DNA Topology and Chromosomes

These flashcards cover key concepts from the lecture on DNA topology and chromosomes, including structures, roles, and essential definitions.

What are chromosomes composed of?

Chromosomes include dedicated sequences that ensure their replication, transcription, packaging, and transmission from one generation to the next.

What does torsional stress in DNA refer to?

It refers to the state of DNA being underwound relative to the stable B-form structure, facilitating both the packaging and access to genetic information.

What role do topoisomerases play in DNA structure?

Topoisomerases control DNA underwinding, helping to manage torsional stress.

What is the difference between introns and exons in eukaryotic genes?

Introns are non-coding segments that interrupt the coding sequences (exons), which actually code for proteins.

What are telomeres?

Telomeres are sequences at the ends of eukaryotic chromosomes that help stabilize the chromosome and prevent degradation.

What is the function of the centromere?

The centromere serves as an attachment point for proteins that link the chromosome to the mitotic spindle during cell division.

How is the human genome organized in terms of chromosomes?

Humans have two sets of 23 linear chromosomes in each diploid cell.

Define genome.

The genome is the complete (haploid) set of genetic material of an organism.

What is the primary sequence of a gene?

The primary sequence of a gene encodes for a polypeptide or RNA with a structural or catalytic function.

What is meant by the 'one gene-one polypeptide hypothesis'?

It means that a gene is a segment of genetic material that defines or codes for one specific polypeptide.

What type of DNA structure do most eukaryotic genes contain?

Most eukaryotic genes contain both introns and exons.

What is supercoiling in relation to DNA?

Supercoiling is the coiling of a coil, which can occur in DNA as a result of tension and torsional stress.

Explain the concept of linking number (Lk) in DNA.

Linking number (Lk) quantifies the topological state of circular DNA and is affected by the DNA's twist and writhe.

What happens to the linking number when DNA is underwound?

The linking number (Lk) decreases; underwound DNA has a lower Lk compared to relaxed DNA.

What is the average number of amino acids in a typical human polypeptide chain?

On average, a typical human polypeptide chain contains 350 amino acid residues.

Describe nucleosomes in eukaryotic DNA.

Nucleosomes are the fundamental structural units of chromatin, composed of core histone proteins bound to approximately 146 base pairs of DNA.

Why are histones important in the organization of DNA?

Histones are basic proteins that package and order the DNA, facilitating its compact organization in the chromatin.

What effect does negative supercoiling have on DNA accessibility?

Negative supercoiling increases access to DNA strands, facilitating processes like transcription.

What is a characteristic feature of bacterial chromosomes?

Bacterial chromosomes are typically circular and organized into looped domains.

What is the role of intercalating agents in DNA structure?

Intercalating agents, like ethidium bromide, can bind to DNA and alter its structure by affecting twist and writhe.

What is Twist ($Tw$) in DNA topology?

Twist refers to the number of helical turns in the DNA structure.

What is Writhe ($Wr$) in DNA topology?

Writhe refers to the number of superhelical turns, representing the coiling of the DNA axis upon itself.

How is the Linking Number ($Lk$) related to Twist and Writhe?

The topological state is defined by the equation $Lk = Tw + Wr$.

What defines 'relaxed' DNA?

DNA is considered relaxed when it has no superhelical tension, meaning $Wr = 0$ and $Lk$ is equal to the number of base pairs divided by the helical repeat ($10.5 bp/turn$).

What is the difference between positive and negative supercoiling?

Positive supercoiling results from overwinding the DNA ($Lk$ increases), while negative supercoiling results from underwinding ($Lk$ decreases).

How does RNA polymerase affect DNA topology during elongation?

Movement of RNA polymerase generates positive supercoils ahead of the transcription bubble and negative supercoils behind it.

What is the catalytic mechanism of topoisomerases?

They utilize a nucleophilic tyrosine to break the phosphodiester backbone, pass a DNA strand or duplex through the break, and then religate the DNA.

What distinguishes Type II topoisomerases?

Type II topoisomerases break both strands of the DNA double helix and require ATP to change the linking number by steps of $2$.

What is the function of DNA Gyrase?

DNA Gyrase is a bacterial Type II topoisomerase that specifically introduces negative supercoils into DNA.

Compare plectonemic and solenoidal supercoiling.

Plectonemic supercoiling involves the DNA axis twisting around itself (extended, thin fibers), whereas solenoidal supercoiling involves DNA wrapping around a core (like a garden hose on a reel).

What is the composition of the histone core?

The histone core is an octamer composed of two copies each of histones $H2A$, $H2B$, $H3$, and $H4$.

How many base pairs per turn ($bp/turn$) are in standard B-DNA?

Standard B-DNA contains approximately $10.5$ base pairs per helical turn.

What are histone tails?

Histone tails are flexible, disordered $N$-terminal regions of histone proteins that extend outside the nucleosome core.

What is the role of post-translational modifications (PTMs) on histones?

PTMs, such as acetylation, methylation, and phosphorylation of histone tails, regulate chromatin compaction and gene expression.