DNA Organization, Replication, and Repair (Lecture 1; Lecture generated)

Flashcard set covering DNA organization, replication machinery, eukaryotic polymerases, telomerase, and DNA repair pathways based on lecture notes.

What three molecular components make up a single DNA nucleotide?

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

Which nitrogenous bases found in DNA belong to the purine class?

Adenine (A) and Guanine (G).

Which nitrogenous bases found in DNA belong to the pyrimidine class?

Cytosine (C) and Thymine (T).

What specific pentose sugar is present in DNA nucleotides?

Deoxyribose.

What covalent bond links the $3'$\text{-OH} group of one sugar to the $5'$\text{-OH} group of the next sugar in a DNA polynucleotide strand?

A phosphodiester bond.

What components constitute the backbone structure of a DNA strand?

Deoxyribose sugars and phosphate groups (deoxyribose-phosphate backbone).

How many hydrogen bonds form between Adenine and Thymine base pairs in DNA?

$2$ hydrogen bonds.

How many hydrogen bonds form between Guanine and Cytosine base pairs in DNA?

$3$ hydrogen bonds.

What term describes the structural arrangement where two complementary DNA strands run in opposite $5' \rightarrow 3'$ directions?

Antiparallel.

What process occurs when heat or alkali reagents break the hydrogen bonds joining complementary DNA strands?

DNA denaturation.

Why do phosphodiester bonds remain intact during heat or alkali denaturation of DNA?

Because phosphodiester bonds are strong covalent bonds that are resistant to heat and alkali reagents.

What term describes the reversible re-joining of separated single-stranded DNA upon removal of denaturing conditions?

Renaturation (or reannealing).

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

The temperature at which $50\%$ of the DNA molecule exists as single strands.

How does base composition influence the melting temperature ($T_m$) of a DNA double helix?

A higher GC content increases the $T_m$ because G:C base pairs are joined by $3$ hydrogen bonds rather than $2$.

What is DNA hybridization?

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

What are the two grooves formed along the surface of the double-helical DNA molecule?

The major groove and the minor groove.

How are base pairs positioned relative to the central helical axis of DNA?

Base pairs are oriented perpendicular to the helical axis.

Which compound serves as the precursor for the phosphate groups in the DNA backbone?

Phosphoric acid.

Which carbon position on the deoxyribose ring lacks a hydroxyl group ($\text{-OH}$) compared to ribose?

The $2'$ carbon position.

At which carbon atom of deoxyribose is the nitrogenous base attached in a nucleotide?

The $1'$ carbon atom.

What percentage of total cellular DNA is comprised of mitochondrial DNA?

Approximately $1\%$.

What is the structural shape and strandedness of mitochondrial DNA?

Circular and double-stranded.

Which evolutionary hypothesis accounts for the origin and circular nature of mitochondrial DNA?

The endosymbiotic theory.

Does mitochondrial DNA contain histone packaging proteins?

No, mitochondrial DNA lacks histones.

How does the base composition of mitochondrial DNA differ from typical nuclear DNA?

Mitochondrial DNA is GC-rich.

How many total genes are present in human mitochondrial DNA?

$37$ genes.

Of the $37$ genes in mitochondrial DNA, how many encode proteins for energy production?

$13$ genes.

Of the $37$ genes in mitochondrial DNA, how many encode rRNA and tRNA?

$24$ genes.

From which parent is mitochondrial DNA inherited in humans?

Exclusively from the mother (maternal inheritance).

Why is mitochondrial DNA useful as a molecular marker for tracking human ancestry?

Because it undergoes no genetic recombination and is inherited strictly along the maternal lineage.

What percentage of human nuclear genomic DNA is non-coding?

Approximately $98\%$.

What is the approximate total length of linear nuclear DNA contained inside a single human cell?

Approximately $6\text{ ft}$ (about $1.8\text{ m}$) per cell.

Approximately how many protein-coding genes are encoded in the human nuclear genome?

Approximately $22,000$ genes.

What structural role does the centromere play during eukaryotic cell division?

