat sterilization is typically the more effective protocol because it penetrates cells better than dry heat does.
Pasteurization is used to kill pathogens and reduce the number of microbes that cause food spoilage. High-temperature, short-time pasteurization is commonly used to pasteurize milk that will be refrigerated; ultra-high temperature pasteurization can be used to pasteurize milk for long-term storage without refrigeration.
Refrigeration slows microbial growth; freezing stops growth, killing some organisms. Laboratory and medical specimens may be frozen on dry ice or at ultra-low temperatures for storage and transport.
High-pressure processing can be used to kill microbes in food. Hyperbaric oxygen therapy to increase oxygen saturation has also been used to treat certain infections.
Desiccation has long been used to preserve foods and is accelerated through the addition of salt or sugar, which decrease water activity in foods.
Lyophilization combines cold exposure and desiccation for the long-term storage of foods and laboratory materials, but microbes remain and can be rehydrated.
Ionizing radiation, including gamma irradiation, is an effective way to sterilize heat-sensitive and packaged materials. Nonionizing radiation, like ultraviolet light, is unable to penetrate surfaces but is useful for surface sterilization.
HEPA filtration is commonly used in hospital ventilation systems and biological safety cabinets in laboratories to prevent transmission of airborne microbes. Membrane filtration is commonly used to remove bacteria from heat-sensitive solutions.

13.3 Using Chemicals to Control Microorganisms

Heavy metals, including mercury, silver, copper, and zinc, have long been used for disinfection and preservation, although some have toxicity and environmental risks associated with them.
Halogens, including chlorine, fluorine, and iodine, are also commonly used for disinfection. Chlorine compounds, including sodium hypochlorite, chloramines, and chlorine dioxide, are commonly used for water disinfection. Iodine, in both tincture and iodophor forms, is an effective antiseptic.
Alcohols, including ethyl alcohol and isopropyl alcohol, are commonly used antiseptics that act by denaturing proteins and disrupting membranes.
Phenolics are stable, long-acting disinfectants that denature proteins and disrupt membranes. They are commonly found in household cleaners, mouthwashes, and hospital disinfectants, and are also used to preserve harvested crops.
The phenolic compound triclosan, found in antibacterial soaps, plastics, and textiles is technically an antibiotic because of its specific mode of action of inhibiting bacterial fatty-acid synthesis..
Surfactants, including soaps and detergents, lower the surface tension of water to create emulsions that mechanically carry away microbes. Soaps are long-chain fatty acids, whereas detergents are synthetic surfactants.
Quaternary ammonium compounds (quats) are cationic detergents that disrupt membranes. They are used in household cleaners, skin disinfectants, oral rinses, and mouthwashes.
Bisbiguanides disrupt cell membranes, causing cell contents to gel. Chlorhexidine and alexidine are commonly used for surgical scrubs, for handwashing in clinical settings, and in prescription oral rinses.
Alkylating agents effectively sterilize materials at low temperatures but are carcinogenic and may also irritate tissue. Glutaraldehyde and o-phthalaldehyde are used as hospital disinfectants but not as antiseptics. Formaldehyde is used for the storage of tissue specimens, as an embalming fluid, and in vaccine preparation to inactivate infectious agents. Ethylene oxide is a gas sterilant that can permeate heat-sensitive packaged materials, but it is also explosive and carcinogenic.
Peroxygens, including hydrogen peroxide, peracetic acid, benzoyl peroxide, and ozone gas, are strong oxidizing agents that produce free radicals in cells, damaging their macromolecules. They are environmentally safe and are highly effective disinfectants and antiseptics.
Pressurized carbon dioxide in the form of a supercritical fluid easily permeates packaged materials and cells, forming carbonic acid and lowering intracellular pH. Supercritical carbon dioxide is nonreactive, nontoxic, nonflammable, and effective at low temperatures for sterilization of medical devices, implants, and transplanted tissues.
Chemical preservatives are added to a variety of foods. Sorbic acid, benzoic acid, propionic acid, and their more soluble salts inhibit enzymes or reduce intracellular pH.
Sulfites are used in winemaking and food processing to prevent browning of foods.
Nitrites are used to preserve meats and maintain color, but cooking nitrite-preserved meats may produce carcinogenic nitrosamines.
Nisin and natamycin are naturally produced preservatives used in cheeses and meats. Nisin is effective against gram-positive bacteria and natamycin against fungi.

13.4 Testing the Effectiveness of Antiseptics and Disinfectants

Chemical disinfectants are grouped by the types of microbes and infectious agents they are effective against. High-level germicides kill vegetative cells, fungi, viruses, and endospores, and can ultimately lead to sterilization. Intermediate-level germicides cannot kill all viruses and are less effective against endospores. Low-level germicides kill vegetative cells and some enveloped viruses, but are ineffective against endospores.
The effectiveness of a disinfectant is influenced by several factors, including length of exposure, concentration of disinfectant, temperature, and pH.
Historically, the effectiveness of a chemical disinfectant was compared with that of phenol at killing Staphylococcus aureus and Salmonella enterica serovar Typhi, and a phenol coefficient was calculated.
The disk-diffusion method is used to test the effectiveness of a chemical disinfectant against a particular microbe.
The use-dilution test determines the effectiveness of a disinfectant on a surface. In-use tests can determine whether disinfectant solutions are being used correctly in clinical settings.14.1 History of Chemotherapy and Antimicrobial Discovery
- Antimicrobial drugs produced by purposeful fermentation and/or contained in plants have been used as traditional medicines in many cultures for millennia.
- The purposeful and systematic search for a chemical “magic bullet” that specifically target infectious microbes was initiated by Paul Ehrlich in the early 20th century.
- The discovery of the natural antibiotic, penicillin, by Alexander Fleming in 1928 started the modern age of antimicrobial discovery and research.
- Sulfanilamide, the first synthetic antimicrobial, was discovered by Gerhard Domagk and colleagues and is a breakdown product of the synthetic dye, prontosil.
14.2 Fundamentals of Antimicrobial Chemotherapy
- Antimicrobial drugs can be bacteriostatic or bactericidal, and these characteristics are important considerations when selecting the most appropriate drug.
- The use of narrow-spectrum antimicrobial drugs is preferred in many cases to avoid superinfection and the development of antimicrobial resistance.
- Broad-spectrum antimicrobial use is warranted for serious systemic infections when there is no time to determine the causative agent, when narrow-spectrum antimicrobials fail, or for the treatment or prevention of infections with multiple types of microbes.
- The dosage and route of administration are important considerations when selecting an antimicrobial to treat and infection. Other considerations include the patient’s age, mass, ability to take oral medications, liver and kidney function, and possible interactions with other drugs the patient may be taking.
14.3 Mechanisms of Antibacterial Drugs
- Antibacterial compounds exhibit selective toxicity, largely due to differences between prokaryotic and eukaryotic cell structure.
- Cell wall synthesis inhibitors, including the β-lactams, the glycopeptides, and bacitracin, interfere with peptidoglycan synthesis, making bacterial cells more prone to osmotic lysis.
- There are a variety of broad-spectrum, bacterial protein synthesis inhibitors that selectively target the prokaryotic 70S ribosome, including those that bind to the 30S subunit (aminoglycosides and tetracyclines) and others that bind to the 50S subunit (macrolides, lincosamides, chloramphenicol, and oxazolidinones).
- Polymyxins are lipophilic polypeptide antibiotics that target the lipopolysaccharide component of gram-negative bacteria and ultimately disrupt the integrity of the outer and inner membranes of these bacteria.
- The nucleic acid synthesis inhibitors rifamycins and fluoroquinolones target bacterial RNA transcription and DNA replication, respectively.
- Some antibacterial drugs are antimetabolites, acting as competitive inhibitors for bacterial metabolic enzymes. Sulfonamides and trimethoprim are antimetabolites that interfere with bacterial folic acid synthesis. Isoniazid is an antimetabolite that interferes with mycolic acid synthesis in mycobacteria.
14.4 Mechanisms of Other Antimicrobial Drugs
- Because fungi, protozoans, and helminths are eukaryotic organisms like human cells, it is more challenging to develop antimicrobial drugs that specifically target them. Similarly, it is hard to target viruses because human viruses replicate inside of human cells.
- Antifungal drugs interfere with ergosterol synthesis, bind to ergosterol to disrupt fungal cell membrane integrity, or target cell wall-specific components or other cellular proteins.
- Antiprotozoan drugs increase cellular levels of reactive oxygen species, interfere with protozoal DNA replication (nuclear versus kDNA, respectively), and disrupt heme detoxification.
- Antihelminthic drugs disrupt helminthic and protozoan microtubule formation; block neuronal transmissions; inhibit anaerobic ATP formation and/or oxidative phosphorylation; induce a calcium influx in tapeworms, leading to spasms and paralysis; and interfere with RNA synthesis in schistosomes.
- Antiviral drugs inhibit viral entry, inhibit viral uncoating, inhibit nucleic acid biosynthesis, prevent viral escape from endosomes in host cells, and prevent viral release from infected cells.
- Because it can easily mutate to become drug resistant, HIV is typically treated with a combination of several antiretroviral drugs, which may include reverse transcriptase inhibitors, protease inhibitors, integrase inhibitors, and drugs that interfere with viral binding and fusion to initiate infection.
14.5 Drug 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.
- Common modes of antimicrobial drug resistance include drug modification or inactivation, prevention of cellular uptake or efflux, target modification, target overproduction or enzymatic bypass, and target mimicry.
- 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.
14.6 Testing the Effectiveness of Antimicrobials
- The Kirby-Bauer disk diffusion test helps determine the susceptibility of a microorganism to various antimicrobial drugs. However, the zones of inhibition measured must be correlated to known standards to determine susceptibility and resistance, and do not provide information on bactericidal versus bacteriostatic activity, or allow for direct comparison of drug potencies.
- Antibiograms are useful for monitoring local trends in antimicrobial resistance/susceptibility and for directing appropriate selection of empiric antibacterial therapy.
- There are several laboratory methods available for determining the minimum inhibitory concentration (MIC) of an antimicrobial drug against a specific microbe. The minimal bactericidal concentration (MBC) can also be determined, typically as a follow-up experiment to MIC determination using the tube dilution method.
14.7 Current Strategies for Antimicrobial Discovery
- Current research into the development of antimicrobial drugs involves the use of high-throughput screening and combinatorial chemistry technologies.
- New technologies are being developed to discover novel antibiotics from soil microorganisms that cannot be cultured by standard laboratory methods.
- Additional strategies include searching for antibiotics from sources other than soil, identifying new antibacterial targets, using combinatorial chemistry to develop novel drugs, developing drugs that inhibit resistance mechanisms, and developing drugs that target virulence factors and hold infections in check.

