MODULE C2: DNA Metabolism Overview

This set of flashcards covers key concepts in DNA metabolism, including replication, repair, and the roles of specific enzymes involved in these processes.

What is DNA metabolism?

A set of enzyme-catalyzed and tightly regulated processes involving DNA replication, repair, and recombination.

What is the significance of the Meselson-Stahl experiment?

It demonstrated semiconservative DNA replication by showing that the nitrogen incorporated into new dsDNA is equally divided between daughter genomes.

What does DNA elongation require?

A DNA polymerase enzyme, a template parental DNA strand, and a primer with a free 3' OH group.

How does DNA polymerase I correct errors during DNA synthesis?

By 3' → 5' exonuclease activity, allowing proofreading of mispaired bases.

What are Okazaki fragments?

Short pieces of DNA synthesized discontinuously on the lagging strand during DNA replication.

What are the main functions of the three types of DNA polymerases in E. coli?

Polymerase I is for cleanup and repair, Polymerase II is for DNA repair, and Polymerase III is for DNA replication.

What is a replisome?

The entire complex of proteins and enzymes involved in DNA replication.

What are the three stages of DNA replication?

Initiation, elongation, and termination.

What role does DNA ligase play in DNA replication?

It seals nicks in the DNA phosphodiester backbone, especially on the lagging strand.

What is the function of nucleases?

Enzymes that degrade DNA or RNA, with types including DNase for DNA and RNase for RNA.

What is DNA replication?

The process by which DNA makes a copy of itself before cell division.

What is semiconservative replication?

A method of DNA replication where each new DNA molecule consists of one old strand and one newly synthesized strand.

What role do helicases play in DNA replication?

Helicases are enzymes that unwind the double-stranded DNA, separating the strands so replication can occur.

What is a primer in DNA replication?

A short nucleic acid sequence required to initiate DNA synthesis by providing a free 3' OH group for DNA polymerase.

What is the leading strand in DNA replication?

The strand of DNA that is synthesized continuously in the same direction as the replication fork movement.

What is the lagging strand in DNA replication?

The strand of DNA that is synthesized in short segments (Okazaki fragments) in the opposite direction of the replication fork movement.

What is the role of topoisomerases in DNA replication?

Topoisomerases relieve the torsional strain generated ahead of the replication fork by cutting and rejoining DNA strands.

How is RNA involved in DNA replication?

RNA primers are laid down by primase to provide starting points for DNA synthesis.

What is the function of DNA ligase?

DNA ligase seals nicks in the DNA phosphodiester backbone, especially on the lagging strand.

What are Okazaki fragments?

Short pieces of DNA synthesized discontinuously on the lagging strand during DNA replication.

What are the main functions of DNA polymerase I, II, and III in E. coli?

Polymerase I is for cleanup and repair, Polymerase II is for DNA repair, and Polymerase III is for DNA replication.

What is a replisome?

The entire complex of proteins and enzymes involved in DNA replication.

What is the role of nucleases in DNA metabolism?

Nucleases are enzymes that degrade DNA or RNA, with types including DNase for DNA and RNase for RNA.

What is the significance of the Meselson-Stahl experiment?

It demonstrated semiconservative DNA replication by showing that the nitrogen incorporated into new dsDNA is equally divided between daughter genomes.

How does DNA polymerase I correct errors during DNA synthesis?

By 3' → 5' exonuclease activity, allowing proofreading of mispaired bases.

What does DNA elongation require?

DNA elongation requires a DNA polymerase enzyme, a template parental DNA strand, and a primer with a free 3' OH group.

What is the role of single-strand binding proteins in DNA replication?

Single-strand binding proteins bind to unpaired DNA strands during replication to prevent them from re-annealing or forming secondary structures.

What is the origin of replication?

The specific location on the DNA molecule where DNA replication begins, characterized by specific DNA sequences.

What is the function of primase in DNA replication?

Primase is an enzyme that synthesizes short RNA primers needed to initiate DNA synthesis.

How is the accuracy of DNA replication maintained?

The accuracy is maintained through the inherent fidelity of DNA polymerases and proofreading mechanisms such as the 3' → 5' exonuclease activity.

What happens during termination of DNA replication?

Termination occurs when DNA replication is complete, the newly synthesized strands are separated, and all replication machinery is disassembled.

What is the function of DNA polymerase?

DNA polymerases synthesize new DNA strands by adding nucleotides complementary to the template strand.

What are telomeres and their role in DNA replication?

Telomeres are repetitive nucleotide sequences at the ends of chromosomes that protect the chromosome from degradation during replication.

What are mutagens and their effect on DNA?

Mutagens are agents that cause changes or mutations in DNA, potentially leading to cancer or genetic disorders.

What are the key enzymes involved in DNA replication?

Key enzymes include DNA polymerase, helicase, primase, ligase, and topoisomerase.

What is the function of DNA helicase?

DNA helicase unwinds and separates the double-stranded DNA into two single strands for replication.

How do DNA polymerases work during DNA replication?

DNA polymerases add nucleotides in a sequence complementary to the template strand, synthesizing new DNA.

What is the significance of the 5’ to 3’ direction in DNA replication?

DNA synthesis occurs in the 5’ to 3’ direction, meaning nucleotides are added to the 3’ end of the growing strand.

What role does the sliding clamp play in DNA replication?

The sliding clamp holds DNA polymerase in place on the DNA strand, increasing the processivity of DNA replication.

What is the lagging strand's synthesis process?

The lagging strand is synthesized discontinuously in short segments called Okazaki fragments, later joined by DNA ligase.

Why are Okazaki fragments produced during DNA replication?

Okazaki fragments are produced because the lagging strand is oriented in the opposite direction of the replication fork's movement.

What happens if DNA ligase is inhibited?

If DNA ligase is inhibited, the nicks between Okazaki fragments cannot be sealed, leading to incomplete and unstable DNA strands.

What types of DNA polymerases exist in E. coli?

There are three types: DNA polymerase I for cleanup and repair, DNA polymerase II for DNA repair, and DNA polymerase III for DNA replication.

What are the components of a nucleotide?

A nucleotide consists of a phosphate group, a five-carbon sugar (deoxyribose in DNA), and a nitrogenous base (adenine, thymine, cytosine, or guanine).

How does leading strand synthesis differ from lagging strand synthesis?

Leading strand synthesis occurs continuously towards the replication fork, while lagging strand synthesis occurs discontinuously away from the fork in Okazaki fragments.

What is the role of okazaki fragments in DNA replication?

Okazaki fragments are short DNA segments synthesized on the lagging strand; they are later joined together by DNA ligase to form a continuous strand.

What is the significance of the replication fork?

The replication fork is the area where the double-stranded DNA is unwound, allowing for the synthesis of the new DNA strands to occur.

What role does primase play in PCR (Polymerase Chain Reaction)?

In PCR, primase is not used; instead, specific primers are designed to anneal to the target DNA sequence, initiating replication during the amplification process.

How does DNA repair occur post-replication?

DNA repair mechanisms, including mismatch repair and nucleotide excision repair, correct errors that escape proofreading during replication.

What is homologous recombination?

A process where two similar DNA strands exchange genetic information, often used in DNA repair and during meiosis in eukaryotes.