Molecular Structure of Chromosomes and Transposable Elements

Comprehensive vocabulary flashcards covering the molecular structure, compaction levels, and organizational machinery of prokaryotic and eukaryotic chromosomes, as well as the mechanisms and evolutionary consequences of transposable elements.

Nucleoid

The irregularly shaped, non-membrane-enclosed region within a prokaryotic cell where the single circular chromosome is situated in direct contact with the cytoplasm.

Loop Domains (Microdomains)

Structural folds of bacterial chromosomal DNA—typically approximately $10{,}000\,\text{bp}$ in size—that compact the genome about 1,000-fold so that it fits inside the bacterial cell.

Nucleoid-Associated Proteins (NAPs)

Bacterial DNA-binding proteins that bend DNA or form cross-bridges between distant DNA regions to establish microdomains and macrodomains, facilitating compaction, organization, segregation, and gene regulation.

DNA Supercoiling

The underwinding or overwinding of the DNA double helix into higher-order torsional coils; bacterial chromosomal DNA is maintained in a negatively supercoiled state (about one negative supercoil per $40$ helical turns in Escherichia coli).

Negative Supercoiling

The left-handed twisting/underwinding of the double helix that compacts chromosomal DNA and creates localized torsional tension that promotes complementary strand separation for replication and transcription.

DNA Gyrase (DNA Topoisomerase II)

A bacterial enzyme that uses energy from $2\,\text{ATP}$ molecules to introduce negative supercoils into circular DNA, relax positive supercoils, and untangle intertwined DNA molecules.

DNA Topoisomerase I

A bacterial enzyme that relieves torsional tension by relaxing negative supercoils without consuming ATP.

Quinolones

A class of antibacterial drugs that selectively inhibit bacterial DNA gyrase, impairing negative supercoiling, the relaxation of positive supercoils, chromosome compaction, and strand separation.

Origins of Replication

Specific nucleotide sequences where replication fork assembly and DNA synthesis begin; eukaryotic chromosomes possess many origins along their linear length, whereas prokaryotic chromosomes typically have one.

Centromere

A constricted eukaryotic chromosomal region essential for correct chromosome segregation during mitosis and meiosis that serves as the attachment site for kinetochore proteins.

Telomeres

Specialized repetitive DNA sequences located at the physical ends of linear eukaryotic chromosomes that confer stability and protect chromosomal ends from degradation or fusion.

Unique (Non-repetitive) Sequences

Genomic sequences present in only one or a few copies per haploid genome, including protein-coding exons, introns, and unique intergenic regions; they constitute roughly $41\%$ of the human genome.

Moderately Repetitive Sequences

DNA sequences occurring from a few hundred to several thousand times throughout the genome, including genes for rRNA and core histones, regulatory elements, and transposable elements.

Highly Repetitive Sequences

Short DNA sequences present in tens of thousands to millions of copies across the genome, such as tandem arrays in centromeric heterochromatin and the human Alu family.

Chromatin

The eukaryotic nucleoprotein complex consisting of chromosomal double-stranded DNA packaged around histones and non-histone proteins.

Nucleosome

The fundamental repeating structural subunit of eukaryotic chromatin, consisting of $146$ or $147\,\text{bp}$ of DNA wrapped $1.65$ negative superhelical turns around an octamer of core histone proteins.

Histone Octamer

The protein core complex of a nucleosome composed of two copies each of four core histones: H2A, H2B, H3, and H4.

Core Histones

The basic, positively charged proteins (H2A, H2B, H3, and H4) enriched in lysine and arginine residues that form electrostatic bonds with the negatively charged phosphodiester backbone of DNA.

Linker Histone (H1)

A histone protein that binds to linker DNA adjacent to the nucleosome core particle, less tightly bound than core histones, which assists in compacting nucleosomes into higher-order fibers.

Zigzag Model

A chromatin folding model in which linker DNA remains relatively straight and consecutive nucleosomes adopt an alternating zigzag conformation over short stretches of $2$ to $4$ nucleosomes.

Structural Maintenance of Chromosomes (SMC) Proteins

A family of dimeric ATPases that form ring-like structures around DNA duplexes to extrude loop domains and organize the internal architecture of interphase and metaphase chromosomes.

CCCTC-Binding Factor (CTCF)

A sequence-specific DNA-binding zinc-finger protein that binds chromatin and homodimerizes to halt loop extrusion by SMC complexes, acting as an architectural boundary/insulator for TADs.

Topologically Associating Domains (TADs)

Structural chromosomal domains measuring approximately $100\,\text{kb}$ to $1\,\text{Mb}$ within which DNA sequences physically interact with one another much more frequently than with sequences in neighboring domains.

Heterochromatin

Tightly packed, condensed regions of chromosomal chromatin that are generally transcriptionally inactive and inaccessible to RNA polymerases.

