BCOR 103 1st Edition Lecture 23 Outline of Last LectureI. Nuclear TransportII. Regulation and RNAIII. Open Mitosis Outline of Current Lecture I. GenomicsII. Alternative SplicingIII. Gene FamiliesCurrent Lecture- Key concept: complexity of an organism does not correlate directly with genome size or the total number of genes in the genome.- Genomics: the systematic analysis of entire cell genomes- First human genome sequence (2000): ~10 years of work, cost $2.7 billiion- Key concept: Organism complexity does correlate with the percentage of the genome that encodes protein (inverse correlation).o Example: human dystrophin gene (encodes a protein that is part of the complex that connects the cytoskeleton to the extracellular matrix) dystrophin gene: 2.5 million bases, 79 exons, final mRNA is 14,000 bases (0.61% of the pre-mRNA)- Alternative Splicing: Production of Multiple Proteins from single geneo Alternative splicing >90% of human genes- Bottom line: alternative mRNA processing allows the production of >100,000 distinct human proteins from ~20,000 genes- DSCAM: each neuron expresses a single type of DSCAM mRNA, and thus each neuron expresses a single type of DSCAM protein; DSCAM allows neurons to distinguish self from non-self (each DSCAM type is functionally distinct)o Note: within each cluster of cassette exons, there is a high degree of similarity, but each cassette exon encodes a slightly different protein sequence- Transposable elements: DNA sequences capable of moving within the genomeThese notes represent a detailed interpretation of the professor’s lecture. GradeBuddy is best used as a supplement to your own notes, not as a substitute.- Mitochondrial DNA is composed of a single double stranded circular molecule. There are several copies in each mitochondrion and there are many mitochondria in most human cells. Mitochondria originated by endosymbiosis of a prokaryotic cell early in the evolution of eukaryotic cells. Mitochondrial DNA is similar to prokaryotic DNA. There are no histones or any other protein associated with mt DNA. The genes contain no introns. Because it is in a highly oxidizing environment it has a much higher rate of mutation thannuclear DNA. The genes in mt DNA code for mitochondrial ribosomes and transfer RNAs.Some genes code for polypeptide subunits of the electron transport chain common to allmitochondria. The mitochondrion relies on nuclear gene products for replication and transcription.o Key point: the human mitochondrion is inherited only from the mother.- Dispersed gene families arising from gene duplication: diversified functionso Following gene duplication: additional gene copy may acquire new functions: tissue specific expression, developmental regulation, altered enzymatic activity.o Example: human fetal globin genes – fetal globin proteins possess a higher affinity for oxygen than adult globin proteins, therefore allow the fetus to obtain sufficient oxygen from the maternal circulation.- Tandem gene families: encode gene products needed in large quantities, on short notice(examples: histone genes, rRNA genes, tRNA, 5S rRNA)- FISH: fluorescence in situ hybridizationo Human telomeres: ~1500 repeats of the sequence AGGGTT per telomere (total 92 telomeres)o Telomeres enable linear eukaryotic genomes to resolve the ‘end problem’ resulting from lagging strand DNA synthesis- ALL DNA polymerases require a primer.- ALL DNA polymerases synthesize DNA 5’ to 3’- Telomeres: solve the problem of replicating the ends of a linear DNA genome- Telomerase: reverse transcriptase that carries its own RNA template.o Note: most human cells do not express telomerase- DNA repeats of no known function: initially referred to as ‘junk DNA’ or ‘selfish DNA’- Repetitive DNA sequences: likely played (and continue to play) an essential role in the evolution of complex organisms – provide a mechanism for genetic change (a prerequisite for evolution)- Transposable elements: sequences that can move in the genome- Basic types:o 1) DNA transposons (prokaryotic-like transposable elements) move by a cut and paste mechanism (no net gain of transposable elements)o 2) Retrotransposons move by use of an RNA intermediate (net gain of transposable elements)- Key concept: all transposable elements generate a short direct repeat (5 – 10 bp) of target DNA sequences upon integration at a new site.- Transposase is a DNA endonuclease that recognizes the inverted repeats at the ends of the transposon and cleaves the transposon from the genome. Transposase then makes a staggered cut in the target DNA allowing for the insertion of the transposon at a new site.- Key concept: DNA transposons move by a cut and paste mechanism, therefore they are ‘cut out’ of their original position in the genome and ‘pasted’ in some other position within the genome- Transposase: enzyme responsible for cutting the DNA transposon out of its original position and cutting the target DNA into which the DNA transposon will be ‘pasted’o Repair of DNA gap carried out by host cell DNA repair enzymeso Note: most DNA transposons in the human genome are inactive- Retrotransposable elements: move within a genome through an RNA intermediate Enzymes required for retrotransposition:o 1) RNA polymerase IIo 2) reverse transcriptaseo 3) integraseo 4) host cell DNA repair machinery- Once inserted into the host cell genome, retrotransposable elements are not excised (thus retrotransposition is essentially irreversible)- Viral-like retrotransposable elements: possess the basic structural features of retroviruses: o 1) long terminal repeats (LTRs) o 2) complete or partial gene structure: gag, pol, env, o 3) short flanking direct repeats of host DNA sequence at the site of integration- HERVs: human endogenous retroviruses – entered the human genome through infectionof germ cells at some point during human evolution- Provirus: term for the retrovirus genome that is integrated into the host cell genome- Retrotransposition requires the synthesis of a capped and polyadenylated RNA by RNA polymerase II - RNAse H: degrades RNA of a hybrid RNA:DNA helix- Pseudogenes arise from the accidental reverse transcription of normal cellular mRNAs. Following insertion into the genome, pseudogenes are usually not expressed (they generally lack flanking regulatory sequences necessary for transcription initiation and mRNA 3’ processing). However, if expressed, they may provide the basis for the evolution of