Microbio Module 1-3

Causative agent of TB

Mycobacterium tuberculosis

Hemoptysis

Coughing up blood

Sputum sample

A mix of saliva and mucus from the respiratory tract

Signs

Observable, objectively measurable health issues such as a rash or blood pressure

Symptoms

Subjective feelings reported by the patient such as fatigue or nausea

Microbe

An organism of microscopic or ultramicroscopic size requiring a microscope to be seen

Acellular microbes

Non-cellular infectious entities including viruses and prions

Prokaryotes

Simple single-celled microbes lacking a true nucleus and membrane-bound organelles

Eukaryotes

Complex microbes possessing a true membrane-bound nucleus and organelles

Robert Hooke

Built the first compound microscope and first used the term cells

Anton van Leeuwenhoek

First observed bacteria using a single-lens microscope

Louis Pasteur

Proved bacteria are living things capable of reproducing and causing disease

Germ Theory of Disease

The principle that specific diseases are caused by microscopic germs

Florence Nightingale

Used statistics to demonstrate the significance of mortality due to infectious disease

Bacillus anthracis

The bacterium that causes anthrax

Robert Koch

Developed postulates linking specific pathogens to specific diseases

Pure culture

A population of bacteria grown from a single colony

Antiseptics and Asepsis

Chemical treatments used to prevent infection during medical procedures

Monomer

A single subunit used as a building block for macromolecules

Carbohydrates

Primary energy sources formed from carbon and water molecules

Peptidoglycan

A structural carbohydrate-protein polymer forming bacterial cell walls

Amino acids

The 20 distinct monomer building blocks of proteins

Primary protein structure

The linear sequence of amino acids held by peptide bonds

Secondary protein structure

Local coiling and folding into alpha helices and beta sheets

Tertiary protein structure

A unique three-dimensional shape formed by hydrogen bonds

Quaternary protein structure

Functional complexes formed by multiple protein chains together

Triglycerides

Long-term energy storage lipids composed of glycerol and three fatty acids

Phospholipids

Lipids that make up the primary structure of cell membranes

Nucleotides

Monomers composed of a five-carbon sugar, phosphate group, and nucleobase

mRNA

Messenger RNA transcribed from DNA to encode genetic information

Protozoa

Unicellular eukaryotic microbes that include amoebas and flagellates.

Dimorphic fungi

Fungi that can switch between a yeast form and hyphae based on environmental needs.

Helminths

Parasitic worms divided into nematodes, trematodes, and cestodes.

Arthropods

Invertebrate animals with an exoskeleton and jointed appendages that can act as disease vectors.

Entamoeba histolytica

An amoeba causing amebic dysentery, characterized by ingested red blood cells.

Giardia lamblia

A flagellated protozoal parasite transmitted via contaminated water, causing giardiasis.

Cestodes

Parasitic flatworms known as tapeworms that absorb nutrients through their skin.

Major bacterial shapes

Cocci (round), bacilli (rod), and spirilla (spiral).

Gram-positive cell wall

Thick, multiple layers of peptidoglycan that retain purple dye.

Gram-negative outer membrane

Contains lipopolysaccharides (LPS) and Lipid A, acting as an endotoxin.

Coupled transport

The use of energy from one gradient to drive transport up another.

Acid-fast stain

Specialized stain used for mycobacteria with hydrophobic mycolic acid walls.

Chemotaxis

The rotation of flagella to propel cells in response to stimuli.

Endospores

Dormant, highly resistant structures formed by bacteria like Bacillus and Clostridium to survive harsh environmental conditions.

Bacterial plasmids

Small, circular DNA molecules separate from the bacterial chromosome that often carry advantageous genes such as antibiotic resistance.

Biofilms

Structured microbial communities encased in an extracellular polymeric matrix that adhere to surfaces and resist immune clearance and disinfection.

Viral replication cycle

The sequential stages of viral infection: attachment, penetration, uncoating, macromolecular synthesis, assembly, and release.

Lytic vs. lysogenic cycles

Lytic phages destroy host cells immediately, whereas lysogenic phages integrate their DNA into the host chromosome as a dormant prophage.

