Microbiology Contributions by Romans and Muslims

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Questions and Answers

What concept regarding disease did Marcus Terentius Varro propose?

Microorganisms can cause disease. (correct)

Only large animals can transmit diseases.

Imbalances in the body's humors are the sole cause of disease.

Diseases are only caused by visible entities.

What innovative method did Abū Bakr al-Rāzī use to determine the ideal location for a hospital?

He analyzed the temperature of the water supplies.

He constructed models to simulate patient flow.

He conducted a survey of the local population's health.

He hung raw meat around the city to observe decay rates. (correct)

What notable distinction did al-Razi make in his medical studies?

The separation of mental and physical illnesses.

The classification of chronic and acute diseases.

The distinction between measles and smallpox. (correct)

The difference between viral and bacterial infections.

What was one of the main contributions of Ibn Sina (Avicenna) in his work, the Canon of Medicine?

He compiled a comprehensive index of illnesses. Signup and view all the answers

Which practice did Ibn Sina advance that has influenced contemporary methods?

The isolation of sick individuals as a means of quarantine. Signup and view all the answers

Why is the Canon of Medicine considered an important medical text worldwide?

It systematically organized medical knowledge for teaching. Signup and view all the answers

What did Varro suggest about certain creatures found in swamps?

They could cause serious diseases when inhaled or ingested. Signup and view all the answers

Which civilization's scholars significantly built upon the medical understandings of earlier cultures, including those of Hippocrates?

Islamic scholars in Persia. Signup and view all the answers

What is the primary purpose of growth media in microbiology?

To supply nutrients for microbial growth Signup and view all the answers

Which of the following best describes a Petri dish?

A dish used to hold solid growth media Signup and view all the answers

What must occur before using an inoculation loop to transfer microorganisms?

It must be sterilized to prevent contamination Signup and view all the answers

Why have many labs phased out the use of Bunsen burners?

They present safety risks with open flames Signup and view all the answers

Which factor influences the effectiveness of certain stains on microbes?

The cellular chemical composition of the microbes Signup and view all the answers

What are test tubes primarily used for in microbiology labs?

To grow microbes in various media Signup and view all the answers

Which of the following is a key ingredient in most growth media?

Source of carbon Signup and view all the answers

What is the role of a rubber tube in a Bunsen burner setup?

To carry gas (fuel) to the burner Signup and view all the answers

What is the shape of bacteria that are typically described as spherical?

Coccus Signup and view all the answers

Which of the following is a characteristic of archaeal cell walls?

They are made of pseudopeptidoglycan. Signup and view all the answers

Some bacteria are photosynthetic. Which of the following is NOT an example mentioned?

Bacillus anthracis Signup and view all the answers

What major characteristic distinguishes eukaryotes from prokaryotes?

Presence of a nucleus Signup and view all the answers

Which type of bacteria is a combination of spherical and rod shapes?

Coccobacillus Signup and view all the answers

Which of the following statements about archaea is true?

They can live in extreme environments. Signup and view all the answers

Which of the following types of bacteria are nonphotosynthetic?

Bacillus cereus Signup and view all the answers

What general shape is a bacteria described as rod-shaped?

Bacillus Signup and view all the answers

What is the primary function of Bergey’s Manual of Determinative Bacteriology?

To classify and identify different prokaryotes Signup and view all the answers

Why are biochemical tests essential in bacterial identification?

They can identify chemicals unique to specific bacterial species. Signup and view all the answers

What role does DNA and rRNA sequencing play in bacteriology?

It aids in both identifying specific bacterial species and classifying new ones. Signup and view all the answers

What is a significant characteristic of different strains within the same species of microorganism?

They can have significantly different attributes. Signup and view all the answers

What is one common source of E.coli O157:H7 infection in humans?

Contaminated water sources Signup and view all the answers

Which of the following statements about E.coli strains is true?

Some E.coli strains are beneficial for digestion. Signup and view all the answers

How have Bergey’s manuals evolved since their first publication?

They have been updated many times to include new species. Signup and view all the answers

What is the purpose of serological tests in bacterial identification?

To identify specific antibodies in a sample. Signup and view all the answers

Which of the following accurately defines protozoa?

Unicellular organisms with complex cell structures Signup and view all the answers

What is binomial nomenclature used for?

Assigning organisms a scientific name with a genus and species designation Signup and view all the answers

Which of these organisms is NOT a unicellular microorganism?

Helminths Signup and view all the answers

Who is known for proposing the addition of a kingdom for protists?

Ernst Haeckel Signup and view all the answers

Which phylogenetic tree classification includes five kingdoms?

Robert Whittaker's tree Signup and view all the answers

What organism requires a host to reproduce?

Helminths Signup and view all the answers

What characteristic does NOT apply to viruses?

They can reproduce independently Signup and view all the answers

What is the primary focus of microbiologists?

A specific subfield within the broad field of microbiology Signup and view all the answers

What historical evidence suggests about early human interactions with fermentation?

They used fermentation to enhance food flavors and preserve them. Signup and view all the answers

Which type of microorganism is often too small to be seen without a microscope?

Bacteria Signup and view all the answers

What method was primarily used to collect cerebrospinal fluid for testing?

Lumbar puncture Signup and view all the answers

What characteristic defines microorganisms or microbes?

Most require a microscope for visibility. Signup and view all the answers

Which of the following fermented products has been made by humans for thousands of years?

Yogurt Signup and view all the answers

During which period did humans first likely develop fermented beverages, according to archaeological findings?

7000 BC Signup and view all the answers

What can cloudy cerebrospinal fluid indicate about a patient's health?

Possible infection Signup and view all the answers

What crucial role did early knowledge of microorganisms play in human civilization?

Facilitated the development of essential food preservation techniques. Signup and view all the answers

What role do microorganisms play in ecosystems?

They serve as the backbone of many food webs. Signup and view all the answers

How did our ancestors utilize invisible microbes to enhance food?

By using fermentation processes in food production. Signup and view all the answers

Which statement regarding the history of microbiology is accurate?

The discovery of bacteria occurred in the 19th century. Signup and view all the answers

What is a significant benefit associated with Alcanivorax borkumensis after the Deepwater Horizon oil spill?

It helps in breaking down oil effectively. Signup and view all the answers

What proportion of microorganisms typically reside on human skin?

Ranging between ten trillion to one hundred trillion. Signup and view all the answers

Which of the following best describes the majority of microorganisms in terms of their effect on humans?

Most are beneficial and essential for health. Signup and view all the answers

In what way are microbiologists expanding our knowledge of microbial life?

By investigating the applications of microbes in technology. Signup and view all the answers

What type of microorganisms are critical for the production of food items like bread, cheese, and beer?

Yeasts and bacteria involved in fermentation. Signup and view all the answers

What significant difference led to the classification of organisms into three domains by Woese and Fox?

Variations in ribosomal RNA gene sequences Signup and view all the answers

Which group of organisms is most closely related based on the findings of the phylogenetic tree?

Archaea and Eukarya Signup and view all the answers

What complicates the determination of evolutionary relationships among organisms?

Horizontal gene transfer Signup and view all the answers

What does the concept of 'webs of life' imply for scientists studying evolution?

There are multiple directions of evolution among species Signup and view all the answers

Which of the following accurately describes the naming system developed by Linnaeus?

A two-word naming system with capitalization rules Signup and view all the answers

In binomial nomenclature, how is the genus name presented?

It is always capitalized and italicized Signup and view all the answers

Why do scientists emphasize rRNA in the classification of organisms?

It is a highly conserved sequence across different organisms Signup and view all the answers

What part of the scientific name for an organism is not capitalized in binomial nomenclature?

Species epithet Signup and view all the answers

What differentiates various strains within the same species of microorganism?

They have identical genetic makeup but different attributes. Signup and view all the answers

Which method is primarily used to identify specific proteins in bacteria during serological tests?

Reaction with specific antibodies Signup and view all the answers

How does Bergey’s Manual contribute to bacteriology?

It serves as a comprehensive classification system for prokaryotes. Signup and view all the answers

Which characteristic does NOT help in the identification of bacteria?

Capacities for photosynthesis in the bacteria Signup and view all the answers

Which statement is true regarding the pathogenic strains of E.coli?

Some E.coli strains are helpful for human digestion. Signup and view all the answers

Which method can establish the classification of newly discovered bacterial species?

DNA and rRNA sequencing Signup and view all the answers

What is the primary application of biochemical tests in bacteriology?

To identify the presence of certain chemical compounds unique to species Signup and view all the answers

What major benefit does binomial nomenclature provide in microbiology?

It eliminates confusion caused by common names. Signup and view all the answers

Which unit of length is equivalent to one millionth of a meter?

Micrometer Signup and view all the answers

What key feature distinguishes prokaryotic microorganisms from eukaryotic microorganisms?

Absence of a true nucleus Signup and view all the answers

What structural component is commonly found in the cell walls of most bacteria?

Peptidoglycan Signup and view all the answers

Which of the following domains contains microorganisms that are entirely acellular?

Viruses Signup and view all the answers

Which of the following units is equivalent to one billionth of a meter?

Nanometer Signup and view all the answers

Which characteristic is true for prokaryotic microorganisms found in the domains Bacteria and Archaea?

They lack a true nucleus. Signup and view all the answers

What is the primary difference between Bacteria and Archaea?

Genetic material organization Signup and view all the answers

Which statement about microorganisms is true?

Microorganisms can be found in all three domains of life. Signup and view all the answers

Why is it important to identify the shape and growth patterns of cells in a specimen?

To understand their characteristics and how they behave, which can aid in identification and treatment. Signup and view all the answers

What other types of microscopy could be used effectively to view this specimen?

Phase-contrast microscopy, differential interference contrast (DIC) microscopy, fluorescence microscopy, and confocal microscopy. Signup and view all the answers

What are some advantages of phase-contrast and DIC microscopy?

Both techniques enhance contrast of living specimens without staining and allow for visualization of fine details. Signup and view all the answers

Why must fluorochromes be used to examine a specimen under a fluorescence microscope?

Fluorochromes absorb energy from a light source and emit visible light, creating a contrast necessary for visualization. Signup and view all the answers

How does a confocal microscope enhance image clarity?

By using a narrow aperture to eliminate light not from the desired z-plane. Signup and view all the answers

Which microscopy technique uses interference patterns to enhance contrast?

Differential interference contrast microscopy Signup and view all the answers

Phase-contrast microscopy is often used to observe live ______ specimens.

specimens Signup and view all the answers

Who is regarded as the first person to formally postulate that disease was spread by tiny invisible seminaria?

Girolamo Fracastoro Signup and view all the answers

What term did Antonie van Leeuwenhoek use to describe microorganisms he observed?

Animalcules Signup and view all the answers

Galileo Galilei is primarily known for his contributions to microscopy.

False Signup and view all the answers

What book did Robert Hooke publish that contained many observations made with compound microscopes?

Micrographia Signup and view all the answers

What modern microscope did Joseph Jackson Lister create in 1830?

Light microscope Signup and view all the answers

What part of a microscope determines the total magnification?

Objective lens Signup and view all the answers

The early simple microscopes were created by __________ in the late 1500s.

eyeglass makers Signup and view all the answers

What modification is made to a brightfield microscope to create a darkfield microscope?

An opaque light stop is added. Signup and view all the answers

What type of microscopy uses an ultraviolet light source?

Fluorescence microscopy Signup and view all the answers

What does the term 'chromophores' refer to in microscopy?

Pigments that absorb and reflect particular wavelengths of light Signup and view all the answers

What can we learn about bacteria by looking at them under a microscope?

We can identify species and diagnose disease. Signup and view all the answers

Which property of light describes the distance between one peak of a wave and the next peak?

Wavelength Signup and view all the answers

What happens when light waves interact with materials?

They can be reflected, absorbed, or transmitted. Signup and view all the answers

Absorbance occurs when a material captures the energy of a light wave.

True Signup and view all the answers

Define refraction in the context of light waves.

Refraction is the change in direction that light waves undergo when they enter a new medium. Signup and view all the answers

Which of the following describes the property that affects how much light a lens can gather?

Numerical aperture Signup and view all the answers

What is magnification?

Magnification is the ability of a lens to enlarge the image of an object compared to its real size. Signup and view all the answers

The lowest frequency of visible light appears as the color ______.

red Signup and view all the answers

What is dispersion in the context of visible light?

The separation of colors when white light passes through a prism Signup and view all the answers

Name a factor that can affect the resolution of a microscope.

Wavelength or numerical aperture. Signup and view all the answers

Higher-frequency waves have longer wavelengths.

False Signup and view all the answers

What are the key points of the cell theory?

The cell theory states that all living organisms are composed of cells, that the cell is the fundamental unit of life, and that all cells arise from pre-existing cells. Signup and view all the answers

What contributions did Rudolf Virchow make to the development of the cell theory?

Rudolf Virchow popularized the principle that all cells arise from other cells, famously stating 'Omnis cellula e cellula'. Signup and view all the answers

What contributions did Robert Remak make to the development of the cell theory?

Robert Remak was the first to publish the idea that all cells originate from other cells in 1852. Signup and view all the answers

What does the modern endosymbiotic theory state?

The modern endosymbiotic theory states that mitochondria and chloroplasts arose as a result of prokaryotic cells establishing a symbiotic relationship within a eukaryotic host. Signup and view all the answers

What evidence supports the endosymbiotic theory?

Evidence includes the presence of their own DNA in mitochondria and chloroplasts, similarities in ribosome structure to bacteria, and replication processes resembling bacterial binary fission. Signup and view all the answers

Compare and contrast the miasma theory of disease with the germ theory of disease.

The miasma theory proposed that diseases were caused by 'bad air' from decomposing matter, while the germ theory states that diseases are caused by microbial infection. Signup and view all the answers

How did Joseph Lister’s work contribute to the debate between the miasma theory and germ theory?

Joseph Lister implemented handwashing and sanitation practices during surgery, reducing postsurgical infections and providing evidence for the germ theory. Signup and view all the answers

What infectious agents are known to cause pneumonia?

Common infectious agents that cause pneumonia include bacteria (like Streptococcus pneumoniae), viruses (like influenza), and fungi. Signup and view all the answers

What is the theory of spontaneous generation?

The theory that life can arise from nonliving matter. Signup and view all the answers

Who was one of the earliest scholars to articulate the theory of spontaneous generation?

Aristotle Signup and view all the answers

What experiment did Francesco Redi perform to challenge spontaneous generation?

He placed meat in jars, some covered and some uncovered, to show that maggots came from flies, not spontaneous generation. Signup and view all the answers

What were the findings of John Needham's experiments?

He proposed that microbes arose spontaneously in boiled broth that became cloudy. Signup and view all the answers

What did Lazzaro Spallanzani demonstrate in his experiments?

He showed that sealed flasks with heated broth remained clear, implying no spontaneous generation. Signup and view all the answers

What innovative design did Louis Pasteur use in his experiments?

He used swan-neck flasks to allow air in but prevent microbial contamination. Signup and view all the answers

What is one of the key tenets of modern cell theory?

All cells only come from other cells. Signup and view all the answers

Who first used the term 'cells' to describe what he observed under a microscope?

Robert Hooke Signup and view all the answers

What did Matthias Schleiden contribute to cell theory?

He described plant tissues as being composed of cells. Signup and view all the answers

What did Rudolf Virchow state in his 1855 publication?

Omnis cellula a cellula, meaning all cells arise from cells. Signup and view all the answers

Which scientist is often remembered as the 'Father of Pathology'?

Rudolf Virchow Signup and view all the answers

True or False: The theory of spontaneous generation was conclusively proven by Redi's experiments.

False Signup and view all the answers

Prokaryotic cells are typically larger than eukaryotic cells.

False Signup and view all the answers

What structures are typically found in prokaryotic cells?

Cell membrane, chromosomal DNA, ribosomes, and cell wall. Signup and view all the answers

Which domain do prokaryotic microorganisms belong to?

Both B and C Signup and view all the answers

Prokaryotic chromosomes are typically ______ and not bound by a complex nuclear membrane.

circular Signup and view all the answers

What is the significance of plasmids in prokaryotic cells?

They often carry genes that confer advantageous traits such as antibiotic resistance. Signup and view all the answers

All prokaryotic cells have a cell wall.

False Signup and view all the answers

What process do vegetative cells undergo to form endospores?

Sporulation Signup and view all the answers

What occurs in a hypertonic medium?

Water diffuses out of the cell Signup and view all the answers

Inclusions in prokaryotic cells provide ______ by storing excess nutrients.

nutrient storage Signup and view all the answers

What is the role of the cell wall in prokaryotic cells?

It protects the cell from changes in osmotic pressure and helps maintain cell shape. Signup and view all the answers

Which of the following statements is true about ribosomes in prokaryotic cells?

They are smaller than eukaryotic ribosomes. Signup and view all the answers

What is the fluid mosaic model describing regarding the plasma membrane?

The ability of membrane components to move fluidly within the membrane Signup and view all the answers

What type of linkages are found in archaeal membrane phospholipids?

Ether linkages Signup and view all the answers

Archaeal plasma membranes are always bilayers.