15.1 Characteristics of Infectious Disease

In an infection, a microorganism enters a host and begins to multiply. Some infections cause disease, which is any deviation from the normal function or structure of the host.
Signs of a disease are objective and are measured. Symptoms of a disease are subjective and are reported by the patient.
Diseases can either be noninfectious (due to genetics and environment) or infectious (due to pathogens). Some infectious diseases are communicable (transmissible between individuals) or contagious (easily transmissible between individuals); others are noncommunicable, but may be contracted via contact with environmental reservoirs or animals (zoonoses)
Nosocomial diseases are contracted in hospital settings, whereas iatrogenic disease are the direct result of a medical procedure
An acute disease is short in duration, whereas a chronic disease lasts for months or years. Latent diseases last for years, but are distinguished from chronic diseases by the lack of active replication during extended dormant periods.
The periods of disease include the incubation period, the prodromal period, the period of illness, the period of decline, and the period of convalescence. These periods are marked by changes in the number of infectious agents and the severity of signs and symptoms.

15.2 How Pathogens Cause Disease

Koch’s postulates are used to determine whether a particular microorganism is a pathogen. Molecular Koch’s postulates are used to determine what genes contribute to a pathogen’s ability to cause disease.
Virulence, the degree to which a pathogen can cause disease, can be quantified by calculating either the ID₅₀ or LD₅₀ of a pathogen on a given population.
Primary pathogens are capable of causing pathological changes associated with disease in a healthy individual, whereas opportunistic pathogens can only cause disease when the individual is compromised by a break in protective barriers or immunosuppression.
Infections and disease can be caused by pathogens in the environment or microbes in an individual’s resident microbiota.
Infections can be classified as local, focal, or systemic depending on the extent to which the pathogen spreads in the body.
A secondary infection can sometimes occur after the host’s defenses or normal microbiota are compromised by a primary infection or antibiotic treatment.
Pathogens enter the body through portals of entry and leave through portals of exit. The stages of pathogenesis include exposure, adhesion, invasion, infection, and transmission.

15.3 Virulence Factors of Bacterial and Viral Pathogens

Virulence factors contribute to a pathogen’s ability to cause disease.
Exoenzymes and toxins allow pathogens to invade host tissue and cause tissue damage. Exoenzymes are classified according to the macromolecule they target and exotoxins are classified based on their mechanism of action.
Bacterial toxins include endotoxin and exotoxins. Endotoxin is the lipid A component of the LPS of the gram-negative cell envelope. Exotoxins are proteins secreted mainly by gram-positive bacteria, but also are secreted by gram-negative bacteria.
Bacterial pathogens may evade the host immune response by producing capsules to avoid phagocytosis, surviving the intracellular environment of phagocytes, degrading antibodies, or through antigenic variation.
Viral pathogens use adhesins for initiating infections and antigenic variation to avoid immune defenses.
Influenza viruses use both antigenic drift and antigenic shift to avoid being recognized by the immune system.

15.4 Virulence Factors of Eukaryotic Pathogens

Fungal and parasitic pathogens use pathogenic mechanisms and virulence factors that are similar to those of bacterial pathogens
Fungi initiate infections through the interaction of adhesins with receptors on host cells. Some fungi produce toxins and exoenzymes involved in disease production and capsules that provide protection of phagocytosis.
Protozoa adhere to target cells through complex mechanisms and can cause cellular damage through release of cytopathic substances. Some protozoa avoid the immune system through antigenic variation and production of capsules.
Helminthic worms are able to avoid the immune system by coating their exteriors with glycan molecules that make them look like host cells or by suppressing the immune system.

16.1 The Language of Epidemiologists

Epidemiology is the science underlying public health.
Morbidity means being in a state of illness, whereas mortality refers to death; both morbidity rates and mortality rates are of interest to epidemiologists.
Incidence is the number of new cases (morbidity or mortality), usually expressed as a proportion, during a specified time period; prevalence is the total number affected in the population, again usually expressed as a proportion.
Sporadic diseases only occur rarely and largely without a geographic focus. Endemic diseases occur at a constant (and often low) level within a population. Epidemic diseases and pandemic diseases occur when an outbreak occurs on a significantly larger than expected level, either locally or globally, respectively.
Koch’s postulates specify the procedure for confirming a particular pathogen as the etiologic agent of a particular disease. Koch’s postulates have limitations in application if the microbe cannot be isolated and cultured or if there is no animal host for the microbe. In this case, molecular Koch’s postulates would be utilized.
In the United States, the Centers for Disease Control and Prevention monitors notifiable diseases and publishes weekly updates in the Morbidity and Mortality Weekly Report.

16.2 Tracking Infectious Diseases

Early pioneers of epidemiology such as John Snow, Florence Nightingale, and Joseph Lister, studied disease at the population level and used data to disrupt disease transmission.
Descriptive epidemiology studies rely on case analysis and patient histories to gain information about outbreaks, frequently while they are still occurring.
Retrospective epidemiology studies use historical data to identify associations with the disease state of present cases. Prospective epidemiology studies gather data and follow cases to find associations with future disease states.
Analytical epidemiology studies are observational studies that are carefully designed to compare groups and uncover associations between environmental or genetic factors and disease.
Experimental epidemiology studies generate strong evidence of causation in disease or treatment by manipulating subjects and comparing them with control subjects.

