Feature	Prokaryotic (bacteria)	Eukaryotic (fungi, protozoa, human cells)
Cell size	Small, ~1-5 μm	Larger, ~10-100 μm
Nucleus	Absent, no nuclear membrane	Present, membrane-bound
DNA organisation	Single circular chromosome, no histones	Multiple linear chromosomes, histone-associated
Organelles	None membrane-bound	Membrane-bound organelles (mitochondria, ER, Golgi)
Ribosomes	70S (30S + 50S subunits)	80S (40S + 60S subunits)
Cell division	Binary fission	Mitosis (somatic) / meiosis (gametes)
Cell wall	Peptidoglycan (most bacteria)	Chitin (fungi); absent in protozoa and human cells
Cytoskeleton	Simple, limited homologues	Complex: actin, microtubules, intermediate filaments
Energy production	Cell membrane (no mitochondria)	Mitochondria

The structural differences between prokaryotic and eukaryotic cells are the entire basis of selective toxicity, the ability of an antimicrobial to kill or inhibit the pathogen while sparing the human host cell.
Ribosome difference (70S vs 80S) is the target of an entire drug class: aminoglycosides, macrolides, tetracyclines, and chloramphenicol all bind bacterial 70S ribosomal subunits and do not significantly affect the structurally distinct human 80S ribosome.
Cell wall (peptidoglycan) absence in human cells is the basis of beta-lactams (penicillins, cephalosporins, carbapenems) and glycopeptides (vancomycin). These drugs disrupt peptidoglycan synthesis or cross-linking, a target that simply does not exist in human cells, giving a wide therapeutic margin.
Fungal cells are eukaryotic, sharing far more structural similarity with human cells than bacteria do. This is why antifungal drugs have a narrower selective target and a comparatively higher rate of host toxicity than antibacterial drugs. Antifungals exploit the specific eukaryotic features that do differ (ergosterol instead of cholesterol in the fungal membrane, chitin instead of the absent fungal-type wall in human cells), covered in full in Fungal Structure and Basic Biology and in Antimicrobial Agents and Resistance.
Protozoa and helminths are also eukaryotic, which is why antiparasitic drugs, like antifungals, generally have a narrower therapeutic index than antibacterials and rely on more specific metabolic or structural differences rather than a wholesale absent-in-host target.

Prokaryotes Versus Eukaryotes

Comparison Table

Prokaryotic Cells

Eukaryotic Cells

Clinical Significance: Antimicrobial Selectivity