False Signup and view all the answers

What is responsible for cell-to-cell communication and sensing environmental conditions?

Membrane proteins Signup and view all the answers

What is the primary function of the cell wall in prokaryotic cells?

To protect the cell from harsh conditions Signup and view all the answers

The major component of bacterial cell walls is called ______.

peptidoglycan Signup and view all the answers

Which bacterial structure can make it more difficult for phagocytic cells to engulf the microbe?

Capsule Signup and view all the answers

Gram-positive bacteria have a thin layer of peptidoglycan.

False Signup and view all the answers

What component of the outer membrane in gram-negative bacteria functions as an endotoxin?

Lipopolysaccharide (LPS) Signup and view all the answers

What is one method that can be used to identify specific pathogenic strains of bacteria?

Serological or immunological tests Signup and view all the answers

Match the following structures with their primary function:

Capsules = Aiding in pathogenicity by evading immune response Fimbriae = Attaching to surfaces Peptidoglycan = Providing structural integrity to bacterial cell walls S-layers = Withstanding osmotic pressure Signup and view all the answers

Which stage of the mitotic phase is known as nuclear division?

Karyokinesis Signup and view all the answers

Which of the following stages of karyokinesis occurs first?

Prophase Signup and view all the answers

Mitosis results in four genetically distinct daughter cells.

False Signup and view all the answers

What is the purpose of meiosis?

To create four genetically distinct gametes. Signup and view all the answers

Where does ribosomal RNA (rRNA) biosynthesis occur?

In the nucleolus. Signup and view all the answers

What type of ribosomes are found in eukaryotic organelles such as mitochondria?

70S Signup and view all the answers

The ______ system is unique to eukaryotic cells and is responsible for synthesizing many cell components.

endomembrane Signup and view all the answers

What are the two types of endoplasmic reticulum (ER)?

Smooth and Rough Signup and view all the answers

Who discovered the Golgi apparatus?

Camillo Golgi Signup and view all the answers

What is the primary function of the Golgi apparatus?

Modification of lipids and proteins Signup and view all the answers

What is the function of pili in pathogenic bacteria?

Adherence to host cells for colonization, infectivity, and virulence. Signup and view all the answers

What is the F pilus and its significance?

The F pilus or sex pilus is important in the transfer of DNA between bacterial cells. Signup and view all the answers

How do fimbriae differ from pili?

Fimbriae are more numerous and shorter compared to pili. Signup and view all the answers

Which group of Strep is associated with a variety of human diseases?

Group A Strep Signup and view all the answers

What are flagella used for in bacterial cells?

Movement in aqueous environments. Signup and view all the answers

What protein composes bacterial flagella?

Flagellin. Signup and view all the answers

Which bacterium is an example of a monotrichously flagellated pathogen?

Vibrio cholerae Signup and view all the answers

What type of flagella are tufts found at each end of the cell?

Amphitrichous Signup and view all the answers

Which bacterium displays a peritrichous arrangement of flagella?

Escherichia coli Signup and view all the answers

What chemical signaling can bacteria respond to for movement?

Chemotaxis. Signup and view all the answers

Match the following flagellar arrangements with their examples:

Monotrichous = Vibrio cholerae Amphitrichous = Spirillum minor Lophotrichous = Pseudomonas aeruginosa Peritrichous = Escherichia coli Signup and view all the answers

What is the main difference in genome structure between eukaryotic and prokaryotic cells?

Eukaryotic cells have multiple linear chromosomes, while prokaryotic cells typically have a single circular chromosome. Signup and view all the answers

Eukaryotic cells are characterized by the absence of membrane-bound organelles.

False Signup and view all the answers

What is the primary role of the nucleus in eukaryotic cells?

Control cell activities and house DNA Signup and view all the answers

Who discovered that certain bacteria can live in boiling water?

Thomas Brock Signup and view all the answers

Which domains of life do prokaryotes belong to?

Both B and C Signup and view all the answers

What is carbon fixation?

The conversion of carbon dioxide into organic carbon products. Signup and view all the answers

In what type of environments can prokaryotes be found?

All of the above Signup and view all the answers

Prokaryotes can be found in the __________, deep oceans, and extreme environments.

soil Signup and view all the answers

Prokaryotic microorganisms are only found in soil and water.

False Signup and view all the answers

What negative impact can prokaryotes have?

They can cause illness or infection in humans. Signup and view all the answers

What type of relationship involves one organism benefiting while harming another?

Parasitism Signup and view all the answers

Match the following types of symbiotic relationships:

Mutualism = Both benefit Amensalism = One harmed, one unaffected Commensalism = One benefits, the other unaffected Parasitism = One benefits, one harmed Signup and view all the answers

What is the primary role of nitrogen-fixing bacteria like Rhizobium?

To convert atmospheric nitrogen into ammonia. Signup and view all the answers

Transient microbiota are permanently established in the human body.

False Signup and view all the answers

What does Agrobacterium tumefaciens cause in plants?

tumors Signup and view all the answers

What type of bacteria is Bartonella?

Gram-negative, facultative intracellular bacteria Signup and view all the answers

What disease does Brucella cause in humans?

brucellosis Signup and view all the answers

What characteristic of Caulobacter makes it useful in studies?

its peculiar life cycle Signup and view all the answers

What does Ehrlichia cause in humans?

ehrlichiosis Signup and view all the answers

What bacterium causes Legionnaires disease?

Legionella pneumophila Signup and view all the answers

What is unique about the morphology of Neisseria?

cocci that form pairs resembling coffee beans Signup and view all the answers

What type of bacteria are Methylomonas?

Gram-negative bacillus Signup and view all the answers

Which species of bacteria causes whooping cough?

Bordetella pertussis Signup and view all the answers

Which of the following is a characteristic of Proteus?

Motile Signup and view all the answers

What is a common characteristic of Enterobacteriaceae?

facultative anaerobes Signup and view all the answers

Pseudomonas species are non-pathogenic.

False Signup and view all the answers

What disease is caused by Shigella?

Dysentery Signup and view all the answers

What is the causative agent of typhoid fever?

Salmonella enterica serovar typhi Signup and view all the answers

What type of bacterium is Pseudomonas aeruginosa?

strictly aerobic, nonfermenting Signup and view all the answers

Which class of Proteobacteria includes sulfate-reducing bacteria?

Deltaproteobacteria Signup and view all the answers

Which of the following bacteria cause respiratory infections? (Select all that apply)

Bordetella pertussis Signup and view all the answers

What is the impact of oxygen exposure on microbiota diversity in the oral cavity?

The inner surface of the cheek has the least diverse microbiota due to its exposure to oxygen, while the crypts of the tongue and spaces between teeth have more diverse microbiota because they have limited oxygen exposure. Signup and view all the answers

What unique reproductive method do Planctomycetes use?

Budding Signup and view all the answers

Which of the following genera is known to cause food poisoning?

Campylobacter Signup and view all the answers

Which bacteria are associated with the gums?

Fusobacterium Signup and view all the answers

Humans acquire their first inoculations of normal flora during vaginal birth.

True Signup and view all the answers

What type of bacteria can cause chronic gastritis and stomach ulcers?

Helicobacter pylori Signup and view all the answers

Match the following genera with their characteristics:

Bdellovibrio = Parasitic bacteria that infect other bacteria Myxobacterium = Forms fruiting bodies and lives in soil Bacteroides = Abundant in the human gastrointestinal tract Chlamydia = Obligate intracellular pathogen causing trachoma Signup and view all the answers

The classification of prokaryotes is based on their __________ and physiological differences.

shape Signup and view all the answers

How can antibiotic therapy disrupt microbiota?

Antibiotic therapy can decrease the population of resident microbiota, leading to an increase in pH which may favor the growth of pathogenic microorganisms. Signup and view all the answers

The main feature of spirochetes is their ______ shape.

spiral Signup and view all the answers

What is one main goal of the Human Microbiome Project?

To create a large repository of gene sequences of important microbes Signup and view all the answers

What distinguishes gram-positive bacteria from gram-negative bacteria?

Gram-positive bacteria possess a thick peptidoglycan cell wall that retains the primary stain (crystal violet), while gram-negative bacteria have a thin peptidoglycan cell wall that does not retain this stain. Signup and view all the answers

Match the following classes of Proteobacteria with their defining feature:

Alphaproteobacteria = Obligate or facultative intracellular bacteria Betaproteobacteria = Slightly less defined but includes many pathogens Gammaproteobacteria = Includes many important human pathogens Deltaproteobacteria = Often includes sulfate-reducing bacteria Epsilonproteobacteria = Includes microaerobic bacteria Signup and view all the answers

What type of photosynthesis do the majority of phototrophic bacteria perform?

Anoxygenic photosynthesis Signup and view all the answers

What pigments do purple and green bacteria use for photosynthesis?

Bacteriochlorophylls Signup and view all the answers

Nonsulfur bacteria use sulfites as electron donors.

False Signup and view all the answers

Which genus is a type of purple sulfur bacterium?

Chromatium Signup and view all the answers

What do cyanobacteria produce through their photosynthesis?

Oxygen Signup and view all the answers

What special cells in cyanobacteria are involved in nitrogen fixation?

Heterocysts Signup and view all the answers

Which bacterium is known to cause tuberculosis?

Mycobacterium tuberculosis Signup and view all the answers

The class __________ includes low G+C gram-positive bacteria.

Bacilli Signup and view all the answers

Match each bacterium with its characteristic:

Actinomyces = Causes gum disease Corynebacterium = Produces diphtheria toxin Mycobacterium tuberculosis = Causes tuberculosis Bifidobacterium = Common in gut microbiota Signup and view all the answers

What bacteria causes diphtheria?

Corynebacterium diphtheriae Signup and view all the answers

Which of these genera is known for being nitrogen-fixing bacteria that live in symbiosis with legumes?

Frankia Signup and view all the answers

What is the morphology of Mycobacterium?

Gram-positive, acid-fast bacillus Signup and view all the answers

Micrococcus is an opportunistic pathogen.

True Signup and view all the answers

What causes tuberculosis?

Mycobacterium tuberculosis Signup and view all the answers

What type of bacteria is Clostridium?

Obligate anaerobes that produce endospores Signup and view all the answers

Which bacterium is known for causing gas gangrene?

Clostridium perfringens Signup and view all the answers

S.pneumoniae is classified under Lancefield groups.

False Signup and view all the answers

The toxin produced by C.botulinum is responsible for ________.

flaccid paralysis Signup and view all the answers

What is the main characteristic of Streptococcus pyogenes?

Causes bacterial pharyngitis Signup and view all the answers

What is the unique feature of Actinobacteria?

High G+C content in DNA Signup and view all the answers

What type of pathogen causes ringworm?

Fungus Signup and view all the answers

What is the most common nematode infection in the United States?

Ascaris lumbricoides Signup and view all the answers

Platyhelminths are segmented flatworms.

False Signup and view all the answers

What infection is caused by Schistosoma mansoni?

Schistosomiasis Signup and view all the answers

Which of the following are medically important flatworms?

Both A and B Signup and view all the answers

Match the following fungi with their diseases:

Histoplasma capsulatum = Histoplasmosis Candida albicans = Vaginal yeast infections Taenia saginata = Beef tapeworm infection Taenia solium = Pork tapeworm infection Signup and view all the answers

What structure do fungi typically use to absorb nutrients?

Hyphae Signup and view all the answers

Dimorphic fungi can change their form based on environmental conditions.

True Signup and view all the answers

What component is found in the cell walls of fungi?

Chitin Signup and view all the answers

How are spores produced in fungi?

Through sexual and asexual reproduction Signup and view all the answers

Which of the following apicomplexans causes intestinal symptoms and can lead to epidemic diarrhea when cysts contaminate drinking water?

Cryptosporidium parvum Signup and view all the answers

What percentage of individuals in the United States have antibodies for toxoplasmosis?

11% Signup and view all the answers

Balantidium coli is the only ciliate that can parasitize humans.

True Signup and view all the answers

What distinguishes oomycetes from true fungi?

Cell walls made of cellulose Signup and view all the answers

Which of the following nematodes is the largest intestinal parasite found in humans?

Ascaris lumbricoides Signup and view all the answers

What is the main cause of Chagas’ disease?

Triatoma spp. (kissing bugs) Signup and view all the answers

Trichomonas vaginalis often causes symptoms in males.

False Signup and view all the answers

The genus _ causes African sleeping sickness.

Trypanosoma brucei Signup and view all the answers

Which type of parasites are included in the study of microbiology?

Parasitic Helminths Signup and view all the answers

What is a common symptom of pinworm infection caused by Enterobius vermicularis?

Sleeplessness and itching around the anus Signup and view all the answers

Match the following parasites with their characteristics:

Giardia lamblia = Causes diarrheal illness Toxoplasma gondii = Associated with serious birth defects Trichinella spiralis = Causes trichinosis from undercooked meat Dirofilaria immitis = Causes heartworm disease in dogs Signup and view all the answers

What disease is caused by the eukaryotic parasite Plasmodium?

Malaria Signup and view all the answers

What is a major public health challenge associated with malaria?

It causes morbidity and mortality in billions worldwide. Signup and view all the answers

Malaria is primarily transmitted through contact with contaminated water.

False Signup and view all the answers

What is the term used for the life stage of protozoa during their feeding and growth?

Trophozoites Signup and view all the answers

Which of the following is NOT a reproductive method used by protozoans?

Mitosis Signup and view all the answers

The organism responsible for amoebic dysentery is called _.

Entamoeba histolytica Signup and view all the answers

What process allows a trophozoite to become a cyst under harsh environmental conditions?

Encystment Signup and view all the answers

Which of the following groups of protists includes the medically important E. histolytica?

Amoebozoa Signup and view all the answers

What is cilia used for?

Locomotion Signup and view all the answers

What is the name of the protective structure that some protozoa form when conditions become unfavorable?

Cyst Signup and view all the answers

What method can be suggested for the prevention of Schistosoma disease?

Improving sanitation and reducing exposure to contaminated water. Signup and view all the answers

Protozoans are always photosynthetic organisms.

False Signup and view all the answers

What is the primary cause of keratitis linked to amoebas?

Acanthamoeba Signup and view all the answers

Which of the drawings shows septate hyphae?

Refer to Figure 5.40. Signup and view all the answers

How has protist taxonomy changed in recent years?

It has been re-examined using newer approaches. Signup and view all the answers

Match the protozoan genus to its associated disease:

Plasmodium = Malaria Giardia = Giardiasis Entamoeba = Amoebic Dysentery Acanthamoeba = Keratitis Signup and view all the answers

What is the benefit of researching the pathways involved in the synthesis of chitin in fungi?

It provides insights into fungal biology and potential applications in biotechnology. Signup and view all the answers

What are chytrids primarily associated with?

Declines in amphibian populations Signup and view all the answers

Which of the following groups of fungi is known for using sporangiospores for asexual reproduction?

Zygomycota Signup and view all the answers

What is the significance of zygospores in Zygomycota?

They are used for sexual reproduction. Signup and view all the answers

Which fungus is an important bread mold and also causes rice seedling blight?

Rhizopus stolonifer Signup and view all the answers

Which of the following fungi is known to produce aflatoxin?

Aspergillus flavus Signup and view all the answers

What are dermatophytes?

Pathogenic fungi capable of causing skin infections. Signup and view all the answers

Which fungus is associated with causing blastomycosis?

Blastomyces dermatitidis Signup and view all the answers

Microsporidia are multicellular fungi.

False Signup and view all the answers

Which group of fungi is known to be involved in food spoilage?

Ascomycota Signup and view all the answers

What type of algae is primarily responsible for the production of approximately 70% of oxygen in aquatic environments?

All algae Signup and view all the answers

What causes red tides?

Dense populations of dinoflagellates Signup and view all the answers

All forms of marine algae are pathogenic.

False Signup and view all the answers

Which of the following is a characteristic of brown algae?

Multicellular seaweeds Signup and view all the answers

Which genus includes the causative agent for malaria?

Plasmodium vivax Signup and view all the answers

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

Giardia lamblia Signup and view all the answers

A fluke is classified within which of the following?

Platyhelminthes Signup and view all the answers

A nonsegmented worm found during a routine colonoscopy is likely which type?

fluke Signup and view all the answers

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

Candida albicans Signup and view all the answers

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

Histoplasma capsulatum Signup and view all the answers

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

foliose Signup and view all the answers

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

theca Signup and view all the answers

Which protists are associated with red tides?

dinoflagellates Signup and view all the answers

The plasma membrane of a protist is called the __________.

pellicle Signup and view all the answers

Animals belong to the same supergroup as the kingdom __________.

Animalia Signup and view all the answers

Flukes are in class __________.