16.3 Modes of Disease Transmission

Reservoirs of human disease can include the human and animal populations, soil, water, and inanimate objects or materials.
Contact transmission can be direct or indirect through physical contact with either an infected host (direct) or contact with a fomite that an infected host has made contact with previously (indirect).
Vector transmission occurs when a living organism carries an infectious agent on its body (mechanical) or as an infection host itself (biological), to a new host.
Vehicle transmission occurs when a substance, such as soil, water, or air, carries an infectious agent to a new host.
Healthcare-associated infections (HAI), or nosocomial infections, are acquired in a clinical setting. Transmission is facilitated by medical interventions and the high concentration of susceptible, immunocompromised individuals in clinical settings.

16.4 Global Public Health

The World Health Organization (WHO) is an agency of the United Nations that collects and analyzes data on disease occurrence from member nations. WHO also coordinates public health programs and responses to international health emergencies.
Emerging diseases are those that are new to human populations or that have been increasing in the past two decades. Reemerging diseases are those that are making a resurgence in susceptible populations after previously having been controlled in some geographic areas.

17.1 Physical Defenses

Nonspecific innate immunity provides a first line of defense against infection by nonspecifically blocking entry of microbes and targeting them for destruction or removal from the body.
The physical defenses of innate immunity include physical barriers, mechanical actions that remove microbes and debris, and the microbiome, which competes with and inhibits the growth of pathogens.
The skin, mucous membranes, and endothelia throughout the body serve as physical barriers that prevent microbes from reaching potential sites of infection. Tight cell junctions in these tissues prevent microbes from passing through.
Microbes trapped in dead skin cells or mucus are removed from the body by mechanical actions such as shedding of skin cells, mucociliary sweeping, coughing, peristalsis, and flushing of bodily fluids (e.g., urination, tears)
The resident microbiota provide a physical defense by occupying available cellular binding sites and competing with pathogens for available nutrients.

17.2 Chemical Defenses

Numerous chemical mediators produced endogenously and exogenously exhibit nonspecific antimicrobial functions.
Many chemical mediators are found in body fluids such as sebum, saliva, mucus, gastric and intestinal fluids, urine, tears, cerumen, and vaginal secretions.
Antimicrobial peptides (AMPs) found on the skin and in other areas of the body are largely produced in response to the presence of pathogens. These include dermcidin, cathelicidin, defensins, histatins, and bacteriocins.
Plasma contains various proteins that serve as chemical mediators, including acute-phase proteins, complement proteins, and cytokines.
The complement system involves numerous precursor proteins that circulate in plasma. These proteins become activated in a cascading sequence in the presence of microbes, resulting in the opsonization of pathogens, chemoattraction of leukocytes, induction of inflammation, and cytolysis through the formation of a membrane attack complex (MAC).
Cytokines are proteins that facilitate various nonspecific responses by innate immune cells, including production of other chemical mediators, cell proliferation, cell death, and differentiation.
Cytokines play a key role in the inflammatory response, triggering production of inflammation-eliciting mediators such as acute-phase proteins, histamine, leukotrienes, prostaglandins, and bradykinin.

17.3 Cellular Defenses

The formed elements of the blood include red blood cells (erythrocytes), white blood cells (leukocytes), and platelets (thrombocytes). Of these, leukocytes are primarily involved in the immune response.
All formed elements originate in the bone marrow as stem cells (HSCs) that differentiate through hematopoiesis.
Granulocytes are leukocytes characterized by a lobed nucleus and granules in the cytoplasm. These include neutrophils (PMNs), eosinophils, and basophils.
Neutrophils are the leukocytes found in the largest numbers in the bloodstream and they primarily fight bacterial infections.
Eosinophils target parasitic infections. Eosinophils and basophils are involved in allergic reactions. Both release histamine and other proinflammatory compounds from their granules upon stimulation.
Mast cells function similarly to basophils but can be found in tissues outside the bloodstream.
Natural killer (NK) cells are lymphocytes that recognize and kill abnormal or infected cells by releasing proteins that trigger apoptosis.
Monocytes are large, mononuclear leukocytes that circulate in the bloodstream. They may leave the bloodstream and take up residence in body tissues, where they differentiate and become tissue-specific macrophages and dendritic cells.

17.4 Pathogen Recognition and Phagocytosis

Phagocytes are cells that recognize pathogens and destroy them through phagocytosis.
Recognition often takes place by the use of phagocyte receptors that bind molecules commonly found on pathogens, known as pathogen-associated molecular patterns (PAMPs).
The receptors that bind PAMPs are called pattern recognition receptors, or PRRs. Toll-like receptors (TLRs) are one type of PRR found on phagocytes.
Extravasation of white blood cells from the bloodstream into infected tissue occurs through the process of transendothelial migration.
Phagocytes degrade pathogens through phagocytosis, which involves engulfing the pathogen, killing and digesting it within a phagolysosome, and then excreting undigested matter.

17.5 Inflammation and Fever

Inflammation results from the collective response of chemical mediators and cellular defenses to an injury or infection.
Acute inflammation is short lived and localized to the site of injury or infection. Chronic inflammation occurs when the inflammatory response is unsuccessful, and may result in the formation of granulomas (e.g., with tuberculosis) and scarring (e.g., with hepatitis C viral infections and liver cirrhosis).
The five cardinal signs of inflammation are erythema, edema, heat, pain, and altered function. These largely result from innate responses that draw increased blood flow to the injured or infected tissue.
Fever is a system-wide sign of inflammation that raises the body temperature and stimulates the immune response.
Both inflammation and fever can be harmful if the inflammatory response is too severe.

18.1 Overview of Specific Adaptive Immunity

Adaptive immunity is an acquired defense against foreign pathogens that is characterized by specificity and memory. The first exposure to an antigen stimulates a primary response, and subsequent exposures stimulate a faster and strong secondary response.
Adaptive immunity is a dual system involving humoral immunity (antibodies produced by B cells) and cellular immunity (T cells directed against intracellular pathogens).
Antigens, also called immunogens, are molecules that activate adaptive immunity. A single antigen possesses smaller epitopes, each capable of inducing a specific adaptive immune response.
An antigen’s ability to stimulate an immune response depends on several factors, including its molecular class, molecular complexity, and size.
Antibodies (immunoglobulins) are Y-shaped glycoproteins with two Fab sites for binding antigens and an Fc portion involved in complement activation and opsonization.
The five classes of antibody are IgM, IgG, IgA, IgE, and IgD, each differing in size, arrangement, location within the body, and function. The five primary functions of antibodies are neutralization, opsonization, agglutination, complement activation, and antibody-dependent cell-mediated cytotoxicity (ADCC).

18.2 Major Histocompatibility Complexes and Antigen-Presenting Cells

Major histocompatibility complex (MHC) is a collection of genes coding for glycoprotein molecules expressed on the surface of all nucleated cells.
MHC I molecules are expressed on all nucleated cells and are essential for presentation of normal “self” antigens. Cells that become infected by intracellular pathogens can present foreign antigens on MHC I as well, marking the infected cell for destruction.
MHC II molecules are expressed only on the surface of antigen-presenting cells (macrophages, dendritic cells, and B cells). Antigen presentation with MHC II is essential for the activation of T cells.
Antigen-presenting cells (APCs) primarily ingest pathogens by phagocytosis, destroy them in the phagolysosomes, process the protein antigens, and select the most antigenic/immunodominant epitopes with MHC II for presentation to T cells.
Cross-presentation is a mechanism of antigen presentation and T-cell activation used by dendritic cells not directly infected by the pathogen; it involves phagocytosis of the pathogen but presentation on MHC I rather than MHC II.

