ch 13 g

What is DNA polymerase?

An enzyme that synthesizes DNA by adding nucleotides to the 3' end of a growing strand.

What is primase?

An enzyme that synthesizes RNA primers to initiate DNA replication.

What is DNA ligase?

An enzyme that joins DNA fragments by forming phosphodiester bonds.

What is a primer?

A short DNA or RNA strand that provides a free 3' OH group for DNA polymerase.

What is helicase?

An enzyme that unwinds the DNA double helix.

What is gyrase?

An enzyme that removes supercoils ahead of the replication fork.

What is the leading strand?

The DNA strand synthesized continuously toward the replication fork.

What is the lagging strand?

The DNA strand synthesized discontinuously away from the replication fork.

What are Okazaki fragments?

Short DNA fragments synthesized on the lagging strand.

What is a holoenzyme?

A multi-subunit protein complex that performs DNA replication.

What are subunits?

Individual protein components that make up a larger protein complex.

What is an exonuclease?

An enzyme that removes nucleotides from the ends of DNA strands.

What is the origin of replication (Ori)?

The location on DNA where replication begins.

What is a telomere?

Repetitive DNA sequences at the ends of eukaryotic chromosomes that protect chromosome ends.

What is telomerase?

An enzyme that maintains telomeres by adding repetitive DNA sequences to chromosome ends.

What is semiconservative DNA replication?

Each new DNA molecule contains one original strand and one newly synthesized strand.

What did the Meselson-Stahl experiment demonstrate?

DNA replication is semiconservative.

How was the Meselson-Stahl experiment performed?

E. coli were grown in heavy nitrogen (15N), transferred to light nitrogen (14N), and DNA density was examined after replication.

What happened after one generation in the Meselson-Stahl experiment?

All DNA had intermediate density (15N/14N hybrid DNA).

What happened after two generations in the Meselson-Stahl experiment?

50% hybrid DNA (15N/14N) and 50% light DNA (14N/14N).

What happens to hybrid DNA after additional generations?

The proportion of hybrid DNA decreases by half each generation.

What factors are required for DNA replication?

DNA template, DNA polymerase, dNTPs (dATP, dTTP, dCTP, dGTP), primer, buffer, and Mg2+.

In what direction does DNA polymerase synthesize DNA and read the template?

Synthesizes 5' to 3' and reads the template 3' to 5'.

Why does DNA polymerase require a primer?

It cannot initiate DNA synthesis without an existing 3' OH group.

How does DNA replication begin?

Initiation proteins bind the origin, helicase unwinds DNA, primase synthesizes primers, and DNA polymerase begins synthesis.

What is bidirectional DNA replication?

Replication proceeds in two opposite directions from the origin, forming two replication forks.

How are the leading and lagging strands synthesized?

Leading strand continuously; lagging strand discontinuously as Okazaki fragments.

Why is the lagging strand synthesized discontinuously?

DNA polymerase only synthesizes 5' to 3', so it must synthesize short fragments away from the replication fork.

What are the four main components of the DNA polymerase III holoenzyme?

Core enzyme, dimerizing subunit, clamp loader, and sliding clamp.

What are the functions of the DNA Pol III holoenzyme components?

Core enzyme = DNA synthesis; Dimerizing subunit = holds two cores together; Clamp loader = loads clamp; Sliding clamp = increases processivity.

What is processivity?

The ability of DNA polymerase to synthesize DNA without repeatedly detaching from the template.

How do DNA polymerases coordinate leading and lagging strand synthesis?

The lagging strand forms a loop so both polymerase cores can move together.

What is the main difference between DNA polymerase I and III?

Pol III synthesizes the leading and lagging strands; Pol I removes RNA primers, fills gaps with DNA, and participates in repair.

What is the function of 5' to 3' exonuclease activity?

Removes RNA primers; found in DNA polymerase I.

What is the function of 3' to 5' exonuclease activity?

Proofreading by removing incorrectly incorporated nucleotides; found in DNA polymerases I and III.

What is the overall DNA replication error rate?

Approximately 1 error per 10^9 bases copied.

What is the error rate of DNA Pol III without proofreading?

Approximately 10 errors per 10^6 bases copied.

What happens after DNA polymerase I removes RNA primers?

Pol I fills the gaps with DNA, and ligase seals the remaining nicks.

How do you write a new DNA strand from a template sequence?

Use complementary base pairing (A-T, G-C), make the strands antiparallel, and write the new strand 5' to 3'.

If the template is 5'-ATCGGACTCC-3', what is the new strand written 5' to 3'?

5'-GGAGTCCGAT-3'.

Why do telomeres shorten during DNA replication?

After the final RNA primer is removed, DNA polymerase cannot fill the remaining gap at the chromosome end.

What is the repetitive sequence of human telomeres?

TTAGGG repeated thousands of times.

What is the composition and function of telomerase?

A reverse transcriptase containing a protein component and its own RNA template; it adds DNA repeats to the 3' end of telomeres.

How are telomeres related to aging?

Telomeres shorten as somatic cells divide, and cells senesce (decline) when telomeres become critically short.

How are telomeres related to cancer?

About 90% of cancer cells produce telomerase, allowing continued cell division; stem cells also produce telomerase.