It acts as the constricted region of the chromosome and the attachment site for spindle microtubules necessary for correct mitosis.

What are telomeres?

Repetitive DNA sequence caps located at the terminal ends of linear eukaryotic chromosomes.

What specific hexanucleotide sequence is repeated at human telomeres?

\text{TTAGGG}.

Approximately how many times is the \text{TTAGGG} sequence repeated at human telomeres?

Approximately $1,000$ times.

What occurs to telomere length during successive cell divisions in somatic cells?

Telomeres progressively shorten with each cell division.

In cytogenetics, what letter is used to designate the short arm of a chromosome?

The p arm.

In cytogenetics, what letter is used to designate the long arm of a chromosome?

The q arm.

What term describes the super-compacted DNA-protein complex that forms chromosomes?

Chromatin.

How does the degree of condensation compare between euchromatin and heterochromatin?

Euchromatin is less condensed, whereas heterochromatin is more condensed.

Where is euchromatin typically located on a chromosome?

On chromosome arms.

Where is heterochromatin predominantly located on a chromosome?

At centromeres, telomeres, and other specific regions.

What type of DNA sequences predominates in euchromatin?

Unique sequences.

What type of DNA sequences predominated in heterochromatin?

Repeated sequences.

How does gene density compare between euchromatin and heterochromatin?

Euchromatin contains many genes, whereas heterochromatin contains few genes.

How does transcription frequency compare between euchromatin and heterochromatin?

Euchromatin is transcribed often, whereas heterochromatin is transcribed infrequently.

What is the fundamental structural unit of chromatin?

The nucleosome.

Which histone proteins comprise the core octamer of a nucleosome?

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

How many times does double-stranded DNA wrap around a histone octamer core in a nucleosome?

$1.65$ times (or approximately $2$ full turns).

Which histone protein binds to linker DNA to connect adjacent nucleosome cores?

Histone H1.

What term describes the structural appearance of chromatin when nucleosomes are connected by linker DNA?

The "beads-on-a-string" model.

What structure is formed when nucleosomes undergo supercoiling into tubular coils?

Chromatin fibers (or solenoids / $30\text{-nm}$ fibers).

What is the diameter of an uncompacted double-stranded DNA double helix?

$2\text{ nm}$.

What is the structural diameter of a single nucleosome core fiber?

$11\text{ nm}$.

What is the diameter of the solenoidal chromatin fiber formed by folded nucleosomes?

$30\text{ nm}$.

What is the average length of the loops formed by $30\text{-nm}$ chromatin fibers?

$300\text{ nm}$.

Compression and folding of $300\text{-nm}$ chromatin loops yields a fiber of what width?

$250\text{ nm}$ wide.

What is the final width of a fully condensed chromatid in a chromosome?

$700\text{ nm}$ (producing a $1400\text{-nm}$ wide chromosome).

During which phase of the cell cycle does DNA replication take place?

S phase (Synthesis phase).

During which phase of the cell cycle does the majority of DNA repair occur?

G2 phase.

Approximately how long does total genome duplication take in a proliferating human cell?

Approximately $9\text{ hours}$.

What are the specific chromosomal sequences where DNA replication initiates called?

Origins of replication (ori).

Approximately how many origins of replication exist per chromosome in eukaryotic cells?

Approximately $100$ origins per chromosome.

How many origins of replication are found in a typical prokaryotic chromosome?

Only $1$ origin of replication.

Why is DNA replication defined as semiconservative?

Because each newly generated double-stranded DNA molecule contains one original parental strand and one newly synthesized daughter strand.

Why is DNA replication defined as bidirectional?

Because replication forks proceed outward in both directions from the origin of replication.

What is the Y-shaped structure formed as DNA unwinds for replication called?

The replication fork.

What is the enzymatic function of helicase at the replication fork?

It breaks hydrogen bonds between nitrogenous base pairs to separate the two parental DNA strands.

What is the function of DNA topoisomerase during replication?

It relaxes torsional stress and unwinds supercoiled DNA ahead of the advancing replication fork.

What is the function of Single-Stranded Binding Proteins (SSBP)?

