200 cards
This deck focuses on the foundational concepts of microbiology, with a strong emphasis on bacterial cell structure, staining techniques, and key cellular components. You'll work through questions about the differences between Gram-positive and Gram-negative bacteria, the chemistry of the Gram stain procedure, and the roles of structures like flagella, pili, capsules, and endospores. Together, these cards build a clear picture of how bacteria are classified and identified in the lab.
The material is well suited for students in introductory microbiology, nursing, pre-med, or general biology courses, as well as anyone preparing for exams that include bacteriology basics. Even if you already have some lab experience, working through these cards is a great way to cement terminology and make sure you can recall key distinctions quickly under pressure.
To get the most out of your study sessions, try reviewing the deck in short, frequent bursts rather than long cramming sessions, since spaced repetition helps move facts into long-term memory. It can also help to group related cards in your mind, for example linking all the questions about Gram staining together so the procedure and its outcomes make sense as one story rather than isolated facts. When you get a card wrong, take a moment to picture the structure or process in your head before moving on, as visualizing these tiny components makes them much easier to remember.
The bacterial cell envelope is one of the most important diagnostic and therapeutic features in microbiology. The Gram stain, developed by Hans Christian Gram, classifies bacteria based on cell wall architecture. Gram-positive bacteria possess a thick peptidoglycan layer and lack an outer membrane, retaining the crystal violet-iodine complex and appearing purple. Gram-negative bacteria have a thin peptidoglycan layer plus an outer membrane containing lipopolysaccharide (LPS); the alcohol/acetone decolorizer washes out the crystal violet, and the safranin counterstain renders them pink. The Gram stain procedure proceeds in four steps: crystal violet (primary stain), Gram's iodine (mordant), alcohol/acetone (decolorizer), and safranin (counterstain).
Peptidoglycan (murein), a polymer of alternating NAG and NAM sugars cross-linked by peptide chains, gives the cell wall its rigidity and is the target of lysozyme, an enzyme found in tears and saliva. Gram-positive walls also contain teichoic acid, a polymer that extends through the peptidoglycan and contributes to virulence and immune stimulation. In contrast, the LPS of Gram-negative organisms, specifically the lipid A component, acts as an endotoxin upon cell lysis. Two notable exceptions to the typical peptidoglycan-containing cell wall are Mycoplasma, which lacks a cell wall entirely and is therefore resistant to penicillin, and Mycobacterium, whose waxy mycolic acid layer renders it acid-fast and identifiable using the Ziehl-Neelsen stain, appearing bright red/pink against a blue background.
Bacteria also display characteristic external structures. Flagella provide motility through rotation of a flagellar motor, while pili (fimbriae) mediate adherence to host cells, with specialized sex pili enabling DNA transfer. A capsule is a tightly bound, well-organized polysaccharide layer that aids in adherence and immune evasion, whereas a slime layer is loosely attached and diffuse. Under stressful conditions, certain genera, notably Bacillus and Clostridium, form endospores, dormant, highly resistant structures visualized using malachite green in the Schaeffer-Fulton stain. Morphologically, bacteria appear as cocci (spherical), bacilli (rod-shaped), or spirilla/spirochetes (spiral), and they arrange into patterns such as diplococci (pairs), streptococci (chains), and staphylococci (grape-like clusters).
Bacterial genetic material is organized as a single circular chromosome compacted in the nucleoid, alongside smaller extrachromosomal circular DNA fragments called plasmids that often carry antibiotic resistance genes and replicate independently. Genetic information can be exchanged through horizontal gene transfer between bacteria rather than parent to offspring. Transformation is the uptake of free, naked DNA from the environment by a competent cell. Transduction involves the transfer of bacterial DNA from one cell to another via a bacteriophage. Conjugation is the direct transfer of DNA, often a plasmid, between two bacteria connected by a sex pilus or mating bridge.
