Control of Micro-organisms: Chemotherapy and Antibiotics
2. Classification of antibiotics by target
Antibiotics are classified by chemical family and, more usefully for GATE, by cellular target. The target explains the spectrum, whether the drug is cidal or static, the side effects and the likely resistance route.
| Target | Drug class and examples | Molecular action |
|---|---|---|
| Cell wall | β-lactams: penicillins, cephalosporins, carbapenems | Acylate penicillin-binding proteins (transpeptidases), so peptidoglycan is not cross-linked |
| Cell wall | Glycopeptides (vancomycin); bacitracin | Vancomycin caps the D-Ala–D-Ala terminus of the precursor; bacitracin blocks carrier recycling |
| 30S ribosome | Aminoglycosides (gentamicin); tetracyclines | Aminoglycosides cause misreading and are cidal; tetracyclines block the A site and are static |
| 50S ribosome | Macrolides (erythromycin); chloramphenicol; clindamycin; linezolid | Macrolides block translocation; chloramphenicol blocks peptidyl transferase; linezolid blocks initiation |
| Nucleic acids | Fluoroquinolones (ciprofloxacin); rifampicin | Quinolones inhibit DNA gyrase/topoisomerase IV; rifampicin inhibits bacterial RNA polymerase |
| Folate pathway | Sulfonamides; trimethoprim | Sulfonamides inhibit dihydropteroate synthase; trimethoprim inhibits dihydrofolate reductase |
| Cell membrane | Polymyxins (colistin); daptomycin | Polymyxins disrupt the Gram-negative outer membrane; daptomycin depolarises Gram-positive membranes |
A few families fall outside the ribosome-centred scheme but are worth knowing: the oxazolidinones (linezolid) are fully synthetic 50S-initiation blockers reserved for resistant Gram-positives, and the cyclic lipopeptide daptomycin is bactericidal against Gram-positives by membrane depolarisation. Learning each drug by its target, rather than by name alone, lets you predict its spectrum and the one resistance route that matters most for it.
3. Molecular modes of action
Cell-wall inhibitors attack peptidoglycan, which only bacteria possess. β-lactams are structural analogues of the D-Ala–D-Ala terminus of the peptide side-chain; they acylate the active-site serine of the transpeptidase (penicillin-binding protein), so cross-bridges never form and the growing wall ruptures under turgor — hence they kill only dividing cells. Vancomycin instead binds the D-Ala–D-Ala substrate itself, hiding it from the enzyme. Because peptidoglycan is absent in humans, these agents have the widest safety margin.
Protein-synthesis inhibitors exploit the 70S ribosome. Aminoglycosides bind the 30S and cause mRNA misreading and faulty proteins; tetracyclines block the aminoacyl-tRNA from entering the A site; chloramphenicol blocks the 50S peptidyl-transferase; macrolides block the exit tunnel and translocation; linezolid blocks assembly of the initiation complex. Nucleic-acid inhibitors split by polymerase: fluoroquinolones trap DNA gyrase/topoisomerase IV and snap the chromosome, while rifampicin binds the β subunit of bacterial RNA polymerase and halts transcription. Antimetabolites block folate: sulfonamides are PABA analogues that competitively inhibit dihydropteroate synthase, and trimethoprim inhibits dihydrofolate reductase one step later; given together they block two sequential steps and act synergistically (co-trimoxazole). Membrane-active drugs (polymyxins, daptomycin) disorganise the membrane and are cidal but less selective.
4. Mechanisms of resistance and its spread
Resistance may be intrinsic (a species inherently lacks the target or is impermeable — mycoplasmas have no wall and ignore β-lactams) or acquired by mutation or by gene transfer. There are four biochemical strategies.
- Enzymatic inactivation: β-lactamases hydrolyse the β-lactam ring (penicillinases, extended-spectrum β-lactamases, carbapenemases); aminoglycoside-modifying enzymes and chloramphenicol acetyltransferase add groups that abolish binding.