Prions

Infectious proteinaceous particles lacking nucleic acids that cause fatal neurodegenerative diseases like Creutzfeldt-Jakob disease.

TB case: How was Kaylee infected, and what finding is a key clue to TB?

Answer: She acquired tuberculosis by inhaling airborne Mycobacterium tuberculosis—not from a handshake, a doorknob, or sharing a drink. Key clues are weeks of cough, fatigue, weight loss, hemoptysis (coughing up blood), and a cavitary lung lesion on X-ray. The appropriate diagnostic specimen for a respiratory TB infection is sputum (a saliva/mucus mixture from the lower respiratory tract).

TB case: What test identified the organism, what drugs are first-line in this case, and what does MDR-TB mean?

Answer: PCR amplified a DNA sequence from the sputum and identified M. tuberculosis. The lecture's first-choice therapy is isoniazid plus rifampin. MDR-TB means multidrug-resistant TB: the strain is resistant to multiple antimicrobial drugs, so standard therapy may fail. In the case, resistance was severe enough that part of the lung had to be removed.

Why were so many people screened after Kaylee's diagnosis?

Answer: TB spreads through inhalation of infectious airborne particles, so close contacts can become infected even before they feel sick. A student had been misdiagnosed for two years, and more than 200 school contacts were infected. Screening and treatment of infected contacts helps prevent progression to active disease and interrupts further spread.

Differentiate a sign from a symptom. Classify: fever, rash, chest pain, fatigue, tachycardia, nausea.

Answer: A sign is objective and observable/measurable by another person (for example, fever, rash, vomiting observed by a clinician, blood pressure, or tachycardia). A symptom is a subjective experience reported by the patient (for example, chest pain, fatigue, nausea, feeling hot/cold, headache, or loss of taste/smell). On an exam, ask: "Could a clinician directly measure or observe it?"

What is a microbe, and why are microbes important even though some cause disease?

Answer: A microbe (microorganism) is an organism of microscopic or ultramicroscopic size; bacteria, protozoa, fungi, and algae are included. Viruses are debated because they are not cells. Most microbes are not "germs." They are environmentally and medically important: microbes bind nitrogen into plant-usable forms and produce vitamins that humans consume. Only a relatively small subset are pathogens.

What is the difference between cellular and acellular microbes?

Answer: Cellular organisms have a cell membrane or wall, cytoplasm, and genetic material in either a nucleus or nucleoid; eukaryotes also have membrane-bound organelles. Acellular agents include viruses and prions. Viruses have no organelles and cannot perform independent metabolism or reproduce independently; they must invade a host cell. A virion is the dormant, extracellular virus particle.

Compare prokaryotic and eukaryotic microbes.

Answer: Prokaryotes (bacteria and archaea) lack a true membrane-bound nucleus; DNA is in a nucleoid. They lack membrane-bound organelles but do have ribosomes, and they are smaller/simpler. Eukaryotic microbes (fungi, protozoa, helminths) have a membrane-bound nucleus, protected DNA, and organelles such as mitochondria, ER, Golgi, and ribosomes; they are larger and more metabolically complex.

Name the major clinically relevant microbial groups and classify each as cellular or acellular.

Answer: Cellular: bacteria (single-celled prokaryotes); fungi (yeasts/molds); protozoa (single-celled eukaryotes); helminths (parasitic worms); and arthropods as invertebrate vectors/ectoparasites. Acellular: viruses and prions. Bacteria are prokaryotic; fungi, protozoa, helminths, and arthropods are eukaryotic.

How is a microbial species named and what is a genome?

Answer: Scientific names use a capitalized genus followed by a lowercase species, both italicized: Staphylococcus aureus. Species are classified by shared genes and traits, especially genetic relatedness based on genome comparisons. A genome is the total DNA content of an organism.

Match these pioneers to their contribution: Hooke, van Leeuwenhoek, Pasteur, Koch, Nightingale, Semmelweis, Lister.