Bacterial growth in batch culture follows a predictable four-phase curve. During the lag phase, cells adapt to their environment, synthesizing enzymes and metabolites with little to no cell division. The log (exponential) phase follows, in which cells divide at a constant maximal rate and the population doubles at regular intervals called generation or doubling time. As nutrients deplete and waste accumulates, growth rate equals death rate in the stationary phase, where population size plateaus. Finally, the death (decline) phase occurs as cells die faster than they divide. Most bacteria require a carbon source, a nitrogen source, an energy source, water, minerals, and appropriate pH, temperature, and osmotic conditions. Autotrophs synthesize organic compounds from CO2, while heterotrophs obtain organic carbon from other organisms. Mesophiles, which grow between roughly 20-45 degrees C, include most human pathogens because this range encompasses body temperature.
Bacteria vary widely in their oxygen requirements. Obligate aerobes require oxygen for growth, while obligate anaerobes are killed or inhibited by its presence. Facultative anaerobes can grow with or without oxygen, preferring aerobic respiration when available. Aerotolerant anaerobes do not use oxygen but tolerate its presence, and capnophiles, such as Neisseria gonorrhoeae, grow best with elevated carbon dioxide. Some organisms, termed extremophiles, are adapted to harsh environments, including thermophiles (heat), psychrophiles (cold), halophiles (high salt), and acidophiles (low pH). In anaerobic conditions without an electron transport chain, many bacteria perform fermentation, breaking down substrates such as glucose while using an organic molecule as the final electron acceptor. Biofilm formation, in which structured bacterial communities embedded in a self-produced matrix adhere to surfaces like catheters and implants, is clinically important because biofilms dramatically increase antibiotic resistance and underlie many chronic infections.
Microbial identification relies on staining techniques, biochemical tests, and specialized culture media. The oxidase test detects cytochrome c oxidase, differentiating Pseudomonas (positive) from Enterobacteriaceae (negative). The catalase test detects the catalase enzyme that breaks hydrogen peroxide into water and oxygen, distinguishing Staphylococcus (positive) from Streptococcus (negative). The coagulase test identifies Staphylococcus aureus (positive) by detecting an enzyme that clots plasma, separating it from coagulase-negative species like S. epidermidis. The oxidative-fermentative (O-F) test distinguishes fermenters, which produce acid under anaerobic conditions, from strict oxidizers.
Culture media can be selective, differential, or both. Selective media such as MacConkey agar inhibit unwanted organisms while permitting growth of Gram-negatives. Differential media allow visual distinction based on biochemical reactions; MacConkey agar also differentiates lactose fermenters (pink colonies) from non-fermenters (colorless). Blood agar reveals hemolytic patterns: beta-hemolysis produces a clear zone of complete red blood cell lysis, as seen with Streptococcus pyogenes, while alpha-hemolysis causes partial lysis with a greenish discoloration, characteristic of Streptococcus pneumoniae and viridans streptococci. The Quellung reaction, a capsule-swelling test, is used to serotype encapsulated bacteria such as S. pneumoniae.
Controlling microbial growth requires distinguishing between sterilization, which kills all microbial life including spores, and disinfection, which reduces pathogens to a safe level but may spare spores. Autoclaving uses pressurized steam, typically at 121 degrees C and 15 psi for 15-20 minutes, reliably destroying endospores. Pasteurization employs milder heat, such as 63 degrees C for 30 minutes or 72 degrees C for 15 seconds, to kill most pathogens without sterilizing the product. Antiseptics are chemicals safe for living tissue, while disinfectants are used on inanimate surfaces and may be too harsh for skin. Alcohols at 60-90% concentration denature proteins and disrupt lipid membranes, while chlorine-based agents like bleach oxidize proteins and nucleic acids through hypochlorous acid formation. HEPA filtration removes airborne bacteria in operating rooms and biosafety cabinets, while ionizing radiation such as gamma rays damages DNA and generates destructive free radicals to sterilize disposable medical supplies. Ethylene oxide gas sterilizes heat-sensitive equipment by alkylating proteins and nucleic acids.
