dna replication and repair: key concepts amd mechanisms

What is the role of base-pairing in DNA replication?

Base-pairing ensures that adenine (A) pairs with thymine (T) and guanine (G) pairs with cytosine (C), allowing the new strand to be complementary to the template strand.

What is semi-conservative replication?

Semi-conservative replication is when the parent DNA double helix separates, and each original strand serves as a template for a new complementary strand, resulting in two identical DNA double helices.

What initiates DNA replication?

DNA replication begins at specific sequences called origins of replication, recognized by initiator proteins that unwind the double helix.

What are replication forks?

Replication forks are Y-shaped structures formed during DNA synthesis at replication origins, where two forks move in opposite directions to unwind the DNA.

How does DNA polymerase synthesize DNA?

DNA polymerase catalyzes the addition of nucleotides to the 3′ end of a growing DNA strand, using deoxyribonucleoside triphosphates (dNTPs) as the nucleotide source.

In what direction is new DNA synthesized?

New DNA is synthesized in the 5′ → 3′ direction because nucleotides can only be added to the free 3′ hydroxyl group.

What is the significance of the antiparallel nature of DNA strands?

The antiparallel nature of DNA strands means that new strands have opposite polarities, affecting how leading and lagging strands are synthesized.

What are Okazaki fragments?

Okazaki fragments are short DNA segments synthesized on the lagging strand during replication, created in the 5′ → 3′ direction.

How are Okazaki fragments joined together?

Okazaki fragments are joined together by DNA ligase, which seals nicks between adjacent fragments to form a continuous DNA strand.

What is the role of primase in DNA replication?

Primase synthesizes short RNA primers that allow DNA polymerase to initiate DNA synthesis without needing an existing 3′ end.

What is the proofreading function of DNA polymerase?

DNA polymerase checks for errors during DNA synthesis, removing mispaired nucleotides and replacing them with the correct ones using its 3′→5′ exonuclease activity.

What happens during the removal of RNA primers?

Nucleases remove RNA primers, and a repair DNA polymerase fills in the gaps with DNA.

What is the energy source for DNA synthesis?

The energy for DNA synthesis comes from the hydrolysis of high-energy phosphate bonds in incoming dNTPs, releasing pyrophosphate (PPi).

What is the function of DNA ligase?

DNA ligase seals the nicks between adjacent Okazaki fragments, forming a continuous sugar-phosphate backbone in the DNA strand.

What is the significance of bidirectional replication?

Bidirectional replication allows two replication forks to synthesize new DNA strands simultaneously, increasing the efficiency of the replication process.

What is torsional stress in DNA replication?

Torsional stress occurs when DNA helicase unwinds the double helix, causing the DNA ahead of the replication fork to become overwound.

How does the replication machine function?

The replication machine involves a complex of proteins that coordinate the synthesis of leading and lagging strands, ensuring rapid DNA synthesis.

What is the role of single-stranded templates in DNA replication?

Single-stranded templates serve as the basis for complementary strand synthesis once the double helix is unwound at the replication fork.

What occurs during the three stages of fork progression in DNA replication?

Stage 1: Origins open and forks move outward; Stage 2: Forks advance, producing new DNA while parental strands remain; Stage 3: Forks meet, completing replication.

What is the function of the 5′ phosphate end in DNA ligase activity?

The 5′ phosphate end of one DNA fragment is activated by ATP hydrolysis, allowing it to join to the 3′ hydroxyl end of the next fragment.

What is the role of the lagging strand polymerase during Okazaki fragment synthesis?

The lagging strand polymerase moves to the next RNA primer after finishing one Okazaki fragment, ensuring efficient synthesis of the lagging strand.

What visual evidence supports the DNA replication process?

Electron micrographs show replication bubbles and nucleosomes along replicating DNA, confirming the process of DNA replication.

What is the significance of multiple origins of replication?

Multiple origins of replication allow for faster replication of the entire DNA molecule by enabling simultaneous synthesis at various points.

What creates torsional strain during DNA replication?

The unwinding of the double helix by DNA helicase ahead of the replication fork.

How does DNA supercoiling relate to torsional stress?

Supercoiling temporarily relieves some torsional stress but is insufficient for continuous replication.

What is the role of DNA topoisomerase during replication?

It resolves torsional stress by introducing transient single-strand breaks, allowing DNA to rotate freely.

What is the function of DNA polymerase?

It adds nucleotides to the 3′ end of the growing DNA strand using the parental strand as a template.

What does DNA helicase do?

It unwinds the DNA double helix ahead of the replication fork using ATP energy.

What is the purpose of single-strand DNA-binding protein?

It binds to exposed single-stranded DNA, preventing it from re-annealing before replication.

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

It keeps DNA polymerase attached to the template for efficient, continuous synthesis.

What does the clamp loader do?

It uses ATP to load the sliding clamp onto DNA.

What does DNA ligase do?

It seals nicks between Okazaki fragments on the lagging strand using ATP.

What is the function of telomerase?

It extends the 3′ end of the parental DNA template, allowing DNA polymerase to complete replication of the lagging strand.

What happens to the lagging strand during DNA replication?

It cannot be completely replicated, leaving a gap at the chromosome end after the final RNA primer is removed.

What is depurination in DNA damage?

It removes guanine or adenine from the DNA backbone, resulting in a missing base.

What occurs during deamination?

It converts cytosine to uracil by removing an amino group, altering base-pairing properties.

What is a thymine dimer?

A covalent bond formed between two adjacent thymine bases, distorting DNA structure and interfering with replication.

What is the consequence of unrepaired thymine dimers?

They may lead to mutations and increase the risk of skin cancers such as melanoma.

What is the mismatch repair system?

It removes replication errors by recognizing and correcting incorrect bases using the original parent strand as a template.

What is Nonhomologous End Joining (NHEJ)?

A repair mechanism that trims broken DNA ends and directly joins them, often resulting in loss of nucleotides.

What is Homologous Recombination (HR)?

A precise repair mechanism that uses a duplicated DNA molecule as a template to restore the original sequence.

What is the relationship between sickle-cell anemia and DNA mutations?

A single nucleotide change in the β-globin gene leads to abnormal hemoglobin structure and sickle-cell anemia.

How does the accumulation of mutations relate to cancer?

Cancer arises from the accumulation of multiple mutations over time, leading to uncontrolled cell growth.

What evolutionary advantage do carriers of sickle-cell anemia have?

They have resistance to malaria, as the parasite grows poorly in sickle-cell hemoglobin.