Trematoda Signup and view all the answers

Nonseptate hyphae are also called __________.

coenocytic Signup and view all the answers

What are the three growth forms of lichens?

crustose, foliose, fruticose Signup and view all the answers

What is a distinctive feature of diatoms?

silica cell walls Signup and view all the answers

What is the best defense against tapeworm infections?

proper cooking of meat Signup and view all the answers

What are kinetoplastids?

single-celled organisms with a unique mitochondrion structure Signup and view all the answers

Which groups contain the multicellular algae?

brown algae, red algae, green algae Signup and view all the answers

What are three ways that lichens are environmentally valuable?

soil production, air pollution indicators, early colonizers Signup and view all the answers

Aside from a risk of birth defects, what other effect might a toxoplasmosis infection have?

may cause flu-like symptoms Signup and view all the answers

What is the function of the ciliate macronucleus?

regulate cellular metabolism and growth Signup and view all the answers

Why are algae not considered parasitic?

they primarily photosynthesize and do not harm other organisms Signup and view all the answers

Match the following types of lichens with their descriptions:

Crustose = Lichen with a crusty appearance tightly attached to substrate Foliose = Lichen with leaf-like lobes attached at one point Fruticose = Lichen with rounded structures and a branched appearance Signup and view all the answers

What are acellular pathogens?

Infectious agents that are not composed of cells, such as viruses. Signup and view all the answers

What is the genome type of viruses?

Either DNA or RNA, but never both Signup and view all the answers

What did Edward Jenner do in relation to smallpox?

He inoculated patients with cowpox to prevent smallpox. Signup and view all the answers

Viruses that infect bacteria are called ______.

bacteriophages Signup and view all the answers

Viruses can infect every type of host cell.

False Signup and view all the answers

What is phage therapy?

Using bacteriophages to treat bacterial infections Signup and view all the answers

Which of the following is a characteristic of viruses?

They are obligate intracellular parasites Signup and view all the answers

What was the first virus investigated and what did it cause?

Tobacco mosaic virus; it caused tobacco mosaic disease. Signup and view all the answers

Match the viruses with their characteristics:

Naked viruses = Viruses formed from nucleic acid and capsid only Enveloped viruses = Viruses with a lipid layer surrounding the capsid Bacteriophages = Viruses that infect bacteria Zoonotic viruses = Viruses transmitted from animals to humans Signup and view all the answers

What phase corresponds to a period when an individual cannot transmit a virus?

Eclipse phase Signup and view all the answers

How is the Ebola virus transmitted?

Through direct contact with bodily fluids Signup and view all the answers

Public health officials did not trace Duncan's contacts during his infection.

False Signup and view all the answers

What types of training can prepare health professionals to contain emerging epidemics?

Infection control training, outbreak management training Signup and view all the answers

What is the difference between a contagious pathogen and an infectious pathogen?

Contagious pathogens can be transmitted through casual contact, while infectious pathogens require a specific route of transmission. Signup and view all the answers

What size filter pore is needed to collect a virus?

Pores smaller than the virus size Signup and view all the answers

What property of cells makes periodic dilutions of primary cell cultures necessary?

Contact inhibition Signup and view all the answers

What is significant about the HeLa cell line?

It is the first immortal cell line. Signup and view all the answers

What are cytopathic effects (CPEs)?

Observable cell abnormalities due to viral infection. Signup and view all the answers

What is the outcome of a positive hemagglutination inhibition (HAI) test?

Agitation of erythrocytes is inhibited, appearing as a red dot in the well. Signup and view all the answers

What are nucleic acid amplification tests (NAAT) used for?

To detect unique nucleic acid sequences of viruses in patient samples. Signup and view all the answers

What do capsids somewhat resemble?

a soccer ball Signup and view all the answers

Which types of viruses can have envelopes?

both helical and polyhedral viruses Signup and view all the answers

What is the main task of the International Committee on Taxonomy of Viruses (ICTV)?

to develop, refine, and maintain a universal virus taxonomy Signup and view all the answers

How many known viral orders has the ICTV classified to date?

seven orders Signup and view all the answers

Which of the following is NOT a type of virus genome mentioned?

triple-stranded RNA Signup and view all the answers

What do virus family names end with?

-viridae Signup and view all the answers

Viruses can replicate by themselves without host cells.

False Signup and view all the answers

What is the attachment stage in the lytic cycle?

the first stage where the phage interacts with specific bacterial surface receptors Signup and view all the answers

What is a prophage?

the integrated phage genome within a bacterial chromosome Signup and view all the answers

What type of test was performed on David to check for rabies virus?

Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis Signup and view all the answers

Why does the immunofluorescent staining technique look for rabies antibodies?

to detect the immune response against the rabies virus Signup and view all the answers

What may cause the prophage to enter the lytic cycle?

environmental stressors such as starvation or exposure to toxic chemicals Signup and view all the answers

Transduction involves the transfer of genetic material between two bacteria via a bacteriophage.

True Signup and view all the answers

What type of transduction occurs during the lytic cycle?

Generalized transduction Signup and view all the answers

What triggers the prophage to undergo induction?

Ultraviolet light exposure or chemical exposure Signup and view all the answers

Specialized transduction involves random packaging of DNA.

False Signup and view all the answers

What is tissue tropism in viruses?

The specificity of a virus to infect certain types of cells within tissues. Signup and view all the answers

Animal viruses express their genes using the normal flow of genetic information.

False Signup and view all the answers

+ssRNA viruses can be translated directly to make viral proteins while -ssRNA requires synthesis of ______.

+ssRNA Signup and view all the answers

What is a provirus?

An integrated viral genome in the host chromosome Signup and view all the answers

What leads to the reactivation of latent viruses?

Certain triggers, often after many years of dormancy. Signup and view all the answers

Which virus is an example of a virus that produces chronic infection?

HIV Signup and view all the answers

What is polymerase chain reaction (PCR) used for?

To detect the presence of viral DNA in a patient's tissue or body fluid sample. Signup and view all the answers

What are the two primary categories of persistent infections?

Latent infection and chronic infection. Signup and view all the answers

What enzyme is used in reverse transcriptase-PCR (RT-PCR)?

Reverse transcriptase Signup and view all the answers

What aspect of viral life cycle leads to a sudden increase in the growth curve?

Release of new virions Signup and view all the answers

What tests did Michelle’s physician recommend?

Pap smear and HPV test Signup and view all the answers

What is a common consequence of a chronic infection?

Symptoms that are recurrent or persistent over a long time. Signup and view all the answers

Plant viruses may have either a DNA or ______ genome.

RNA Signup and view all the answers

Why is a single diagnostic test often insufficient?

Because results depend on the sensitivity of the assay, the quantity of virions present, and timing. Signup and view all the answers

What indicates a positive enzyme immunoassay (EIA) test?

The presence of a colored end product Signup and view all the answers

What is the genome of a viroid made of?

A short strand of circular RNA Signup and view all the answers

What is a key difference between viroids and virusoids?

Viroids are self-replicating while virusoids require a helper virus to replicate. Signup and view all the answers

Prions contain DNA or RNA.

False Signup and view all the answers

What diseases in humans are caused by prions?

Kuru, Creutzfeldt-Jakob disease, fatal familial insomnia, Gerstmann-Straussler-Scheinker disease Signup and view all the answers

What do transmissible spongiform encephalopathies (TSEs) cause?

Degeneration of neural tissue Signup and view all the answers

What does the Pap smear test screen for?

Presence of HPV Signup and view all the answers

Viroids have a protein coat.

False Signup and view all the answers

The rabies virus can be transmitted through casual contact.

False Signup and view all the answers

The component(s) of a virus that is/are extended from the envelope for attachment is/are the:

Glycoprotein Signup and view all the answers

Which of the following does a virus lack? Select all that apply.

Cytoplasm Signup and view all the answers

In naming viruses, the family name ends with and genus name ends with .

−viridae; −virus Signup and view all the answers

What is another name for a nonenveloped virus?

Naked virus Signup and view all the answers

Which of the following leads to the destruction of the host cells?

Lytic cycle Signup and view all the answers

A virus obtains its envelope during which of the following phases?

Release Signup and view all the answers

Which of the following components is brought into a cell by HIV?

Reverse transcriptase Signup and view all the answers

A positive-strand RNA virus:

Can be used directly to translate viral proteins. Signup and view all the answers

Scientists have identified viruses that are able to infect fungal cells.

True Signup and view all the answers

A virus that infects a bacterium is called a/an __________.

Bacteriophage Signup and view all the answers

A/an __________ virus possesses characteristics of both.

Viroid Signup and view all the answers

Which of these organisms is known for using cytochrome c oxidase?

Both B and C Signup and view all the answers

E. coli is positive for the oxidase test.

False Signup and view all the answers

What is one circumstance under which aerobic respiration is not possible?

The cell lacks a sufficient amount of oxygen. Signup and view all the answers

Which process uses an inorganic molecule as a final electron acceptor?

Anaerobic respiration Signup and view all the answers

How many ATP molecules can be generated from one molecule of NADH during aerobic respiration?

Three ATP molecules Signup and view all the answers

What is the theoretical maximum yield of ATP during the complete aerobic respiration of glucose?

38 ATP molecules Signup and view all the answers

Which type of bacteria are known to perform lactic acid fermentation?

Lactobacillus Signup and view all the answers

Fermentation does not require __________.

oxygen Signup and view all the answers

What type of fermentation do Saccharomyces cerevisiae perform?

Alcohol fermentation Signup and view all the answers

When would a metabolically versatile microbe perform fermentation rather than cellular respiration?

When oxygen is scarce or absent, and the microbe needs to generate ATP without using oxygen. Signup and view all the answers

How can lipases and phospholipases contribute to virulence in microbes?

By breaking down lipids and phospholipids in host cells, providing nutrients and facilitating infection. Signup and view all the answers

How can protein catabolism help identify microbes?

By distinguishing pathogens based on their ability to produce specific proteases and degrade proteins. Signup and view all the answers

Which products are produced by the butanediol fermentation pathway?

2,3-butanediol Signup and view all the answers

Which of these microbes is associated with the production of lactic acid?

Lactobacillus Signup and view all the answers

What is the primary product of alcoholic fermentation?

Ethanol Signup and view all the answers

Microbial photosynthesis is only significant in plants.

False Signup and view all the answers

A Gram stain can help identify the bacterium Neisseria meningitidis.

True Signup and view all the answers

What is the term used to describe all of the chemical reactions inside a cell?

Metabolism Signup and view all the answers

What is the difference between catabolism and anabolism?

Catabolism breaks down complex molecules to release energy, whereas anabolism builds complex molecules from simpler ones, requiring energy. Signup and view all the answers

Which of the following correctly describes autotrophs?

Organisms that convert inorganic carbon dioxide into organic carbon compounds. Signup and view all the answers

What are the primary electron carriers mentioned in the text?

FAD and NADP+ Signup and view all the answers

All organisms are chemoheterotrophs.

False Signup and view all the answers

What is the function of an electron carrier?

To shuttle high-energy electrons between compounds in metabolic pathways. Signup and view all the answers

An enzyme lowers the ______ of a chemical reaction.

activation energy Signup and view all the answers

Temperature and pH can affect enzyme activity.

True Signup and view all the answers

______ are organic helper molecules required for enzyme action.

Coenzymes Signup and view all the answers

What role do enzymes play in a chemical reaction?

Enzymes act as catalysts to speed up chemical reactions without being consumed in the process. Signup and view all the answers

Explain the difference between a competitive inhibitor and a noncompetitive inhibitor.

A competitive inhibitor resembles the substrate and competes for the active site, while a noncompetitive inhibitor binds to an allosteric site, reducing the enzyme's activity. Signup and view all the answers

What is an apoenzyme?

An enzyme that is inactive without its cofactor Signup and view all the answers

Which of the following are examples of coenzymes?

NADH Signup and view all the answers

What is glycolysis?

Glycolysis is the metabolic pathway that converts glucose into pyruvate, producing ATP and NADH. Signup and view all the answers

In which part of the cell does glycolysis occur?

Cytoplasm Signup and view all the answers

What is the net gain of ATP from glycolysis?

The net gain from the breakdown of a single glucose molecule is two ATP molecules. Signup and view all the answers

What are the main products of the Krebs cycle?

All of the above Signup and view all the answers

A competitive inhibitor can permanently deactivate an enzyme.

False Signup and view all the answers

The Krebs cycle regenerates the compound used in the ______ step.

first Signup and view all the answers

What is the importance of feedback inhibition?

Feedback inhibition helps regulate metabolic pathways by using the end product of a pathway to inhibit an earlier step. Signup and view all the answers

Where does photosynthesis take place in a phototrophic eukaryote?

Chloroplasts Signup and view all the answers

Why would a photosynthetic bacterium have different pigments?

To absorb energy from more wavelengths of light Signup and view all the answers

Describe the three stages of the Calvin cycle.

Fixation, reduction, regeneration Signup and view all the answers

What are the four steps of the nitrogen cycle?

Nitrogen fixation, ammonification, nitrification, and denitrification Signup and view all the answers

The process of photophosphorylation generates _____ by chemiosmosis.

ATP Signup and view all the answers

Oxygen is generated as a byproduct in anoxygenic photosynthesis.

False Signup and view all the answers

Match the following pigments with their corresponding colors:

Bacteriochlorophylls = Green, purple, or red Carotenoids = Orange, red, or yellow Chlorophylls = Green Phycocyanins = Blue Phycoerythrins = Red Signup and view all the answers

What is the primary function of the electron transport system (ETS) in photosynthesis?

To transfer high-energy electrons to produce NADH or NADPH Signup and view all the answers

What molecules are used in the Calvin cycle for the fixation of CO2?

Ribulose bisphosphate (RuBP) Signup and view all the answers

What is produced during cyclic photophosphorylation?

ATP Signup and view all the answers

Which of the following biogeochemical cycles does NOT involve redox chemistry?

Phosphorus cycle Signup and view all the answers

Human activities introducing excessive nutrients can lead to eutrophication.

True Signup and view all the answers

What is bioremediation?

The process of using microbial metabolism to remove pollutants. Signup and view all the answers

Which of the following contaminants is particularly concerning as a carcinogenic xenobiotic?

Polycyclic aromatic hydrocarbons (PAH) Signup and view all the answers

What are the two categories of bioremediation?

In situ and ex situ. Signup and view all the answers

What role do bacteria like Rhodococcus and Pseudomonas play in bioremediation?

They degrade environmental contaminants. Signup and view all the answers

What is the common method used to categorize bioremediation?

By whether it is in situ or ex situ. Signup and view all the answers

The prevalence of N.meningitidis is particularly low in the 'meningitis belt.'

False Signup and view all the answers

What is recommended for young people living in close quarters, such as dormitories?

Vaccination against N.meningitidis Signup and view all the answers

What should be monitored after recovery from bacterial meningitis?

Developmental issues. Signup and view all the answers

Study Notes

Roman and Islamic Contributions to Microbiology

Marcus Terentius Varro (116-27 BC) proposed the concept of invisible organisms causing disease.
In his book "On Farming", Varro described how "minute creatures" in swamps could enter the body and cause illnesses.
Abū Bakr al-Rāzī (Rhazes) used experimental methods to assess medical treatments.
He identified the differences between measles and smallpox.
Al-Razi's approach focused on identifying causes rather than just symptoms, a significant shift in medical thinking.
Ibn Sina (Avicenna) wrote "The Canon of Medicine", a significant text with detailed descriptions of diseases, medicinal substances, and treatments.
The Canon described mechanisms of contagion and the potential transmission of illness through breath.
Ibn Sina emphasized the crucial role of isolation in preventing disease spread, foundational for quarantines.
The Canon of Medicine influenced medical education worldwide for centuries.

Microbiological Techniques and Tools

Staining techniques allow for visualizing microbes.
Some dyes require pre-treating the specimens with heat or chemicals.
Different staining methods work on different types of microbes due to variation in cellular composition.
Growth media provide essential nutrients for microorganism growth in a laboratory setting.
Petri dishes are commonly used for growing microbes on agar.
Test tubes are used for cultivating microbes in different types of media.
Bunsen burners provide flame sterilization for equipment.
Inoculation loops are used for streaking microbes on agar or transferring them between containers.
Sterilization of inoculation loops between uses is crucial for preventing contamination.

Naming and Classifying Microorganisms

Binomial nomenclature assigns organisms Latinized scientific names with a genus and species designation.
Bergey's Manual of Determinative Bacteriology and Bergey's Manual of Systematic Bacteriology are standard references for identifying and classifying prokaryotes.
Biochemical tests detect chemicals unique to certain species, crucial for identification.
Serological tests use antibodies that react with specific bacterial proteins for identification.
DNA and rRNA sequencing are used for identification and classifying newly discovered bacterial species.

Microbial Diversity

Strains are subtypes within a microorganism species, differing in attributes.
Escherichia coli is an example of a species with different strains, with variation in their ability to cause disease.
E. coli strains are found in the human gut where they aid digestion, provide beneficial chemicals, and fight against pathogens.
Bacteria are classified by shape: spherical (coccus), rod-shaped (bacillus), or curved (spirillum, spirochete, or vibrio).
They have a wide range of metabolic abilities and can thrive in various environments.
Archaea are single-celled prokaryotic organisms.
They are distinct from bacteria in evolutionary history, genetic makeup, metabolic pathways, and cell wall/membrane structure.
Unlike bacteria, archaeal cell walls do not contain peptidoglycan.
Archaea inhabit diverse environments, including extreme conditions like extreme temperatures, pH, and salinity.

