4.

SSB proteins (Single-Strand

Binding proteins)
I. INITIATION STAGE
●​ Function: Stabilize single-stranded
(Bacteria – E. coli) DNA
●​ Role in order: After helicase opens
strands
1. DnaA protein
●​ What it does:
●​ Function: Initiator protein; binds to ○​ Prevents strands from
origin (oriC) at specific DNA re-annealing

⭐
sequences. ●​ Key note: Keeps DNA open for
●​ Role in order: FIRST STEP replication
●​ What it does:
○​ Binds to high- and low-affinity
sites (DNA boxes)
5. Topoisomerases
○​ Unwinds AT-rich region (DNA
unwinding element)
a. DNA gyrase
●​ Key note: Starts the whole
replication process. ●​ Function: Relieves supercoiling
ahead of fork
●​ Role: Works continuously during
unwinding
2. DnaC protein
●​ Function: Helicase loader b. Topoisomerase IV
●​ Role in order: After DnaA
●​ Function: Separates interlinked
●​ What it does:
daughter DNA
○​ Loads DnaB (helicase) onto
●​ Role: Late stage (termination)
DNA
●​ Key note: Doesn’t unwind DNA
itself—just helps helicase bind.
6. Primase (DnaG protein)
●​ Function: Synthesizes RNA primers
3. DnaB (Helicase) ●​ Role in order: After DNA is opened
●​ What it does:
●​ Function: Unwinds the DNA double
○​ Adds short RNA sequence
helix
(~10 nucleotides)
●​ Role in order: After DnaC loads it
●​ Key note: DNA polymerase cannot
●​ What it does:
start without it
○​ Breaks hydrogen bonds
between base pairs
○​ Creates replication fork
●​ Key note: Moves along DNA using
ATP
🧬 II. ELONGATION ●​ What it does:
○​ Displaces SSB proteins
STAGE ○​ Allows primase binding

7. DNA Polymerase III (Main 10. DNA Polymerase I

enzyme) ●​ Function: Replaces RNA primers
●​ Function: Synthesizes new DNA with DNA

⭐
strand ●​ Role in order: After Pol III finishes
●​ Role in order: MAIN replication fragment
enzyme ●​ What it does:
●​ What it does: ○​ Removes RNA primer (5’→3’
○​ Adds nucleotides in 5’ → 3’ exonuclease)
direction ○​ Fills gap with DNA
○​ Works on: ●​ Key note: Cleanup enzyme
■​ Leading strand
(continuous)
■​ Lagging strand
11. DNA Ligase
(Okazaki fragments)
●​ Special features: ●​ Function: Seals gaps between DNA
○​ Has proofreading (3’→5’ fragments
exonuclease activity) ●​ Role in order: Last step of elongation
●​ Key note: Most important enzyme in ●​ What it does:
replication ○​ Joins Okazaki fragments
○​ Forms phosphodiester bonds
●​ Key note: Makes DNA strand
continuous
8. Sliding Clamp + Clamp Loader

🧬 III. TERMINATION
●​ Function: Keeps DNA Pol III
attached to DNA
●​ Role: During elongation
●​ What it does:
○​ Prevents polymerase from STAGE
falling off
●​ Key note: Increases speed and
12. Tus protein
efficiency
●​ Function: Stops replication fork
●​ Role: Termination
●​ What it does:
9. PriA protein ○​ Binds to Ter sites
●​ Function: Helps restart replication ○​ Blocks helicase movement
(lagging strand priming) ●​ Key note: Ensures replication ends
●​ Role: Before primase acts on properly
lagging strand
13. Topoisomerase IV (again)
●​ Function: Separates daughter
🧬 V. EUKARYOTIC
chromosomes DNA REPLICATION
●​ Role: Final separation
●​ What it does: ENZYMES
○​ Decatenates (untangles)
circular DNA
Initiation

🧬 IV. NUCLEOTIDE 17. ORC (Origin Recognition

Complex)
SYNTHESIS ENZYMES ●​ Function: Recognizes origin of
replication
●​ Role: First step in eukaryotes
14. Ribonucleotide reductase
●​ Function: Converts RNA nucleotides
→ DNA nucleotides 18. Cdc6 & Cdt1
●​ Role: Before replication
●​ Function: Recruit helicase
●​ What it does:
●​ Role: After ORC
○​ Produces
deoxyribonucleotides
(dNTPs)
19. MCM complex (helicase)
●​ Function: Unwinds DNA
15. Kinase ●​ Equivalent to: DnaB in bacteria
●​ Function: Adds phosphate groups
●​ Role: Activation step
●​ What it does: 20. CDK (Cyclin-dependent
○​ Converts nucleotides → kinase)
triphosphates (dATP, dGTP,
●​ Function: Activates replication
etc.)
proteins
●​ Role: Controls timing

16. Thymidylate synthase

(implied) 21. Cdc45, Sld proteins, GINS
●​ Function: Produces thymidine (T) complex
●​ Role: Nucleotide formation
●​ Function: Activate helicase and
●​ What it does:
replication machinery
○​ Converts uridine →
thymidine using THF
22. Mcm10 30. DNA Ligase (Eukaryotic)
●​ Function: Stabilizes replication ●​ Same function as in bacteria
complex

Special Case
Elongation (Eukaryotes)
31. Telomerase
23. DNA Polymerase α (alpha) ●​ Function: Extends chromosome
●​ Function: Makes RNA + short DNA ends (telomeres)
primer ●​ Role: Solves end-replication problem
●​ Role: First polymerase used ●​ Key note: Uses RNA template

24. DNA Polymerase δ (delta)

●​ Function: Synthesizes lagging strand
🧠 SIMPLE ORDER
SUMMARY (Bacteria)
1.​ DnaA → binds origin
25. DNA Polymerase ε (epsilon)
2.​ DnaC → loads helicase
●​ Function: Synthesizes leading strand 3.​ DnaB (helicase) → unwinds DNA
4.​ SSB → stabilizes strands
5.​ Topoisomerase → relieves tension
26. RPA (Replication Protein A) 6.​ Primase (DnaG) → makes primer
7.​ DNA Pol III → elongates DNA
●​ Function: Stabilizes single-stranded
8.​ DNA Pol I → replaces primers
DNA
9.​ Ligase → seals fragments
●​ Equivalent to: SSB in bacteria
10.​Tus + Topo IV → terminate &
separate

27. RFC (Replication Factor C)

●​ Function: Loads sliding clamp

28. PCNA (Sliding clamp)

●​ Function: Holds polymerase in place

29. Fen1 & Dna2

●​ Function: Remove RNA primers