18.3 T Lymphocytes and Cellular Immunity

Immature T lymphocytes are produced in the red bone marrow and travel to the thymus for maturation.
Thymic selection is a three-step process of negative and positive selection that determines which T cells will mature and exit the thymus into the peripheral bloodstream.
Central tolerance involves negative selection of self-reactive T cells in the thymus, and peripheral tolerance involves anergy and regulatory T cells that prevent self-reactive immune responses and autoimmunity.
The TCR is similar in structure to immunoglobulins, but less complex. Millions of unique epitope-binding TCRs are encoded through a process of genetic rearrangement of V, D, and J gene segments.
T cells can be divided into three classes—helper T cells, cytotoxic T cells, and regulatory T cells—based on their expression of CD4 or CD8, the MHC molecules with which they interact for activation, and their respective functions.
Activated helper T cells differentiate into T_H1, T_H2, T_H17, or memory T cell subtypes. Differentiation is directed by the specific cytokines to which they are exposed. T_H1, T_H2, and T_H17 perform different functions related to stimulation of adaptive and innate immune defenses. Memory T cells are long-lived cells that can respond quickly to secondary exposures.
Once activated, cytotoxic T cells target and kill cells infected with intracellular pathogens. Killing requires recognition of specific pathogen epitopes presented on the cell surface using MHC I molecules. Killing is mediated by perforin and granzymes that induce apoptosis.
Superantigens are bacterial or viral proteins that cause a nonspecific activation of helper T cells, leading to an excessive release of cytokines (cytokine storm) and a systemic, potentially fatal inflammatory response.

18.4 B Lymphocytes and Humoral Immunity

B lymphocytes or B cells produce antibodies involved in humoral immunity. B cells are produced in the bone marrow, where the initial stages of maturation occur, and travel to the spleen for final steps of maturation into naïve mature B cells.
B-cell receptors (BCRs) are membrane-bound monomeric forms of IgD and IgM that bind specific antigen epitopes with their Fab antigen-binding regions. Diversity of antigen binding specificity is created by genetic rearrangement of V, D, and J segments similar to the mechanism used for TCR diversity.
Protein antigens are called T-dependent antigens because they can only activate B cells with the cooperation of helper T cells. Other molecule classes do not require T cell cooperation and are called T-independent antigens.
T cell-independent activation of B cells involves cross-linkage of BCRs by repetitive nonprotein antigen epitopes. It is characterized by the production of IgM by plasma cells and does not produce memory B cells.
T cell-dependent activation of B cells involves processing and presentation of protein antigens to helper T cells, activation of the B cells by cytokines secreted from activated T_H2 cells, and plasma cells that produce different classes of antibodies as a result of class switching. Memory B cells are also produced.
Secondary exposures to T-dependent antigens result in a secondary antibody response initiated by memory B cells. The secondary response develops more quickly and produces higher and more sustained levels of antibody with higher affinity for the specific antigen.

18.5 Vaccines

Adaptive immunity can be divided into four distinct classifications: natural active immunity, natural passive immunity, artificial passive immunity, and artificial active immunity.
Artificial active immunity is the foundation for vaccination and vaccine development. Vaccination programs not only confer artificial immunity on individuals, but also foster herd immunity in populations.
Variolation against smallpox originated in the 10^th century in China, but the procedure was risky because it could cause the disease it was intended to prevent. Modern vaccination was developed by Edward Jenner, who developed the practice of inoculating patients with infectious materials from cowpox lesions to prevent smallpox.
Live attenuated vaccines and inactivated vaccines contain whole pathogens that are weak, killed, or inactivated. Subunit vaccines, toxoid vaccines, and conjugate vaccines contain acellular components with antigens that stimulate an immune response.

19.1 Hypersensitivities

An allergy is an adaptive immune response, sometimes life-threatening, to an allergen.
Type I hypersensitivity requires sensitization of mast cells with IgE, involving an initial IgE antibody response and IgE attachment to mast cells. On second exposure to an allergen, cross-linking of IgE molecules on mast cells triggers degranulation and release of preformed and newly formed chemical mediators of inflammation. Type I hypersensitivity may be localized and relatively minor (hives and hay fever) or system-wide and dangerous (systemic anaphylaxis).
Type II hypersensitivities result from antibodies binding to antigens on cells and initiating cytotoxic responses. Examples include hemolytic transfusion reaction and hemolytic disease of the newborn.
Type III hypersensitivities result from formation and accumulation of immune complexes in tissues, stimulating damaging inflammatory responses.
Type IV hypersensitivities are not mediated by antibodies, but by helper T-cell activation of macrophages, eosinophils, and cytotoxic T cells.

19.2 Autoimmune Disorders

Autoimmune diseases result from a breakdown in immunological tolerance. The actual induction event(s) for autoimmune states are largely unknown.
Some autoimmune diseases attack specific organs, whereas others are more systemic.
Organ-specific autoimmune diseases include celiac disease, Graves disease, Hashimoto thyroiditis, type I diabetes mellitus, and Addison disease.
Systemic autoimmune diseases include multiple sclerosis, myasthenia gravis, psoriasis, rheumatoid arthritis, and systemic lupus erythematosus.
Treatments for autoimmune diseases generally involve anti-inflammatory and immunosuppressive drugs.

19.3 Organ Transplantation and Rejection

Grafts and transplants can be classified as autografts, isografts, allografts, or xenografts based on the genetic differences between the donor’s and recipient’s tissues.
Genetic differences, especially among the MHC (HLA) genes, will dictate the likelihood that rejection of the transplanted tissue will occur.
Transplant recipients usually require immunosuppressive therapy to avoid rejection, even with good genetic matching. This can create additional problems when immune responses are needed to fight off infectious agents and prevent cancer.
Graft-versus-host disease can occur in bone marrow transplants, as the mature T cells in the transplant itself recognize the recipient’s tissues as foreign.
Transplantation methods and technology have improved greatly in recent decades and may move into new areas with the use of stem cell technology to avoid the need for genetic matching of MHC molecules.

19.4 Immunodeficiency

Primary immunodeficiencies are caused by genetic abnormalities; secondary immunodeficiencies are acquired through disease, diet, or environmental exposures
Primary immunodeficiencies may result from flaws in phagocyte killing of innate immunity, or impairment of T cells and B cells.
Primary immunodeficiencies include chronic granulomatous disease, X-linked agammaglobulinemia, selective IgA deficiency, and severe combined immunodeficiency disease.
Secondary immunodeficiencies result from environmentally induced defects in B cells and/or T cells.
Causes for secondary immunodeficiencies include malnutrition, viral infection, diabetes, prolonged infections, and chemical or radiation exposure.

19.5 Cancer Immunobiology and Immunotherapy

Cancer results from a loss of control of the cell cycle, resulting in uncontrolled cell proliferation and a loss of the ability to differentiate.
Adaptive and innate immune responses are engaged by tumor antigens, self-molecules only found on abnormal cells. These adaptive responses stimulate helper T cells to activate cytotoxic T cells and NK cells of innate immunity that will seek and destroy cancer cells.
New anticancer therapies are in development that will exploit natural adaptive immunity anticancer responses. These include external stimulation of cytotoxic T cells and therapeutic vaccines that assist or enhance the immune response.

20.1 Polyclonal and Monoclonal Antibody Production

Antibodies bind with high specificity to antigens used to challenge the immune system, but they may also show cross-reactivity by binding to other antigens that share chemical properties with the original antigen.
Injection of an antigen into an animal will result in a polyclonal antibody response in which different antibodies are produced that react with the various epitopes on the antigen.
Polyclonal antisera are useful for some types of laboratory assays, but other assays require more specificity. Diagnostic tests that use polyclonal antisera are typically only used for screening because of the possibility of false-positive and false-negative results.
Monoclonal antibodies provide higher specificity than polyclonal antisera because they bind to a single epitope and usually have high affinity.
Monoclonal antibodies are typically produced by culturing antibody-secreting hybridomas derived from mice. mAbs are currently used to treat cancer, but their exorbitant cost has prevented them from being used more widely to treat infectious diseases. Still, their potential for laboratory and clinical use is driving the development of new, cost-effective solutions such as plantibodies.