Answer: Hooke: first compound microscope and "cells" in cork. van Leeuwenhoek: observed bacteria using a single-lens microscope. Pasteur: disproved spontaneous generation and showed microbes reproduce. Koch: scientific method/postulates linking a microbe to disease. Nightingale: used statistics to show infectious-disease mortality. Semmelweis: antiseptic hand practices protect patients. Lister: chemical treatment of surgical instruments; helped establish aseptic operating rooms.

What was spontaneous generation, and how did Pasteur change microbiology?

Answer: Spontaneous generation was the idea that microbes arise spontaneously from nonliving material. Pasteur demonstrated that bacteria are living organisms capable of reproduction. This supported germ theory: specific microscopic germs can cause disease rather than disease arising spontaneously.

What is germ theory and how do public health/epidemiology use it?

Answer: Germ theory states that specific diseases are caused by microscopic germs. Public health examines infectious disease in populations, while epidemiology uses statistics to determine disease causes and patterns. In the U.S., the CDC monitors public health; for example, it tracks seasonal influenza and helps predict strains that should be included in vaccines.

What are Koch's four postulates?

Answer: 1) The microbe is abundant in diseased organisms and absent from healthy ones. 2) Isolate it from a diseased organism and grow it in pure culture. 3) The cultured microbe causes the same disease when introduced into a healthy host. 4) Re-isolate the same microbe from the newly diseased host. A pure culture comes from a single bacterial colony.

Why can Koch's postulates fail in real clinical practice?

Answer: Not every infection causes disease in every infected person: M. tuberculosis causes symptoms in only about 10% of infected people. Some pathogens are difficult to detect early, and some have only human hosts. Intentionally infecting humans with HIV to satisfy postulates would be unethical. Therefore, modern evidence can link pathogens and disease without completing every postulate.

How did the anthrax case demonstrate pathogen identification and treatment?

Answer: After handling dead cattle, Caleb developed a nodule with a purple ring and black eschar—classic cutaneous-anthrax clues. Serum testing detected antibodies to a bacterial antigen, confirming Bacillus anthracis. Ciprofloxacin, the lecture's standard treatment for cutaneous anthrax, was continued and he improved.

Name the four macromolecule families and explain polymerization.

Answer: The four families are carbohydrates, lipids, proteins, and nucleic acids. Polymerization joins monomers (single building units) into longer polymers. The lecture emphasizes that all macromolecule families are built by polymerization except lipids. Know the monomer/polymer relationship rather than simply listing terms.

What are the major functions and categories of carbohydrates?

Answer: Carbohydrates (CHO; hydrated carbon chains) are a major energy source, store energy, help form structural parts of DNA/RNA, and provide structural strength in cellulose and chitin. Monosaccharides: glucose, fructose, galactose. Disaccharides: sucrose = glucose + fructose; lactose = glucose + galactose. Polysaccharides: glycogen for stored energy, cellulose for structural fiber, chitin for arthropod exoskeletons.

How do NAG and NAM relate to bacterial cell walls and antibiotics?

Answer: N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) are modified carbohydrate units that form bacterial peptidoglycan. Peptidoglycan combines sugar chains with peptide links and gives the bacterial wall strength. The lecture notes that drugs such as vancomycin and bacitracin disrupt production/bonds involving these wall components, weakening or killing bacteria.

What are proteins made of? Distinguish peptide, polypeptide, and protein.

Answer: Proteins are predominant organic molecules in cells and are built from amino-acid monomers. Essential amino acids must be obtained from diet because the organism cannot make them; nonessential amino acids can be synthesized. A peptide is roughly 2-50 amino acids; a polypeptide is usually more than 50 amino acids and may be a protein subunit; a protein usually contains at least about 100 amino acids. DNA directs amino-acid sequence.

Describe the four levels of protein structure with examples.

Answer: Primary: linear amino-acid sequence held by peptide bonds ("string of pearls"). Secondary: local alpha helices or beta sheets; keratin is an alpha-helix example. Tertiary: one polypeptide's unique 3-D shape, stabilized in part by hydrogen bonds; examples include myoglobin and enzymes such as lipase. Quaternary: multiple protein subunits form one functional complex; examples include hemoglobin and antibodies.