Eukaryotic Microorganisms

The Eukarya domain includes all eukaryotes, both single-celled (protists) and multi-celled organisms (plants, animals, and fungi).
The defining characteristic of eukaryotes is the nucleus in their cells.
Protozoa are single-celled with complex cellular structures and are mainly motile.
Microscopic fungi include molds and yeasts.
Helminths are parasitic worms with microscopic eggs and larvae, included in microbiology because of this microscopic stage.
Viruses are acellular, meaning they are not composed of cells, require a host to reproduce.

Key Figures in Microbiology History

Antonie van Leeuwenhoek was the first to observe "animalcules" (microorganisms) under the microscope.
Robert Koch established the germ theory of disease, demonstrating that specific bacteria cause specific diseases.
Louis Pasteur developed the process of pasteurization to kill harmful bacteria in food, and contributed to the understanding of vaccination and germ theory.
Edward Jenner developed the first successful vaccine against smallpox.

The Germ Theory of Disease

The germ theory of disease postulates that specific microorganisms called germs cause specific diseases.
Koch's Postulates, a set of criteria used to establish a causal relationship between a microbe and a disease.
Pasteur's work validated the Germ Theory of Disease, which revolutionized medicine and public health.

The Development of Vaccination and Antiseptics

Jenner's work with the first vaccine against smallpox laid the foundation for modern immunology and the development of vaccines.
Lister's work on antiseptic techniques helped prevent infection in surgical procedures.
Advances in vaccination and antiseptic practices drastically reduced disease rates and improved public health.

What Our Ancestors Knew

Humans have benefitted from microorganisms long before understanding them.
Fermented foods and beverages like beer, wine, bread, yogurt, cheese, and pickled vegetables have been consumed throughout history.
Archaeological evidence suggests people utilized fermentation to preserve and improve food as early as 7000 BC.
Some early civilizations associated disease with invisible organisms, like the "miasma theory" that attributed illness to foul air.

A Systematic Approach

The invention of the microscope in the 17th century marked a new era in microbiology.
Antonie van Leeuwenhoek used his handmade microscopes to observe microorganisms, leading to major advancements in understanding microorganisms.
Louis Pasteur’s work in the 19th century refuted spontaneous generation, proving that life arises from pre-existing life.
Robert Koch laid the foundation for the germ theory of disease, identifying specific microbes responsible for specific diseases.

Types of Microorganisms

Microorganisms are found in all three domains of life: Archaea, Bacteria, and Eukarya.
Prokaryotes (bacteria and archaea) lack a nucleus, while eukaryotes have a nucleus.
Some microorganisms, like viruses, are acellular (not composed of cells).
Bacteria are found in a wide variety of habitats, including within and on humans.
Most bacteria are harmless or beneficial, but some are pathogenic (cause disease).
Bacteria are typically prokaryotic with cell walls containing peptidoglycan.

How We See the Invisible World

Light is a form of electromagnetic radiation (EMR) which exhibits various properties such as reflection, absorption, and transmission.
Wavelength, amplitude, and frequency are key characteristics that determine how light interacts with objects.
Different materials exhibit different refractive indices, which affect the speed and direction of light passing through them.
Lenses utilize refraction to focus light, magnifying images and adjusting focal length with curvature and object distance.
Visible light occupies a narrow band on the electromagnetic spectrum, with each color representing a specific frequency and wavelength.
Fluorescent dyes absorb specific wavelengths of light and emit different colors, used to enhance contrast in microscopy.
Magnification refers to the enlargement of an image, while resolution is the ability to distinguish between two closely spaced objects.
Higher resolution is achieved with shorter wavelengths and greater numerical aperture, which measures a lens’ ability to gather light.
Contrast is enhanced through techniques that highlight differences in the optical properties of various specimen components.
Girolamo Fracastoro was one of the first to propose the existence of tiny invisible "seeds of contagion" responsible for disease spread.
Antonie van Leeuwenhoek, using homemade simple microscopes, revolutionized microscopy by being the first person to observe and describe bacteria and other single-celled organisms.

Early Microscopy

Antonie van Leeuwenhoek is credited with the discovery of microorganisms.
Early microscopes were developed by eyeglass makers in the Netherlands in the late 1500s.
Galileo Galilei used a compound microscope to examine insect parts.
Van Leeuwenhoek used a simple microscope, with one lens.
Galileo's compound microscope used two sets of lenses.
Robert Hooke published observations using a compound microscope in his 1665 book Micrographia.
Hooke was the first to observe cells, describing the structures in cork as resembling "Honey-comb," "small Boxes or Bladders of Air," and "Cavern, Bubble, or Cell.”
Hooke's observations were likely of dead cells, with only the rigid cell walls providing the structure.
Hans and Zaccharias Janssen, Dutch spectacle-makers, may have invented the telescope, simple microscope, and compound microscope during the late 1500s or early 1600s.
Historical evidence for the Janssens' contributions is inconclusive.

Brightfield Microscopy

Brightfield microscopes are the most commonly used type of microscope.
Brightfield microscopes are compound microscopes with two or more lenses.
The lenses produce a dark image on a bright background.
They have an objective lens and an ocular lens.
The objective lens typically magnifies 4⨯ to 100⨯.
The ocular lens typically magnifies 10⨯.
The total magnification is the product of the ocular magnification times the objective magnification.
Brightfield microscopes use an illuminator, which is typically a high-intensity bulb.
Light from the illuminator passes through a condenser lens, which focuses light on the specimen.
The condenser focus knob allows optimization of the condenser's position.
A diaphragm between the condenser and the specimen adjusts the amount of light striking the specimen.
Some brightfield microscopes have a rheostat to adjust the intensity of the illuminator.
Structures in the specimen appear darker than the bright background.
The maximum magnification for brightfield microscopes is about 1000⨯.
Brightfield microscopy allows us to see objects as small as bacteria.
Immersions oil with an oil immersion lens increases the maximum angle at which light can strike the lens, improving the resolution of the image.

Microscope Maintenance

Clean the lenses with lens paper.
Do not allow lenses to contact the slide.
Protect the illuminator bulb.
Do not push an objective onto a slide.
Do not use the coarse focusing knob with the 40⨯ or greater objective lenses.
Only use immersion oil with a specialized oil objective (usually the 100⨯ objective).
Clean oil from immersion lenses after use.
Clean oil accidentally transferred from other lenses.
Cover the microscope when not in use.

Darkfield Microscopy

Darkfield microscopy is a brightfield microscopy with a modification in the condenser.
Darkfield microscopes use an opaque light stop placed between the illuminator and the condenser lens.
The opaque light stop blocks most light from the illuminator.
The resulting light forms a hollow cone of light focused on the specimen.
Only light reflected or refracted by structures in the specimen reaches the objective lens.
Images appear as bright objects on a dark background.
Darkfield microscopy is effective for viewing unstained live specimens.
Treponema pallidum, the causative agent of syphilis, is best viewed using a darkfield microscope.

Phase-Contrast Microscopy

Phase-contrast microscopes use refraction and interference caused by structures in a specimen to create high-contrast images without staining.
An annular stop is used in the condenser to produce a hollow cone of light focused on the specimen.
The objective contains a phase plate with a phase ring.
Light traveling directly from the illuminator passes through the phase ring, while light refracted or reflected by the specimen passes through the phase plate.
This creates waves that are about one-half of a wavelength out of phase.
Out-of-phase waves can cancel each other out (destructive interference).
Structures that refract light appear dark against a bright background of only unrefracted light.
Phase-contrast microscopy is often used to observe live specimens.

Differential Interference Contrast (DIC) Microscopy

DIC microscopy is similar to phase-contrast microscopy, using interference patterns to enhance contrast.
DIC uses two beams of light with different polarizations.
After passing through the specimen, the beams are recombined.
Differences in the interference patterns generated by the combining of the beams create high-contrast images of living organisms with a three-dimensional appearance.
DIC microscopy is especially useful for distinguishing structures within live, unstained specimens.

Chromoblastomycosis

A chronic skin infection caused by a fungus.
Common In tropical and subtropical climates.

Phase-contrast and DIC microscopy

Enhance contrast in specimens.
Allow visualization of transparent, unstained structures.

Fluorescence Microscopy

Uses fluorescent chromophores called fluorochromes.
Fluorochromes absorb energy and emit visible light.
Examples of fluorochromes include chlorophylls & fluorescent stains (Texas red, FITC, DAPI, acridine orange).
Uses excitation light (UV or blue) to illuminate the specimen.
The emitted light is then filtered, leaving only visible light for observation.
Produces bright images against a dark background.
Used in clinical microbiology to identify pathogens, locate specific species, identify structures within cells, and distinguish living/dead cells.
Multiple fluorochromes can be used simultaneously to visualize different structures.

Immunofluorescence

A technique used to identify disease-causing microbes.
Direct Immunofluorescence Assay (DFA): Stained antibodies bind directly to the pathogen.
Indirect Immunofluorescence Assay (IFA): Unstained primary antibodies bind to the pathogen, and then fluorescent secondary antibodies bind to the primary antibodies. IFA increases the visibility of the pathogen.

Confocal Microscopes

Use lasers to scan z-planes of the specimen.
Produces multiple two-dimensional images of different depths.
Creates a 3-dimensional image using a computer.
Fluorescent stains are often used to enhance contrast and resolution.
Useful for examining thick specimens, such as biofilms, alive and unfixed.

Two-Photon Microscopes

A specific type of fluorescence microscopy that improves upon traditional approaches.
Uses two photons of long-wavelength light simultaneously to excite fluorochromes.
Reduces scattering and out-of-focus blur.
Allows for deeper penetration into thicker specimens.
Especially useful for imaging living cells and tissues.

Spontaneous Generation

Aristotle proposed that life can arise from nonliving matter containing pneuma (spirit or breath).
Francesco Redi (1668) disproved spontaneous generation of maggots on meat by showing they only appeared when flies could lay eggs on the meat.
John Needham (1745) claimed microbes arose spontaneously from boiled broth, but likely did not boil the broth sufficiently to kill all microbes.
Lazzaro Spallanzani (1768) refuted Needham's claim by showing that heated broth remained clear and sterile if sealed, but became contaminated if opened to air.
Louis Pasteur (1858) conclusively disproved spontaneous generation by filtering air through a gun-cotton filter, finding it full of microorganisms.
Pasteur's swan-neck flask experiment proved that microbes were introduced from the air, not from a "life force," by allowing air into the flasks but preventing airborne microorganisms from entering the sterilized broth.

Foundations of Modern Cell Theory

Robert Hooke (1665) coined the term "cells" while observing small chambers in cork, and noted that each cell was distinct.
Matthias Schleiden (1838) proposed that plant tissues were composed of cells, but believed they formed through crystallization.
Theodor Schwann (1839) observed similar structures in animal tissues, solidifying the foundation for the idea that cells are the fundamental components of all living organisms.
Robert Remak (1852) published evidence for cells arising from other cells through division.
Rudolf Virchow (1855) popularized the concept of cell theory with the phrase omnis cellula a cellula (all cells arise from cells).

Endosymbiotic Theory

Robert Brown (1831) first described observations of nuclei in plant cells.
Andreas Schimper (1880s) discovered chloroplasts in plant cells and their role in starch formation, noting their independent division.
Konstantin Mereschkowski (1905) proposed that chloroplasts may have originated from photosynthetic bacteria living symbiotically inside a eukaryotic cell.

Endosymbiotic Hypothesis

Mereschkowski: proposed a similar origin for plant cell nuclei, suggesting eukaryotic cells evolved from ancestral bacteria
Wallin: experimentally investigated similarities between mitochondria, chloroplasts, and bacteria, supporting Mereschkowski’s hypothesis
Modern Genome Sequencing: disproved Wallin’s claim of culturing mitochondria outside host cells, showing genes were transferred to the host cell’s nucleus
Mitochondrial & Chloroplast DNA Discovery: revived the endosymbiotic hypothesis in the 1960s
Lynn Margulis: published her ideas on the endosymbiotic origin of mitochondria and chloroplasts in 1967, providing evidence from microscopy, genetics, molecular biology, fossils, and geology
Modern Endosymbiotic Theory: states that mitochondria and chloroplasts arose from symbiotic relationships between prokaryotic cells and eukaryotic hosts
Mitochondrial & Chloroplast DNA Similarity: the DNA of these organelles closely resembles their bacterial counterparts in sequence and structure, but is reduced due to gene transfer to the host nucleus
Ribosome Similarity: Mitochondrial and chloroplast ribosomes are structurally similar to bacterial ribosomes, not eukaryotic host ribosomes
Binary Fission: these organelles divide using binary fission, mirroring bacteria, not mitosis used by eukaryotic cells

Germ Theory of Disease

Ancient Greek Miasma Theory: proposed that disease originated from particles emanating from decomposing matter.
Ibn Sina and Ibn Zuhr: Proposed tuberculosis spread through breath and scabies caused by mites.
Girolamo Fracastoro's Germ Theory: proposed that diseases could be transmitted through direct contact, contaminated clothing, or air
Ignaz Semmelweis: observed that childbirth mortality rates were higher in hospital wards staffed by physicians than midwife-staffed wards
Semmelweis' Handwashing Theory: proposed that physicians carried disease from autopsies to patients, suggesting handwashing to prevent transmission.
John Snow's Epidemiological Study: traced cholera outbreaks to contaminated water sources in London, refuting the miasma theory
Louis Pasteur: demonstrated that microbes, not spontaneous generation, caused food spoilage, suggesting they could also cause infection
Joseph Lister: advocated for handwashing and cleanliness during surgery to reduce postsurgical infections.
Lister's use of Carbolic Acid: reduced postsurgical infection, becoming a standard medical practice
Robert Koch’s Postulates: established a protocol to identify the causes of specific diseases, linking specific microbes to specific diseases, culminating in the germ theory of disease

Prokaryotic Cells

Prokaryotic Cell Structure: possesses cytoplasm enclosed by a plasma membrane, one or more chromosomes, and ribosomes
Prokaryotic vs. Eukaryotic Cell Differences: Prokaryotic cells lack a nucleus surrounded by a nuclear membrane and have a single, circular chromosome. Eukaryotic cells have a complex nuclear membrane containing multiple rod-shaped chromosomes.
Prokaryotic Cell Morphology: cells from a specific organism typically share similar shapes (e.g., coccus, bacillus, spirillum)
Prokaryotic Cell Arrangement: cells of the same species may group together in specific arrangements based on their plane of division (e.g., diplococci, streptococci, staphylococci)
Cell Wall Function: maintains morphology and protects the cell from osmotic pressure changes.
Osmotic Pressure: occurs due to differences in solute concentration on opposing sides of a semipermeable membrane, leading to water movement to equilibrate the concentration.

Osmosis and Tonicity

Osmosis is the diffusion of water, which can create osmotic pressure on a cell during environmental changes.
Isotonic medium: solute concentrations inside and outside the cell are equal, no water movement.
Hypertonic medium: solute concentration outside cell is higher, water moves out, potentially causing crenation.
Hypotonic medium: solute concentration inside cell is higher, water moves in, potential cell swelling and lysis.
Tonicity: the capacity of a cell to withstand changes in osmotic pressure.
Cells with cell walls are more resistant to osmotic pressure changes and maintain their shape.
In hypertonic environments, cells without cell walls might undergo crenation (shrivel).
In hypertonic environments, cells with cell walls undergo plasmolysis (plasma membrane detaches from the cell wall).
Cells without cell walls are more prone to lysis in hypotonic environments.

Prokaryotic Cell Structure

Prokaryotic cells have a nucleoid region containing circular, haploid DNA.
Nucleoid-associated proteins (NAPs) help organize and package prokaryotic DNA, similar to histones in eukaryotic cells.
Plasmids are extrachromosomal DNA in prokaryotes, often carrying beneficial genes like antibiotic resistance.
Ribosomes in prokaryotes are 70S, smaller than eukaryotic 80S ribosomes.
Inclusions are cytoplasmic structures in prokaryotes for storing excess nutrients.
Examples of inclusions include glycogen/starch, volutin granules, sulfur granules, polyhydroxybutyrate (PHB).
Gas vacuoles are inclusions for buoyancy regulation in water.
Magnetosomes are inclusions containing magnetic iron oxides/sulfides for magnetic field alignment.
Carboxysomes are protein-based inclusions containing RuBisCO and carbonic anhydrase, important for carbon metabolism.

Endospores

Endospores are dormant structures formed by some bacteria under unfavorable conditions.
They protect the bacterial genome and allow survival without food/water, chemicals, extreme temperatures, or radiation.
Endospores are formed through sporulation, a process starting with asymmetric cell division and the formation of a forespore.
Endospores are dehydrated and metabolically inactive.
Endospores germinate when conditions become favorable, returning to a vegetative state.
Clinically significant endospore-forming bacteria include Bacillus and Clostridium, including B.anthracis, C.tetani, C.difficile, C.perfringens, and C.botulinum.

Plasma Membrane

Plasma membrane encloses the cytoplasm and other internal structures of cells.
The fluid mosaic model describes its structure: a bilayer of phospholipids and proteins that can move freely.
In bacteria and eukaryotes, phospholipids usually have ester linkages.
Archaeal membranes have ether linkages, branched chains, and can be bilayers or monolayers.
Membrane proteins play roles in cell-to-cell communication, environmental sensing, and virulence.
Glycoproteins and glycolipids extend from the cell surface, allowing interaction with the environment.

