Additional Questions on Genomes

What does DnaA do in bacterial DNA replication?

Binds oriC and helps initiate DNA strand separation at an AT-rich region.

What is oriC?

The bacterial origin of replication, where DNA replication begins.

What does DnaB do?

Acts as the helicase that unwinds DNA at the replication bubble.

What is the DnaBC complex?

The bacterial helicase complex that is loaded at the replication bubble; DnaB provides helicase activity.

What does DnaG do?

Bacterial primase; makes RNA primers so DNA polymerase can begin DNA synthesis.

What is the replisome?

A multiprotein complex assembled at each replication fork; includes at minimum the helicase complex, DNA polymerase complex, and primase.

What is the direction of new DNA synthesis?

5′ → 3′ at both replication forks.

What is the leading strand?

The strand synthesized continuously in the 5′ → 3′ direction.

What is the lagging strand?

The strand synthesized discontinuously as short Okazaki fragments.

Why does the lagging strand need repeated RNA primers?

Each Okazaki fragment needs its own starting point, made by primase.

What is the main replicative DNA polymerase in bacteria?

Pol III, also called DnaE.

What does bacterial Pol I do?

Participates in DNA synthesis and repair and replaces RNA primers with DNA.

What does bacterial Pol II do?

Participates in DNA synthesis and repair.

Which archaeal polymerases are listed in the lecture?

PolB and PolD; PolD is marked as a main replicative polymerase.

What does archaeal PolB do, according to the lecture?

Aids in DNA synthesis and repair.

Which eukaryotic polymerases are listed in the lecture?

Pol α, Pol β, Pol γ, Pol δ, and Pol ε.

Which eukaryotic polymerases are marked as main replicative polymerases?

Pol δ and Pol ε.

What does eukaryotic Pol γ replicate?

Mitochondrial circular DNA.

What polymerase does the lecture list for plant chloroplast circular DNA?

Plant organellar polymerase (POP).

What initiates bacterial DNA replication?

DnaA binding at oriC.

What initiator system is used in eukaryotes instead of DnaA?

An origin recognition complex (ORC) made of several proteins.

Which initiators are examples in archaea?

Orc1 and Cdc6; the lecture says archaea use one or two initiators.

What helicase-related complex do archaea and eukaryotes use instead of bacterial DnaBC?

The MCM (minichromosome maintenance) complex.

How many replication origins do eukaryotes have, according to the lecture?

Hundreds to thousands.

What do topoisomerases do?

Change DNA topology and help manage DNA supercoiling.

What do Tus and RTP do?

Bind ter termination sites in some bacteria and block helicase movement.

What are ter sites?

Non-coding DNA termination sites; the lecture describes them as 20-30 nucleotide tandem repeats, with 2-6 sites in some bacterial genomes.

How does replication usually terminate when there are no specific termination sites?

The two replication forks collide; the replisomes pause and disassemble.

How can plasmids replicate?

Most replicate bidirectionally; they can also use rolling-circle replication.

What is the key difference between bidirectional and rolling-circle replication?

Bidirectional replication proceeds from an origin in two directions; rolling-circle replication uses a different mechanism in which synthesis proceeds around a circular template.