Antimicrobial agents are described using two key suffixes: -cidal agents such as bactericidal drugs directly kill the organism, whereas -static agents such as bacteriostatic drugs inhibit growth and rely on the host immune system to clear the infection. Different antibiotic classes target distinct bacterial processes. Beta-lactams including penicillins and cephalosporins inhibit peptidoglycan cross-linking by binding penicillin-binding proteins, weakening the cell wall and causing lysis. Vancomycin binds the D-Ala-D-Ala terminus of peptidoglycan precursors, blocking cell wall synthesis, and is effective mainly against Gram-positives. Aminoglycosides such as gentamicin irreversibly bind the 30S ribosomal subunit, causing mRNA misreading and inhibiting protein synthesis. Tetracyclines also bind the 30S subunit, blocking aminoacyl-tRNA attachment, while macrolides like erythromycin and azithromycin bind the 50S subunit to block translocation.
Other antibiotics target nucleic acid and metabolic pathways. Fluoroquinolones such as ciprofloxacin inhibit DNA gyrase and topoisomerase IV, blocking DNA replication. Rifampin inhibits bacterial DNA-dependent RNA polymerase, halting transcription. Sulfonamides competitively inhibit dihydropteroate synthase, blocking folic acid synthesis required for nucleotide production. Metronidazole forms toxic free radicals in anaerobic and microaerophilic organisms, damaging their DNA and making it useful against anaerobes and certain protozoa. Two drugs that act on the same pathway can produce antibiotic synergy, an effect greater than the sum of individual contributions, as exemplified by trimethoprim-sulfamethoxazole, which sequentially blocks two steps of folate synthesis.
Four general mechanisms underlie antibiotic resistance: enzymatic drug inactivation, altered target sites, decreased drug uptake or permeability, and increased efflux pump activity. Beta-lactamase (penicillinase) hydrolyzes the beta-lactam ring, inactivating penicillins; beta-lactamase inhibitors such as clavulanic acid are combined with penicillins, as in Augmentin (amoxicillin-clavulanate), to protect the antibiotic. Extended-spectrum beta-lactamases (ESBLs) confer resistance to a broad range of beta-lactams including cephalosporins. Methicillin-resistant Staphylococcus aureus (MRSA) arises from altered penicillin-binding protein PBP2a, encoded by the mecA gene. Vancomycin-resistant Enterococcus (VRE) replaces the D-Ala-D-Ala terminus of peptidoglycan precursors with D-Ala-D-Lac, which vancomycin cannot bind. Resistance genes spread readily through horizontal gene transfer, commonly mediated by plasmids (R factors), transposons, and integrons transferred via conjugation.
Gram-positive cocci and rods cause many familiar diseases. Streptococcus pyogenes (Group A Streptococcus) is the leading cause of bacterial pharyngitis and can lead to post-streptococcal complications including rheumatic fever and glomerulonephritis; it also produces erythrogenic (pyrogenic) exotoxin responsible for scarlet fever. Streptococcus pneumoniae, alpha-hemolytic, lancet-shaped, and optochin-sensitive, is a major cause of bacterial meningitis and pneumonia. Streptococcus agalactiae (Group B Streptococcus) causes neonatal meningitis and sepsis. Staphylococcus aureus, coagulase-positive and catalase-positive, causes skin infections, food poisoning, and toxic shock syndrome via the superantigen TSST-1. The coagulase-negative Staphylococcus epidermidis commonly infects prosthetic devices and catheters. Bacillus anthracis causes anthrax through three toxin components, protective antigen, edema factor, and lethal factor. Clostridium tetani produces tetanospasmin, which blocks inhibitory neurotransmitters and causes spastic paralysis. Clostridium botulinum releases botulinum toxin that blocks acetylcholine release at the neuromuscular junction, causing flaccid paralysis. Clostridium perfringens causes gas gangrene via alpha toxin, a lecithinase. Clostridioides difficile causes pseudomembranous colitis, often after antibiotic use disrupts normal flora. Corynebacterium diphtheriae produces diphtheria toxin, which ADP-ribosylates elongation factor-2 (EF-2), inhibiting host protein synthesis. The acid-fast Mycobacterium tuberculosis causes tuberculosis, with primary infection sometimes producing a calcified Ghon complex. Mycobacterium leprae causes Hansen's disease (leprosy). Listeria monocytogenes causes listeriosis with characteristic growth at refrigeration temperatures and transplacental transmission, leading to neonatal meningitis.