20.2 Detecting Antigen-Antibody Complexes

When present in the correct ratio, antibody and antigen will form a precipitin, or lattice that precipitates out of solution.
A precipitin ring test can be used to visualize lattice formation in solution. The Ouchterlony assay demonstrates lattice formation in a gel. The radial immunodiffusion assay is used to quantify antigen by measuring the size of a precipitation zone in a gel infused with antibodies.
Insoluble antigens in suspension will form flocculants when bound by antibodies. This is the basis of the VDRL test for syphilis in which anti-treponemal antibodies bind to cardiolipin in suspension.
Viral infections can be detected by quantifying virus-neutralizing antibodies in a patient’s serum.
Different antibody classes in plasma or serum are identified by using immunoelectrophoresis.
The presence of specific antigens (e.g., bacterial or viral proteins) in serum can be demonstrated by western blot assays, in which the proteins are transferred to a nitrocellulose membrane and identified using labeled antibodies.
In the complement fixation test, complement is used to detect antibodies against various pathogens.

20.3 Agglutination Assays

Antibodies can agglutinate cells or large particles into a visible matrix. Agglutination tests are often done on cards or in microtiter plates that allow multiple reactions to take place side by side using small volumes of reagents.
Using antisera against certain proteins allows identification of serovars within species of bacteria.
Detecting antibodies against a pathogen can be a powerful tool for diagnosing disease, but there is a period of time before patients go through seroconversion and the level of antibodies becomes detectable.
Agglutination of latex beads in indirect agglutination assays can be used to detect the presence of specific antigens or specific antibodies in patient serum.
The presence of some antibacterial and antiviral antibodies can be confirmed by the use of the direct Coombs’ test, which uses Coombs’ reagent to cross-link antibodies bound to red blood cells and facilitate hemagglutination.
Some viruses and bacteria will bind and agglutinate red blood cells; this interaction is the basis of the direct hemagglutination assay, most often used to determine the titer of virus in solution.
Neutralization assays quantify the level of virus-specific antibody by measuring the decrease in hemagglutination observed after mixing patient serum with a standardized amount of virus.
Hemagglutination assays are also used to screen and cross-match donor and recipient blood to ensure that the transfusion recipient does not have antibodies to antigens in the donated blood.

20.4 EIAs and ELISAs

Enzyme immunoassays (EIA) are used to visualize and quantify antigens. They use an antibody conjugated to an enzyme to bind the antigen, and the enzyme converts a substrate into an observable end product. The substrate may be either a chromogen or a fluorogen.
Immunostaining is an EIA technique for visualizing cells in a tissue (immunohistochemistry) or examining intracellular structures (immunocytochemistry).
Direct ELISA is used to quantify an antigen in solution. The primary antibody captures the antigen, and the secondary antibody delivers an enzyme. Production of end product from the chromogenic substrate is directly proportional to the amount of captured antigen.
Indirect ELISA is used to detect antibodies in patient serum by attaching antigen to the well of a microtiter plate, allowing the patient (primary) antibody to bind the antigen and an enzyme-conjugated secondary antibody to detect the primary antibody.
Immunofiltration and immunochromatographic assays are used in lateral flow tests, which can be used to diagnose pregnancy and various diseases by detecting color-labeled antigen-antibody complexes in urine or other fluid samples

20.5 Fluorescent Antibody Techniques

Immunofluorescence assays use antibody-fluorogen conjugates to illuminate antigens for easy, rapid detection.
Direct immunofluorescence can be used to detect the presence of bacteria in clinical samples such as sputum.
Indirect immunofluorescence detects the presence of antigen-specific antibodies in patient sera. The fluorescent antibody binds to the antigen-specific antibody rather than the antigen.
The use of indirect immunofluorescence assays to detect antinuclear antibodies is an important tool in the diagnosis of several autoimmune diseases.
Flow cytometry uses fluorescent mAbs against cell-membrane proteins to quantify specific subsets of cells in complex mixtures.
Fluorescence-activated cell sorters are an extension of flow cytometry in which fluorescence intensity is used to physically separate cells into high and low fluorescence populations.

21.1 Anatomy and Normal Microbiota of the Skin and Eyes

Human skin consists of two main layers, the epidermis and dermis, which are situated on top of the hypodermis, a layer of connective tissue.
The skin is an effective physical barrier against microbial invasion.
The skin’s relatively dry environment and normal microbiota discourage colonization by transient microbes.
The skin’s normal microbiota varies from one region of the body to another.
The conjunctiva of the eye is a frequent site for microbial infection, but deeper eye infections are less common; multiple types of conjunctivitis exist.

21.2 Bacterial Infections of the Skin and Eyes

Staphylococcus and Streptococcus cause many different types of skin infections, many of which occur when bacteria breach the skin barrier through a cut or wound.
S. aureus are frequently associated with purulent skin infections that manifest as folliculitis, furuncles, or carbuncles. S. aureus is also a leading cause of staphylococcal scalded skin syndrome (SSSS).
S. aureus is generally drug resistant and current MRSA strains are resistant to a wide range of antibiotics.
Community-acquired and hospital-acquired staphyloccocal infections are an ongoing problem because many people are asymptomatic carriers.
Group A streptococci (GAS), S. pyogenes, is often responsible for cases of cellulitis, erysipelas, and erythema nosodum. GAS are also one of many possible causes of necrotizing fasciitis.
P. aeruginosa is often responsible for infections of the skin and eyes, including wound and burn infections, hot tub rash, otitis externa, and bacterial keratitis.
Acne is a common skin condition that can become more inflammatory when Cutibacterium acnes infects hair follicles and pores clogged with dead skin cells and sebum.
Cutaneous anthrax occurs when Bacillus anthracis breaches the skin barrier. The infection results in a localized black eschar on skin. Anthrax can be fatal if B. anthracis spreads to the bloodstream.
Common bacterial conjunctivitis is often caused by Haemophilus influenzae and usually resolves on its own in a few days. More serious forms of conjunctivitis include gonococcal ophthalmia neonatorum, inclusion conjunctivitis (chlamydial), and trachoma, all of which can lead to blindness if untreated.
Keratitis is frequently caused by Staphylococcus epidermidis and/or Pseudomonas aeruginosa, especially among contact lens users, and can lead to blindness.
Biofilms complicate the treatment of wound and eye infections because pathogens living in biofilms can be difficult to treat and eliminate.

21.3 Viral Infections of the Skin and Eyes

Papillomas (warts) are caused by human papillomaviruses.
Herpes simplex virus (especially HSV-1) mainly causes oral herpes, but lesions can appear on other areas of the skin and mucous membranes.
Roseola and fifth disease are common viral illnesses that cause skin rashes; roseola is caused by HHV-6 and HHV-7 while fifth disease is caused by parvovirus 19.
Viral conjunctivitis is often caused by adenoviruses and may be associated with the common cold. Herpes keratitis is caused by herpesviruses that spread to the eye.

21.4 Mycoses of the Skin

Mycoses can be cutaneous, subcutaneous, or systemic.
Common cutaneous mycoses include tineas caused by dermatophytes of the genera Trichophyton, Epidermophyton, and Microsporum. Tinea corporis is called ringworm. Tineas on other parts of the body have names associated with the affected body part.
Aspergillosis is a fungal disease caused by molds of the genus Aspergillus. Primary cutaneous aspergillosis enters through a break in the skin, such as the site of an injury or a surgical wound; it is a common hospital-acquired infection. In secondary cutaneous aspergillosis, the fungus enters via the respiratory system and disseminates systemically, manifesting in lesions on the skin.
The most common subcutaneous mycosis is sporotrichosis (rose gardener’s disease), caused by Sporothrix schenkii.
Yeasts of the genus Candida can cause opportunistic infections of the skin called candidiasis, producing intertrigo, localized rashes, or yellowing of the nails.