- Target alteration: methicillin-resistant Staphylococcus aureus carries mecA encoding PBP2a, which β-lactams barely bind; ribosomal methylation (erm) resists macrolides; point mutations in gyrase or RNA polymerase resist quinolones and rifampicin; replacing D-Ala–D-Ala with D-Ala–D-Lac gives vancomycin resistance (vanA).
- Reduced uptake and efflux: loss of outer-membrane porins keeps Gram-negative drugs out, and active efflux pumps export tetracyclines, macrolides and fluoroquinolones before they act.
- Target bypass or overproduction: making extra target enzyme or an alternative pathway, as when bacteria overproduce PABA or dihydrofolate reductase to overcome folate inhibitors.
The same organism often carries several mechanisms at once, which is why a single isolate can be resistant to many unrelated drugs (multidrug resistance). An integron can line up cassettes for a β-lactamase, an aminoglycoside-modifying enzyme and a sulfonamide-resistant target on one mobile element, so that selecting for any one drug co-selects the rest. This is also why a resistance gene first seen in a harmless environmental bacterium can, over time, appear in a clinical pathogen.
5. Antifungal drugs
Fungi are eukaryotes, so selective toxicity is harder than for bacteria: useful targets are the ones that differ from human cells — the membrane sterol ergosterol (humans use cholesterol) and the fungal cell wall of β-1,3-glucan and chitin, which humans lack entirely.
| Class (example) | Target / action |
|---|---|
| Polyenes (amphotericin B, nystatin) | Bind ergosterol and form membrane pores, leaking ions; fungicidal but nephrotoxic |
| Azoles (fluconazole, itraconazole, voriconazole) | Inhibit lanosterol 14-α-demethylase (CYP51), blocking ergosterol synthesis |
| Echinocandins (caspofungin) | Inhibit β-1,3-glucan synthase, so the cell wall fails |
| Allylamines (terbinafine) | Inhibit squalene epoxidase early in ergosterol synthesis |
| Flucytosine (5-FC) | Converted inside the fungus to 5-fluorouracil, which blocks nucleic-acid synthesis |
| Griseofulvin | Disrupts the mitotic spindle (microtubules); used for dermatophyte skin infections |
Key takeaways
- Selective toxicity is the central idea: hit a target the host lacks (peptidoglycan, 70S ribosome, gyrase, folate synthesis). Drugs are bactericidal or bacteriostatic, narrow- or broad-spectrum.
- MIC is the lowest concentration stopping visible growth (read from a two-fold dilution series); MBC kills ≥99.9%; Kirby–Bauer reads a zone diameter against breakpoints.
- Therapeutic index = TD₅₀/ED₅₀; a larger value is safer. With first-order kinetics the plasma level halves each half-life, which sets the dosing interval.
- Antibiotics group by target: cell wall (β-lactams, vancomycin), 30S (aminoglycosides, tetracyclines), 50S (macrolides, chloramphenicol, linezolid), nucleic acids (quinolones, rifampicin), folate (sulfonamides, trimethoprim), membrane (polymyxins).
- Resistance works by enzymatic inactivation (β-lactamases), target alteration (PBP2a/mecA, vanA, erm), reduced uptake/efflux, or target bypass, and spreads by horizontal gene transfer on plasmids, transposons and integrons.
- Antifungals target ergosterol (polyenes, azoles, allylamines) or the glucan wall (echinocandins); antivirals target virus-specific enzymes (acyclovir, reverse-transcriptase/protease/integrase/neuraminidase inhibitors) and are combined to curb resistance.
Practice questions (16)
Attempt each one before opening the answer. Every explanation names the tempting wrong option as well as the right one, because that is where marks are lost.
