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A detailed scientific diagram of a prokaryotic cell with labeled structures including cell wall, cell membrane, cytoplasm, nucleoid region with DNA, ribosomes, flagella, pili, capsule, and plasmids. Clean educational illustration style with clear labels and arrows.
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Prokaryotic replication
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Here is a full breakdown of prokaryotic DNA replication, sourced from Biochemistry, 8th ed. - Lippincott Illustrated Reviews.
Prokaryotic DNA Replication
Overview
Prokaryotic DNA replication is semiconservative - the two parental strands separate, and each serves as a template for a new complementary strand. The result is two daughter duplexes, each with one old strand and one newly synthesized strand.
Step 1 - Initiation at the Origin (oriC)
Prokaryotes have a single origin of replication called oriC (in E. coli). This is a consensus sequence that is AT-rich, which makes it easier to melt (separate) since A-T base pairs have only 2 hydrogen bonds vs. 3 for G-C.
- DnaA protein binds to DnaA boxes within oriC, causing the AT-rich DNA unwinding element to melt open, creating short regions of ssDNA.
Step 2 - Replication Fork Formation
Two replication forks form and move bidirectionally outward from oriC, creating a replication bubble. Three key proteins maintain the open complex:
| Protein | Function |
|---|---|
| DnaB helicase | Unwinds the double helix using ATP hydrolysis |
| SSB proteins (single-stranded DNA-binding) | Bind cooperatively to ssDNA to keep strands separated and protect from nucleases |
| Topoisomerases | Relieve torsional stress (positive supercoils) that builds ahead of the fork |
- Type I topoisomerases: nick one strand, rotate, and reseal - no ATP needed
- Type II topoisomerases (DNA gyrase): cut both strands, pass a segment through, and reseal - uses ATP; introduces negative supercoils to neutralize positive ones
Clinical note: Fluoroquinolones (e.g., ciprofloxacin) inhibit bacterial DNA gyrase - a type II topoisomerase unique to bacteria. This makes it an excellent antibiotic target.
Step 3 - Priming
DNA polymerases cannot start a new chain de novo - they can only extend an existing strand. A short RNA primer is required:
- Primase (part of the primosome complex) synthesizes a short RNA primer in the 5'→3' direction
- The primosome = prepriming complex + primase
- RNA primers are made for the leading strand (once) and for each Okazaki fragment on the lagging strand
Step 4 - Elongation by DNA Pol III
DNA polymerase III is the main replicative polymerase in E. coli. It:
- Extends from the 3'-OH of the RNA primer
- Synthesizes in the 5'→3' direction only
- Is highly processive - stays on the template without dissociating, due to its β-subunit sliding clamp (a ring that encircles the template strand)
- Uses dNTPs (dATP, dTTP, dCTP, dGTP); releases PPi which is hydrolyzed to 2 Pi (making the reaction irreversible)
Leading strand - synthesized continuously toward the replication fork (3'→5' template read, 5'→3' new strand).
Lagging strand - synthesized discontinuously away from the fork as Okazaki fragments (each preceded by an RNA primer).
Step 5 - Primer Removal and Gap Filling (DNA Pol I)
DNA polymerase I has two critical activities:
- 5'→3' exonuclease: removes the RNA primer ahead of it
- 5'→3' polymerase: simultaneously fills the gap with DNA
This combined action is called nick translation.
Step 6 - Ligation
After gap filling, a nick remains between the new DNA segment and the existing DNA (a missing phosphodiester bond). DNA ligase seals this nick using NAD⁺ (in prokaryotes) as a cofactor.
Summary Table of Key Enzymes
| Enzyme | Role |
|---|---|
| DnaA | Initiates opening at oriC |
| DnaB (helicase) | Unwinds double helix, ATP-dependent |
| SSB proteins | Stabilize ssDNA at replication fork |
| DNA gyrase (Topo II) | Relieves positive supercoils ahead of fork |
| Primase | Synthesizes RNA primers |
| DNA Pol III | Main chain elongation (5'→3'), high fidelity, processive |
| DNA Pol I | Removes RNA primers; fills gaps (nick translation) |
| DNA ligase | Seals nicks between Okazaki fragments |
Source: Biochemistry, 8th ed. - Lippincott Illustrated Reviews, pp. 1145-1163
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