What are the key lipid types and functions?

Answer: Lipids are organic molecules that form membranes and other cell components. Triglycerides store long-term energy: one glycerol plus three fatty acids, yielding about twice as much energy per gram as carbohydrates. Phospholipids form cell membranes. Steroids are ringed compounds involved in membranes and hormone backbones; cholesterol reinforces animal-cell membranes and occurs in certain bacteria. Waxes have an ester bond between a long-chain alcohol and saturated fatty acid.

Why are waxes/lipids clinically important in Mycobacterium?

Answer: The cell wall of Mycobacteria such as M. tuberculosis and M. leprae contains waxy, long-chain lipid material. This contributes to disease-causing potential and makes the envelope unusually resistant. In the bacteria lecture, the related mycolic-acid-rich envelope is highly hydrophobic and resists Gram staining, which is why acid-fast staining is used.

What is a nucleotide, and compare DNA and RNA?

Answer: A nucleotide contains a five-carbon sugar, phosphate group, and nitrogenous base. DNA is generally double-stranded, forms chromosomes, and encodes genetic information in genes. RNA transfers genetic information toward protein production. mRNA is transcribed from DNA, rRNA is part of the ribosome, and tRNA carries amino acids to mRNA. Influenza and HIV are examples of viruses with RNA genomes.

What are the three major bacterial shapes? Give key arrangement terms for bacilli.

Answer: Cocci are round/pearl-shaped, bacilli are rod-shaped, and spirilla are spiral-shaped. Bacilli can occur as a single bacillus, diplobacilli (pairs), streptobacilli (chains), or palisades. Variations in shape, number, and grouping create useful morphology terms. Other shapes shown include filamentous, star-shaped, and rectangular forms.

What structures make up the bacterial cell envelope?

Answer: The envelope includes the cell (plasma) membrane and peptidoglycan cell wall; Gram-negative bacteria also have an outer membrane. Cytoplasm is contained by the cell membrane. The cell wall lies outside it, and the Gram-negative outer membrane lies outside the wall. Do not call every outside layer a "cell wall"—the outer membrane is a distinct Gram-negative structure.

What is the bacterial nucleoid?

Answer: The nucleoid is the DNA-containing region of a bacterial cell. It is not enclosed by a nuclear membrane. The bacterial chromosome is organized within the cytoplasm as looped coils, with DNA-binding/bridging proteins helping organize it. Bacteria therefore have DNA but no true nucleus.

What is the bacterial plasma membrane made of and why is it essential?

Answer: It is a phospholipid bilayer with proteins and separates cytoplasm from the outside environment—thus defining the cell. Its proteins support external structures such as flagella/pili, signal and communicate, export toxins/virulence factors, transport substances, and establish concentration gradients for energy transfer.

Compare passive transport, active transport, and coupled transport.

Answer: Passive transport (diffusion/osmosis) moves substances down a concentration gradient and does not require energy input. Active transport uses ATP to move substances against a concentration gradient. Coupled transport uses energy released from movement down one gradient to move another substance up its gradient. Always state direction relative to the gradient on exam answers.

Differentiate symport from antiport; give the examples used in lecture.

Answer: Symport moves two molecules/ions in the same direction across a membrane; the lecture example is glucose plus Na+ or H+ moving into a cell. Antiport moves two molecules/ions in opposite directions; the sodium-potassium pump example pumps Na+ out while K+ moves in. Both are forms of coupled transport.

Describe peptidoglycan as a bacterial wall material.

Answer: The bacterial cell wall is a single, interlinked molecule enclosing the entire cell. It has parallel glycan chains (polymers of disaccharides) cross-linked by short peptides. This net-like structure provides physical strength; the lecture compares it to a chain-link fence. Its bacterial specificity makes it an important antibiotic target.

How do cell-wall antibiotics damage bacteria?

