Module 11 - DNA replication and repair

DNA replication

The process by which a cell duplicates its DNA, resulting in two identical copies of the DNA molecule.

Semiconservative

A method of DNA replication in which each new DNA molecule consists of one original strand and one newly synthesized strand.

Origin of replication

The specific location on the DNA molecule where replication begins.

DNA gyrase

An enzyme that relieves the strain of unwinding DNA during replication by introducing negative supercoils.

DNA polymerase

An enzyme responsible for synthesizing new DNA strands by adding nucleotides complementary to the template strand.

Okazaki fragments

Short segments of DNA synthesized on the lagging strand during DNA replication.

Lagging strand

The DNA strand that is synthesized discontinuously in short segments during replication.

Leading strand

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

SSB proteins

Single-strand binding proteins that stabilize unwound DNA during replication to prevent it from re-annealing.

Exonuclease

An enzyme that removes nucleotides from the ends of a DNA strand, playing a role in proofreading and repair.

Beta-clamp

A protein that encircles DNA and holds DNA polymerase in place during replication, enhancing processivity.

DNA polymerase III

The primary enzyme involved in DNA replication in prokaryotes, responsible for synthesizing new DNA strands.

Nucleotide excision repair

A DNA repair mechanism that removes damaged nucleotides and replaces them with the correct ones.

Base excision repair

A DNA repair process that corrects damaged or mismatched bases by removing and replacing them.

Mismatch repair

A system for recognizing and repairing erroneous insertion, deletion, and misincorporation of bases that can occur during DNA replication.

Double-strand breakage repair

A repair mechanism that fixes breaks in both strands of the DNA helix, often involving homologous recombination or non-homologous end joining.

DNA replication in bacterial cells

The process by which bacteria replicate their circular DNA, typically starting at a single origin of replication and proceeding bidirectionally.

The structure and functions of DNA polymerases

DNA polymerases are multi-subunit enzymes that synthesize DNA by adding nucleotides to a growing strand, with various types performing distinct roles in replication and repair.

Fidelity of replication

The accuracy of DNA replication, which is ensured by the proofreading ability of DNA polymerases and various repair mechanisms.

Replication in Eukaryotic cells

Eukaryotic DNA replication involves multiple origins of replication, complex regulation, and the involvement of various proteins and enzymes to ensure accurate duplication of linear chromosomes.

Proteins required for replication

Various proteins, including helicases, primases, DNA polymerases, and ligases, are essential for the initiation, elongation, and completion of DNA replication.

DNA repair (NER and BER)

Nucleotide excision repair (NER) removes bulky DNA lesions, while base excision repair (BER) corrects non-helix-distorting base damage.

Cholera toxin exerts its effect on epithelial cells in the intestinal lumen by:

inhibiting GTPase activity in the Gα subunit.

The oriC sequence is to E. coli as _______ is to yeast.

autonomous replicating sequence (ARS)

Which amino acids are known to be phosphorylated by most protein kinases?

serine, threonine, tyrosine

Okazaki fragments are synthesized using the _______ strand as a template in the _______ direction.

lagging; 5′ to 3′

Which type of DNA repair removes via a cut-and-patch mechanism a variety of bulky lesions, like pyrimidine dimers and nucleotides to which various chemical groups have been attached?

nucleotide excision repair.

When the cyclin concentration _____, cyclin-dependent kinase is activated, causing the cell to:

rises: enter the M phase

Which of the following is NOT true regarding the kinetochore?

It is the same as the centromere.

Replication of a DNA strand, whether it is a leading or lagging strand, is initiated by the enzyme:

primase

Sometimes an enzyme is activated by a receptor and brings about the cellular response by generating a second messenger. Such an enzyme is called a(n) __________.

effector

The small portions in which eukaryotic cells replicate their genomes are called _______.

replicons

Explain how semiconservative principle of DNA relates to genomic fidelity

Since DNA replication uses the old strand as a template for the new one, it is a near perfect copy of the genetic code, reducing mutations and more accurate genetic info

DNA replication steps in eukaryotes: initiation, elongation and termination (explain each)

initiate with multiple origins, uses a CMG helicase complex to open helix

Elongation: DNA pol e and sigma, continoues and discontinous synthesis

Termination: where the forks meets, requires replisome disassembly

DNA pol alpha

RNA Primase for Eukaryotes, has some pol activity, no proofreading activity

DNA pol epsilon

leading strand synthesis and proofreasing

DNA pol gamma

replicates mitochondrial DNA

DNA pol sigma

lagging strand synthesis, fills gaps during DNA repair

DNA pol beta

BER repair, filling small gaps, removal of damaged bases