Q&A: DNA Organization, Replication, and Repair

Practice Q&A flashcards covering DNA structure, organization, eukaryotic replication machinery, telomerase, and repair pathways based on lecture notes.

What are the three main structural characteristics of the DNA double helix model?

It is a double helix that is antiparallel and complementary.

What three chemical components make up a nucleotide monomer in DNA?

A nitrogenous base, a pentose sugar (deoxyribose), and a phosphate group.

Which nitrogenous bases belong to the purine class?

Adenine (A) and Guanine (G).

Which nitrogenous bases belong to the pyrimidine class?

Cytosine (C) and Thymine (T).

What chemical bond joins the 3'-OH group of one sugar to the 5'-OH group of the next sugar in a polynucleotide chain?

A phosphodiester bond.

How many hydrogen bonds join Adenine to Thymine, and Guanine to Cytosine in double-stranded DNA?

Two hydrogen bonds join Adenine to Thymine (A:T), and three hydrogen bonds join Guanine to Cytosine (G:C).

How is the melting temperature ($T_m$) of DNA defined?

The temperature at which 50% of the DNA is present as single strands.

How does base composition affect the melting temperature ($T_m$) of DNA?

DNA with high GC-content has a higher $T_m$ because GC pairs have three hydrogen bonds compared to two in AT pairs.

What is hybridization in the context of nucleic acids?

The tendency of single-stranded DNA to bind complementary sequences of DNA or RNA.

What are the key structural characteristics of mitochondrial DNA?

It is circular, double-stranded, lacks histones, and is GC rich.

How many total genes are in human mitochondrial DNA, and how are they divided by function?

37 genes total: 13 for energy production and 24 for rRNA and tRNA.

From which parent is mitochondrial DNA exclusively inherited?

It is derived exclusively from the mother.

What percentage of nuclear DNA is non-coding, and approximately how many genes does nuclear DNA encode?

Approximately 98% is non-coding, and it encodes approximately 22,000 genes.

What is the function of a chromosome's centromere?

It serves as the attachment site for spindle microtubules and is required for correct mitosis.

What specific sequence repeat is found at chromosome telomeres, and how many times is it repeated?

The sequence TTAGGG is repeated approximately 1,000 times.

How do euchromatin and heterochromatin differ in condensation, gene density, and transcription frequency?

Euchromatin is less condensed, contains many genes, and is transcribed often; heterochromatin is more condensed, contains few genes, and is transcribed infrequently.

Which histone proteins compose the octamer core of a nucleosome?

Two molecules each of histones H2A, H2B, H3, and H4.

What is the role of histone H1 in chromatin packaging?

Histone H1 binds to linker DNA and connects adjacent nucleosomes.

During which cell cycle phases do DNA replication and DNA repair primarily occur?

DNA replication occurs during S phase, and DNA repair occurs during $G_2$ phase.

How long does cell genome duplication take, and how many origins of replication exist per chromosome in eukaryotes versus prokaryotes?

It takes approximately 9 hours. Eukaryotes have approximately 100 origins per chromosome, while prokaryotes have only 1.

What two descriptive terms characterize the mechanism and directionality of DNA replication?

Semiconservative and bidirectional.

What is the specific function of DNA helicase during replication?

It breaks hydrogen bonds and separates the two strands of DNA.

What is the function of DNA topoisomerase ahead of the replication fork?

It relaxes coils and unwinds DNA ahead of the replication fork.

What is the function of single-stranded binding proteins (SSBP) during replication?

They attach to each single strand to prevent reannealing.

Which enzyme synthesizes the RNA primer for DNA replication, and how long is the primer?

Primase (a subunit of DNA polymerase) synthesizes an RNA primer of approximately 15 nucleotides.

In what direction does DNA polymerase read parental DNA, and in what direction does it synthesize daughter DNA?

It reads parental DNA 3' to 5' and synthesizes daughter DNA 5' to 3'.

Which enzymatic activity enables DNA polymerase to proofread mismatched nucleotides?

3' to 5' exonuclease activity.

What are the primary roles of Pol $\delta$ and Pol $\epsilon$ in eukaryotic DNA replication?

Pol $\delta$ elongates Okazaki fragments on the lagging strand, and Pol $\epsilon$ elongates the leading strand.

Which DNA polymerase is responsible for replicating mitochondrial DNA?

Pol $\gamma$ (gamma).

What chemical reaction is catalyzed by DNA ligase?

It joins a free 3'-OH group and a free 5'-phosphate group to form a phosphodiester bond.

How does lagging strand synthesis differ from leading strand synthesis?

The leading strand is synthesized continuously toward the replication fork; the lagging strand is synthesized discontinuously away from the fork as Okazaki fragments (approx. 200 nucleotides) from multiple RNA primers.

What causes the end-replication problem in eukaryotic chromosomes?

Removal of the terminal RNA primer from the 3'-end of the daughter strand during lagging strand synthesis leaves a gap that cannot be filled, leading to progressive telomere shortening.

What are the two components of the ribonucleoprotein telomerase, and what genes encode them?

Reverse transcriptase encoded by the TERT gene, and an RNA template encoded by the TERC gene.

In which cell types is telomerase expressed?

It is expressed in germline cells and cancer cells (it is not expressed in somatic cells).

What is the overall error rate (fidelity) of DNA replication?

Approximately 1 error in every $10^9$ to $10^{10}$ nucleotides.

How does direct damage reversal repair $O^6\text{-methylguanine}$ lesions?

Methyltransferase removes the methyl group from $O^6\text{-methylguanine}$; the methylated enzyme becomes permanently inactive, requiring one enzyme per methyl group removed.

What four sequential steps make up a generic DNA excision repair pathway?

1. Detection of damage;

2. Excision of damaged DNA by endo-/exonucleases;

3. Replacement of excised region by DNA polymerase;

4. Nick sealing by DNA ligase.

What spontaneous DNA lesions are repaired by Base Excision Repair (BER), and at what daily rates do they occur?

Depurination (>1000/day) and deamination of Cytosine to Uracil (>100/day).

What type of DNA damage is repaired by Nucleotide Excision Repair (NER), and what disorder results from NER defects?

Bulky damage distorting the helix (such as benzo[a]pyrene-guanine adducts and UV-induced pyrimidine/T-T dimers); defects result in xeroderma pigmentosum.

How do Homologous Recombination (HR) and Non-homologous end-joining (NHEJ) differ in accuracy and template requirement?

HR uses information from the sister chromatid as a template and is precise (mostly during S phase); NHEJ joins breaks without sequence similarity, works throughout the cell cycle, and is error-prone (causing deletions or small insertions).