Organisation & Control of Eukaryotic Genome Vocabulary

Vocabulary flashcards covering the structure, packing, non-coding elements, and multi-level control of gene expression in the eukaryotic genome.

Euchromatin

The less compact, transcriptionally active form of chromatin where the $30\text{ nm}$ fibre has dissociated into a "beads-on-a-string" structure, allowing access to transcription factors and RNA polymerase.

Heterochromatin

Highly condensed, transcriptionally inactive regions of chromatin that are usually localized to the periphery of the eukaryotic nucleus.

Nucleosome

The basic unit of eukaryotic chromosomal packing, consisting of negatively charged DNA wound 1.65 times ($146\text{ base pairs}$) around an octamer core of 8 positively charged histone proteins (two each of H2A, H2B, H3, and H4).

Linker DNA

The region of DNA that connects adjacent nucleosomes in chromatin.

30 nm chromatin fibre (Solenoid)

A chromatin structure formed when the $10\text{-nm}$ nucleosome fibre coils upon itself with 6 to 8 nucleosomes per turn, stabilized by histone H1.

Histone H1

A fifth type of histone protein (linker protein) that attaches near the nucleosome bead to stabilize the $30\text{ nm}$ chromatin fibre by neutralizing negative charges on DNA and interacting with histone octamers.

Looped domains (300 nm fibre)

Loops formed by the $30\text{ nm}$ chromatin fibre attached to a chromosome scaffold composed of non-histone proteins.

Metaphase chromosome

The maximally condensed and compacted state of chromatin seen during cell division, consisting of a pair of sister chromatids held together at the centromere.

Non-coding DNA

Portions of a genome that do not code for proteins or functional RNA products (e.g., rRNA, tRNA); includes promoters, enhancers, silencers, introns, centromeres, and telomeres.

Promoter

A specific non-coding proximal control sequence located upstream of the transcription start site where RNA polymerase II and general transcription factors bind to initiate transcription.

TATA box

A conserved non-coding DNA sequence ($\text{5'-TATAAA-3'}$) within many eukaryotic promoters located 20 to 30 base pairs upstream of the start site, crucial for determining the precise site of transcription initiation.

Terminator

A specific sequence of non-coding DNA located at the end of a gene that signals RNA polymerase to stop transcription and release the pre-mRNA transcript.

Enhancer

A distal non-coding regulatory DNA sequence bound by specific transcription factors called activators, which increases the rate of transcription by promoting transcription initiation complex assembly.

Silencer

A distal non-coding regulatory DNA sequence bound by specific transcription factors called repressors, which decreases or inhibits the rate of transcription by blocking transcription initiation complex assembly.

Introns

Non-coding DNA sequences interspersed between coding regions (exons) within eukaryotic genes that are transcribed into pre-mRNA and excised prior to translation.

Exons

Coding regions of a eukaryotic gene that remain in mature mRNA after splicing and encode amino acid sequences for polypeptide synthesis.

Alternative RNA splicing

A post-transcriptional process in which different combinations of exons from a single pre-mRNA are joined together, enabling one gene to produce multiple protein isoforms.

Telomere

A non-coding region composed of non-coding tandem repeats (e.g., $\text{5'-TTAGGG-3'}$ in humans) found at the ends of linear eukaryotic chromosomes that protects genes from end-replication degradation.

Telomerase

A ribonucleoprotein enzyme consisting of TERC (RNA template) and TERT (reverse transcriptase) that lengthens telomeres at the 3' end in germ cells, stem cells, and cancer cells.

Centromere

The constricted non-coding region of a chromosome containing tandem repeats where sister chromatids are joined and where kinetochores assemble for spindle attachment.

Kinetochore

A multiprotein complex assembled on the centromere that binds to spindle microtubules to enable chromosome segregation during mitosis and meiosis.

Differential gene expression

The expression of different sets of genes by cells containing identical genomes, providing temporal and spatial regulation for cellular differentiation.

DNA methylation

The addition of methyl groups ($\text{-CH}_3$) to cytosine bases in CpG islands catalysed by DNA methyltransferases, leading to chromatin condensation and transcriptional silencing.

Histone acetylation

The addition of acetyl groups to positively charged lysine residues on histone tails by histone acetyltransferase (HAT), neutralizing lysine's charge to loosen chromatin structure and activate transcription.

General transcription factors

Essential proteins (such as TFIID) required for the transcription of all protein-coding genes that bind directly to the promoter or each other to assemble the transcription initiation complex.

Specific transcription factors

Gene-specific proteins (activators or repressors) that bind to distal control elements (enhancers or silencers) to regulate the rate of transcription initiation.

Combinatorial control

The regulation of gene expression determined by a specific combination of control elements and transcription factors present in a particular cell type or developmental stage.

Coordinately controlled genes

Genes with related functions dispersed across different chromosomes that possess identical control elements, enabling their simultaneous expression in response to a single signal.

5' capping

The co-transcriptional addition of 7-methylguanosine to the 5' end of pre-mRNA via a $5' \rightarrow 5'$ triphosphate bridge, which protects mRNA from degradation and promotes translation initiation.

3' polyadenylation

The post-transcriptional addition of approximately 200 adenine nucleotides (poly-A tail) to the 3' end of pre-mRNA following transcription of the AAUAAA signal sequence, enhancing mRNA stability and export.

Spliceosome

A large complex consisting of snRNPs and proteins that recognizes splice sites, excises introns as lariats, and splices exons together to produce mature mRNA.

Ubiquitin

A small regulatory protein covalently attached to target proteins to mark them for degradation by proteasomes.

Proteasome

A protein complex that recognizes ubiquitin-tagged proteins, unfolds them, and hydrolyses them into small peptide fragments.