# Genome Structure ## Genome Complexity (Size vs Density) - Genome size is correlated with the complexity of an organism, but the actual number of genes is more closely linked to it. - Genome density refers to how close together the exonic regions of DNA and how many noncoding intronic sequences exist between them - A pseudogene is a segment of DNA that structurally resembles a gene, but isn’t capable of coding for a protein (are not expressed and contain no regulatory regions) - Often arise from: gene duplication/divergence, unequal crossing over, nondisjunction, or reverse transcription of mRNA - Typically silenced by methylation - Can be considered “molecular fossils” of our ancestors’ genomes - Genes can be overlapping within a genome. - Depends on the reading frame as well as which strand the gene is on ![[Pasted image 20240307131030.png]] - Introns (and genome complexity) increases with the complexity of the species - The mitochondrial genome has genes with overlapping exons --- - Introns are non-coding regions within a gene. - Intergenic regions are non-coding regions between genes. - Genes can be transferred horizontally between species (plants, bacteria, animals) - Whole genome duplications can occur, such as diploid cells and cancer cells (to increase growth factors). Genes are then lost that are negative selectors (*fractionation*) ## Genes and Intergenic DNA - While only ~1.5% of the genome contains protein coding sequences, an estimated 80% of the genome is still biochemically active - It is likely that these non-coding genes still contribute to overall gene expression by acting as regulatory switches ![[Pasted image 20240329001807.png|400]] **Repetitive Intergenic DNA** - ~50% of the human genomic DNA is repetitive, ranging from short repeats - *Microsatellites:* 5-50 repeating units that are ≤ 13 bp each - *DNA Slippage:* strands can slip when repetitive **Transposable Elements and Retroelements** - One third of the genome - Capable of moving to new positions, often leaving their original copy behind leading to a duplication event ![[Pasted image 20240329003945.png|300]] - Transposon: replicating DNA and inserting it somewhere else - Retrotransposon: transcribing DNA into mRNA, which is later reverted back into DNA via reverse transcriptase and then inserted to a new location - Bacteria and other less complex organisms tend to have far less repetitive DNA - Due to: repair systems, gene disruption due to lack of introns, stronger selection due to larger population sizes **Function of Noncoding DNA** - Mice are >97% similar to our genomes, yet we diverged ~65 mya. This homology is largely attributed to noncoding DNA, rather than actual proteins - Some of our pseudogenes have been shown to have significant function (defensins → HIV immunity) when artificially induced - Regulation: microRNA, cis-regulatory elements (DNA that serves as a binding site) - Variation is believed to allow for rapid evolution - point mutations are typically fatal to a proteins structure - Endogenous Retroviruses (ERVs) are previously inserted segments of DNA from viruses that have persisted over generations while staying dormant > “And then he Alu-ed all over our genome and got his elements all up in our junk” - Alu element is a retrotransposon that has ~1.5 million copies and makes up 11% of our genome - Accounts for 30% of methylation - Known as genomic instability factors as they are hot spots for recombination/exon shuffling - Theorized for why we no longer have Vitamin C; somewhat compensated for by the loss of uricase enzyme (although also has potential of developing gout) ![[Pasted image 20240329005703.png|375]] > “We (our genomes) are the mediums through which genes are jumping through over time.” --- Prokaryotes: - Do not contain [[Introns and Exons|introns]] within their DNA - Can have genes organized into [[Operons]] Eukaryotes -