21.5 Protozoan and Helminthic Infections of the Skin and Eyes

The protozoan Acanthamoeba and the helminth Loa loa are two parasites that can breach the skin barrier, causing infections of the skin and eyes.
Acanthamoeba keratitis is a parasitic infection of the eye that often results from improper disinfection of contact lenses or swimming while wearing contact lenses.
Loiasis, or eye worm, is a disease endemic to Africa that is caused by parasitic worms that infect the subcutaneous tissue of the skin and eyes. It is transmitted by deerfly vectors.

22.1 Anatomy and Normal Microbiota of the Respiratory Tract

The respiratory tract is divided into upper and lower regions at the epiglottis.
Air enters the upper respiratory tract through the nasal cavity and mouth, which both lead to the pharynx. The lower respiratory tract extends from the larynx into the trachea before branching into the bronchi, which divide further to form the bronchioles, which terminate in alveoli, where gas exchange occurs.
The upper respiratory tract is colonized by an extensive and diverse normal microbiota, many of which are potential pathogens. Few microbial inhabitants have been found in the lower respiratory tract, and these may be transients.
Members of the normal microbiota may cause opportunistic infections, using a variety of strategies to overcome the innate nonspecific defenses (including the mucociliary escalator) and adaptive specific defenses of the respiratory system.
Effective vaccines are available for many common respiratory pathogens, both bacterial and viral.
Most respiratory infections result in inflammation of the infected tissues; these conditions are given names ending in -itis, such as rhinitis, sinusitis, otitis, pharyngitis, and bronchitis.

22.2 Bacterial Infections of the Respiratory Tract

A wide variety of bacteria can cause respiratory diseases; most are treatable with antibiotics or preventable with vaccines.
Streptococcus pyogenes causes strep throat, an infection of the pharynx that also causes high fever and can lead to scarlet fever, acute rheumatic fever, and acute glomerulonephritis.
Acute otitis media is an infection of the middle ear that may be caused by several bacteria, including Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis. The infection can block the eustachian tubes, leading to otitis media with effusion.
Diphtheria, caused by Corynebacterium diphtheriae, is now a rare disease because of widespread vaccination. The bacteria produce exotoxins that kill cells in the pharynx, leading to the formation of a pseudomembrane; and damage other parts of the body.
Bacterial pneumonia results from infections that cause inflammation and fluid accumulation in the alveoli. It is most commonly caused by S. pneumoniae or H. influenzae. The former is commonly multidrug resistant.
Mycoplasma pneumonia results from infection by Mycoplasma pneumoniae; it can spread quickly, but the disease is mild and self-limiting.
Chlamydial pneumonia can be caused by three pathogens that are obligate intracellular parasites. Chlamydia pneumoniae is typically transmitted from an infected person, whereas C. psittaci is typically transmitted from an infected bird. Chlamydia trachomatis, may cause pneumonia in infants.
Several other bacteria can cause pneumonia in immunocompromised individuals and those with cystic fibrosis.
Tuberculosis is caused by Mycobacterium tuberculosis. Infection leads to the production of protective tubercles in the alveoli and calcified Ghon complexes that can harbor the bacteria for a long time. Antibiotic-resistant forms are common and treatment is typically long term.
Pertussis is caused by Bordetella pertussis. Mucus accumulation in the lungs leads to prolonged severe coughing episodes (whooping cough) that facilitate transmission. Despite an available vaccine, outbreaks are still common.
Legionnaires disease is caused by infection from environmental reservoirs of the Legionella pneumophila bacterium. The bacterium is endocytic within macrophages and infection can lead to pneumonia, particularly among immunocompromised individuals.
Q fever is caused by Coxiella burnetii, whose primary hosts are domesticated mammals (zoonotic disease). It causes pneumonia primarily in farm workers and can lead to serious complications, such as endocarditis.

22.3 Viral Infections of the Respiratory Tract

Viruses cause respiratory tract infections more frequently than bacteria, and most viral infections lead to mild symptoms.
The common cold can be caused by more than 200 viruses, typically rhinoviruses, coronaviruses, and adenoviruses, transmitted by direct contact, aerosols, or environmental surfaces.
Due to its ability to rapidly mutate through antigenic drift and antigenic shift, influenza remains an important threat to human health. Two new influenza vaccines are developed annually.
Several viral infections, including respiratory syncytial virus infections, which frequently occur in the very young, can begin with mild symptoms before progressing to viral pneumonia.
SARS and MERS are acute respiratory infections caused by coronaviruses, and both appear to originate in animals. SARS has not been seen in the human population since 2004 but had a high mortality rate during its outbreak. MERS also has a high mortality rate and continues to appear in human populations.
Measles, rubella, and chickenpox are highly contagious, systemic infections that gain entry through the respiratory system and cause rashes and fevers. Vaccines are available for all three. Measles is the most severe of the three and is responsible for significant mortality around the world. Chickenpox typically causes mild infections in children but the virus can reactivate to cause painful cases of shingles later in life.

22.4 Respiratory Mycoses

Fungal pathogens rarely cause respiratory disease in healthy individuals, but inhalation of fungal spores can cause severe pneumonia and systemic infections in immunocompromised patients.
Antifungal drugs like amphotericin B can control most fungal respiratory infections.
Histoplasmosis is caused by a mold that grows in soil rich in bird or bat droppings. Few exposed individuals become sick, but vulnerable individuals are susceptible. The yeast-like infectious cells grow inside phagocytes.
Coccidioidomycosis is also acquired from soil and, in some individuals, will cause lesions on the face. Extreme cases may infect other organs, causing death.
Blastomycosis, a rare disease caused by a soil fungus, typically produces a mild lung infection but can become disseminated in the immunocompromised. Systemic cases are fatal if untreated.
Mucormycosis is a rare disease, caused by fungi of the order Mucorales. It primarily affects immunocompromised people. Infection involves growth of the hyphae into infected tissues and can lead to death in some cases.
Aspergillosis, caused by the common soil fungus Aspergillus, infects immunocompromised people. Hyphal balls may impede lung function and hyphal growth into tissues can cause damage. Disseminated forms can lead to death.
Pneumocystis pneumonia is caused by the fungus P. jirovecii. The disease is found in patients with AIDS and other immunocompromised individuals. Sulfa drug treatments have side effects, but untreated cases may be fatal.
Cryptococcosis is caused by Cryptococcus neoformans. Lung infections may move to the brain, causing meningitis, which can be fatal.

23.1 Anatomy and Normal Microbiota of the Urogenital Tract

The urinary system is responsible for filtering the blood, excreting wastes, and helping to regulate electrolyte and water balance.
The urinary system includes the kidneys, ureters, urinary bladder, and urethra; the bladder and urethra are the most common sites of infection.
Common sites of infection in the male reproductive system include the urethra, as well as the testes, prostate and epididymis.
The most commons sites of infection in the female reproductive system are the vulva, vagina, cervix, and fallopian tubes.
Infections of the urogenital tract can occur through colonization from the external environment, alterations in microbiota due to hormonal or other physiological and environmental changes, fecal contamination, and sexual transmission (STIs).

23.2 Bacterial Infections of the Urinary System

Bacterial cystitis is commonly caused by fecal bacteria such as E. coli.
Pyelonephritis is a serious kidney infection that is often caused by bacteria that travel from infections elsewhere in the urinary tract and may cause systemic complications.
Leptospirosis is a bacterial infection of the kidney that can be transmitted by exposure to infected animal urine, especially in contaminated water. It is more common in tropical than in temperate climates.
Nongonococcal urethritis (NGU) is commonly caused by C. trachomatis, M. genitalium, Ureaplasma urealyticum, and M. hominis.
Diagnosis and treatment for bacterial urinary tract infections varies. Urinalysis (e.g., for leukocyte esterase levels, nitrite levels, microscopic evaluation, and culture of urine) is an important component in most cases. Broad-spectrum antibiotics are typically used.