They bind to single-stranded parental DNA to prevent the strands from reannealing.

What enzyme synthesizes short RNA primers to initiate DNA synthesis?

Primase (a subunit of DNA polymerase alpha).

What is the approximate length of the RNA primer generated by primase?

Approximately $15\text{ nucleotides}$.

To which chemical group on a growing strand does DNA polymerase attach incoming dNTPs?

The free $3'$\text{-OH} group.

In which direction does DNA polymerase read the parental template strand?

In the $3' \rightarrow 5'$ direction.

In which direction does DNA polymerase synthesize a new daughter DNA strand?

In the $5' \rightarrow 3'$ direction.

Which enzymatic activity allows DNA polymerases to excise RNA primers?

$5' \rightarrow 3'$ exonuclease activity.

Which enzymatic activity provides proofreading capabilities to DNA polymerases?

$3' \rightarrow 5'$ exonuclease activity.

How does $3' \rightarrow 5'$ exonuclease proofreading correct mispaired nucleotides?

It retreats to excise the mismatched nucleotide at the $3'$ end, allowing correct $5' \rightarrow 3'$ synthesis to resume.

Which enzyme joins adjacent DNA fragments by forming phosphodiester bonds between free $3'$\text{-OH} and $5'$\text{-phosphate} ends?

DNA ligase.

In what direction does the leading strand run relative to the replication fork?

It runs $3' \rightarrow 5'$ toward the replication fork.

How is the leading strand synthesized relative to the movement of the replication fork?

Continuously from a single RNA primer by DNA polymerase.

In what direction does the lagging strand run relative to the replication fork?

It runs $3' \rightarrow 5'$ away from the replication fork.

How is the lagging strand synthesized relative to the movement of the replication fork?

Discontinuously from multiple RNA primers, producing Okazaki fragments.

What is the typical length of Okazaki fragments in eukaryotic replication?

Approximately $200\text{ nucleotides}$.

What are the two main functions of DNA Polymerase alpha (Pol $\alpha$)?

It contains primase activity and initiates DNA synthesis.

Does DNA Polymerase alpha (Pol $\alpha$) possess proofreading activity?

No, Pol $\alpha$ lacks proofreading activity.

What is the primary cellular function of DNA Polymerase beta (Pol $\beta$)?

DNA repair.

Does DNA Polymerase beta (Pol $\beta$) possess proofreading activity?

No, Pol $\beta$ lacks proofreading activity.

What is the main function of DNA Polymerase delta (Pol $\delta$)?

Elongation of Okazaki fragments on the lagging strand.

Does DNA Polymerase delta (Pol $\delta$) possess proofreading activity?

Yes, Pol $\delta$ has $3' \rightarrow 5'$ exonuclease proofreading activity.

What is the main function of DNA Polymerase epsilon (Pol $\epsilon$)?

Elongation of the leading strand.

Does DNA Polymerase epsilon (Pol $\epsilon$) possess proofreading activity?

Yes, Pol $\epsilon$ has $3' \rightarrow 5'$ exonuclease proofreading activity.

What is the main function of DNA Polymerase gamma (Pol $\gamma$)?

Replication of mitochondrial DNA.

Does DNA Polymerase gamma (Pol $\gamma$) possess proofreading activity?

Yes, Pol $\gamma$ has $3' \rightarrow 5'$ exonuclease proofreading activity.

What sequence of events processes Okazaki fragments into a continuous strand?

RNA primers are removed by $5' \rightarrow 3'$ exonuclease, gaps are filled by DNA polymerase, and remaining nicks are sealed by DNA ligase.

What causes the end-replication problem in linear eukaryotic chromosomes?

The removal of the terminal RNA primer from the $3'$ end of the lagging strand template leaves an uncopyable gap, leading to strand shortening.

What chemical product is released when incoming dNTPs are attached to a growing DNA chain?

Pyrophosphate ($PP_i$).

What specific chemical link is generated when an incoming nucleotide monophosphate is added to a DNA strand?

A $3' \rightarrow 5'$ phosphodiester bond.