DNA Replication: Semiconservative, Bidirectional, Origins, and Enzymes

Practice flashcards covering core concepts of DNA replication: semiconservative and bidirectional replication, origins (bacterial and eukaryotic), key enzymes (DnaA/B/C, Pol III/I, helicase, primase, ligase, SSB, sliding clamp), Okazaki fragments, and recent observations on replication dynamics.

What does semiconservative replication mean?

Each daughter DNA molecule contains one parental (original) strand and one newly synthesized strand.

What are the three attributes of DNA replication shared by all organisms?

1) Each parental strand remains intact; 2) Each parental strand serves as a template for an antiparallel, complementary daughter strand; 3) Replication yields two identical daughter duplexes with one parental and one daughter strand.

Where does bacterial DNA replication typically initiate and in what direction does it proceed?

From a single origin of replication, proceeding bidirectionally.

Do eukaryotic chromosomes have a single origin or multiple origins?

Multiple origins of replication.

Who provided the first evidence of bacterial origins of replication and when?

John Cairns in 1963.

What is a replication bubble and what is a replication fork?

A replication bubble forms by expansion around the origin; replication forks are at the ends of the bubble where DNA unwinds and replication proceeds.

What is oriC and its key features in E. coli?

The origin of replication in E. coli; about 245 bp of A-T rich DNA, subdivided by three 13-bp sequences followed by four 9-bp sequences.

What is the common 9-mer consensus sequence found at many bacterial origins?

TTATCCACA (with some species showing variations such as TGATCCACA or TTGTCCACA).

How many origins can the human genome contain?

More than 50,000 origins of replication.

Name the enzymes DnaA, DnaB, and DnaC and their roles in E. coli replication initiation.

DnaA binds the 9-mer sequences at oriC and helps bend/open the 13-mer region; DnaB is the helicase that unwinds the DNA; DnaC assists loading DnaB onto the DNA.

What enzyme prevents reannealing of single-stranded DNA during replication?

Single-stranded binding protein (SSB).

Which enzyme synthesizes the leading strand continuously?

DNA polymerase III.

Which enzyme synthesizes the lagging strand in short Okazaki fragments and what completes the process?

DNA polymerase III synthesizes the Okazaki fragments; DNA polymerase I removes RNA primers and fills in with DNA, then DNA ligase seals the gaps.

What is the role of DNA ligase in replication?

Joins Okazaki fragments to form a continuous DNA strand.

What is the purpose of the sliding clamp in DNA replication?

To increase the processivity of DNA polymerase III by tethering it to the DNA.

Describe the structure of the sliding clamp.

A ring-shaped, doughnut-like clamp with a hole (~35 Å) through which DNA passes, anchoring the polymerase to the template.

What did Kowalczykowski and colleagues observe about replication in 2017?

Leading and lagging strands are synthesized at roughly the same rate, but with many starts and stops; replication speed varies over time; highly coordinated synthesis was not observed, and the precise mechanism is not fully understood.

What is meant by replication origins having conserved sequences?

Origins contain specific nucleotide sequences that attract replication enzymes; conserved sequences help identify origins across species.

What are ARS in yeast and why are they important?

Autonomously replicating sequences (ARS); multiple origins of replication in Saccharomyces cerevisiae, with ARS organization similar across the genome.

In E. coli replication initiation, what is the sequence of events involving oriC and Dna proteins?

DnaA binds the 9-mer sequences at oriC, bends the DNA, and destabilizes the A-T rich 13-mer; DnaB helicase unwinds the strands, aided by DnaC; SSB prevents reannealing.

What is the role of topoisomerase during replication?

Relaxes supercoiling that arises from unwinding the double helix.

How do leading and lagging strand syntheses differ in direction relative to fork movement?

The leading strand is synthesized continuously in the same direction as fork progression; the lagging strand is synthesized discontinuously in the opposite direction via Okazaki fragments.