Membrane Transport

Plasma membranes control molecular transport into and out of cells.
Simple diffusion (passive transport) moves molecules down a concentration gradient.
Facilitated diffusion uses carriers or channels to transport molecules down a concentration gradient.
Active transport moves molecules against the concentration gradient, requiring energy (ATP).
Group translocation modifies a molecule upon entry, preventing transport against an unfavorable gradient.
The phosphotransferase system phosphorylates sugar upon entry, considered energy neutral.

Photosynthetic Membrane Structures

Cyanobacteria and photosynthetic bacteria have photosynthetic membrane structures.
Thylakoids in cyanobacteria and chromatophores/lamellae/chlorosomes in photosynthetic bacteria enclose photosynthetic pigments.
These structures are invaginations of the plasma membrane.

Cell Wall

The main function of the cell wall is to protect the cell from harsh external conditions.

Cell Walls

Bacterial cell walls are composed of peptidoglycan, a unique polymer not found in other organisms.
Peptidoglycan is a mesh-like structure made of alternating N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) molecules.
Tetrapeptide chains extending from each NAM unit are cross-linked, creating a strong tensile strength.
Gram-positive bacteria have thick layers of peptidoglycan, often embedded with teichoic acids, which contribute to cell wall rigidity.
Gram-negative bacteria have a thinner peptidoglycan layer and an outer membrane, which contains lipopolysaccharide (LPS), an endotoxin that can trigger immune responses.
Archaeal cell walls differ from bacterial cell walls, lacking peptidoglycan and instead containing pseudopeptidoglycan or glycoproteins.

### Glycocalyces and S-Layers

Glycocalyces are sugar coats that can surround prokaryotic cells.
Capsules are organized, firmly attached glycocalyces, often composed of polysaccharides, that can protect cells from phagocytosis.
Slime layers are less organized and loosely attached, aiding in adhesion and biofilm formation.
Biofilms can protect microbes from environmental stressors and antibiotics.
S-layers are composed of structural proteins and glycoproteins and can contribute to cell wall integrity and interaction with the immune system.

Filamentous Appendages

Fimbriae and pili are short, bristle-like protein appendages involved in attachment to surfaces and other cells.
Pili are longer and less numerous than fimbriae, and a specific type called the F pilus is essential for DNA transfer between bacteria.
Flagella are long, spiral-shaped filaments that provide movement for bacterial cells.
Flagella are composed of flagellin protein subunits and rotate like propellers, powered by a basal body embedded in the cell membrane.
Different types of flagella arrangements exist, including monotrichous (single flagellum), amphitrichous (flagella at both ends), lophotrichous (flagella tuft at one end), and peritrichous (flagella covering the cell surface).
Bacteria use flagella for chemotaxis, moving toward attractants and away from repellents.
Flagellar rotation in a counterclockwise direction results in a "run," while clockwise rotation causes a "tumble," allowing for directional movement.

Eukaryotic Cells

Eukaryotic organisms include protozoa, algae, fungi, plants, and animals.
Eukaryotic cells possess a nucleus and other membrane-bound organelles, absent in prokaryotic cells.
Eukaryotic cells are generally larger than prokaryotic cells.
Eukaryotic cells undergo mitosis and meiosis for cell division, contrasting with prokaryotic binary fission.

Eukaryotic Cells

Eukaryotic cells possess a nucleus enclosed by a nuclear membrane
Eukaryotic cells have a cytoplasm that contains membrane-bound organelles like mitochondria, endoplasmic reticulum (ER), Golgi apparatus, lysosomes, and peroxisomes
The cytoskeleton is an internal network that supports the transport of intracellular components and maintains cell shape
The genome of eukaryotic cells is organized into multiple, rod-shaped chromosomes
Eukaryotic cells display diverse cell morphologies, including spheroid, ovoid, cuboidal, cylindrical, flat, lenticular, fusiform, discoidal, crescent, ring stellate, and polygonal shapes
The shape of a eukaryotic cell can be influenced by its function, cytoskeleton structure, cytoplasm viscosity, cell membrane or wall rigidity, and external environmental pressure

Nucleus

Eukaryotic cells have a nucleus that houses the DNA genome
The nucleus functions in controlling cellular activities, reproduction, and heredity
The DNA in the nucleus is organized into multiple linear chromosomes and is wrapped around proteins called histones
The nucleus is bound by a double-layered nuclear membrane (nuclear envelope) which is contiguous with the cell's endoplasmic reticulum
The nuclear envelope contains nuclear pores, protein complexes that control the movement of materials in and out of the nucleus
The nuclear lamina, a meshwork of intermediate filaments, determines the shape of the nucleus

Cell Cycle

Eukaryotic cells multiply through asexual reproduction known as mitosis
The cell cycle consists of two phases: interphase and the mitotic phase
Interphase is divided into G1, S, and G2 stages, during which the cell grows and DNA replicates
The mitotic phase involves chromosome alignment, separation, movement to opposite poles, and division into two identical daughter cells
Karyokinesis, or nuclear division, occurs during the mitotic phase, involving prophase, prometaphase, metaphase, anaphase, and telophase
Cytokinesis, the physical separation of the cytoplasmic components into the two daughter cells, completes the mitotic phase

Meiosis

Meiosis is a type of sexual reproduction in eukaryotic microorganisms
Unlike mitosis, meiosis involves two separate nuclear divisions to create four genetically distinct gametes, each containing half the number of chromosomes found in the original cell

Nucleolus

The nucleolus is a dense area in the nucleus where ribosomal RNA (rRNA) biosynthesis occurs
The nucleolus is also the site where ribosome assembly begins
Pre-ribosomal complexes are assembled in the nucleolus and transported to the cytoplasm for complete ribosome assembly

Ribosomes

Eukaryotic organelles like mitochondria or chloroplasts have 70S ribosomes, similar to prokaryotic ribosomes
However, non-organelle-associated ribosomes in eukaryotic cells are 80S, being different in size and composition compared to prokaryotic ribosomes
Ribosomes are classified as free ribosomes (found in the cytoplasm and synthesizing water-soluble proteins) or membrane-bound ribosomes (attached to the endoplasmic reticulum and producing proteins for membranes or export)

Endomembrane System

The endomembrane system is a network of membranous tubules, sacs, and flattened disks that synthesize and transport cellular components
The endomembrane system includes the endoplasmic reticulum, Golgi apparatus, lysosomes, and vesicles

Endoplasmic Reticulum (ER)

The ER is an interconnected network of tubules and cisternae (flattened sacs)
There are two types of ER: rough endoplasmic reticulum (RER) and smooth endoplasmic reticulum (SER)
RER is studded with ribosomes and synthesizes proteins destined for the plasma membrane
These proteins are inserted into the RER membrane and transported by vesicles to the Golgi apparatus, plasma membrane, other organelles, or outside the cell
SER lacks ribosomes, and is involved in lipid biosynthesis, carbohydrate metabolism, and detoxification of toxic compounds

Golgi Apparatus

The Golgi apparatus is composed of stacked membranous disks called dictyosomes
It modifies lipids and proteins transported from the ER, often adding carbohydrate components to form glycolipids, glycoproteins, or proteoglycans
Glycolipids and glycoproteins are inserted into the plasma membrane and are essential for cell recognition and signal transduction

Prokaryote Habitats and Functions

Prokaryotes are found in diverse environments, including hot springs, Antarctic ice, deep ocean, and even soil.
Prokaryotes are abundant in the human body, outnumbering human cells.
Key functions of prokaryotes in the ecosystem include:
- Soil formation and stabilization
- Nutrient cycling (nitrogen fixation and carbon fixation)
- Degradation of organic matter
- Remediation of environmental pollutants

Symbiotic Relationships

Mutualism: Both organisms benefit.
- Example: Humans and Bacteroides thetaiotaomicron (break down complex plant materials in the gut).
Amensalism: One organism harms the other, while the former remains unaffected.
- Example: Staphylococcus epidermidis and Propionibacterium acnes (produce antibacterial compounds that kill other bacteria).
Commensalism: One organism benefits, while the other is unaffected.
- Example: Staphylococcus epidermidis (use dead skin cells as nutrients).
Neutralism: Neither organism is affected.
- Example: Vegetating bacteria and endospores.
Parasitism: One organism benefits, while the other is harmed.
- Example: Pathogenic prokaryotes that cause diseases like tetanus and tuberculosis.

Microbiota

The human microbiome consists of all prokaryotic and eukaryotic microorganisms and their genetic material.
Resident microbiota: Organisms that permanently live in or on the body.
Transient microbiota: Organisms that temporarily reside in the body, often including pathogens.
Microbiota diversity varies depending on the body site (e.g., mouth, skin, intestines) and individual factors (diet, hygiene).

Microbiota Variations

Diversity of microbiota is higher in the crypts of the tongue and spaces between teeth due to limited oxygen exposure.
The inner surface of the cheek has a predominance of Streptococcus, while the throat, tonsil, and saliva have more Fusobacterium.
In the intestines, the genus Bacteroides is predominant.
Acquisition of microbiota begins during birth and continues after birth from parents, healthcare providers, and other individuals.

Microbiome

Microbiome changes throughout life as microbes colonize and exit the body.
Within 9 hours, half of the microbial inhabitants of the small intestine can change.
Vaginal birth is important for establishing a healthy microbiome.
Babies born vaginally are primarily colonized by Lactobacillus.
Babies born by cesarean section are often colonized by skin microbes, including hospital-acquired pathogens.
Resident microbiota are important for health by occupying niches that could be used by pathogens.
Lactobacillus contributes to vaginal acidity, inhibiting yeast growth.
Antibiotic use can disrupt the microbiome, increasing risk of infections and pathogen carriage.

Prokaryote Classification

Prokaryote classification is challenging due to their asexual reproduction and limited morphological features.
Traditional classification relies on shape, staining patterns, and biochemistry.
Modern classification incorporates genetic sequencing for more accurate categorization.
Bergey's Manual of Systematic Bacteriology is a comprehensive guide for prokaryote taxonomy.
Staining patterns are used to categorize bacteria:
- Gram-positive: retain crystal violet stain, thick peptidoglycan layer.
- Gram-negative: lose crystal violet stain, thin peptidoglycan layer.
- Atypical: cannot be stained by standard methods.
Gram-negative bacteria are categorized into additional groups:
- Deeply branching bacteria: early evolutionary forms, found in extreme environments.
- Proteobacteria: diverse group, including many human pathogens.
- Cytophaga-Flavobacterium-Bacteroides (CFB): gut microbiota components.
- Spirochetes: spiral-shaped bacteria, including the syphilis pathogen.
Gram-positive bacteria are classified by the presence of guanine and cytosine (G+C) nucleotides in their DNA.
- Low G+C bacteria: less than 50% G+C, include pathogens causing anthrax, tetanus, and listeriosis.
- High G+C bacteria: more than 50% G+C, include pathogens causing diphtheria and tuberculosis.

Human Microbiome Project

Launched in 2008 by the National Institutes of Health (NIH).
Aims to create a database of human microbiome gene sequences.
Addresses challenges of culturing microbes by using metagenomic analysis.
Found unexpected presence of pathogenic microbes in healthy people.
Revealed a significant number of uncultured organisms.
Future goals include analyzing the microbiome in diseased patients and finding relationships between microbiota and disease risk.

Proteobacteria

A phylum of gram-negative bacteria.
Includes diverse groups with varying metabolic strategies.
Divided into five classes: Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Epsilonproteobacteria.

Alphaproteobacteria

Many are obligate or facultative intracellular bacteria.
Can survive in low-nutrient environments.
Includes rickettsias, obligate intracellular pathogens.
Rickettsia spp. cause serious diseases like Rocky Mountain spotted fever and epidemic typhus.

Betaproteobacteria

Diverse group with various metabolic capabilities.
Some genera include human pathogens.
Neisseria genera contain pathogens causing gonorrhea and bacterial meningitis.
Bordetella pertussis causes pertussis (whooping cough).

Gram-Negative Bacteria

Pertussis: Caused by the bacteria Bordetella pertussis, which is a coccobacillus, a gram-negative bacillus. This bacteria is known for causing whooping cough.
Burkholderia: Burkholderia are Gram-negative bacilli, they are aerobic and aquatic. They cause various diseases in humans and animals, especially in those with compromised immune systems.
Leptothrix: Leptothrix are Gram-negative, sheathed, filamentous bacteria, typically found in aquatic environments. They contribute to oxidizing iron and manganese within wastewater treatment plants.
Neisseria: Neisseria bacteria are Gram-negative, shaped like a coffee bean. They require moist environments and high carbon dioxide levels for growth. They can be identified by the oxidase reaction. Many Neisseria species are pathogenic, causing common diseases like gonorrhea and meningitis.
Thiobacillus: Thiobacillus are Gram-negative bacilli that are thermophilic, acidophilic, and require oxygen (they are strictly aerobic). They oxidize iron and sulfur.

Gammaproteobacteria

The most diverse class of Gram-negative bacteria.
Includes a wide range of pathogens.
Pseudomonas: Pseudomonas are strictly aerobic, non-fermenting, and highly motile; they often infect wounds and burns, as well as being responsible for chronic urinary tract infections and respiratory infections.
Pseudomonas bacteria are known for being resistant to many antibiotics and their ability to form biofilms.
Pasteurellaceae: Pasteurellaceae are a family of bacteria that can be found in humans and animals.
Pasteurella haemolytica causes pneumonia in sheep and goats.
P.multocida is another species of Pasteurellaceae that can be transmitted from animals to humans through bites, usually causing skin and tissue infections.
Haemophilus: Haemophilus are a genus of bacteria that includes two known human pathogens:
H.influenzae is a common cause of upper and lower respiratory tract infections that include sinusitis, bronchitis, ear infections, and pneumonia.
H.ducreyi can cause a sexually transmitted infection called chancroid.
Vibrionales: This group includes a variety of aquatic bacteria that are known for causing various diseases in humans,
- Vibrio cholerae causes cholera by producing toxins that cause electrolytes and water to be released into the intestines, leading to diarrhea and dehydration.
- V. parahaemolyticus can cause gastrointestinal diseases in humans, while V.vulnificus causes serious and potentially life-threatening infections in humans that include cellulitis and blood-borne infections.
- Aliivibrio fischeri has a symbiotic relationship with squid, providing essential nutrients for the squid while reducing risks from predators with bioluminescence.
- Legionella are aquatic bacteria that can cause a respiratory disease called Legionnaires disease. The bacteria are typically found in warm water, such as pools or air conditioning units, that can become contaminated with Legionella bacteria, causing outbreaks.
Enterobacteriaceae: Enterobacteriaceae are a large family of intestinal bacteria. They are facultative anaerobes that ferment carbohydrates for energy. They are categorized into either “coliform” or “noncoliform” bacteria.
- Coliforms: Coliform bacteria ferment lactose completely.
- Noncoliforms: Noncoliform bacteria are unable to ferment lactose completely, or can only ferment lactose partially. This group includes several human pathogens like Salmonella spp., Shigella spp., and Yersinia pestis.
- Escherichia coli (E.coli) is one of the most studied bacteria. Most E.coli strains can benefit humans, but some strains produce the Shiga toxin, a dangerous toxin that can cause cellular death and hemorrhagic colitis. Other strains of E.coli can cause traveler’s diarrhea.
- Salmonella: Salmonella are non-coliform bacteria that can cause various symptoms, including fever, vomiting, and diarrhea. Some strains, such as Salmonella typhi, can cause typhoid fever.

### Deltaproteobacteria

A small class of Gram-negative bacteria.
Sulfate-reducing bacteria are a group of bacteria that use sulfate for energy.
Desulfovibrio orale causes periodontal disease, an inflammatory disease that affects the gums.
Bdellovibrio: Bdellovibrio bacteria are parasites that infect other Gram-negative bacteria.
Myxobacteria: Myxobacteria live in the soil. They are known for their social interactions with each other and their ability to form fruiting bodies.
Myxobacteria are also known for forming myxospores.

Epsilonproteobacteria

The smallest class of the Proteobacteria class.
Epsilonproteobacteria are microaerophilic bacteria that require small amounts of oxygen to grow. They are known for their helical shape.
Campylobacter: Campylobacter bacteria are found in poultry and can be ingested from undercooked foods. They cause food poisoning and severe enteritis.
Helicobacter: * Helicobacter* bacteria are also commonly found in poultry and can cause food poisoning. Helicobacter pylori is known for its ability to survive in the acidic environments of the stomach.
H.pylori is associated with gastritis, peptic ulcers, and stomach cancer.

Chlamydia

C.trachomatis is a human pathogen that causes trachoma, an eye disease often leading to blindness.
C.trachomatis also causes the sexually transmitted disease lymphogranuloma venereum (LGV).
LGV is often mildly symptomatic, manifesting as regional lymph node swelling, or asymptomatic, but is highly contagious and common on college campuses.
Members of the genus Chlamydia are gram-negative, obligate intracellular pathogens that are resistant to cellular defenses.
Elementary bodies are the endospore-like form of intracellular bacteria that enter epithelial cells and become active.

