DNA Structure, Genome Organization, and Chromatin Architecture

Flashcards covering DNA structure, comparative viral, bacterial, and eukaryotic genome architecture, chromatin packaging levels, and epigenetic modifications.

What are the three core structural components of a nucleotide?

A phosphate group, a five-carbon sugar, and a nitrogenous base.

Which nitrogenous bases are classified as purines and which are classified as pyrimidines?

Purines include Adenine and Guanine. Pyrimidines include Cytosine, Uracil (in RNA only), and Thymine (in DNA only).

How is a purine ring structure defined in comparison to a pyrimidine ring structure?

A purine consists of a pyrimidine ring fused to an imidazole ring, whereas a pyrimidine is a heterocyclic aromatic compound with a single six-membered ring containing two nitrogen atoms at positions $1$ and $3$.

How many base pairs per turn are in standard B-DNA, and what grooves are featured along its structure?

B-DNA has $10\text{ pb}$ (base pairs) per turn and features both a major groove and a minor groove.

What is the typical range of genome size for viruses?

Viral genomes range in size from $2\text{ Kb}$ to $2\text{ Mb}$ (or $4\text{ Kb}$ to $2\text{ Mb}$).

How does the organization of the E. coli chromosome differ between the exponential phase and the stationary phase of growth?

In the exponential phase, the chromosome forms transcriptionally active loops organized around transcription factories, Fis, and RNA polymerase at promoters. In the stationary phase, it reorganizes into a relaxed loop conformation bound with H-NS and reduced active transcription centers.

How do prokaryotic and eukaryotic gene structures differ regarding non-coding sequences?

Eukaryotic genes contain non-coding intervening sequences called introns within their Open Reading Frame (ORF), whereas prokaryotic genes lack introns and are often organized into operons.

What proportions of the human nuclear genome consist of repetitive versus non-repetitive DNA sequences?

The human nuclear genome consists of $53.94$% repetitive DNA sequences and $46.06$% non-repetitive DNA sequences.

What histone proteins form the core of a nucleosome, and what is its net charge?

The core octamer consists of two copies each of histones $H2A$, $H2B$, $H3$, and $H4$. Histones carry a positive charge.

What constitutes a chromatosome?

A chromatosome consists of a nucleosome core octamer wrapped $1.65$ times by DNA, plus an $H1$ linker histone protein attached.

What are the primary differences between euchromatin and heterochromatin?

Euchromatin represents relaxed, open chromatin (~$90$% of total), is gene-rich, transcriptionally active, heavily acetylated, and has loose $H1$ association. Heterochromatin represents condensed, closed chromatin (~$10$% of total), is gene-poor, remains condensed during interphase, and has tight $H1$ association.

What are the structural dimensions associated with the sequential levels of eukaryotic chromatin condensation?

DNA double helix ($2\text{ nm}$) $\rightarrow$ Nucleosome ($11\text{ nm}$) $\rightarrow$ Chromatin fiber ($30\text{ nm}$) $\rightarrow$ Chromatin loops ($300\text{ nm}$) $\rightarrow$ Compressed fiber ($250\text{ nm}$ to $700\text{ nm}$) $\rightarrow$ Chromatid/Chromosome ($1400\text{ nm}$).

What is a Topologically Associating Domain (TAD) and what is its typical size?

A TAD is a self-interacting genomic region bound by specific boundaries within which regulatory elements interact with target genes. Its average size is ~$1\text{ Mb}$ (ranging from several hundred $\text{Kb}$ to $2\text{ Mb}$).

What is the definition of epigenetics in molecular genetics?

Epigenetics refers to non-sequence changes to the DNA molecule that impact gene expression, such as DNA methylation, histone modification, and nucleosome positioning.

Which post-translational modifications occur on histone tails?

Histone tail modifications include Acetylation (Ac), Phosphorylation (P), Methylation (Me), Citrullination (Ci), and Ubiquitination (Ub).

How do viruses, E. coli, and eukaryotes compare in terms of location of genome, chromosome structure, and ploidy?

Viruses: inside capsid, linear or circular, $1n$. E. coli: cytoplasm (nucleoid region), circular dsDNA, $1n$. Eukaryotes: nucleus (and mitochondria/chloroplast), linear nuclear genome (circular mtDNA/cpDNA), $2n$.