Euchromatin

Less condensed, openly organized chromatin regions where loop domains are accessible to transcriptional machinery, enabling active gene transcription.

Constitutive Heterochromatin

Chromosomal regions (such as centromeric and telomeric DNA) that remain permanently compacted, transcriptionally inactive, and rich in highly repetitive sequences in all cell types.

Facultative Heterochromatin

Chromatin segments that can reversibly transition between euchromatin and heterochromatin states depending on developmental timing and cell type.

Chromosome Territories

Distinct, non-overlapping spatial compartments within the interphase nucleus occupied by specific individual chromosomes, bounded by links to neighboring domains and the nuclear lamina.

Metaphase Chromosome Scaffold

A non-histone protein framework containing SMC proteins that anchors the bases of radial loop arrays in fully condensed $1{,}400\,\text{nm}$ mitotic chromosomes.

Condensin II

An SMC complex located within the nucleus during early prophase that forms a central spiral scaffold and organizes large loops into radial arrays.

Condensin I

An SMC complex that gains access to chromatin only after nuclear envelope breakdown (NEBD), generating nested smaller loops inside the larger loops organized by Condensin II.

Cohesin

A multiprotein complex containing SMC1 and SMC3 that holds sister chromatids together from S phase onward, remaining at the centromere until it is cleaved and degraded at the start of anaphase.

Transposition

The biochemical process by which small, mobile segments of DNA integrate into new genomic locations; discovered by Barbara McClintock in corn (Zea mays).

Transposable Elements (TEs)

Mobile genetic elements ("jumping genes") capable of shifting locations within a genome, found widely across bacteria, archaea, fungi, plants, and animals.

Simple Transposition

A non-replicative "cut-and-paste" transposition pathway in which transposase excises a DNA transposable element from its original location and inserts it into a new target site.

Retrotransposition

A transposition pathway found exclusively in eukaryotes where a retrotransposon is transcribed into an RNA intermediate, reverse transcribed into DNA, and integrated into a new site.

Transposase

An enzyme encoded by DNA transposons that binds inverted terminal repeats, dimerizes to loop out the transposon, cuts it out of the host DNA, and inserts it into a staggered target locus.

Inverted Repeats (IR)

Identical or near-identical sequences ($9$ to $40\,\text{bp}$ long) at both ends of a transposon that point in opposite directions and are recognized and cleaved by transposase.

Direct Repeats (DR)

Identical flanking nucleotide sequences oriented in the same 5'-to-3' direction created when host DNA repair synthesis fills staggered cuts at the insertion site of a transposable element.

Autonomous Elements

Transposable elements that contain intact, functional genes encoding all enzymes (such as transposase or reverse transcriptase) necessary to catalyze their own transposition.

Nonautonomous Elements

Transposable elements lacking genes for mobility-related enzymes that rely on proteins expressed by autonomous elements elsewhere in the genome to mobilize.

LTR Retrotransposons

Retroelements evolutionarily related to retroviruses that are flanked by long terminal repeats (LTRs) and encode reverse transcriptase and integrase.

Integrase

An enzyme encoded by LTR retrotransposons that recognizes LTR ends, cleaves host target DNA, and catalyzes the integration of newly synthesized retroelement cDNA.

Non-LTR Retrotransposons

Retroelements that do not possess long terminal repeats and move via target-site primed reverse transcription, often encoding a protein with both endonuclease and reverse transcriptase activities.

Target-Site Primed Reverse Transcription (TPRT)

The mobility mechanism of non-LTR retrotransposons wherein an endonuclease nicks genomic target DNA, enabling the element's poly(A) tail to anneal so the cleaved DNA strand primes reverse transcription directly at the chromosome insertion site.

Long Interspersed Elements (LINEs)

Autonomous non-LTR retroelements measuring $1{,}000$ to $10{,}000\,\text{bp}$ in length (such as human L1) present in $20{,}000$ to $1{,}000{,}000$ copies, comprising roughly $17\%$ of the human genome.

Short Interspersed Elements (SINEs)

Nonautonomous retroelements shorter than $500\,\text{bp}$ (such as the approximately $300\,\text{bp}$ human Alu sequence derived from 7SL RNA) that make up approximately $10\%$ of the human genome.

P Element

A transposable element in Drosophila melanogaster introduced into wild populations around 1950 that rapidly swept through global fly populations; absent only in lab strains collected prior to 1950.

Exon Shuffling

The evolutionary mechanism by which transposable elements facilitate the excision, transposition, and incorporation of coding exons into new genes, generating novel protein functions.

TBXT Gene AluY Insertion

An ancestral hominoid-specific insertion of an AluY element into an intron of the TBXT gene that pairs with an upstream AluSx1 element to cause alternative splicing (exclusion of exon 6), leading to the evolutionary loss of the external tail.