Spirochetes

Spirochetes are characterized by long, spiral-shaped bodies (up to 250 μm).
They are often very thin, making them difficult to examine under a conventional brightfield microscope.
Darkfield fluorescent microscopy is typically used to visualize spirochetes.
They are highly motile, using an axial filament to propel themselves.
The axial filament is similar to a flagellum but wraps around the cell, running inside the cell body in the periplasmic space.
Several genera of spirochetes include human pathogens, including Treponema and Borrelia.

Treponema

T.pallidum pallidum causes syphilis, the third most prevalent sexually transmitted bacterial infection in the United States.
Other subspecies of T.pallidum cause tropical infectious diseases of the skin, bones, and joints.

Borrelia

B.burgdorferi causes Lyme disease, which is transmitted by ticks (notably Ixodes and Amblyomma).
Lyme disease often produces a "bull's eye" rash, fever, fatigue, and sometimes, debilitating arthritis.
B.recurrens causes relapsing fever.

Cytophaga, Fusobacterium, and Bacteroides (CFB group)

These bacteria are classified together as the CFB group and share similarities in their DNA sequences.
They are rod-shaped bacteria adapted to anaerobic environments, such as the tissue of the gums, gut, and rumen of ruminating animals.
CFB bacteria are avid fermenters, able to process cellulose in the rumen.

Cytophaga

Cytophaga are motile aquatic bacteria that glide.

Fusobacteria

Fusobacteria inhabit the human mouth and may cause severe infectious diseases.

Bacteroides

Bacteroides is the largest genus of the CFB group, with dozens of species prevalent in the human large intestine (up to 30% of the entire gut microbiome).
One gram of human feces contains up to 100 billion Bacteroides cells.
Most Bacteroides are mutualistic, benefiting from gut nutrients and preventing pathogens from colonizing the large intestine.
A few species of Bacteroides are pathogenic, like B.melaninogenicus, which can cause wound infections.

Planctomycetes

Found in aquatic environments (freshwater, saltwater, and brackish water).
Reproduce by budding, where a mother cell forms a bud that detaches and lives independently.
Swarmer cells are motile and not attached to a surface.
They differentiate into sessile (immobile) cells with a holdfast for attachment to surfaces.
Only sessile cells can reproduce.

Phototrophic Bacteria

This diverse group uses sunlight as their primary energy source, including both Proteobacteria and nonproteobacteria.
They synthesize ATP via photosynthesis.
Most phototrophic bacteria perform anoxygenic photosynthesis (do not produce oxygen).

Purple and Green Bacteria

These bacteria use bacteriochlorophylls for photosynthesis, giving them a range of colors from orange to purple to green.
Classified into sulfur and nonsulfur bacteria.

Purple Sulfur Bacteria

Oxidize hydrogen sulfide into elemental sulfur and sulfuric acid.
Chromatium is a model organism for bacterial photosynthesis studies.

Green Sulfur Bacteria

Use sulfide for oxidation and produce large amounts of green bacteriochlorophyll.
Bacteriochlorophyll is stored in specialized organelles called chlorosomes.
Chlorobium is an example of a green sulfur bacterium.

Purple Non-Sulfur Bacteria

Similar to purple sulfur bacteria but use hydrogen for oxidation.
Rhodospirillum is a facultative anaerobe that can fix nitrogen and produce biological plastic and hydrogen fuel.

Green Non-Sulfur Bacteria

Similar to green sulfur bacteria but use substrates other than sulfides for oxidation.
Chloroflexus is an example of a green non-sulfur bacterium.
It is thermophilic and can glide like Cytophaga.

Cyanobacteria

This phylum has blue-green color from chlorophyll in their cells.
They are responsible for oxygenic photosynthesis, producing large amounts of oxygen.
Scientists believe cyanobacteria played a critical role in changing the Earth's atmosphere from anoxic to oxygen-rich.
Cyanobacteria exhibit amazing adaptability, thriving in various habitats like marine and freshwater environments, soils, and even rocks.
They can live as unicellular organisms, in colonies, or filamentous, forming sheaths or biofilms.
Many fix nitrogen, converting molecular nitrogen into nitrites and nitrates.
Photosynthesis in Cyanobacteria is oxygenic, using chlorophyll a as a primary pigment.
They also use phycocyanin and cyanophycin, secondary photosynthetic pigments that give them their blue color.
Microcystis can form harmful cyanobacterial blooms, producing toxins harmful to wildlife and humans.

Gram-Positive Bacteria

Gram-positive bacteria have a thick peptidoglycan layer in their cell wall, allowing them to retain crystal violet stain and appear purple under a microscope.
Two main groups of gram-positive bacteria are classified based on their guanine-cytosine (G+C) content in DNA:
- High G+C gram-positive bacteria (Actinobacteria): Have a G+C content higher than 50%.
- Low G+C gram-positive bacteria (Bacilli): Have a G+C content lower than 50%.

High G+C Gram-Positive Bacteria (Actinobacteria)

Diverse group with various shapes including branching rods, coccobacilli, and complex structures.
Primarily found in soil and aquatic environments.
Mostly aerobic.
Cell walls contain diverse peptidoglycans.
Examples:
- Actinomyces: Found in soil and human mouth, can cause periodontitis and oral abscesses.
- Mycobacterium: Covered with a waxy mycolic acid coat, resists drying and some antibiotics, require an acid-fast staining procedure.
- Mycobacterium tuberculosis: Causes tuberculosis, a lung infection that can spread to other organs.
- Mycobacterium leprae: Causes Hansen’s disease (leprosy), affecting peripheral nerves, skin, and respiratory tract.
- Corynebacterium: Rod-shaped bacteria forming V-shaped pairs, contain metachromatic granules, most species are harmless, but C.diphtheria causes diphtheria.
- Bifidobacterium: Filamentous anaerobes, commonly found in the human gut, used as probiotics in yogurt production.
- Gardnerella vaginalis: Gram-variable coccobacilli, colonize the human vagina, causes bacterial vaginosis.

Low G+C Gram-Positive Bacteria (Bacilli)

Include a number of pathogenic genera.
Examples:
- Clostridia: Rod-shaped, obligate anaerobes, form endospores, found in anaerobic environments.
- Clostridium perfringens: Causes gas gangrene, releasing toxins that damage tissue.
- Clostridium tetani: Causes tetanus, producing a neurotoxin that blocks nerve impulses causing spastic paralysis.
- Clostridium botulinum: Produces botulinum toxin, the deadliest known toxin, blocks acetylcholine release causing flaccid paralysis.
- Clostridium difficile: Cause severe colitis and diarrhea, often in patients taking antibiotics.
- Lactobacillales: Include bacilli and cocci, found in the human gut.
- Streptococcus: Spherical or ovoid bacteria forming chains.
- Streptococcus pyogenes: Belongs to Lancefield group A, β-hemolytic, causes strep throat, impetigo and flesh-eating disease.
- Streptococcus pneumoniae: Diplococci, does not belong to a Lancefield group, causes pneumonia, meningitis, septicemia, osteomyelitis, and endocarditis.
- Bacillus: Rod-shaped bacteria, form endospores, include aerobes and facultative anaerobes.
- Bacillus anthracis: Causes anthrax, affecting animals and humans, leading to skin ulcers, enterocolitis, pneumonia, and brain damage.
- Bacillus cereus: Causes food poisoning.
- Bacillus thuringiensis: Produces substances used as insecticides.
- Staphylococcus: Cocci forming grape-like clusters.
- Staphylococcus epidermidis: Common on skin.
- Staphylococcus aureus: Can cause serious infections.

### Unicellular Eukaryotic Parasites

Microscopic eukaryotic organisms are responsible for many serious human diseases.
Protozoa are nonphotosynthetic, motile, and always unicellular.
Many protozoa are free-living, but some are parasitic and can cause illness.
Some protozoa have a cyst stage that allows them to survive harsh environmental conditions.
Protozoa reproduce using a variety of methods: binary fission, budding, schizogony, sexual reproduction through syngamy or conjugation.
Protozoa have a plasma membrane, or plasmalemma. Some have a pellicle, bands of protein that add rigidity.
Protozoa may have a cytostome (specialized structure for taking in food), a cytoproct (for exocytosis of wastes), or an oral groove lined with cilia to sweep in food particles.
Protozoa are heterotrophic and can be either holozoic, ingesting whole food particles through phagocytosis, or saprozoic, ingesting small, soluble food molecules.
Protozoa can use cilia, flagella, or pseudopodia for locomotion.
Protozoa may have contractile vacuoles for osmotic regulation.
Protozoa may lack mitochondria or have modified mitochondria.
The classification of protists is changing due to recent discoveries about their evolutionary history.
There are six supergroups of eukaryotes, and many protozoa are scattered across many different taxonomic groups.

Amoebozoa

The supergroup Amoebozoa includes protozoans that use amoeboid movement.
Amoebas use pseudopodia for locomotion, extending cytoplasm to move the cell forward.
Members of the genus Entamoeba include commensal and parasitic species, including E. histolytica, the primary cause of amoebic dysentery.
Acanthamoeba can cause keratitis (corneal inflammation) and blindness.
Slime molds, which previously were classified as animals, fungi, or plants, are in the phylum Eumycetozoa.
Slime molds can be cellular or plasmodial.

Chromalveolata

The supergroup Chromalveolata is united by the similar origins of its members’ plastids.
Apicomplexans are intra- or extracellular parasites that have an apical complex at one end of the cell.
The apical complex helps the parasite to enter host cells.
Many apicomplexans have complex life cycles that involve multiple hosts.
Plasmodium is a genus of apicomplexans that causes malaria.
Other medically important apicomplexans include:
- Cryptosporidium parvum: causes intestinal symptoms and epidemic diarrhea.
- Theileria (Babesia) microti: causes recurring fever and is a common transfusion-transmitted pathogen.
- Toxoplasma gondii: causes toxoplasmosis, which can be transmitted from cat feces, unwashed fruit and vegetables, or undercooked meat.
Toxoplasmosis can be associated with serious birth defects.
A national survey found that 11% of people in the United States have antibodies for toxoplasmosis.
There is evidence that Toxoplasma gondii can alter infected humans’ behavior and personality traits.

Ciliates

Ciliates are a diverse group of microorganisms with cilia for locomotion and feeding
Balantidium coli is the only parasitic ciliate affecting humans, causing intestinal illness primarily in immunocompromised individuals
Common ciliate examples include Paramecium and Stentor
Ciliates have a diploid micronucleus for sexual reproduction and a polyploid macronucleus derived from the micronucleus with a reduced set of metabolic genes
Ciliates reproduce through conjugation where two cells exchange haploid micronuclei, resulting in genetically diverse offspring

Öomycetes

Öomycetes are also known as water molds.
They have cellulose cell walls, unlike the chitinous walls of fungi, and are generally diploid.
Phytophthora, responsible for the Irish potato famine, is a prominent example of this group.

Excavata

The Excavata supergroup contains primitive eukaryotes and parasites with limited metabolic abilities
Excavates have complex cell shapes and structures, including a depression called an excavate
Excavates are divided into three subgroups: Fornicata, Parabasalia, and Euglenozoa
Fornicata lack mitochondria but have flagella, with Giardia lamblia causing diarrheal illness as a notable example
Parabasalia are animal endosymbionts like Trichomonas vaginalis, the cause of trichomoniasis, a sexually transmitted disease
Euglenozoa include photosynthetic and nonphotosynthetic species, with Euglena having two flagella, a pellicle, stigma, and chloroplasts
Trypanosoma, within the Euglenozoa, is a parasitic pathogen responsible for African trypanosomiasis (sleeping sickness) and American trypanosomiasis (Chagas disease)
Trypanosoma brucei, responsible for African sleeping sickness, is spread by tsetse flies and affects the blood and brain
Trypanosoma cruzi, causing Chagas disease, is transmitted by kissing bugs and affects the heart or digestive system
Leishmania, another trypanosome, causes skin diseases and systemic illness

Parasitic Helminths

Parasitic helminths are animals studied in microbiology due to their microscopic eggs and larvae
The major groups are roundworms (Nematoda) and flatworms (Platyhelminthes), about half of which are parasitic
Unlike free-living helminths, parasitic forms have limited digestive, nervous, and locomotor abilities
They often have complex lifecycles with multiple hosts and some are monoecious (both sexes in one individual) while others are dioecious (separate sexes)

Nematoda

Nematoda includes over 15,000 species, several being human parasites
These unsegmented worms have a complete digestive system
Ascaris lumbricoides is the largest nematode intestinal parasite in humans, causing symptoms ranging from mild to severe
Pinworm (Enterobius vermicularis) is the most common nematode infection in the United States, causing sleeplessness and anal itching
Toxocara canis and T.cati are dog and cat nematodes, respectively, that can cause toxocariasis in humans, leading to larval migrans
Hookworm, caused by Necator americanus and Ancylostoma duodenale, results in abdominal pain, diarrhea, anemia, and fatigue
Trichinellosis (trichinosis), caused by Trichinella spiralis, is acquired from undercooked meat and causes fever, muscle pain, and digestive issues
Heartworm in dogs is caused by Dirofilaria immitis, transmitted by mosquitoes, and causes fatigue, cough, and potentially death

Platyhelminthes

Platyhelminthes, flatworms, include flukes (trematodes) and tapeworms (cestodes) as medically important parasites
Flukes are nonsegmented flatworms with oral suckers for attaching to the intestines, lungs, blood vessels, or liver
Trematodes have complex life cycles, with multiple hosts
Schistosoma mansoni, S.haematobium, andS.japonicum, found in freshwater snails, are responsible for schistosomiasis
Schistosomiasis symptoms include anemia, malnutrition, fever, abdominal pain, and fluid buildup
Tapeworms (cestodes) are segmented flatworms with suckers or hooks on their scolex for attachment
Tapeworms have an intermediate host where eggs hatch into larval oncospheres that develop into cysticerci
Proglottids detach and release fertilized eggs, completing the cycle

Tapeworms

The beef tapeworm, Taenia saginata, and the pork tapeworm, T. solium, can be ingested by humans through undercooked contaminated meat.
The beef tapeworm is generally benign, but can cause digestive issues and allergic reactions.
The pork tapeworm can have more severe effects when the larvae enter other tissues, including the central nervous system.
Diphylobothrium latum is the largest human tapeworm, can grow to 15 meters long, and is ingested through undercooked fish.
Echinococcus granulosus, the dog tapeworm, can infect humans and requires dogs as a host.

Flatworms

Some medically important flatworms are segmented, and some are not.

### Helminth Infections

Worldwide, approximately 807–1,221 million people are infected with Ascaris lumbricoides.
Almost 600-800 million people have whipworm (Trichuris) infections worldwide.
About 576–740 million people are infected with hookworm (Necator americanus and Ancylostoma duodenale).
Over 200 million people globally have schistosomiasis.
Helminths are a significant global public health concern.
Helminths may cause subclinical illnesses or more severe, chronic illnesses.

Guinea Worm Eradication

Guinea worm disease is caused by Dracunculus medinensis, a nematode.
When individuals consume contaminated water, they ingest larvae.
Larvae migrate, mate, and females emerge, often through feet.
An eradication campaign led by WHO, the CDC, UNICEF, and the Carter Center has been highly successful.
In 2014, only 126 cases were reported.

Fungi

Fungi are heterotrophic and typically saprozoic.
They are important decomposers and play a role in food production and antibiotic development.
They include microscopic (yeasts and spores) and macroscopic organisms (mushrooms and molds).
Some fungi are pathogenic and cause mycoses.
Some pathogenic fungi are opportunistic, meaning they only cause infections when a host's immune system is compromised.

### Fungal Characteristics

Multicellular fungi, called molds, are made of filaments called hyphae.
Hyphae form a network called a mycelium, which makes up the thallus of fleshy fungi.
Hyphae can be septate (with walls) or nonseptate (without walls).
Yeasts are unicellular fungi that reproduce asexually by budding.
Some fungi are dimorphic, meaning they can exist as both yeasts and molds, depending on the environment.
Fungal cell walls contain chitin.
Fungal cell membranes have ergosterols instead of cholesterol.

Fungal Reproduction

Fungi reproduce sexually through cross- or self-fertilization.
Different mating types combine to create a dikaryotic cell, followed by karyogamy to form a diploid zygote.
The zygote undergoes meiosis to produce spores that germinate into haploid mycelia.
In asexual reproduction, fungi may use mitosis, budding, fragmentation of hyphae, or the formation of asexual spores.

Fungal Diversity

Fungi are very diverse and include seven major groups.
Urediniomycetes and Ustilagomycetes cause plant rusts and smuts, respectively.
Glomeromycota are mycorrhizal fungi that are symbionts with plant roots, promoting plant growth.
Chytridiomycetes are aquatic fungi with flagellated, motile gametes.
Zygomycota, Ascomycota, Basidiomycota and Microsporidia are also significant groups of fungi.

