Chromatin Structure, DNA Replication, and Cell Cycle Key Concepts W2

What is chromatin?

The complex of DNA and proteins (primarily histones) that makes up eukaryotic chromosomes.

What is the primary function of histones?

Histones act as spools around which DNA winds to condense and package it into compact structures like nucleosomes.

What does the 'beads on a string' conformation represent?

It represents the first level of DNA packaging where DNA is wrapped around histone octamers, forming nucleosomes connected by linker DNA.

How much DNA is typically associated with one nucleosome?

Approximately 200 base pairs of DNA.

What are the four core histones?

H2A, H2B, H3, and H4.

What is the role of histone H1?

Histone H1 binds to the linker DNA and the nucleosome core, facilitating the folding of the 'beads on a string' into a more compact 30nm chromatin fiber.

What are the three essential components of a functional eukaryotic chromosome?

An origin of replication (ORI), a centromere, and telomeres.

What is the function of the origin of replication (ORI)?

It is the specific DNA sequence where the replication machinery assembles to initiate DNA synthesis.

What is the role of the centromere?

It serves as the attachment site for kinetochore proteins, ensuring proper chromosome segregation during cell division.

What is the 'end replication problem'?

The inability of DNA polymerase to replicate the very ends of linear chromosomes, leading to progressive shortening of DNA with each round of replication.

How do telomeres address the end replication problem?

Telomeres consist of repetitive non-coding sequences at the ends of chromosomes that protect essential genetic information from being lost during replication.

What is the purpose of a selection marker in a plasmid transformation experiment?

It allows researchers to identify and isolate cells that have successfully taken up the plasmid by enabling them to grow under specific selective conditions (e.g., lacking a nutrient).

What was the conclusion of the Meselson-Stahl experiment?

It demonstrated that DNA replication is semi-conservative, meaning each new DNA molecule consists of one original parent strand and one newly synthesized strand.

What are the three hypothesized models of DNA replication tested by Meselson and Stahl?

Conservative, semi-conservative, and dispersive replication.

What does DNA polymerase require to initiate synthesis?

It requires a template DNA strand and an RNA primer to provide a free 3'-OH group.

What are dNTPs?

Deoxynucleotide triphosphates, which serve as the building blocks (substrates) for DNA synthesis.

In which direction is a new DNA strand synthesized?

DNA synthesis always occurs in the 5' to 3' direction, meaning nucleotides are added to the 3' end of the growing strand.

What is the role of pyrophosphatase in DNA synthesis?

It hydrolyzes the pyrophosphate (PPi) released during phosphodiester bond formation into two inorganic phosphates, driving the reaction forward thermodynamically.

Why is an RNA primer used instead of a DNA primer?

RNA primers are synthesized by primase, which does not require a pre-existing 3'-OH group to initiate synthesis, unlike DNA polymerase.

What is the structural basis for histone/DNA interaction?

Histones are rich in positively charged amino acids, which form strong electrostatic attractions with the negatively charged phosphate backbone of DNA.

What are histone tails?

Flexible N-terminal extensions of histones that are subject to various chemical modifications (e.g., acetylation, methylation) that regulate chromatin structure and gene expression.

What happens to a yeast cell that fails to acquire a plasmid with a selection marker on selective media?

It will not grow because it lacks the necessary gene provided by the plasmid to survive under those specific conditions.

How does the density gradient centrifugation distinguish between 15N and 14N DNA?

15N-labeled DNA is denser and migrates further down the density gradient tube compared to the lighter 14N-labeled DNA.

What would the results look like after one generation if replication were conservative?

There would be two distinct bands: one corresponding to heavy (15N) DNA and one to light (14N) DNA, with no intermediate density.

What is the role of the chromosome scaffold?

It is a protein-based structure that helps organize and condense chromatin into the highly compact form of a mitotic chromosome.

Does DNA polymerase facilitate phosphodiester bond formation in a sequence-specific manner?

No, DNA polymerase binds DNA non-specifically, relying on base-pairing rules to ensure the correct nucleotide is added to the template.

What is the chemical mechanism of phosphodiester bond formation?

The 3'-OH group of the growing DNA strand performs a nucleophilic attack on the alpha-phosphate of the incoming dNTP, releasing pyrophosphate.