Answer: Penicillins, methicillin, and cephalosporins interfere with peptidoglycan repair/production, including peptide cross-bridge formation. Vancomycin blocks a different wall-assembly step. The result is a weakened wall that cannot resist forces on the cytoplasm; cell-wall damage or enzyme-driven hydrolysis can create holes and kill the bacterium. These drugs target bacterial wall features, not a human cell wall.

What are fixation and staining for?

Answer: Fixation and staining improve detection and resolution of microbial cells. Fixation kills cells and stabilizes the sample on the slide. Stains bind negative charges on the bacterial envelope and absorb visible light, creating contrast. A simple stain colors cells dark but not the background; methylene blue is the lecture example.

What is a differential stain and what does the Gram stain distinguish?

Answer: A differential stain makes two kinds of cells distinguishable. The Gram stain divides bacteria into Gram-positive and Gram-negative classes based on envelope/cell-wall properties. It is not merely a color test: the color outcome reflects whether the cell retains the crystal-violet-iodine complex after decolorization.

List the Gram-stain sequence and final colors.

Answer: 1) Fix cells. 2) Crystal violet primary stain. 3) Iodine, which forms a complex with crystal violet. 4) Decolorizer: Gram-positive cells retain the complex while Gram-negative cells lose it. 5) Safranin counterstain: Gram-positive cells remain dark purple; Gram-negative cells become pale red/pink. Learn both sequence and reason.

Compare Gram-positive and Gram-negative envelopes.

Answer: Gram-positive bacteria have a thick, multilayered peptidoglycan wall and no outer membrane; they retain purple Gram stain and are generally more directly affected by cell-wall-active antibiotics. Gram-negative bacteria have a thin peptidoglycan layer plus an outer membrane. They stain pink/red after safranin and are often harder for antibiotics to penetrate because of the added outer barrier.

Give examples associated with Gram-positive vs Gram-negative bacteria in lecture.

Answer: Gram-positive: Streptococcus, Staphylococcus, Clostridium (including C. diff), some Listeria, Bacillus anthracis, and Streptococcus pyogenes. Gram-negative: Escherichia coli, Pseudomonas aeruginosa (a hospital-associated pneumonia example), gonococci (gonorrhea), and meningococci (bacterial meningitis). Remember: morphology and Gram status are separate classification clues.

What is LPS and why can it worsen a patient after bacteria die?

Answer: Lipopolysaccharide (LPS) is in the outer leaflet of the Gram-negative outer membrane. It has lipid A plus polysaccharide chains. When Gram-negative cells lyse, lipid A acts as an endotoxin; therefore antibiotics may kill bacteria but release material that can contribute to endotoxic shock. The key association is Gram-negative outer membrane → LPS → lipid A endotoxin.

Why are Mycobacteria "acid-fast" rather than reliably Gram stained?

Answer: Mycobacteria have a complex envelope with peptidoglycan plus arabinogalactan and long-chain mycolic acids. The lipid-rich, extremely hydrophobic material resists Gram-stain penetration. Acid-fast staining is used instead. Clinically important examples are Mycobacterium tuberculosis and Mycobacterium leprae.

Summarize bacterial cell division.

Answer: Bacterial division begins with DNA replication. Protein synthesis and expansion of cytoplasm elongate the cell. A septum forms, then the cell divides. In a rapid-growing cell, DNA replication and cell division are coordinated so daughter cells receive genetic material. The process is prokaryotic cell division—not mitosis with a nucleus.

Compare fimbriae, conjugation pili, and stalks.

Answer: Pili are made of pilin protein. Fimbriae (attachment pili) help bacterial cells attach to surfaces. A conjugation pilus facilitates transfer of DNA between cells. Stalks are membranous cytoplasmic extensions that secrete adhesion factors. All can support colonization, but only the conjugation pilus is specifically linked to DNA transfer.

What do flagella do? Define chemotaxis.

Answer: Rotary flagella provide motility. Chemotaxis is movement in response to stimuli, driven by changes in flagellar rotation. On an exam, distinguish flagella (motility/chemotaxis) from pili/fimbriae (attachment and, for conjugation pili, DNA transfer).

Match specialized bacterial structures to their function: thylakoids, gas vesicles, storage granules, magnetosomes.