Zygomycota

Zygomycetes are primarily saprophytic with coenocytic hyphae.
They reproduce asexually with sporangiospores and sexually with zygospores.
Rhizopus stolonifer is a bread mold that causes rice seedling blight.
Mucor is a genus that can cause necrotizing infections, but most species are intolerant of mammalian body temperatures.

Ascomycota

Ascomycota are found in food, food spoilage, and human pathogens.
They can have septate hyphae and produce ascospores and conidia.
Aspergillus causes allergies and infections and is used in beverage production.
Aspergillus flavus produces aflatoxin, a potent carcinogen.
Neurospora crassa is used in genetics research.
Penicillium produces penicillin.
Dermatophytes, such as Trichophyton, Microsporum, and Epidermophyton, cause skin infections.
Blastomyces dermatitidis causes blastomycosis, a respiratory infection.
Histoplasma capsulatum causes histoplasmosis, another respiratory infection.
Coccidioides immitis causes Valley fever.
Candida albicans causes yeast infections.
Saccharomyces yeasts are unicellular and used in brewing.

Basidiomycota

Basidiomycota have basidia that produce basidiospores.
They are important decomposers and food sources.
Cryptococcus neoformans can cause serious lung infections.
Agricus campestris is an edible mushroom.
Amanita phalloides is a poisonous mushroom known as the death cap.

Microsporidia

Microsporidia are unicellular, obligate intracellular parasites.
They lack mitochondria, peroxisomes, and centrioles.
They have a polar tubule that allows them to enter host cells.
Microsporidiosis is caused by microsporidia infections.

Basidiomycota

Produce deadly toxins
Important differences in fungal cells can be targets for antifungal medications
Similarities between human and fungal cells make it difficult to find medication targets which results in toxic adverse effects

Protists

Vary in how they get their nutrition, morphology, method of locomotion, and method of reproduction
Important structures include contractile vacuoles, cilia, flagella, pellicles, and pseudopodia
Some lack organelles such as mitochondria
The taxonomy of protists is changing rapidly
Include important pathogens and parasites

Parasitic Helminths

Often identified by looking for microscopic eggs and larvae
Two major groups: roundworms (Nematoda) and flatworms (Platyhelminthes)
Nematodes are common intestinal parasites often transmitted through undercooked foods
Platyhelminths include tapeworms and flukes often transmitted through undercooked meat

Fungi

Diverse saprotrophic eukaryotic organisms with chitin cell walls
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

Algae

Diverse group of photosynthetic eukaryotic protists
May be unicellular or multicellular
Large, multicellular algae are called seaweeds
Have little pathogenicity, but can be associated with toxic algal blooms
Can contaminate seafood with toxins
Important for producing agar and carrageenan.

Lichens

Symbiotic association between a fungus and an algae or a cyanobacterium
Symbiotic association is currently considered to be a controlled parasitism
Slow growing and can live for centuries in a variety of habitats
Environmentally important, helping to create soil, providing food, and acting as indicators of air pollution

Viral Classification

The International Committee on Taxonomy of Viruses (ICTV) classifies viruses into seven orders, 96 families, and 350 genera.
Viral family names end in "-viridae" (e.g., Parvoviridae) and genus names end in "-virus" (e.g., Parvovirus).
Viral orders, families, and genera are italicized.
Viral species are often referred to using a genus and species epithet (e.g., Pandoravirus dulcis or Pandoravirus salinus).

Baltimore Classification System

An alternative classification system to ICTV nomenclature.
Classifies viruses based on their genomes (DNA or RNA, single or double stranded, and mode of replication).
Creates seven groups of viruses with common genetics and biology.

Informal Virus Grouping

Viruses are often grouped informally based on chemistry, morphology, or other shared characteristics.
Examples include:
- Naked or enveloped structure
- Single-stranded (ss) or double-stranded (ds) DNA or ss or ds RNA genomes
- Segmented or nonsegmented genomes
- Positive-strand (+) or negative-strand (−) RNA

Common Pathogenic Viruses

dsDNA, enveloped
- Family: Poxviridae
  - Example Virus: Orthopoxvirus - Skin papules, pustules, lesions
  - Example Virus: Parapoxvirus - Skin lesions
- Family: Herpesviridae
  - Example Virus: Simplexvirus - Cold sores, genital herpes, sexually transmitted disease
- Family: Adenoviridae
  - Example Virus: Atadenovirus - Respiratory infection (common cold)
- Family: Papillomaviridae
  - Example Virus: Papillomavirus - Genital warts, cervical, vulvar, or vaginal cancer
dsDNA, naked
- Family: Papillomaviridae
  - Example Virus: Papillomavirus - Genital warts, cervical, vulvar, or vaginal cancer
- Family: Reoviridae
  - Example Virus: Reovirus - Gastroenteritis, severe diarrhea (stomach flu)
ssDNA, naked
- Family: Parvoviridae
  - Example Virus: Adeno-associated dependoparvovirus A - Respiratory tract infection
  - Example Virus: Adeno-associated dependoparvovirus B - Respiratory tract infection
dsRNA, naked
- Family: Reoviridae
  - Example Virus: Rotavirus - Gastroenteritis
+ssRNA, naked
- Family: Picornaviridae
  - Example Virus: Enterovirus C - Poliomyelitis
  - Example Virus: Rhinovirus - Upper respiratory tract infection (common cold)
  - Example Virus: Hepatovirus - Hepatitis
+ssRNA, enveloped
- Family: Togaviridae
  - Example Virus: Alphavirus - Encephalitis, hemorrhagic fever
  - Example Virus: Rubivirus - Rubella
- Family: Retroviridae
  - Example Virus: Lentivirus - Acquired immune deficiency syndrome (AIDS)
−ssRNA, enveloped
- Family: Filoviridae
  - Example Virus: Zaire Ebolavirus - Hemorrhagic fever
- Family: Orthomyxoviridae
  - Example Virus: Influenzavirus A, B, C - Flu
- Family: Rhabdoviridae
  - Example Virus: Lyssavirus - Rabies

International Classification of Diseases (ICD)

A standard taxonomy of disease maintained by the World Health Organization (WHO).
Assigns alphanumeric codes to viral infections, other diseases, medical conditions, and causes of death.
Used to categorize patient conditions for treatment, insurance reimbursement, and epidemiological research.

Rabies Diagnosis and Treatment

Prickling and itching at the site of a dog bite can be early symptoms of rabies.
Rabies diagnosis in live patients involves blood, saliva, and skin testing.
Immunofluorescent staining on skin biopsies detects rabies antibodies in cutaneous nerves.
Serum samples are tested for rabies virus antibodies.
Reverse transcriptase-polymerase chain reaction (RT-PCR) on saliva samples detects viral RNA.
Prophylactic treatment with human rabies immunoglobulin and rabies vaccines is given if rabies antigens are detected in blood.

Viral Life Cycle

Viruses require host cells for reproduction and metabolic processes.
Viruses can commandeer cellular machinery to produce more viral particles.

Bacteriophage Life Cycle

Lytic cycle:
- Attachment - Phage binds to specific bacterial surface receptors.
- Entry or penetration - Phage injects its genome into the cell.
- Biosynthesis - Virus replicates, transcribes, and translates viral components.
- Maturation - New virions are assembled.
- Release - Mature viruses burst out of the host cell, releasing progeny viruses.
Lysogenic cycle:
- Phage genome integrates into the bacterial chromosome, becoming a prophage.
- Prophage replicates with the bacterial genome.
- Induction can trigger the phage to excise from the host chromosome and enter the lytic cycle.

Transduction

Transfer of bacterial DNA from one bacterium to another by bacteriophages.
Generalized transduction: Random piece of bacterial chromosomal DNA transferred during the lytic cycle.
Specialized transduction: Specific piece of bacterial DNA near the site of phage integration transferred during the lysogenic cycle.

Animal Virus Life Cycle

Lytic animal viruses follow similar infection stages as bacteriophages: attachment, penetration, biosynthesis, maturation, and release.
Penetration occurs through endocytosis or membrane fusion.
Viruses are often host specific and exhibit tissue tropism.

Unique Virus Characteristics

Retroviruses: RNA viruses that use reverse transcriptase to convert their RNA genome into DNA, which can then integrate into the host genome.
Latent viruses: Viruses that can remain dormant within a host cell for long periods without causing symptoms.

Virus-Host Cell Interactions

Viruses can have a variety of effects on host cells:
- Lysis: Destruction of the host cell.
- Latency: Dormant infection without symptoms.
- Chronic infection: Persistent infection with ongoing symptoms.
- Transformation: Conversion of a normal host cell into a cancerous cell.

Plant Virus Replication

Plant viruses replicate in the cytoplasm.
They often spread through plant tissues through plasmodesmata.

Key Facts

Phage therapy can be used to target specific bacterial infections.
Lysogenic conversion can alter bacterial phenotypes.
Transduction contributes to bacterial evolution by exchanging genetic information.
Animal viruses can exploit host cell machinery for replication.### Virus Genome Types
Three types of RNA genome: dsRNA, +ssRNA, and −ssRNA.
+ssRNA can be translated directly by host ribosomes to make viral proteins.
−ssRNA needs to be replicated into +ssRNA by viral RdRP before being translated.
RdRP is crucial for dsRNA virus replication, using the negative strand as a template to create +ssRNA.
Newly synthesized +ssRNA copies can be translated by cellular ribosomes.

Retrovirus Nucleic Acid Synthesis

Retroviruses are +ssRNA viruses with a unique enzyme called reverse transcriptase.
Reverse transcriptase synthesizes a complementary ssDNA (cDNA) copy using the +ssRNA genome.
ssDNA is converted into dsDNA and integrates into the host chromosome as a provirus.
Provirus becomes a permanent part of the host genome, establishing a chronic infection.

Persistent Infection

Occurs when a virus is not completely eliminated and stays in certain tissues or organs.
May remain silent or undergo productive infection without seriously harming the host.
Two main types: latent infection and chronic infection.

Latent Infection

Virus remains hidden or dormant inside the cell.
Often causes initial acute infection before becoming dormant.
Example: varicella-zoster virus (chickenpox and shingles).
May exist as circular viral genome molecules or integrate into the host genome (provirus).
Difficult to detect during dormancy and may be asymptomatic.

Chronic Infection

Persistent symptoms over a long time.
Occurs when the body cannot eliminate the virus.
Examples: HIV, hepatitis C virus.
Virus interferes with immune function through various mechanisms: preventing antigen expression, altering immune cells, restricting gene expression, rapid antigen mutation.

Plant Viruses

Similar to animal viruses, can be enveloped or non-enveloped, DNA or RNA.
Majority have +ssRNA genome similar to mRNA.
Host range can be narrow or broad.
Transmission via contact, fungi, nematodes, insects, or wounds.
Biotrophic parasites, establishing infections without killing the host.
Infection can be asymptomatic (latent) or lytic (cell death).

Viral Growth Curve

Different from bacterial growth curve, does not follow a sigmoidal pattern.
Initial stage: inoculum of virus causes infection.
Eclipse phase: viruses bind and penetrate cells, no virions detected in the medium.
Burst: virions released from lysed host cells simultaneously, leading to a steep rise in viral titer.
Decline: viral particles degrade if no viable host cells remain.

Ebola Virus

Incurable and deadly, no approved treatments or vaccines.
Incubation time: 2 to 21 days.
Transmission via direct contact with bodily fluids.
Contagious during symptomatic stage.
Quarantine and contact tracing are crucial to prevent spread.

Virus Isolation and Cultivation

Viruses require living host cells for replication.
Infected host cells can be cultured and grown.
Virions can be separated from host cells by centrifugation or filtration.
Membrane filters remove larger particles, allowing collection of viruses in the filtrate.

Virus Cultivation Techniques

In vivo: within a whole living organism (plant or animal).
In vitro: outside a living organism, in cells in an artificial environment.
Animal viruses require cells from a host animal or tissue culture.
In vivo: animal embryos, embryonated bird eggs, or whole animals.
Tissue tropism: viruses may need to be introduced to specific sites for growth.

Viral Infections

Viral infection can cause tissue damage, lesions, embryonic developmental disruption and death
Viruses can be cultured using chicken eggs, as well as other cells
Chicken eggs can be infected in different locations, including the chorioallantoic membrane, the amniotic cavity, and the yolk sac

Cell Cultures

Primary cell cultures: Freshly prepared from animal tissues, require a solid surface to grow, have a limited lifespan, and can be transferred to another vessel for continued growth
Continuous cell lines: Usually derived from transformed cells or tumors, can be subcultured many times or grown indefinitely, may not exhibit anchorage dependency, may have lost their contact inhibition, can grow in piles or lumps that resemble small tumors
HeLa cell line: An example of an immortal cell line, originally cultivated from tumor cells obtained from Henrietta Lacks, was used to establish tissue culture as an important technology for research in cell biology, virology, and medicine

Detection of a Virus

Cytopathic effects (CPEs): Observable cell abnormalities due to viral infection, examples include loss of adherence, changes in cell shape, shrinkage of nucleus, vacuoles in the cytoplasm, fusion of cytoplasmic membranes, inclusion bodies, and complete cell lysis
Serological assays: Used to detect the presence of certain types of viruses in patient serum, serum is the liquid fraction of blood plasma from which clotting factors have been removed
Hemagglutination assay: A direct serological assay used to detect specific types of viruses in a patient sample, involves agglutination (clumping) of red blood cells, many viruses have hemagglutinins on their surface proteins that can bind to receptors on the membranes of erythrocytes and cause them to agglutinate
Hemagglutination inhibition (HAI) assays: Indirect assays using antibodies to detect specific viruses, antibodies bind to hemagglutinins, preventing erythrocytes from interacting with the virus, agglutination is inhibited
Nucleic acid amplification tests (NAAT): Widely used to detect unique nucleic acid sequences of viruses in patient samples, NAATs are used for molecular biology research
Polymerase chain reaction (PCR): An NAAT used to detect the presence of viral DNA in a patient's tissue or body fluid sample, amplifies (makes many copies) of a viral DNA segment of interest, short nucleotide sequences called primers bind to specific sequences of viral DNA, helping identify the virus
Reverse transcriptase-PCR (RT-PCR): An NAAT used to detect the presence of RNA viruses, uses reverse transcriptase (RT) to make a DNA copy (cDNA) from viral RNA, and then amplifies the cDNA by PCR
Enzyme immunoassays (EIAs): Used to detect viral antigens, rely on the ability of antibodies to detect and attach to specific biomolecules (antigens)
EIA process: Detecting antibodies attach to the target antigen with high specificity, a colorless enzyme is attached to the detecting antibody and acts as a tag, the enzyme interacts with a colorless substrate and produces a colored end product, EIAs often use layers of antibodies to capture and react with antigens, all of which are attached to a membrane filter
Western blot: A more sensitive test that can be used as confirmation for positive EIAs
NAAT: A highly sensitive test that can be used as confirmation for positive EIAs

Viroids

Discovered in 1971 by Theodor Diener, a pathologist working at the Agriculture Research Service
Consist only of a short strand of circular RNA capable of self-replication, do not have a protein coat
Cause diseases in plants, including potato tuber spindle disease, tomato planta macho viroid, avocado sunblotch viroid, and peach latent mosaic viroid

Metabolism

Metabolism encompasses all chemical reactions within a cell, responsible for building and breaking down complex molecules.
Anabolism is the process of building complex molecules from simpler ones, requiring energy input.
Catabolism is the breakdown of complex molecules into simpler ones, releasing energy.
Cells balance anabolism and catabolism to maintain energy levels.

Classifying Organisms

Organisms are classified based on their carbon and energy sources.
Autotrophs use inorganic carbon dioxide (CO2) to produce organic carbon compounds.
Heterotrophs rely on organic carbon compounds initially produced by autotrophs.
Phototrophs get energy for electron transfer from light.
Chemotrophs obtain energy for electron transfer from breaking chemical bonds.
Organotrophs obtain energy from organic compounds.
Lithotrophs get energy from inorganic compounds like hydrogen sulfide.

Oxidation-Reduction Reactions

Transferring electrons between molecules drives energy use in cells.
Oxidation removes electrons from a molecule, leaving it oxidized.
Reduction adds electrons to a molecule, leaving it reduced.
Oxidation and reduction occur together in redox reactions.

Energy Carriers

Electron carriers bind to and shuttle high-energy electrons in metabolic pathways.
NAD+/NADH and FAD/FADH2 are used in energy extraction, while NADP+/NADPH is important in anabolic reactions.
ATP is the cell's energy currency, used to drive endergonic reactions.
Breaking high-energy phosphate bonds in ATP releases energy, ATP is regenerated through phosphorylation.

Enzymes as Catalysts

Enzymes are protein catalysts that speed up biochemical reactions.They lower activation energy, making reactions occur faster.
Enzymes bind to reactants called substrates at their active site, a specific region with a unique chemical environment for substrate binding.
The induced-fit model describes how an enzyme changes shape upon substrate binding to enhance its fit.
Enzymes are highly specific to their substrates and are influenced by environmental factors like temperature and pH.

Enzyme Helpers

Cofactors are inorganic ions like magnesium (Mg2+) that help stabilize enzyme structure and function.
Coenzymes are organic helper molecules often derived from vitamins, facilitating enzyme activity.
Apoenzyme is an inactive enzyme without its necessary cofactor or coenzyme.
Holoenzyme is an active enzyme with its associated cofactor or coenzyme.