23.3 Bacterial Infections of the Reproductive System

Bacterial vaginosis is caused by an imbalance in the vaginal microbiota, with a decrease in lactobacilli and an increase in vaginal pH. G. vaginalis is the most common cause of bacterial vaginosis, which is associated with vaginal discharge, odor, burning, and itching.
Gonorrhea is caused by N. gonorrhoeae, which can cause infection of the reproductive and urinary tracts and is associated with symptoms of urethritis. If left untreated, it can progress to epididymitis, salpingitis, and pelvic inflammatory disease and enter the bloodstream to infect other sites in the body.
Chlamydia is the most commonly reported STI and is caused by C. trachomatis. Most infections are asymptomatic, and infections that are not treated can spread to involve the epididymis of memalesn and cause salpingitis and pelvic inflammatory disease in females.
Syphilis is caused by T. pallidum and has three stages, primary, secondary, and tertiary. Primary syphilis is associated with a painless hard chancre lesion on genitalia. Secondary syphilis is associated with skin and mucous membrane lesions. Tertiary syphilis is the most serious and life-threatening, and can involve serious nervous system damage.
Chancroid is an infection of the reproductive tract caused by H. ducreyi that results in the development of characteristic soft chancres.

23.4 Viral Infections of the Reproductive System

Genital herpes is usually caused by HSV-2 (although HSV-1 can also be responsible) and may cause the development of infectious, potentially recurrent vesicles
Neonatal herpes can occur in babies born to infected people and can cause symptoms that range from relatively mild (more common) to severe.
Human papillomaviruses are the most common sexually transmitted viruses and include strains that cause genital warts as well as strains that cause cervical cancer.

23.5 Fungal Infections of the Reproductive System

Candida spp. are typically present in the normal microbiota in the body, including the skin, respiratory tract, gastrointestinal tract, and female urogenital system.
Disruptions in the normal vaginal microbiota can lead to an overgrowth of Candida, causing vaginal candidiasis.
Vaginal candidiasis can be treated with topical or oral fungicides. Prevention is difficult.

23.6 Protozoan Infections of the Urogenital System

Trichomoniasis is a common STI caused by Trichomonas vaginalis.
T. vaginalis is common at low levels in the normal microbiota.
Trichomoniasis is often asymptomatic. When symptoms develop, trichomoniasis causes urinary discomfort, irritation, itching, burning, discharge from the penis, and vaginal discharge.
Trichomoniasis is treated with the antiflagellate drugs tinidazole and metronidazole.

24.1 Anatomy and Normal Microbiota of the Digestive System

The digestive tract, consisting of the oral cavity, pharynx, esophagus, stomach, small intestine, and large intestine, has a normal microbiota that is important for health.
The constant movement of materials through the gastrointestinal canal, the protective layer of mucus, the normal microbiota, and the harsh chemical environment in the stomach and small intestine help to prevent colonization by pathogens.
Infections or microbial toxins in the oral cavity can cause tooth decay, periodontal disease, and various types of ulcers.
Infections and intoxications of the gastrointestinal tract can cause general symptoms such as nausea, vomiting, diarrhea, and fever. Localized inflammation of the GI tract can result in gastritis, enteritis, gastroenteritis, hepatitis, or colitis, and damage to epithelial cells of the colon can lead to dysentery.
Foodborne illness refers to infections or intoxications that originate with pathogens or toxins ingested in contaminated food or water.

24.2 Microbial Diseases of the Mouth and Oral Cavity

Dental caries, tartar, and gingivitis are caused by overgrowth of oral bacteria, usually Streptococcus and Actinomyces species, as a result of insufficient dental hygiene.
Gingivitis can worsen, allowing Porphyromonas, Streptococcus, and Actinomyces species to spread and cause periodontitis. When Prevotella intermedia, Fusobacterium species, and Treponema vicentii are involved, it can lead to acute necrotizing ulcerative gingivitis.
The herpes simplex virus type 1 can cause lesions of the mouth and throat called herpetic gingivostomatitis.
Other infections of the mouth include oral thrush, a fungal infection caused by overgrowth of Candida yeast, and mumps, a viral infection of the salivary glands caused by the mumps virus, a paramyxovirus.

24.3 Bacterial Infections of the Gastrointestinal Tract

Major causes of gastrointestinal illness include Salmonella spp., Staphylococcus spp., Helicobacter pylori, Clostridium perfringens, Clostridioides difficile, Bacillus cereus, and Yersinia bacteria.
C. difficile is an important cause of hospital acquired infection.
Vibrio cholerae causes cholera, which can be a severe diarrheal illness.
Different strains of E. coli, including ETEC, EPEC, EIEC, and EHEC, cause different illnesses with varying degrees of severity.
H. pylori is associated with peptic ulcers.
Salmonella enterica serotypes can cause typhoid fever, a more severe illness than salmonellosis.
Rehydration and other supportive therapies are often used as general treatments.
Careful antibiotic use is required to reduce the risk of causing C. difficile infections and when treating antibiotic-resistant infections.

24.4 Viral Infections of the Gastrointestinal Tract

Common viral causes of gastroenteritis include rotaviruses, noroviruses, and astroviruses.
Hepatitis may be caused by several unrelated viruses: hepatitis viruses A, B, C, D, and E.
The hepatitis viruses differ in their modes of transmission, treatment, and potential for chronic infection.

24.5 Protozoan Infections of the Gastrointestinal Tract

Giardiasis, cryptosporidiosis, amoebiasis, and cyclosporiasis are intestinal infections caused by protozoans.
Protozoan intestinal infections are commonly transmitted through contaminated food and water.
Treatment varies depending on the causative agent, so proper diagnosis is important.
Microscopic examination of stool or biopsy specimens is often used in diagnosis, in combination with other approaches.

24.6 Helminthic Infections of the Gastrointestinal Tract

Helminths often cause intestinal infections after transmission to humans through exposure to contaminated soil, water, or food. Signs and symptoms are often mild, but severe complications may develop in some cases.
Ascaris lumbricoides eggs are transmitted through contaminated food or water and hatch in the intestine. Juvenile larvae travel to the lungs and then to the pharynx, where they are swallowed and returned to the intestines to mature. These nematode roundworms cause ascariasis.
Necator americanus and Ancylostoma doudenale cause hookworm infection when larvae penetrate the skin from soil contaminated by dog or cat feces. They travel to the lungs and are then swallowed to mature in the intestines.
Strongyloides stercoralis are transmitted from soil through the skin to the lungs and then to the intestine where they cause strongyloidiasis.
Enterobius vermicularis are nematode pinworms transmitted by the fecal-oral route. After ingestion, they travel to the colon where they cause enterobiasis.
Trichuris trichiura can be transmitted through soil or fecal contamination and cause trichuriasis. After ingestion, the eggs travel to the intestine where the larvae emerge and mature, attaching to the walls of the colon and cecum.
Trichinella spp. is transmitted through undercooked meat. Larvae in the meat emerge from cysts and mature in the large intestine. They can migrate to the muscles and form new cysts, causing trichinosis.
Taenia spp. and Diphyllobothrium latum are tapeworms transmitted through undercooked food or the fecal-oral route. Taenia infections cause taeniasis. Tapeworms use their scolex to attach to the intestinal wall. Larvae may also move to muscle or brain tissue.
Echinococcus granulosus is a cestode transmitted through eggs in the feces of infected animals, especially dogs. After ingestion, eggs hatch in the small intestine, and the larvae invade the intestinal wall and travel through the circulatory system to form dangerous cysts in internal organs, causing hydatid disease.
Flukes are transmitted through aquatic plants or fish. Liver flukes cause disease by interfering with the bile duct. Intestinal flukes develop in the intestines, where they attach to the intestinal epithelium.