Answer: Thylakoid membranes: photosynthetic bacteria. Gas vesicles: aquatic bacteria inflate/deflate them for buoyancy. Storage granules: store nutrients such as sulfur, phosphate, or PHA. Magnetosomes: contain magnetite/iron oxides and support magnetotaxis. These are adaptive structures for distinct habitats, not universal bacterial features.

Compare eukaryotic nucleus, ER/Golgi/lysosomes, and mitochondria/chloroplasts.

Answer: A eukaryotic nucleus organizes DNA and has a double nuclear envelope with pores; the outer membrane is continuous with ER. Rough ER, smooth ER, Golgi, and lysosomes form the endomembrane system for processing/trafficking. Mitochondria and chloroplasts convert energy; both contain bacterial-like genomes and ribosomes, supporting endosymbiosis. Bacteria lack these membrane-bound organelles.

What do the eukaryotic cytoskeleton, cilia/flagella, and contractile vacuoles do?

Answer: The cytoskeleton maintains cell shape and includes microfilaments, intermediate filaments, and microtubules. Eukaryotic cilia and flagella are constructed from microtubules. Contractile vacuoles collect and expel water, helping maintain water balance. Do not assume bacterial and eukaryotic flagella have the same construction.

Which eukaryotic groups are studied in clinical microbiology, and what makes an arthropod clinically relevant?

Answer: Protozoa are always unicellular; fungi may be unicellular or multicellular; helminths are multicellular parasitic worms. Arthropods are invertebrate animals often relevant as ectoparasites or vectors: they may bite/sting, feed on blood, or transmit infectious agents. They are not microbes in the same sense as bacteria, but are medically important infectious agents/vectors.

What structures are present in eukaryotic microbial cells?

Answer: The lecture lists a cell membrane, nucleus, mitochondria, rough and smooth ER, Golgi complex, cytoskeleton, cytoplasm, and glycocalyx. This list is high yield for distinguishing eukaryotes from prokaryotes: a true nucleus and membrane-bound organelles are the clearest clues.

Compare yeast and mold forms.

Answer: Clinically important microscopic fungi are primarily yeasts and molds. Yeasts are round/oval, divide rapidly by mitosis, and form surface swellings called buds; buds detach as new yeast cells. Molds grow as long, threadlike hyphae (branched fibers). A morphology question asking "budding, round/oval" indicates yeast; "threadlike hyphae" indicates mold.

What are dimorphic fungi? Name three dangerous examples and their main disease sites.

Answer: Dimorphic fungi ("two bodies") can grow as yeast or hyphal forms depending on conditions such as temperature and moisture. Blastomyces causes blastomycosis affecting lungs, skin, oral, and nasal mucosa. Histoplasma capsulatum causes pulmonary histoplasmosis. Sporothrix schenckii causes sporotrichosis with nodules involving skin and lymph nodes.

Match environmental exposure clues to Blastomyces, Histoplasma, and Sporothrix.

Answer: Blastomyces: inhaled environmental spores associated with construction/digging, wood cutting/clearing, and wilderness exposure such as hiking, hunting, or fishing. Histoplasma: "birds and bats"—bird cages, chicken coops, pet stores, caves, and decaying soil. Sporothrix: "rose gardener's disease"—thorny bushes/briars and infected/decaying soil; dust may also be inhaled.

What is a mycosis, and what three categories of human fungal disease does the CDC use in lecture?

Answer: Mycosis means fungal infection. Categories: community-acquired infections in the general population, often environmental dirt/dust/mold pathogens; hospital-associated infections acquired in clinical settings; and opportunistic fungal infections, typically low-virulence organisms that attack weakened hosts. Host status and setting are key classification clues.

Why would voriconazole most directly affect the fungal cell membrane?

Answer: Voriconazole impairs ergosterol synthesis. Ergosterol is a key membrane sterol in fungi; therefore the eukaryotic structure most directly affected is the cell membrane, not the nucleus, ribosomes, or mitochondria. This illustrates selective antifungal targeting of a fungal membrane component.