Enzyme Inhibition

Competitive inhibitors are molecules similar to a substrate that can compete for binding to the active site, blocking substrate access.
Noncompetitive inhibitors bind to a site other than the active site, changing the enzyme's shape and preventing proper substrate binding.### Enzyme Regulation
Allosteric inhibitors bind to an enzyme at a site other than the active site.
Allosteric inhibitors induce a conformational change in the enzyme, reducing its affinity for the substrate.
Allosteric activators bind to an enzyme at a site other than the active site, increasing the enzyme's affinity for the substrate.
Feedback inhibition occurs when a pathway product acts as an allosteric inhibitor of an enzyme earlier in its pathway.
Feedback inhibition regulates the production of specific molecules by slowing down the production of a pathway product when it becomes abundant.

Glycolysis

Glycolysis is the most common pathway for glucose catabolism.
Glycolysis occurs in the cytoplasm of prokaryotic and eukaryotic cells.
Glycolysis does not require oxygen.
Glycolysis produces two molecules of pyruvate from one glucose molecule.
Glycolysis can be coupled with aerobic or anaerobic respiration.
The Embden-Meyerhof-Parnas (EMP) pathway consists of two phases: the energy investment phase and the energy payoff phase.
The energy investment phase uses two ATP molecules to modify glucose, producing two glyceraldehyde 3-phosphate (G3P) molecules.
The energy payoff phase extracts energy from G3P, producing four ATP molecules, two NADH molecules, and two pyruvate molecules.
ATP is produced during glycolysis by substrate-level phosphorylation.

Alternative Glycolytic Pathways

The Entner-Doudoroff (ED) pathway is an alternative glycolytic pathway used by some prokaryotes.
The pentose phosphate pathway (PPP) produces intermediates used for nucleotide and amino acid biosynthesis.

Transition Reaction, Coenzyme A, and the Krebs Cycle

Pyruvate is decarboxylated to a two-carbon acetyl group in the transition reaction (a.k.a., the bridge reaction).
The transition reaction occurs in the mitochondrial matrix of eukaryotes and the cytoplasm of prokaryotes.
Acetyl groups attach to coenzyme A (CoA) to enter the Krebs cycle.
The Krebs cycle is a closed loop that regenerates the compound used in the first step.
The Krebs cycle produces two CO2 molecules, one ATP molecule (or GTP), three NADH molecules, and one FADH2 molecule per turn.

Cellular Respiration

Cellular respiration uses the electron transport system (ETS) to generate ATP through oxidative phosphorylation.
The ETS is a series of membrane-associated protein complexes and associated mobile accessory electron carriers.
Electrons from NADH and FADH2 are passed through the ETS to a final electron acceptor.
The final electron acceptor in aerobic respiration is oxygen (O2), which is reduced to water (H2O).
Anaerobic respiration uses an inorganic molecule other than oxygen as a final electron acceptor.

Chemiosmosis, Proton Motive Force, and Oxidative Phosphorylation

The ETS pumps hydrogen ions (H+) across a membrane, creating a proton motive force (PMF).
The PMF is used by ATP synthase to produce ATP through oxidative phosphorylation.
Chemiosmosis is the movement of H+ ions across a membrane through ATP synthase.

ATP Synthase

ATP synthase is a membrane-bound enzyme complex that uses the PMF to produce ATP.
ATP synthase is found in the plasma membrane of prokaryotes and the inner mitochondrial membrane of eukaryotes.### ATP Synthase
ATP synthase is a protein that functions like a tiny generator powered by the flow of hydrogen ions (H+) down their electrochemical gradient.
In prokaryotic cells, H+ flows from the outside of the cytoplasmic membrane into the cytoplasm.
In eukaryotic cells, H+ flows from the intermembrane space to the mitochondrial matrix.
The rotation of ATP synthase regenerates ATP from ADP and inorganic phosphate (Pi) through oxidative phosphorylation.

ATP Production

The passage of electrons from one molecule of NADH generates enough proton motive force to produce three ATP molecules.
The passage of electrons from one molecule of FADH2 generates enough proton motive force to produce two ATP molecules.
The theoretical maximum yield of ATP during the complete aerobic respiration of glucose is 38 molecules.

Fermentation

Fermentation is an anaerobic process that does not require oxygen and reoxidizes NADH to NAD+ for reuse in glycolysis.
Fermentation does not directly produce any additional ATP beyond that produced during glycolysis.
Fermenters produce a maximum of two ATP molecules per glucose during glycolysis.

Lactic Acid Fermentation

Lactic acid fermentation, carried out by bacteria like those found in yogurt and sour foods, is key for producing lactic acid.
Bacteria of several genera, including Lactobacillus, Leuconostoc, and Streptococcus, are known as lactic acid bacteria (LAB).
Homolactic fermentation produces only lactic acid, while heterolactic fermentation produces lactic acid, ethanol, acetic acid, and CO2.

Alcohol Fermentation

Alcohol fermentation produces ethanol and is carried out by yeast like Saccharomyces cerevisiae.
The process involves the conversion of pyruvate to acetaldehyde and then to ethanol.
Alcohol fermentation is used in the production of alcoholic beverages and bread.

Other Fermentation Pathways

Various other fermentation pathways exist in prokaryotes to provide NAD+ for glycolysis.
These pathways often produce gas, such as CO2 and hydrogen gas.
Fermentation products are used in the production of various food products and commercial products.

Identifying Bacteria through Fermentation

Different bacteria can be identified based on their ability to ferment specific substrates or produce unique fermentation products.
Biochemical test panels, like the API test panel, can rapidly identify bacteria based on their metabolic profiles.
Fermenting sugars like lactose, sorbitol, and mannitol can distinguish different bacterial strains.

Lipid Catabolism

Lipids are a form of long-term energy storage in animals.
Composed of glycerol and three fatty acids.
Phospholipids compose the cell and organelle membranes of all organisms except the archaea.
Triglycerides and phospholipids are broken down by releasing fatty acid chains.
The reactions breaking down triglycerides are catalyzed by lipases.
Those involving phospholipids are catalyzed by phospholipases.
Lipases and phospholipases contribute to the virulence of certain microbes like Staphylococcus aureus and Cryptococcus neoformans.
Glycerol can be phosphorylated to glycerol-3-phosphate and easily converted to glyceraldehyde 3-phosphate.
Glyceraldehyde 3-phosphate continues through glycolysis.
Fatty acids are catabolized in a process called β-oxidation.
β-oxidation sequentially removes two-carbon acetyl groups from the ends of fatty acid chains.
Acetyl groups produced during β-oxidation are carried by coenzyme A to the Krebs cycle.

Protein Catabolism

Proteins are degraded through the concerted action of a variety of microbial protease enzymes.
Extracellular proteases cut proteins internally at specific sequences, breaking them into smaller peptides.
Some pathogens can be identified by their ability to produce a specific type of extracellular protease.
Gelatinase is produced by Proteus and Serratia.
Caseinase, which degrades casein, is produced by Pseudomonas aeruginosa.
Peptides are broken down further into individual amino acids by additional intracellular proteases.
Each amino acid can be enzymatically deaminated to remove the amino group.
The remaining molecules enter the transition reaction or the Krebs cycle.

Photosynthesis

Photosynthesis is the biochemical process by which phototrophic organisms convert solar energy into chemical energy.
Photosynthesis takes place in two stages: the light-dependent reactions and the light-independent reactions.
Light-dependent reactions convert light energy into stored chemical energy.
Light-independent reactions use the chemical energy to assemble sugar molecules using CO2.
Light-dependent reactions produce ATP and either NADPH or NADH.
These energy carriers are used in the light-independent reactions to fix inorganic CO2 in an organic form.

Photosynthetic Structures

In eukaryotes, photosynthesis takes place inside chloroplasts.
Chloroplasts are enclosed by a double membrane.
The thylakoids, stacked disc-shaped structures within the chloroplast, are the sites of photosynthesis.
In prokaryotes, photosynthetic membranes are infolded regions of the plasma membrane.

Photosynthetic Pigments

Photosynthetic pigments are organized into photosystems.
Photosystems consist of a light-harvesting complex and a reaction center.
The light-harvesting complex absorbs light energy and transfers it to the reaction center.
Different light-harvesting pigments absorb unique wavelengths.
The reaction center contains a pigment molecule that can undergo oxidation upon excitation.
Different types of photosynthetic bacteria are optimized for harvesting the wavelengths of light to which they are commonly exposed.

Oxygenic and Anoxygenic Photosynthesis

In oxygenic photosynthesis, water is split, providing electrons for the reaction center and generating oxygen as a byproduct.
Anoxygenic photosynthesis uses other reduced compounds as electron donors.
These types of photosynthesis do not produce oxygen.
Two light reactions, rather than one, are required to split water and capture energy.
Joan Mary Anderson demonstrated the existence of two types of photosystems: photosystem I (PSI) and photosystem II (PSII).
Cyanobacteria and plant chloroplasts have both photosystems.
Anoxygenic photosynthetic bacteria use only one photosystem.

Noncyclic and Cyclic Photophosphorylation

Noncyclic photophosphorylation occurs when both ATP and NADPH are required.
The electron flow in this process is called the Z-scheme.
Cyclic photophosphorylation occurs when the cell's need for ATP outweighs the need for NADPH.
Only PSI is used during cyclic photophosphorylation.

Light-Independent Reactions

The Calvin-Benson cycle is the biochemical pathway used for fixation of CO2.
The Calvin cycle is located within the cytoplasm of photosynthetic bacteria and in the stroma of eukaryotic chloroplasts.
The three main stages of the Calvin cycle are fixation, reduction, and regeneration.
The enzyme ribulose bisphosphate carboxylase (RuBisCO) catalyzes the addition of a CO2 to ribulose bisphosphate (RuBP).
Six molecules of both ATP and NADPH are used to convert 3-PGA into glyceraldehyde 3-phosphate (G3P).
The remaining G3P not used to synthesize glucose is used to regenerate RuBP.
RuBisCO is the most plentiful enzyme on Earth.
The Calvin cycle is also used by many nonphotosynthetic chemoautotrophs to fix CO2.

Biogeochemical Cycles

Microorganisms are vital for the biogeochemical cycles of carbon, nitrogen, and sulfur.
Bioremediation uses microorganisms to remove pollutants from the environment.

Carbon Cycle

The carbon cycle is a constant exchange of CO2 between heterotrophs (which produce CO2 during respiration or fermentation) and autotrophs (which use CO2 for carbon fixation).
Methanotrophs are bacteria and archaea that use methane as their carbon source.
Methanogens are archaea that produce methane as a byproduct of anaerobic respiration using CO2 as a terminal electron acceptor.

Nitrogen cycle

Prokaryotes play a key role in the nitrogen cycle, transforming nitrogen between different forms.
Nitrogen fixation is the process of converting atmospheric nitrogen (N2) into ammonia (NH3) by certain bacteria and archaea, making it usable by other organisms.
The three main steps in nitrogen conversion back to atmospheric nitrogen are: ammonification, nitrification, and denitrification
Ammonification involves the conversion of nitrogenous waste into ammonia.
Nitrification involves the oxidation of ammonia (NH3) to nitrite (NO2-) and then to nitrate (NO3-) by bacteria.
Denitrification involves the conversion of nitrate (NO3-) into nitrogen gas (N2) by bacteria using nitrate as an electron acceptor.

Sulfur Cycle

Anoxygenic photosynthetic bacteria and chemoautotrophic archaea and bacteria use hydrogen sulfide (H2S) as an electron donor, oxidizing it to elemental sulfur (S0) and then sulfate (SO42-).
The sulfur cycle also involves decomposition of dead organisms by fungi and bacteria, which release hydrogen sulfide back into the environment.

Bioremediation

Bioremediation is the use of microorganisms to remove pollutants from the environment.
Xenobiotics are compounds synthesized by humans that can contaminate the environment and are often difficult to break down.
In situ bioremediation takes place at the site of contamination, without moving the contaminated material.
Ex situ bioremediation involves the removal of contaminated material to a controlled environment for treatment.
Enhanced bioremediation techniques may involve adding nutrients, air, or specific microbes to increase the efficiency of microbial degradation.
Surfactants produced by some bacteria help break down hydrophobic molecules like those found in oil, making them easier for other microbes to degrade.

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Explore the significant contributions of Marcus Terentius Varro, Abū Bakr al-Rāzī, and Ibn Sina to the field of microbiology. This quiz examines their groundbreaking ideas on disease causation, medical treatments, and the foundations of preventive medicine. Test your knowledge on how their works impacted medical practices and education throughout history.

Microbiology Contributions by Romans and Muslims

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Questions and Answers

What concept regarding disease did Marcus Terentius Varro propose?

What innovative method did Abū Bakr al-Rāzī use to determine the ideal location for a hospital?

What notable distinction did al-Razi make in his medical studies?

What was one of the main contributions of Ibn Sina (Avicenna) in his work, the Canon of Medicine?

Which practice did Ibn Sina advance that has influenced contemporary methods?

Why is the Canon of Medicine considered an important medical text worldwide?

What did Varro suggest about certain creatures found in swamps?

Which civilization's scholars significantly built upon the medical understandings of earlier cultures, including those of Hippocrates?

What is the primary purpose of growth media in microbiology?

Which of the following best describes a Petri dish?

What must occur before using an inoculation loop to transfer microorganisms?

Why have many labs phased out the use of Bunsen burners?

Which factor influences the effectiveness of certain stains on microbes?

What are test tubes primarily used for in microbiology labs?

Which of the following is a key ingredient in most growth media?

What is the role of a rubber tube in a Bunsen burner setup?

What is the shape of bacteria that are typically described as spherical?

Which of the following is a characteristic of archaeal cell walls?

Some bacteria are photosynthetic. Which of the following is NOT an example mentioned?

What major characteristic distinguishes eukaryotes from prokaryotes?

Which type of bacteria is a combination of spherical and rod shapes?

Which of the following statements about archaea is true?

Which of the following types of bacteria are nonphotosynthetic?

What general shape is a bacteria described as rod-shaped?

What is the primary function of Bergey’s Manual of Determinative Bacteriology?

Why are biochemical tests essential in bacterial identification?

What role does DNA and rRNA sequencing play in bacteriology?

What is a significant characteristic of different strains within the same species of microorganism?

What is one common source of E.coli O157:H7 infection in humans?

Which of the following statements about E.coli strains is true?

How have Bergey’s manuals evolved since their first publication?

What is the purpose of serological tests in bacterial identification?

Which of the following accurately defines protozoa?

What is binomial nomenclature used for?

Which of these organisms is NOT a unicellular microorganism?

Who is known for proposing the addition of a kingdom for protists?

Which phylogenetic tree classification includes five kingdoms?

What organism requires a host to reproduce?

What characteristic does NOT apply to viruses?

What is the primary focus of microbiologists?

What historical evidence suggests about early human interactions with fermentation?

Which type of microorganism is often too small to be seen without a microscope?

What method was primarily used to collect cerebrospinal fluid for testing?

What characteristic defines microorganisms or microbes?

Which of the following fermented products has been made by humans for thousands of years?

During which period did humans first likely develop fermented beverages, according to archaeological findings?

What can cloudy cerebrospinal fluid indicate about a patient's health?

What crucial role did early knowledge of microorganisms play in human civilization?

What role do microorganisms play in ecosystems?

How did our ancestors utilize invisible microbes to enhance food?

Which statement regarding the history of microbiology is accurate?

What is a significant benefit associated with Alcanivorax borkumensis after the Deepwater Horizon oil spill?

What proportion of microorganisms typically reside on human skin?

Which of the following best describes the majority of microorganisms in terms of their effect on humans?

In what way are microbiologists expanding our knowledge of microbial life?

What type of microorganisms are critical for the production of food items like bread, cheese, and beer?

What significant difference led to the classification of organisms into three domains by Woese and Fox?

Which group of organisms is most closely related based on the findings of the phylogenetic tree?

What complicates the determination of evolutionary relationships among organisms?

What does the concept of 'webs of life' imply for scientists studying evolution?

Which of the following accurately describes the naming system developed by Linnaeus?

In binomial nomenclature, how is the genus name presented?

Why do scientists emphasize rRNA in the classification of organisms?

What part of the scientific name for an organism is not capitalized in binomial nomenclature?

What differentiates various strains within the same species of microorganism?

Which method is primarily used to identify specific proteins in bacteria during serological tests?

How does Bergey’s Manual contribute to bacteriology?

Which characteristic does NOT help in the identification of bacteria?

Which statement is true regarding the pathogenic strains of E.coli?

Which method can establish the classification of newly discovered bacterial species?

What is the primary application of biochemical tests in bacteriology?

What major benefit does binomial nomenclature provide in microbiology?

Which unit of length is equivalent to one millionth of a meter?

What key feature distinguishes prokaryotic microorganisms from eukaryotic microorganisms?

What structural component is commonly found in the cell walls of most bacteria?

Which of the following domains contains microorganisms that are entirely acellular?