DNA Replication: Detailed Mechanism

Comprehensive flashcards covering DNA replication mechanisms in E. coli and eukaryotes, including initiation, elongation, processivity, termination, and telomere maintenance.

What does the term 'initiation of DNA replication' specifically mean in the context of molecular biology?

'primer synthesis.'

What is a 'primosome' and which proteins compose it in E. coli?

A primosome is a collection of proteins needed to make primers for a given replicating DNA. In E. coli, it is composed of DNA helicase (DnaB) and Primase (DnaG).

Describe the composition and length of the E. coli oriC.

The oriC is a $245 ext{-bp}$ DNA element composed of the DUE (DNA Unwinding Element) and the DOR (DnaA-Oligomerization Region).

How does DnaA interact with oriC to initiate melting?

DnaA binds to dnaA boxes (9-mers), which cooperates with RNA polymerase and HU-protein to melt a DNA region (13-mers) adjacent to the leftmost dnaA box.

What are the synthesis rates of Pol III holoenzyme in vitro versus in vivo?

The rate in vitro is about $730 ext{ nts per second}$ and the rate in vivo is $ext{~}1000 ext{ nt/sec}$.

Why is the Pol III core enzyme alone considered a poor polymerase?

It falls off the template after synthesizing only $10 ext{ nt}$ and takes approximately $1 ext{ minute}$ to reassociate with the template and nascent DNA strand.

What is the processivity factor in eukaryotes that forms a ring encircling DNA?

PCNA, which forms a trimer.

How is the double-headed Pol III holoenzyme structured to coordinate leading and lagging strand synthesis?

Two core polymerases are attached through $2 ext{ τ}$ subunits to a $ext{γ}$ complex. One core synthesizes the leading strand continuously while the other performs discontinuous lagging strand synthesis.

What protein binds to the 22-bp terminator sites in the bacterial Terminus region?

TUS (terminus utilization substance).

Which enzyme is responsible for decatenating the two entangled daughter duplexes following bacterial DNA replication?

topo-IV.

What is the function of the enzyme telomerase?

It makes the G-rich telomere strand using a short internal RNA that serves as a template for synthesis.

What are the three steps in the cycle of telomere formation by telomerase?

(a) Elongation (adding bases to the $3'$ end), (b) Translocation (moving to the new $3'$ end), and (c) repeated Elongation.

What is a 't-loop' in telomere structure?

A DNA loop formed when the single-stranded $3'$ end of the telomere invades the double-stranded telomeric DNA upstream.

What is the 'Shelterin complex' and name at least four of its proteins.

A group of telomere-binding proteins in mammals; known proteins include TRF1, TRF2, POT1, TPP1, TIN2, and RAP1.

Distinguish the roles of TRF1 and POT1 in the Shelterin complex.

TRF1 binds the double-stranded (ds) parts of telomeres (TTAGG-repeat binding), while POT1 (Protection of telomeres-1) binds the single-stranded (ss) $3'$ tails.