Cell Cycle & DNA Foundations
During which specific phase of the cell cycle does DNA replication take place?
S phase of Interphase.
What is the Y-shaped region formed when parental DNA strands are unzipped?
The Replication Fork.
Which enzyme physically breaks hydrogen bonds to unwind and unzip the double helix?
DNA Helicase.
Which new DNA strand is synthesized continuously towards the replication fork?
The Leading Strand.
What is the main job of Single-Stranded Binding Proteins (SSBPs) at the replication fork?
They bind to open single strands to physically prevent them from reattaching or re-annealing.
Where is DNA physically located in eukaryotic cells versus prokaryotic cells during replication?
Nucleus in eukaryotes; Nucleoid region in prokaryotes.
What is the term for a newly synthesized DNA strand that is built using an original template strand?
Daughter Strand.
Which enzyme prevents DNA from overwinding or supercoiling ahead of the replication fork?
Topoisomerase.
Which new DNA strand is synthesized discontinuously away from the replication fork?
The Lagging Strand.
In what direction of the DNA strand do DNA polymerases add new nucleotides?
5' to 3' direction.
What term describes a duplicated DNA molecule that consists of one original parent strand and one newly synthesized daughter strand?
Semiconservative replication.
What are the original double-stranded DNA templates called before replication begins?
Parental DNA (or parent strands).
What is the function of DNA Ligase?
It seals gaps in the sugar-phosphate backbone to link DNA fragments together. Usually, combines Okazaki fragments and helps in DNA repair.
What are Okazaki Fragments, and why do they form during replication?
They are short segments of newly synthesized DNA built discontinuously on the lagging strand because DNA polymerase synthesizes away from the advancing replication fork.
Explain the function of RNA Primase and why it is essential for DNA replication to begin.
It lays down a short RNA primer sequence to provide an initial starting point, which is essential because DNA polymerases cannot synthesize a strand from scratch and require an existing 3' end to attach to.
What is the main purpose of replicating the genetic code before a cell divides?
Ensures that every daughter cell receives the full set of genes necessary to synthesize proteins, perform metabolism, and carry out life functions.
What short RNA structure must physically attach to the template before DNA polymerase can begin building?
RNA Primer.
What is the function of exonuclease?
They are specialized enzymes that remove nucleotides one at a time from the end of a DNA or RNA polynucleotide chain by breaking phosphodiester bonds. They help in DNA repair and DNA proofreading and also remove RNA Primers.
What is the specific function of 3' to 5' Exonuclease activity during replication?
It performs proofreading by breaking phosphodiester bonds to cleave and remove incorrect nucleotides one by one from the 3' end of the strand.
What is the function of Mismatch Repair Mechanisms and how do they do it?
They detect and correct base pairing errors in newly synthesized DNA that manage to escape polymerase proofreading. They do it by removing incorrect sections using exonuclease and replacing them using DNA polymerase.
How does the number of origins of replication physically differ between prokaryotic and eukaryotic DNA and why?
Prokaryotic DNA has one origin of replication because it has small circular DNA, while eukaryotic DNA has many origins as it has much longer, linear DNA.
What specific covalent bond forms the physical backbone connecting adjacent nucleotides in a DNA strand?
Phosphodiester bond.
What is the difference between DNA Polymerase I and DNA Polymerase III?
DNA Polymerase III performs the main job of building new DNA strands during elongation while DNA Polymerase I removes RNA primers and replaces them with DNA nucleotides.
What is the function of the Sliding Clamp?
It is a ring-shaped structural protein that encircles double-stranded DNA and tethers DNA polymerase to the template strand so it stays attached.
Explain the key events that happen during the Termination phase of DNA replication.
DNA Polymerase I replaces RNA primers with DNA bases, and DNA Ligase bonds the fragments together to create two complete daughter strands.