BIOL300: Chapter 6 Part 2

What must a cell do before it can divide?

Copy its DNA to share with the next cell.

How long does it take to copy the human genome?

Approximately 8 hours during the S-phase.

What is the nature of DNA replication?

DNA replication is semi-conservative, producing two complete double helices from the original DNA molecule.

What is the role of initiator proteins in DNA replication?

They recognize specific sequences at replication origins and break hydrogen bonds to separate DNA strands.

What is a replisome?

The replication machine that contains all the proteins needed to copy DNA.

What is the function of DNA helicase?

To separate and open DNA strands, allowing access for proteins and enzymes.

In which direction does DNA polymerase synthesize new DNA?

In the 5'-to-3' direction.

What is the purpose of primase in DNA replication?

To generate a short RNA primer that provides a starting point for DNA polymerase.

What are Okazaki fragments?

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

What is the role of DNA ligase?

To join the 5' phosphate of new DNA to the adjacent 3' hydroxyl end of the next segment.

How does DNA polymerase proofread its work?

It corrects errors using a 3' to 5' proofreading activity.

What is the function of the sliding clamp (PCNA)?

To enhance DNA synthesis elongation by associating with DNA polymerase.

What is the role of topoisomerases during DNA replication?

To resolve torsional tension and tangled DNA by making single- or double-stranded breaks.

What is telomerase and its function?

An enzyme that extends the telomeres of chromosomes using an RNA template.

What is a mutation?

A permanent change in the DNA sequence.

What is the difference between non-homologous end-joining (NHEJ) and homologous recombination repair (HRR)?

NHEJ is a fast and easy repair method that often alters DNA, while HRR is precise but slower, using a template for repair.

What types of damage can occur to DNA?

Base damage, oxidative damage, hydrolytic attack, and thymine dimers caused by UV light.

What is the role of the MutS/MutL complex in DNA repair?

To recognize mismatches and make a single-stranded break for repair.

What are some examples of human diseases associated with defective DNA repair?

Werner syndrome, Ataxia Telangiectasia, and BRCA 1/2 defects.

What is the significance of post-translational modifications (PTMs) in cellular response to DNA damage?

They play a critical role in regulating the cellular response to DNA damage.

What happens to DNA when it undergoes oxidative damage?

It can lead to base loss or base changes.

What is the function of single-strand binding proteins (SSB)?

To bind to single-stranded DNA, protecting it from nucleases and stabilizing the strand.

What is the significance of the 5' to 3' direction in DNA synthesis?

It is the only direction in which DNA polymerase can synthesize new DNA strands.

How does the replication fork function in DNA replication?

It is the Y-shaped junction where DNA strands are separated and new strands are synthesized.

What is the role of repair polymerase?

To replace RNA primers with DNA during replication.

What is the impact of mutations on cancer development?

Accumulation of mutations can lead to cancer and aging.

What is the importance of DNA replication in laboratory techniques?

It is the basis for techniques like PCR and DNA sequencing.

DNA polymerase synthesizes from

5' to 3'

Primase

An enzyme that joins RNA nucleotides to make the primer using the parental DNA strand as a template.

Nuclease

breaks apart RNA primer

Repair Polymerase

Replaces RNA with DNA

DNA Ligase

joins 5' phosphate of new DNA to adjacent 3'hydroxyl end of the next - GLUE

Leading strand vs. Lagging strand

works toward replication fork / works away from replication fork; both always move in the 5' ➝ 3' direction

proofreading occurs in what direction?

3-5

What does the single stranded binding protein do?

binds to single-strand DNA; protects it from nucleases and at the same time "straightens out" any secondary structures

What do topoisomerase 1 and 2 do?

resolve tension and tangled DNA by breaking the phosphate backbone.

Which topoisomerase makes a a "nick" in one strand to relieve stress?

1

which topoisomerase makes a double strand DNA break and untangle DNA molecules?

2

What are the two most common types of DNA damage?

Depurination and Deamination

Depurination

the loss of a purine base from a nucleotide

Deamination

Removal of amino group from amino acids. -> leads to a base change

How are DNA repair mechanisms activated?

Some proteins serve as communicators or sensors.

Double stranded DNA breaks can be repaired by two mechanisms. What are they?

Non-homologous end joining and homologous recombination

Non-homologous end joining

A mechanism for repairing double-strand breaks in DNA that involves quickly bringing together, trimming, and rejoining the two broken ends; results in a loss of information at the site of repair.

homologous recombination

process by which a cell replaces a stretch of DNA with a segment that has a similar nucleotide sequence-> slow and difficult but more precise