25.1 Anatomy of the Circulatory and Lymphatic Systems

The circulatory system moves blood throughout the body and has no normal microbiota.
The lymphatic system moves fluids from the interstitial spaces of tissues toward the circulatory system and filters the lymph. It also has no normal microbiota.
The circulatory and lymphatic systems are home to many components of the host immune defenses.
Infections of the circulatory system may occur after a break in the skin barrier or they may enter the bloodstream at the site of a localized infection. Pathogens or toxins in the bloodstream can spread rapidly throughout the body and can provoke systemic and sometimes fatal inflammatory responses such as SIRS, sepsis, and endocarditis.
Infections of the lymphatic system can cause lymphangitis and lymphadenitis.

25.2 Bacterial Infections of the Circulatory and Lymphatic Systems

Bacterial infections of the circulatory system are almost universally serious. Left untreated, most have high mortality rates.
Bacterial pathogens usually require a breach in the immune defenses to colonize the circulatory system. Most often, this involves a wound or the bite of an arthropod vector, but it can also occur in hospital settings and result in nosocomial infections.
Sepsis from both gram-negative and gram-positive bacteria, puerperal fever, rheumatic fever, endocarditis, gas gangrene, osteomyelitis, and toxic shock syndrome are typically a result of injury or introduction of bacteria by medical or surgical intervention.
Tularemia, brucellosis, cat-scratch fever, rat-bite fever, and bubonic plague are zoonotic diseases transmitted by biological vectors
Ehrlichiosis, anaplasmosis, endemic and murine typhus, Rocky Mountain spotted fever, Lyme disease, relapsing fever, and trench fever are transmitted by arthropod vectors.
Because their symptoms are so similar to those of other diseases, many bacterial infections of the circulatory system are difficult to diagnose.
Standard antibiotic therapies are effective for the treatment of most bacterial infections of the circulatory system, unless the bacterium is resistant, in which case synergistic treatment may be required.
The systemic immune response to a bacteremia, which involves the release of excessive amounts of cytokines, can sometimes be more damaging to the host than the infection itself.

25.3 Viral Infections of the Circulatory and Lymphatic Systems

Human herpesviruses such Epstein-Barr virus (HHV-4) and cytomegalovirus (HHV-5) are widely distributed. The former is associated with infectious mononucleosis and Burkitt lymphoma, and the latter can cause serious congenital infections as well as serious disease in immunocompromised adults.
Arboviral diseases such as yellow fever, dengue fever, and chikungunya fever are characterized by high fevers and vascular damage that can often be fatal. Ebola virus disease is a highly contagious and often fatal infection spread through contact with bodily fluids.
Although there is a vaccine available for yellow fever, treatments for patients with yellow fever, dengue, chikungunya fever, and Ebola virus disease are limited to supportive therapies.
Patients infected with human immunodeficiency virus (HIV) progress through three stages of disease, culminating in AIDS. Antiretroviral therapy (ART) uses various combinations of drugs to suppress viral loads, extending the period of latency and reducing the likelihood of transmission.
Vector control and animal reservoir control remain the best defenses against most viruses that cause diseases of the circulatory system.

25.4 Parasitic Infections of the Circulatory and Lymphatic Systems

Malaria is a protozoan parasite that remains an important cause of death primarily in the tropics. Several species in the genus Plasmodium are responsible for malaria and all are transmitted by Anopheles mosquitoes. Plasmodium infects and destroys human red blood cells, leading to organ damage, anemia, blood vessel necrosis, and death. Malaria can be treated with various antimalarial drugs and prevented through vector control.
Toxoplasmosis is a widespread protozoal infection that can cause serious infections in the immunocompromised and in developing fetuses. Domestic cats are the definitive host.
Babesiosis is a generally asymptomatic infection of red blood cells that can causes malaria-like symptoms in elderly, immunocompromised, or asplenic patients.
Chagas disease is a tropical disease transmitted by triatomine bugs. The trypanosome infects heart, neural tissues, monocytes, and phagocytes, often remaining latent for many years before causing serious and sometimes fatal damage to the digestive system and heart.
Leishmaniasis is caused by the protozoan Leishmania and is transmitted by sand flies. Symptoms are generally mild, but serious cases may cause organ damage, anemia, and loss of immune competence.
Schistosomiasis is caused by a fluke transmitted by snails. The fluke moves throughout the body in the blood stream and chronically infects various tissues, leading to organ damage.

26.1 Anatomy of the Nervous System

The nervous system consists of two subsystems: the central nervous system and peripheral nervous system.
The skull and three meninges (the dura mater, arachnoid mater, and pia mater) protect the brain.
Tissues of the PNS and CNS are formed of cells called glial cells and neurons.
Since the blood-brain barrier excludes most microbes, there is no normal microbiota in the CNS.
Some pathogens have specific virulence factors that allow them to breach the blood-brain barrier. Inflammation of the brain or meninges caused by infection is called encephalitis or meningitis, respectively. These conditions can lead to blindness, deafness, coma, and death.

26.2 Bacterial Diseases of the Nervous System

Bacterial meningitis can be caused by several species of encapsulated bacteria, including Haemophilus influenzae, Neisseria meningitidis, Streptococcus pneumoniae, and Streptococcus agalactiae (group B streptococci). H. influenzae affects primarily young children and neonates, N. meningitidis is the only communicable pathogen and mostly affects children and young adults, S. pneumoniae affects mostly young children, and S. agalactiae affects newborns during or shortly after birth.
Symptoms of bacterial meningitis include fever, neck stiffness, headache, confusion, convulsions, coma, and death.
Diagnosis of bacterial meningitis is made through observations and culture of organisms in CSF. Bacterial meningitis is treated with antibiotics. H. influenzae and N. meningitidis have vaccines available.
Clostridium species cause neurological diseases, including botulism and tetanus, by producing potent neurotoxins that interfere with neurotransmitter release. The PNS is typically affected. Treatment of Clostridium infection is effective only through early diagnosis with administration of antibiotics to control the infection and antitoxins to neutralize the endotoxin before they enter cells.
Listeria monocytogenes is a foodborne pathogen that can infect the CNS, causing meningitis. The infection can be spread through the placenta to a fetus. Diagnosis is through culture of blood or CSF. Treatment is with antibiotics and there is no vaccine.
Hansen’s disease (leprosy) is caused by the intracellular parasite Mycobacterium leprae. Infections cause demylenation of neurons, resulting in decreased sensation in peripheral appendages and body sites. Treatment is with multi-drug antibiotic therapy, and there is no universally recognized vaccine.

26.3 Acellular Diseases of the Nervous System

Viral meningitis is more common and generally less severe than bacterial menigitis. It can result from secondary sequelae of many viruses or be caused by infections of arboviruses.
Various types of arboviral encephalitis are concentrated in particular geographic locations throughout the world. These mosquito-borne viral infections of the nervous system are typically mild, but they can be life-threatening in some cases.
Zika virus is an emerging arboviral infection with generally mild symptoms in most individuals, but infections of pregnant people can cause the birth defect microcephaly.
Polio is typically a mild intestinal infection but can be damaging or fatal if it progresses to a neurological disease.
Rabies is nearly always fatal when untreated and remains a significant problem worldwide.
Transmissible spongiform encephalopathies such as Creutzfeldt-Jakob disease and kuru are caused by prions. These diseases are untreatable and ultimately fatal. Similar prion diseases are found in animals.

26.4 Fungal and Parasitic Diseases of the Nervous System

Neuromycoses are uncommon in immunocompetent people, but immunocompromised individuals with fungal infections have high mortality rates. Treatment of neuromycoses require prolonged therapy with antifungal drugs at low doses to avoid side effects and overcome the effect of the blood-brain barrier.
Some protist infections of the nervous systems are fatal if not treated, including primary amoebic meningitis, granulomatous amoebic encephalitis, human African trypanosomiasis, and neurotoxoplasmosis.
The various forms of ameobic encephalitis caused by the different amoebic infections are typically fatal even with treatment, but they are rare.
African trypanosomiasis is a serious but treatable disease endemic to two distinct regions in sub-Saharan Africa caused by the insect-borne hemoflagellate Trypanosoma brucei.
Neurocysticercosis is treated using antihelminthic drugs or surgery to remove the large cysts from the CNS.