16 O&C of Eukaryotic Genome Notes 2024

Proteolytic cleavage can activate proteins by removing signal peptides or pro‑regions and enabling proper folding; example: insulin maturation from pre‑proinsulin -> proinsulin -> active insulin via removal of signal peptide and C‑chain plus disulfide bond formation.

Eukaryotic genomes are generally much larger than prokaryotic or viral genomes, consist of two or more linear chromosomes located in the nucleus, each chromosome is a single double‑stranded linear DNA molecule associated with histones, with multiple origins of replication; genes have introns interrupting coding sequences and each gene has its own promoter; eukaryotes also have smaller circular mitochondrial genomes (and chloroplast genomes in plants).

The first level is winding DNA around groups of eight core histone proteins (histone octamer) to form nucleosomes, producing a bead‑like structure; linker DNA joins nucleosomes and histone H1 stabilises DNA entry/exit.

The 30‑nm chromatin fibre is the second level of packing where nucleosome 'beads' coil into a helical structure, which then forms looped domains with scaffold proteins and further coils into condensed chromosomes during mitosis.

Euchromatin is less condensed, appears lightly stained, contains actively transcribed genes and may be depleted of nucleosomes in promoters; heterochromatin is highly condensed, appears darkly stained, contains repetitive sequences and is transcriptionally inactive; ~10% of mammalian genome is in heterochromatin and it's concentrated at centromeres and telomeres.

Chemical modification (e.g., methylation or acetylation) changes histone charge and alters DNA–histone association, affecting chromatin condensation: modifications can make DNA more or less accessible to transcription factors, thereby regulating transcription.

A mitotic chromosome is a condensed structure of two identical sister chromatids joined at the centromere; the tips are telomeres, which protect chromosome ends.

Introns are non‑coding sections within eukaryotic genes; they enable alternative splicing, allowing one gene to code for multiple polypeptides. Introns commonly begin with 'GT' and end with 'AG'.

Promoter: nucleotide sequence just upstream of a gene where general transcription factors and RNA polymerase bind to initiate transcription. Enhancer: nucleotide sequence that may lie thousands of base pairs away where activator proteins bind to increase transcription. Silencer: distal sequence where repressor proteins bind to suppress transcription.

Centromere is a constricted chromosome region (~220 nucleotides, highly repeated) that mediates sister chromatid cohesion and kinetochore formation, enabling spindle fibre attachment for chromatid separation; centromere dysfunction can cause aneuploidy.

Telomeres protect genes from erosion during replication, maintain chromosomal end integrity by preventing end‑to‑end fusion, and limit cell lifespan by causing apoptosis after critical shortening.

Telomerase carries a short RNA template complementary to the telomeric repeat (e.g., 5'‑TTAGGG‑3' in humans); telomerase reverse transcriptase (TERT) uses this RNA to extend the parental strand by RNA‑templated DNA synthesis, then DNA polymerase fills in the complementary strand, leaving a single‑stranded overhang. Telomerase is active in germ cells but inactive in most somatic cells.

Gene regulation directs development and maintains homeostasis; organisms have thousands of genes but do not express them all at once or in every cell—differential expression enables different cell types and developmental stages to express needed proteins.

Chromatin remodelling, transcriptional control, post‑transcriptional control, translational control, and post‑translational control.

By changing DNA packaging (via histone modifications and DNA methylation), chromatin remodelling alters accessibility of promoters to general transcription factors and RNA polymerase, enabling or preventing transcription initiation.

Histone acetylation (by histone acetyltransferases) decreases histone positive charge, lowers histone–DNA affinity, unravels chromatin into euchromatin, increases accessibility for transcription machinery, and generally activates transcription.

Histone deacetylation (by histone deacetylases) restores positive charge, increases affinity between histones and DNA, condenses chromatin into heterochromatin, reduces accessibility of transcription machinery, and represses transcription.

DNA methylation (by DNA methyltransferase) can block transcription factor binding at CpG‑rich sites, preventing transcription initiation, and can recruit proteins (e.g., histone deacetylases) that induce chromatin condensation into transcriptionally inactive heterochromatin.

Prokaryotes lack chromatin packaging with histones and thus lack histone modifications; while they have DNA methylation for other purposes, they do not use chromatin remodelling for gene regulation. Eukaryotes use histone modification and DNA methylation to control chromatin structure and gene expression.

General transcription factors bind promoters (e.g., TATA box) and recruit RNA polymerase to form a basal transcription initiation complex; specific transcription factors bind control elements (enhancers/silencers) to modulate transcription rate by interacting with the initiation complex.

Activators binding to enhancers or repressors binding to silencers induce DNA looping (aided by DNA‑bending proteins) to bring bound factors into contact with the promoter and transcription initiation complex, thereby increasing or decreasing RNA polymerase activity.

A transcription factor has a DNA‑binding domain for recognition and binding to specific DNA sequences and an activation domain for interacting with other proteins of the transcriptional machinery.

Eukaryotic repressors can: block activator binding to enhancers; mask activator activation domains; interact with general transcription factors to block assembly or release of RNA polymerase; package regions into heterochromatin; recruit histone deacetylases to condense chromatin.

Combinational control is when a gene is regulated by multiple enhancers/silencers and the unique combination of control elements and available activator/repressor proteins in a cell determines precise spatial and temporal gene expression.