The principle that an antimicrobial drug should injure the pathogen at doses the host can tolerate is called:
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Answer: D — Selective toxicity
Selective toxicity is the whole basis of chemotherapy: the drug exploits a difference between microbe and host, such as the bacterial 70S ribosome or peptidoglycan. Competitive inhibition is one molecular mechanism, not the overarching principle; synergism is cooperation between two drugs; bioavailability is how much drug reaches the circulation.β-lactam antibiotics such as penicillin kill bacteria because they:
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Answer: C — inhibit the transpeptidases that cross-link peptidoglycan, so the wall ruptures in dividing cells
β-lactams acylate penicillin-binding proteins (transpeptidases), so peptidoglycan cross-bridges never form and the growing wall bursts under turgor; they therefore act only on dividing cells. The 30S option describes aminoglycosides, dihydrofolate reductase is trimethoprim's target, and ergosterol pores describe the antifungal polyenes.Which antibiotic class binds the 30S ribosomal subunit?
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Answer: A — Tetracyclines, which block aminoacyl-tRNA from entering the A site
Among protein-synthesis inhibitors only aminoglycosides and tetracyclines act on the 30S subunit; tetracyclines block the A site. Macrolides act on the 50S, while fluoroquinolones and rifamycins are nucleic-acid inhibitors, not ribosomal drugs at all — the trap is grouping every translation and transcription inhibitor together.A strain of Staphylococcus aureus is resistant to methicillin and nearly all β-lactams, yet it produces no β-lactamase. The most likely mechanism is:
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Answer: B — an altered penicillin-binding protein (PBP2a, encoded by mecA) that β-lactams bind poorly
Methicillin resistance in S. aureus is classically target alteration: mecA encodes PBP2a, a transpeptidase that β-lactams bind with very low affinity, so wall synthesis continues. A β-lactamase is the tempting answer because enzymatic destruction is the commonest penicillin-resistance route, but the stem rules it out; and porin loss is irrelevant here because S. aureus is Gram-positive and has no outer membrane.Azole antifungals such as fluconazole act by:
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Answer: B — inhibiting lanosterol 14-α-demethylase and so blocking ergosterol synthesis
Azoles inhibit the cytochrome-P450 enzyme lanosterol 14-α-demethylase (CYP51), stopping ergosterol synthesis so the membrane becomes defective. Binding preformed ergosterol to form pores is the mechanism of polyenes like amphotericin B; glucan-synthase inhibition is echinocandins; spindle disruption is griseofulvin.Acyclovir is highly selective against herpesviruses mainly because:
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Answer: A — it is first phosphorylated by the viral thymidine kinase, so it is activated chiefly inside infected cells
Acyclovir is a prodrug: only the viral thymidine kinase efficiently makes the first phosphate, so the active triphosphate accumulates in infected cells, where it inhibits the viral DNA polymerase and terminates the chain. Neuraminidase inhibition describes oseltamivir against influenza, and uncoating blockade describes amantadine; acyclovir does not target host RNA polymerase.A drug that stops bacterial growth without killing the cells, relying on host defences to clear the infection, is best described as:
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Answer: C — Bacteriostatic
A bacteriostatic drug (tetracycline, sulfonamide, chloramphenicol) only inhibits multiplication; clearance then depends on the host's immune system, which is why such drugs can fail in severely immunodeficient patients. Bactericidal means it actually kills; broad-spectrum refers to the range of organisms, not the cidal/static distinction; prophylactic refers to preventive use.Co-trimoxazole combines sulfamethoxazole with trimethoprim. Why are the two given together?
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Answer: D — They block two sequential steps of folate synthesis, acting synergistically
Sulfonamides inhibit dihydropteroate synthase and trimethoprim inhibits dihydrofolate reductase, two consecutive steps of the same folate pathway, so blocking both is synergistic and more bactericidal than either alone. They act on different enzymes, not the same site; neither is a β-lactam, so β-lactamase protection is irrelevant; and neither is a ribosomal drug.Antifungal drugs are harder to design selectively than antibacterial drugs mainly because:
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Answer: B — fungi are eukaryotes and share much of their cell biology with human cells
Fungi are eukaryotes, so they share ribosomes, membranes and many enzymes with human cells, leaving few unique targets; the usable ones are ergosterol and the glucan/chitin wall. Fungi do not grow faster than bacteria, they have no peptidoglycan (that is bacterial), and they do have a sterol — ergosterol — which is in fact a major drug target.Which of the following are genuine biochemical mechanisms of antibiotic resistance?