Gram-negative pathogens span cocci, bacilli, and curved forms. Neisseria gonorrhoeae causes gonorrhea, and Neisseria meningitidis causes bacterial meningitis with a characteristic petechial rash. Escherichia coli is the most common cause of community-acquired urinary tract infections, and enterohemorrhagic E. coli (EHEC), especially O157:H7, produces Shiga-like toxin causing hemolytic uremic syndrome, while enterotoxigenic E. coli (ETEC) causes traveler's diarrhea. Salmonella typhi causes typhoid fever, while non-typhoidal Salmonella such as S. enteritidis causes gastroenteritis from contaminated poultry and eggs. Shigella species cause bacillary dysentery. Vibrio cholerae produces cholera toxin that activates adenylate cyclase, raising cAMP and causing massive watery diarrhea. Campylobacter jejuni, acquired from undercooked poultry, is a leading cause of bacterial gastroenteritis. Helicobacter pylori causes peptic ulcers and gastritis. Pseudomonas aeruginosa, a major opportunistic pathogen in cystic fibrosis and burn patients, produces a characteristic blue-green pigment. Bordetella pertussis causes whooping cough. Legionella pneumophila causes Legionnaires' disease, often from contaminated water systems such as cooling towers. Klebsiella pneumoniae causes community-acquired pneumonia with mucoid colonies. Haemophilus influenzae type b (Hib) causes epiglottitis and meningitis, especially in unvaccinated children. Yersinia pestis causes plague, transmitted by fleas.
Spirochetes and other distinctive pathogens include Treponema pallidum, which causes syphilis through stages of chancre, rash and systemic symptoms, latent disease, and eventually tertiary gummas with cardiovascular and neurological involvement. Borrelia burgdorferi causes Lyme disease, transmitted by Ixodes ticks, with erythema migrans (bullseye rash) as the classic early finding. Leptospira interrogans causes leptospirosis, often from water contaminated with animal urine. Chlamydia trachomatis is an obligate intracellular bacterium causing trachoma and the most common bacterial STI worldwide. Chlamydophila pneumoniae causes atypical pneumonia, as does the cell-wall-deficient Mycoplasma pneumoniae. Among Rickettsia, obligate intracellular bacteria that cannot be cultured on standard media, Rickettsia rickettsii causes Rocky Mountain spotted fever. Coxiella burnetii causes Q fever and uniquely survives outside host cells via a spore-like form. Other notable pathogens include Francisella tularensis (tularemia), Brucella species (brucellosis from unpasteurized dairy), Bartonella henselae (cat scratch disease), and Bacteroides fragilis, an anaerobic rod that causes abscesses when it breaches normal oral or gastrointestinal flora. Bacterial toxins fall into two broad categories: exotoxins, secreted proteins with specific molecular targets and high potency, often produced by Gram-positive organisms, and endotoxins, which are lipopolysaccharide (LPS) released upon Gram-negative cell lysis, causing fever and septic shock. Superantigens such as TSST-1 and streptococcal pyrogenic exotoxin bridge MHC II and T-cell receptors outside the normal antigen-binding groove, triggering massive non-specific T-cell activation and cytokine release.
