Here is the completely updated `question.php`.
I added the missing `$breadcrumbs` array and defined `$category_name` and `$topic_name` right before the header is included. This ensures that `header.php` generates the correct Breadcrumb Schema, page title, and meta description for single question pages.
Replace your entire `question.php` with this:
```php
DNA Replication Questions
Q.
DNA replication is described as semiconservative because:
Both daughter strands are entirely new
Only one daughter molecule is produced
Each daughter molecule has one parental and one newly synthesized strand
Both parental strands stay together in one daughter
Explanation:
Each daughter DNA molecule contains one parental (conserved) strand and one newly synthesized strand.
Q.
The Meselson-Stahl experiment used which isotope to demonstrate semiconservative replication?
Carbon-14 (14C)
Nitrogen-15 (15N)
Sulfur-35 (35S)
Phosphorus-32 (32P)
Explanation:
Meselson and Stahl (1958) labeled DNA with heavy nitrogen (15N) and tracked its distribution in successive generations using density gradient centrifugation.
Q.
Sites on DNA where replication initiates are called:
Origins of replication
Centromeres
Promoters
Telomeres
Explanation:
Origins of replication are specific DNA sequences recognized by initiator proteins that recruit the replication machinery.
Q.
The Y-shaped structure where DNA is being unwound and copied is called the:
Replication fork
Replisome
Promoter region
Okazaki fork
Explanation:
The replication fork is the site where parental DNA is separated into two template strands and new DNA is synthesized.
Q.
Which enzyme unwinds the DNA double helix at the replication fork?
Ligase
Primase
DNA polymerase
DNA helicase
Explanation:
DNA helicase uses ATP hydrolysis to break hydrogen bonds between base pairs and separate the two strands.
Q.
Which enzyme synthesizes RNA primers during DNA replication?
Topoisomerase
DNA polymerase III
DNA ligase
Primase
Explanation:
Primase is an RNA polymerase that creates short RNA primers, providing a 3'-OH for DNA polymerase to extend.
Q.
DNA polymerase can only add nucleotides to which end of a growing strand?
Only the middle of the strand
The 5' end
The 3' end
Both ends simultaneously
Explanation:
DNA polymerases synthesize DNA strictly in the 5'→3' direction, adding to the free 3'-OH end of the growing chain.
Q.
The strand synthesized continuously toward the replication fork is called the:
Lagging strand
Template strand
Leading strand
Coding strand
Explanation:
The leading strand is synthesized in the same direction as fork movement (5'→3'), so it grows continuously with a single primer.
Q.
The strand synthesized discontinuously in short fragments is called the:
Leading strand
Lagging strand
Non-template strand
Sense strand
Explanation:
The lagging strand is synthesized away from the fork direction in short Okazaki fragments, each requiring its own primer.
Q.
The short DNA fragments synthesized on the lagging strand are called:
Kornberg fragments
Watson fragments
Okazaki fragments
Klenow fragments
Explanation:
Okazaki fragments are typically 100–200 nt in eukaryotes and 1000–2000 nt in prokaryotes; they are later joined by DNA ligase.
Q.
The enzyme that joins Okazaki fragments together is:
DNA polymerase I
DNA helicase
DNA ligase
Topoisomerase
Explanation:
DNA ligase seals the nick between adjacent fragments by forming a phosphodiester bond between the 3'-OH and 5'-phosphate.
Q.
In E. coli, which DNA polymerase is primarily responsible for chromosomal DNA replication?
DNA polymerase I
DNA polymerase III
DNA polymerase II
DNA polymerase IV
Explanation:
DNA polymerase III is the main replicative enzyme in E. coli, with high processivity and 3'→5' proofreading exonuclease activity.
Q.
In E. coli, which DNA polymerase removes RNA primers and fills the resulting gaps?
DNA polymerase II
DNA polymerase III
Primase
DNA polymerase I
Explanation:
DNA polymerase I possesses a unique 5'→3' exonuclease activity that removes RNA primers while simultaneously extending the DNA chain.
Q.
Which exonuclease activity enables DNA polymerase to remove mismatched nucleotides during replication?
Endonuclease activity
Helicase activity
3'→5' exonuclease activity
5'→3' exonuclease activity
Explanation:
The 3'→5' exonuclease activity provides proofreading, removing incorrectly incorporated nucleotides and increasing replication fidelity.
Q.
Single-strand binding proteins (SSBs) function during replication to:
Synthesize RNA primers
Cleave phosphodiester bonds
Prevent re-annealing of separated DNA strands
Add supercoils to DNA
Explanation:
SSBs coat single-stranded DNA to prevent premature re-annealing and to protect the strands from nucleases.
Q.
In bacteria, which enzyme introduces negative supercoils ahead of the replication fork?
DNA polymerase I
DNA gyrase
DNA ligase
DNA helicase
Explanation:
DNA gyrase (a type II topoisomerase) uses ATP to introduce negative supercoils, relieving positive torsional stress generated by fork progression.
Q.
Telomerase functions to:
Synthesize mitochondrial DNA
Cleave Okazaki fragments
Remove RNA primers
Extend chromosome ends using an RNA template
Explanation:
Telomerase is a reverse transcriptase that uses its own RNA template to extend telomeric repeats at chromosome ends, compensating for end-replication loss.
Q.
Eukaryotic chromosomes typically have how many origins of replication per chromosome?
No fixed origins
Exactly one origin
Two origins only
Multiple origins
Explanation:
Eukaryotic chromosomes are long and replicate from multiple origins, allowing genome duplication within a single S phase.
Q.
Replication that proceeds in both directions away from a single origin is described as:
Rolling circle replication
Conservative replication
Bidirectional replication
Unidirectional replication
Explanation:
Bidirectional replication creates two replication forks moving in opposite directions from each origin, doubling the rate of genome duplication.
Q.
The high fidelity of DNA replication (error rate ~1 in 10^9) is achieved by:
Base selection, proofreading, and mismatch repair
Only base selection by DNA polymerase
Random chance alone
Only post-replication repair
Explanation:
Base selection, 3'→5' proofreading exonuclease activity, and post-replication mismatch repair together produce the extremely low error rate observed.
Q.
Which of the following is NOT required for DNA replication?
DNA template
dNTPs
Primase
RNA polymerase
Explanation:
RNA polymerase is the enzyme for transcription. DNA replication requires a template, primers, dNTPs, and the replisome proteins, not RNA polymerase.
Q.
Okazaki fragments are found on which strand?
Neither strand
Lagging strand
Both strands equally
Leading strand
Explanation:
Okazaki fragments are exclusively synthesized on the lagging strand because this strand must be synthesized in short segments away from fork movement.
Q.
Primers in DNA replication are made of:
Protein
RNA
DNA
Polysaccharide
Explanation:
Primase synthesizes short RNA primers (not DNA) because DNA polymerases can only extend an existing 3'-OH group, which RNA primers provide.
Q.
The replisome is best described as:
A type of topoisomerase
A DNA repair enzyme
The multiprotein complex that carries out DNA replication
A ribosome-bound complex
Explanation:
The replisome is the multiprotein machine at the replication fork composed of helicase, primase, DNA polymerases, and accessory factors.
Q.
Which of the following organisms uses a theta (θ) structure during DNA replication?
Retroviruses only
Eukaryotic linear chromosomes
Mitochondria only
Bacteria with circular chromosomes
Explanation:
Theta replication occurs in circular DNA molecules such as bacterial chromosomes and plasmids, producing a characteristic θ-shaped intermediate.