DNA Structure and Genome Organization PDF

Organisation of the Human Genome The Human Genome The nuclear genome The mitochondrial genome  The Human Genome The exome 2% of the genome The Human Genome The Mitochondrial Genome A single ds circular chromosome; 2 – 10...

Organisation of the Human Genome The Human Genome The nuclear genome The mitochondrial genome  The Human Genome The exome 2% of the genome The Human Genome The Mitochondrial Genome A single ds circular chromosome; 2 – 10 copies per mitochondrion 16,569 bp 37 genes -13 code for enzymes of oxidative phosphorylation -2 code for mt rRNAs -22 code for mt tRNAs  mtDNA vs. nuclear DNA mtDNA Nuclear DNA Circular Linear No introns Has introns Small intergenic spaces: 1-2 bp Long intergenic spaces: Kb Codon usage: Codon usage: – Stop: UAA, UAG, AGA, AGG – Stop: UAA, UAG, UGA – Tryptophan: UGA – Tryptophan: UGG – Start: AUG, AUA, AUC, AUU – Start: AUG Maternal inheritance Inherited from both parents Rapid DNA replication Slower DNA replication No proof-reading or DNA repair Proof-reading & DNA repair Mutation rate 10 – 100X higher The Human Genome  The Nuclear Genome G-bands: dark staining bands with Geimsa Identifying Chromosomes Chromosomes: Structure Telomere p (short arm) q (long arm) Telomere Chromosomes: Organisation  Histones Small: 10-20kDa Highly conserved Very basic proteins Heavily acetylated/methylated A core of 8 histones (2 each of H2A, H2B, H3 and H4) around which the DNA is wrapped Histone H1 attached to linker DNA between nucleosomes Do not dissociate from DNA during DNA replication Chromosomes: Organisation Chromosomes: Structure Telomere p (short arm) q (long arm) Telomere Heterochromatin & Euchromatin Euchromatin : the fraction of the nuclear genome which contains transcriptionally active DNA and which adopts a relatively extended conformation Hetorochromatin: a chromosomal region that remains highly condensed throughout the cell cycle and shows little or no evidence of active gene expression – Constitutive: always inactive & condensed e.g centromere – Facultative: can exist as either condensed or dispersed e.g. Mammalian X-chromosome Heterochromatin & Euchromatin  The Centromere Constriction in the chromosome Region where the sister chromatids are held together Essential for attachment to the spindle and segregation A specific DNA sequence which is highly repetitive  The Telomere The tip of the chromosome Repetitive DNA sequence Maintain structural integrity of chromosome; Linked to ageing Telomerase needed to prevent loss during DNA replication Structure of DNA Structure of DNA  Nucleotides 2 purines A&G 2 pyrimidines C&T U replaces T in RNA Different sugars in DNA and RNA DNA – RNA - protein  Genes in the human genome Besides protein coding gene, the human genome codes for functional RNAs rRNAs tRNAs small nuclear RNAs small nucleolar RNAs microRNAs … https://www.nature.com/articles/d41586-018-05462-w https://www.ncbi.nlm.nih.gov/pubmed/27573892  ‘Functional’ DNA By Thomas Shafee - Own work, CC BY 4.0, https://commons.wikimedia.org/w/index.php?curid=39441809 Gene Structure direction of transcription RNA synthesis Gene Structure  Sense and antisense DNA strands 5’ 3’ ❖ The SENSE strand is the coding strand; its sequence determines the protein sequence. It is the same sequence as the mRNA for that particular gene except that T is replaced by U ❖ The ANTISENSE strand serves as the template for mRNA production; it is complementary to the RNA transcript ❖ The sense strand is not the same for all genes; some genes are encoded on the forward strand, and some on the reverse but they are always read 5’ → 3’ 3’ 5’ Non-coding RNA Repetitive DNA  Repetitive DNA Tandem repeats A stretch of repeated DNA sequence Satellites Minisatellites Microsatellites  Repetitive DNA Satellites (very large repeats; from 100 kb - 1 Mb long) Accumulate in regions of low recombination e.g. centromere region of chromosomes; a repeat unit of 171 bp which makes up 3 - 5% of each chromosome  Repetitive DNA Short simple repeats (SSR) – Minisatellites (repeats of 10 – 50 bp; repeated up to 1000 x) – Microsatellites (repeats of 2 – 9 bp; repeated 10 – 100 x) Non-coding repeats Disease causing Forensic DNA Huntington’s Disease Paternity testing Myotonic Dystrophy  Repetitive DNA Short simple repeats (SSR) How do Tandem Repeats arise? Replication Slippage (polymerase stuttering)  Slippage Backward slippage Forward slippage Insertion Deletion  Slippage Slippage in Huntington’s disease Slippage  Mobile Genetic Elements Transposons or Transposable elements Jumping Genes  Mobile genetic elements E.g. transposons (transposable elements) DNA fragments flanked by short, inverted repeat sequences which can transfer from one location to the other in the genome  Transposons Use transposase enzymes Transposase cuts to give sticky ends Transposable element is inserted, DNA ligase fills the gaps Transposase site – the repeat sequence – is recreated  Retrotransposons DNA RNA DNA (inserted in a new position in the genome)  Transposable Elements Genomic Repeats Pseudogenes  Pseudogenes Pseudogenes cDNA copies of reverse transcribed mRNA Do not contain any Polymerase II promoter Are always inactive  Pseudogenes Pseudogenes may also arise due to gene duplications  Pseudogenes Serious implications for genetic diagnostics