Viruses are obligate intracellular parasites consisting of nucleic acid enclosed in a protein capsid; a complete infectious particle outside a host cell is called a virion. Enveloped viruses possess a host-derived lipid bilayer surrounding the capsid, while non-enveloped (naked) viruses consist only of a protein capsid and tend to be more resistant to desiccation and disinfectants. Capsid symmetry is either icosahedral or helical, with poxviruses exhibiting complex symmetry. DNA viruses typically replicate in the nucleus (poxviruses being the exception), whereas RNA viruses usually replicate in the cytoplasm, though influenza and retroviruses require nuclear steps. Bacteriophages can replicate through a lytic cycle, immediately producing progeny and lysing the host, or a lysogenic cycle, integrating their DNA into the host genome as a prophage that replicates passively until induced.
Retroviruses such as HIV use reverse transcriptase to convert their RNA genome into DNA. HIV targets CD4+ T helper lymphocytes, as well as macrophages and dendritic cells, by binding CD4 plus co-receptors CCR5 or CXCR4. Disease progression is monitored by CD4+ T cell count, with AIDS diagnosed when counts fall below 200 cells/microliter or when an AIDS-defining illness develops. The respiratory viruses include rhinoviruses (Picornaviridae), the most frequent cause of the common cold, and influenza virus, an orthomyxovirus bearing two major surface antigens, hemagglutinin (HA) and neuraminidase (NA). Antigenic drift involves gradual point mutations in HA and NA, producing seasonal epidemics, while antigenic shift is abrupt reassortment of gene segments between strains and can cause pandemics. Measles virus (Paramyxoviridae) produces characteristic Koplik spots on the buccal mucosa, and mumps virus causes parotitis with swollen salivary glands.
Herpesviruses establish lifelong latency in host cells with potential for reactivation. Varicella-zoster virus (VZV) causes chickenpox on primary infection and shingles upon reactivation. Epstein-Barr virus (EBV) causes infectious mononucleosis and is linked to Burkitt lymphoma and nasopharyngeal carcinoma. Cytomegalovirus (CMV) is associated with congenital hearing loss and severe disease in immunocompromised transplant patients. HSV-1 typically causes oral herpes, while HSV-2 typically causes genital herpes, though both can cause either. Hepatitis viruses differ in transmission and outcome: hepatitis A and E are fecal-oral and generally self-limited, with hepatitis E being particularly dangerous in pregnant women; hepatitis B, a hepadnavirus transmitted by blood and body fluids, can become chronic and increase liver cancer risk; hepatitis C (Flaviviridae) is the most common cause of chronic viral hepatitis in many countries and is transmitted mainly via blood; and hepatitis D is a defective virus requiring co-infection with hepatitis B.
Other medically important viruses include rabies virus (Rhabdaviridae), which produces characteristic Negri body cytoplasmic inclusions; rotavirus, the leading cause of viral gastroenteritis in children; and norovirus, the most common cause of outbreak-associated viral gastroenteritis on cruise ships and similar settings. Poliovirus (Picornaviridae) targets motor neurons in the anterior horn of the spinal cord, causing flaccid paralysis. Arboviruses transmitted by mosquitoes include yellow fever virus (Flaviviridae, vector Aedes mosquitoes), dengue virus, which causes fever, rash, and severe joint pain, and Zika virus, which is associated with congenital microcephaly when contracted during pregnancy. SARS-CoV-2 binds the ACE2 receptor via its spike protein to enter human cells. Vaccination strategies rely on either live-attenuated vaccines, using weakened replicating pathogens that elicit strong and durable immunity but carry small risk in immunocompromised hosts, or inactivated (killed) vaccines, which are safer but often require boosters and adjuvants.
