---

Microbiology Exam Study Notes

---

SECTION 1: BACTERIA

1.1 Structure - Prokaryotes vs. Eukaryotes

Exam tip: The 70S ribosome is the target of many antibiotics (aminoglycosides, tetracyclines, macrolides, chloramphenicol). The 80S ribosome is not affected - that's why these drugs are selective.

---

1.2 Bacterial Classification

1. Staining - Gram stain, acid-fast stain
2. Morphology - cocci (spheres), rods (bacilli), spirals
3. Arrangement - single, chains (strepto-), clusters (staphylo-)
4. Metabolism - aerobic, anaerobic, facultative anaerobe
5. Genotype - 16S rRNA sequencing (gold standard)

Gram Stain - The Big Distinction

• Mycobacterium - acid-fast (waxy mycolic acid wall)
• Mycoplasma - NO cell wall (not targeted by beta-lactams)
• Chlamydia - obligate intracellular
• Rickettsia - obligate intracellular

---

1.3 Cell Wall Components

Peptidoglycan (Murein)

• Meshlike structure made of glycan chains (GlcNAc + MurNAc) cross-linked by peptide bridges
• Gives rigidity and determines bacterial shape
• Target of beta-lactams (penicillin, cephalosporins) and vancomycin
• Degraded by lysozyme (found in tears and mucus)
• Mycoplasmas have no peptidoglycan - that's why beta-lactams don't work against them

Gram-Positive Extras

• Teichoic acid - strengthens wall, sequesters Ca2+ ions
• Lipoteichoic acid - activates innate host defenses

Gram-Negative Extras

• Outer membrane - lipopolysaccharide (LPS) + phospholipids + proteins
• LPS = Endotoxin - the lipid A portion causes fever, sepsis, and shock
• Periplasmic space - contains enzymes like beta-lactamases
• Outer membrane blocks large/hydrophobic molecules and complement

Other Surface Structures

---

1.4 Mechanisms of Bacterial Pathogenesis

"To a bacterium, the human body is a collection of environmental niches providing warmth, moisture, and food." - Medical Microbiology 9e

A. Direct Tissue Damage

• Enzymes: proteases, lipases, hyaluronidase, collagenase
• Type III secretion systems - molecular "needles" inject toxins directly into host cells

B. Toxins

• Clostridium tetani - tetanospasmin blocks inhibitory neurotransmitters (spastic paralysis - "lockjaw")
• Clostridium botulinum - botulinum toxin blocks acetylcholine release (flaccid paralysis)
• Vibrio cholerae - cholera toxin (ADP-ribosylates Gs protein → cAMP↑ → rice-water diarrhea)
• Corynebacterium diphtheriae - diphtheria toxin (ADP-ribosylates EF-2 → inhibits protein synthesis)
• Staphylococcus aureus - multiple toxins: TSST-1 (toxic shock), Panton-Valentine leukocidin (PVL)

C. Immune Evasion

• Capsule - blocks opsonization and phagocytosis
• Protein A (S. aureus) - binds IgG Fc, blocks opsonization
• M protein (Streptococcus) - antiphagocytic
• Thick peptidoglycan (gram-positive) - resists complement membrane attack complex
• O antigen on LPS (gram-negative) - limits complement access

D. Virulence Factors - Key Concepts

• Pathogenicity islands - clusters of virulence genes on chromosomes or plasmids, often transferred together (e.g., SPI-2 in Salmonella)
• Quorum sensing - bacteria "count" their numbers; when a threshold is reached, they coordinate virulence factor expression (e.g., Pseudomonas biofilm using N-acyl homoserine lactone)
• Biofilm - protective matrix; highly resistant to antibiotics and immune responses

---

SECTION 2: VIRUSES

2.1 Basic Properties

• Size: 18-600 nm (most < 200 nm - NOT visible by light microscope)
• Genome: Either DNA or RNA (never both)
• Structure: Nucleic acid + protein capsid (+ lipid envelope in enveloped viruses)
• Obligate intracellular parasites - require host cell machinery to replicate

2.2 Viral Classification

DNA Viruses (mnemonic: HHAPPPy)

RNA Viruses - Selected High-Yield Examples

2.3 Enveloped vs. Non-Enveloped - Clinical Significance

2.4 Viral Replication Steps (General)

1. Attachment - viral surface protein binds host receptor
2. Entry/Penetration - fusion (enveloped) or receptor-mediated endocytosis
3. Uncoating - release of nucleic acid
4. Replication - using host machinery; RNA viruses replicate in cytoplasm (exception: influenza, retroviruses in nucleus)
5. Assembly - new virions assembled
6. Release - budding (enveloped) or cell lysis (naked)

2.5 Mechanisms of Viral Disease

• Direct cytopathic effect - virus destroys the cell it infects
• Immune-mediated damage - host inflammatory response causes tissue damage (can be the primary cause of symptoms)
• Chronic infection / latency - virus persists (e.g., HSV latent in ganglia; VZV reactivates as shingles)
• Oncogenic transformation - viral genes integrate and cause cancer (HPV → cervical cancer; EBV → Burkitt lymphoma; HBV/HCV → hepatocellular carcinoma)
• Immunosuppression - HIV destroys CD4+ T cells; CMV in immunocompromised

---

SECTION 3: FUNGI

3.1 Basic Properties

• Eukaryotes - have nucleus, mitochondria, Golgi, ER
• Cell wall contains chitin (not peptidoglycan)
• Cell membrane contains ergosterol (not cholesterol) - target of antifungals
• Two morphological forms:
  • Yeast - unicellular, reproduce by budding
  • Mold (Hyphae) - filamentous, reproduce sexually and asexually

3.2 Dimorphic Fungi - High Yield!

3.3 Major Fungal Pathogens

3.4 Antifungal Drug Targets

---

SECTION 4: PARASITES

4.1 Overview

• Most complex microbes - eukaryotes, unicellular to multicellular
• Range from 4-5 μm protozoa to 10-meter tapeworms
• Complex life cycles; often require multiple hosts
• Geographic distribution is key to diagnosis (travel history!)

4.2 Classification

Protozoa (Unicellular)

Helminths (Worms)

---

QUICK REFERENCE - HIGH-YIELD MNEMONICS

---

LAST-MINUTE FACTS TO REMEMBER

1. Gram stain exceptions: Mycobacteria (acid-fast), Treponema (too thin - use dark-field microscopy), Rickettsia/Chlamydia (intracellular, can't be Gram stained easily)
2. Cell wall targets: Beta-lactams and vancomycin target gram-positive cell wall synthesis; vancomycin is the last resort for MRSA
3. LPS = endotoxin = gram-negative = causes fever, hypotension, septic shock via IL-1, IL-6, TNF-alpha
4. Exotoxin vs. Endotoxin: Exotoxins are proteins (can be inactivated/made into toxoids for vaccines - tetanus, diphtheria); endotoxins are lipopolysaccharide and cannot be toxoided
5. HIV attacks CD4+ T cells (helper T cells) - when CD4 < 200 cells/μL = AIDS; susceptible to opportunistic infections (PCP, Cryptococcus, Toxoplasma, CMV, MAC)
6. Fungal cell membrane = ergosterol (target of polyenes and azoles) vs. human cell membrane = cholesterol
7. Biofilm - Pseudomonas and Staphylococcus are notorious for forming biofilms on prosthetics/catheters; highly antibiotic resistant

---

• Go deeper on any specific organism or topic
• Generate practice questions (Q&A format)
• Create mnemonics for a hard-to-remember section
• Cover antibiotics/antibiotic mechanisms in more detail