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Answer: A — Enzymatic inactivation of the drug, as by β-lactamases; B — Active efflux of the drug out of the cell; C — Modification of the drug target so the drug binds poorly
Enzymatic inactivation, efflux and target modification are three of the four classic resistance strategies (the fourth is reduced uptake or target bypass). Host antibody against an antibiotic is not a resistance mechanism; resistance is a property of the bacterium, and small drug molecules do not provoke a protective antibody response that clears the drug.Which of the following antibiotics act by inhibiting bacterial nucleic-acid synthesis?
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Answer: A — Ciprofloxacin, through inhibition of DNA gyrase; B — Rifampicin, through inhibition of RNA polymerase
Fluoroquinolones such as ciprofloxacin inhibit DNA gyrase/topoisomerase (DNA synthesis) and rifampicin inhibits RNA polymerase (transcription); both act on nucleic-acid metabolism. Erythromycin and gentamicin are protein-synthesis inhibitors binding the 50S and 30S ribosomal subunits respectively, not nucleic-acid synthesis.Which statements about antiviral chemotherapy are correct?
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Answer: A — Selective antivirals typically target virus-encoded enzymes rather than host ones; B — Oseltamivir inhibits the influenza neuraminidase and blocks virus release; D — Zidovudine is a reverse-transcriptase inhibitor used against HIV
Good antivirals target virus-specific enzymes (reverse transcriptase, protease, neuraminidase), oseltamivir blocks the influenza neuraminidase, and zidovudine is a nucleoside reverse-transcriptase inhibitor. HIV is treated with combination therapy, not a single drug; monotherapy selects resistant mutants rapidly because the viral polymerase is error-prone.In a broth-dilution MIC test, two-fold dilutions give tubes at 128, 64, 32, 16, 8, 4, 2 and 1 µg/mL. Visible growth appears in the tubes at 8, 4, 2 and 1 µg/mL; the tubes at 16 µg/mL and above are clear. The MIC is ____ µg/mL.
Numerical answer — type the value.
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Answer: 16
The MIC is the lowest concentration that prevents visible growth. Growth is seen up to 8 µg/mL, and the lowest clear tube is 16 µg/mL, so the MIC = 16 µg/mL. The highest tube showing growth (8 µg/mL) is a common wrong pick.For a new antimicrobial the dose toxic to 50% of animals is TD₅₀ = 400 mg/kg and the dose effective in 50% is ED₅₀ = 20 mg/kg. Using therapeutic index = TD₅₀ / ED₅₀, the therapeutic index is ____.
Numerical answer — type the value.
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Answer: 20
Therapeutic index = TD₅₀ / ED₅₀ = 400 / 20 = 20. A larger index means the toxic dose is far above the effective dose, so the drug is safer.A drug is eliminated by first-order kinetics with a half-life of 3 hours. Its plasma concentration is 64 mg/L immediately after a dose. Assuming no further dose, the time for the concentration to fall to 2 mg/L is ____ hours.
Numerical answer — type the value.
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Answer: 15
Each half-life halves the concentration: 64 → 32 → 16 → 8 → 4 → 2 mg/L is 5 halvings, i.e. a 32-fold (2⁵) fall. Five half-lives × 3 h = 15 h. Equivalently, 64/2 = 32 = 2⁵, so n = 5 and t = 5 × 3 = 15 h.After exactly 4 half-lives of first-order elimination, the percentage of the original drug amount still remaining in the body is ____ % (to two decimal places).
Numerical answer — type the value.
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Answer: 6.25
After n half-lives the fraction remaining is (1/2)ⁿ. For n = 4, (1/2)⁴ = 1/16 = 0.0625 = 6.25%. This is why roughly 4–5 half-lives are taken as the time for a drug to be essentially cleared.