Fungi differ from bacteria in their cell wall composition: fungal walls contain chitin and glucans, whereas bacterial walls contain peptidoglycan. Fungal cell membranes contain ergosterol as the principal sterol, which serves as the target for many antifungal drugs. Morphologically, yeasts are unicellular and reproduce by budding, while molds are multicellular and form branching filaments called hyphae. Dimorphism is the ability of certain fungi, such as Histoplasma, Blastomyces, and Coccidioides, to switch between yeast and mold forms depending on environmental temperature, growing as molds at room temperature and as yeasts at body temperature. Asexual reproductive spores called conidia form at the tips of specialized hyphae and are useful for laboratory identification.
Major pathogenic fungi include Candida albicans, part of normal flora that causes opportunistic infections such as thrush and vaginal candidiasis, and Cryptococcus neoformans, an encapsulated yeast causing cryptococcal meningitis, especially in HIV/AIDS patients, with the capsule visualized using India ink stain. Histoplasma capsulatum, found in soil enriched with bird or bat droppings in the Ohio and Mississippi river valleys, causes histoplasmosis. Coccidioides immitis, endemic to the southwestern US deserts, causes Valley fever (coccidioidomycosis). Blastomyces dermatitidis causes blastomycosis in the Great Lakes and Mississippi/Ohio river valleys. Aspergillus species produce septate hyphae with acute-angle branching and cause invasive pulmonary infections in immunocompromised hosts, while Aspergillus flavus produces aflatoxins that contaminate food and increase hepatocellular carcinoma risk. Mucor and Rhizopus species (Mucorales) cause mucormycosis with broad, non-septate hyphae branching at wide angles, classically in patients with diabetic ketoacidosis. Pneumocystis jirovecii causes Pneumocystis pneumonia, a classic AIDS-defining illness. Dermatophytes such as Trichophyton, Microsporum, and Epidermophyton infect keratinized tissue, causing tinea (ringworm) infections of skin, hair, and nails.
Antifungal drugs target the unique features of fungal cells. Azoles such as fluconazole inhibit lanosterol 14-alpha-demethylase, blocking ergosterol synthesis and disrupting the fungal membrane. Amphotericin B binds ergosterol directly, forming membrane pores that cause leakage of cell contents. Echinocandins like caspofungin inhibit beta-(1,3)-D-glucan synthase, blocking fungal cell wall synthesis. Griseofulvin disrupts microtubule function and mitosis, making it useful for dermatophyte infections.
Among protozoan parasites, Plasmodium species such as P. falciparum and P. vivax cause malaria, transmitted by female Anopheles mosquitoes; P. falciparum produces the most severe and deadly form. Toxoplasma gondii causes toxoplasmosis, acquired from cat feces or undercooked meat, and is dangerous in pregnancy (causing congenital toxoplasmosis) and in immunocompromised patients. Trypanosoma brucei causes African sleeping sickness via the tsetse fly, while Trypanosoma cruzi causes Chagas disease via triatomine (kissing) bugs. Entamoeba histolytica causes amoebic dysentery and liver abscesses. Giardia lamblia (intestinalis) causes foul-smelling, greasy diarrhea and is transmitted via contaminated water, often affecting hikers. Trichomonas vaginalis is a sexually transmitted protozoan causing vaginitis. Cryptosporidium parvum causes waterborne diarrhea, particularly in immunocompromised patients. Leishmania species cause visceral and cutaneous leishmaniasis, transmitted by sandflies.
Helminthic (worm) infections remain widespread. Trichinella spiralis, acquired from undercooked pork, causes trichinosis. Enterobius vermicularis (pinworm) is the most common helminthic infection in the United States, especially in children. Ascaris lumbricoides, one of the most common helminthic infections worldwide, is acquired via fecal-oral ingestion of eggs. Necator americanus and Ancylostoma duodenale are hookworms that infect humans through skin penetration from contaminated soil. The pork tapeworm Taenia solium can cause cysticercosis when its eggs are ingested, while Taenia saginata is acquired from undercooked beef.
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