Both liver and lens cells have genes for albumin and crystallin, but only liver cells express albumin and lens cells express crystallin because the required activator proteins are present only in the appropriate cell type; different repressors also prevent expression in other cell types.

Prokaryotes often use a single operator proximal to genes (operon) producing polycistronic mRNA and can use positive/negative regulation; eukaryotes use unique combinations of distal control elements (enhancers/silencers) for each gene with monocistronic mRNA and each gene has its own promoter.

5' capping, splicing (including removal of introns), and 3' polyadenylation; these produce mature mRNA that exits the nucleus for translation.

Alternative splicing is a regulated process where different combinations of exons are included/excluded from mature mRNAs derived from the same pre‑mRNA, allowing one gene to produce multiple proteins and increasing proteome diversity beyond the ~20,000 protein‑coding genes.

Different cell types can include or exclude particular exons during splicing, producing protein isoforms with different amino acid sequences and functions from the same gene, enabling tissue‑specific protein expression.

Prokaryotes lack a nuclear envelope so transcription and translation are simultaneous and post‑transcriptional modifications do not occur; eukaryotes separate transcription and translation with nuclear processing steps (capping, splicing, polyadenylation) and can perform alternative splicing.

Longer mRNA half‑life allows it to remain in the cytoplasm longer and be translated more times, producing more protein; mRNA stability is influenced by the 5' cap, 3' poly‑A tail length, and binding proteins or hormones that affect degradation.

The 5' cap protects mRNA from 5' exonucleases and aids translation initiation; the poly‑A tail buffers against 3' exonucleases so a longer tail increases mRNA stability and translation potential.

Translational repressors (sequence‑specific RNA‑binding proteins) can bind the 5' UTR to prevent ribosome binding; complementary RNA molecules can bind the 5' UTR to block ribosome access, inhibiting formation of the translation initiation complex.

Prokaryotic mRNAs lack 5' cap and poly‑A tail and are generally less stable, though stability can be enhanced by 3' stem‑loops; both use translational repressors or complementary RNAs to block ribosome binding, while eukaryotes use 5' cap and poly‑A tail to regulate half‑life and translation.

Post‑translational modification adds chemical groups to proteins after synthesis to regulate function; examples include glycosylation (carbohydrate addition), phosphorylation (phosphate addition), acetylation, methylation, and hydroxylation.

Proteins destined for degradation are tagged with ubiquitin covalently attached to their N‑terminus; ubiquitinated proteins are recognised and degraded by the proteasome, allowing removal of unneeded or damaged proteins and recycling of amino acids.

By post‑translational modifications that control protein activity (e.g., phosphorylation) and by targeted degradation via ubiquitinylation and proteasome action to control protein quantity and remove faulty proteins.

Prokaryotes generally do not have post‑translational modifications like eukaryotes; eukaryotes use biochemical modifications and proteolytic cleavage to regulate activity and ubiquitin‑mediated proteasomal degradation to control protein levels.

Glycosylation: adds carbohydrates to membrane proteins to form glycoproteins; Phosphorylation: adds phosphates, activating many transcription factors and signalling proteins; Acetylation: e.g., histone acetylation and activation of p53; Methylation: activates some enzymes (e.g., phosphatase); Hydroxylation: modifies collagen residues for stability.

Each eukaryotic gene typically has its own promoter and distinct control elements, allowing independent regulation; genes are not necessarily co‑regulated because eukaryotic genomes have complex, cell‑type and temporally specific regulation.

Histone H1 binds to the site where DNA enters and exits the nucleosome and stabilises the nucleosome structure.

Repetitive satellite DNA is concentrated in heterochromatin regions such as centromeres and telomeres and is transcriptionally inactive.

Chromatin remodelling switches expression of certain genes off and others on during differentiation by altering chromatin condensation via histone modifications and DNA methylation, enabling tissue‑specific gene expression.

Proteins that recognise methylated DNA recruit histone deacetylases, which remove acetyl groups from histones, leading to chromatin condensation and gene silencing.

Introns tend to begin with 'GT-' and end with '-AG'.

An operon is a cluster of multiple structural genes under the control of a single promoter and operator in prokaryotes, producing polycistronic mRNA that encodes multiple proteins.

Certain hormones can stimulate or retard mRNA degradation rates, altering mRNA half‑life and thus protein production.

Telomeres cap chromosome ends, preventing DNA repair machinery from recognising chromosome ends as breaks and fusing them; without telomeres broken ends may be joined, disrupting gene regulation.

Cells undergo apoptosis after a limited number (~50) of divisions when telomeres shorten to a critical length, limiting mutation accumulation and cancer development.

Multiple origins allow efficient replication of large linear chromosomes during S phase, ensuring timely duplication of the genome.

Many transcription factors bind CpG‑rich recognition sites; methylation of these CpG sites blocks their binding and suppresses transcription initiation.

DNA looping mediated by DNA‑bending proteins brings enhancer‑bound activators (or silencer‑bound repressors) into proximity with the promoter and transcription initiation complex, modulating RNA polymerase activity.

Each eukaryotic gene has its own promoter and is transcribed into a separate mRNA, producing monocistronic mRNAs that code for a single polypeptide, enabling independent regulation of each gene.

Genes packaged into heterochromatin are usually transcriptionally inactive and resistant to expression due to tight compaction limiting access to transcription machinery.

Chromatin fibres associate with nuclear matrix scaffold proteins to form looped domains and undergo higher‑order coiling, aiding condensation into mitotic chromosomes.