Genome and Genes Overview

Study Notes

A genome encompasses the complete set of chromosomes, including all DNA molecules, encoding genetic information.
Genes, the functional units of the genome, determine specific traits and occupy defined locations on chromosomes, known as genetic loci.
Gene numbers vary widely among organisms, from approximately 500 in mycoplasma to about 40,000 in humans.
Non-coding DNA, comprising considerable portions of eukaryotic genomes, includes functional RNA genes, regulatory elements, introns, and pseudogenes.
The C-value paradox refers to inconsistencies between genome size and organismal complexity, exemplified by the small genome of pufferfish, contrasting with human gene count.

Non-coding functional RNA genes: Include rRNA, tRNA, and microRNAs, which are essential for various cellular functions but do not encode proteins.
Cis and Trans regulatory elements: Control gene expression; cis elements (promoters, enhancers) and trans elements (repressors, operators) direct transcription and regulatory activities.
Introns: Non-coding regions interspersed within genes, excluded from mRNA during processing.
Pseudogenes: Non-functional gene remnants due to mutations, often termed genomic fossils.
Repetitive DNA and telomeres: Non-coding sequences at chromosome ends, with roles in chromosome protection and stability.

Non-coding DNA plays crucial roles in regulating gene expression and chromosomal integrity.
Certain non-coding variants are linked to diseases and are involved in the formation of regulatory RNAs, like microRNA and siRNA.
Non-coding DNA contributes to chromosomal structures, centromere operations, and meiosis.

Prokaryotic genomes, primarily bacterial, are compactly organized within a nucleoid, containing about 80% DNA.
DNA is structured into domains, with nearly 100 loops per genome, facilitating supercoiling and compactness.
DNA is shielded by polyamines to minimize charge repulsion, enabling tight packing within small cellular volumes.

Eukaryotic DNA is extensively packaged into chromatin and chromosomes, accommodating long DNA sequences within cell nuclei.
Chromatin comprises DNA, proteins, and RNA, with histones being central to DNA organization.
Five major histone classes (H1, H2A, H2B, H3, H4) participate in forming nucleosomes, the basic structural units of chromatin.

Nucleosomes consist of histone cores and linker DNA, crucial for DNA compaction, typically repeating every 2,000 base pairs.
Histone tails extend from nucleosomes, playing key roles in chromatin condensation and gene regulation through modifications like acetylation.

Nucleosomes organize into a 30-nm fiber, achieving significant DNA compaction over chromosomes while remaining accessible for replication and transcription.
The structure and compaction can vary, influenced by the transcriptional activity of specific DNA regions.

Certain DNA regions associate with a nuclear scaffold, with scaffold-associated regions separated by loops containing related genes, facilitating functional organization within the nucleus.