Transcript Chapter 19.
Chapter 19: Control of Eukaryotic Genes AP Biology 2007-2008 The BIG Questions… How are genes turned on & off in eukaryotes? How do cells with the same genes differentiate to perform completely different, specialized functions? Differential gene expressions AP Biology 1. DNA packing How do you fit all that DNA into nucleus? DNA coiling & folding double helix nucleosomes chromatin fiber looped domains chromosome from DNA double helix to AP Biology chromosome condensed Nucleosomes 8 histone molecules “Beads on a string” 1st level of DNA packing histone proteins 8 protein molecules positively charged amino acids bind tightly to negatively charged DNA ps://www.youtube.com/watch?v=gbSIBhFwQ4s&list=PLAD3D E96CA98E831E&index=3 AP Biology DNA packing movie DNA packing as gene control Degree of packing of DNA regulates transcription tightly wrapped around histones no transcription genes turned off Heterochromatin (Interphase) darker DNA (H) = tightly packed euchromatin lighter DNA (E) = loosely packed H AP Biology E Points of control The control of gene expression can occur at any step in the pathway from gene to functional protein 1. packing/unpacking DNA 2. Transcription (most common) 3. mRNA processing 4. mRNA transport 5. translation 6. protein processing 7. protein degradation AP Biology Histone Modification Chemical modification of histone tails Can affect the configuration of chromatin and thus gene expression Chromatin changes Transcription RNA processing mRNA degradation Translation Protein processing and degradation Histone tails DNA double helix Figure 19.4a AP Biology Amino acids (N-terminus) available for chemical modification (a) Histone tails protrude outward from a nucleosome Histone acetylation Acetylation of histones unwinds DNA loosely wrapped around histones attachment of acetyl groups (–COCH3) to postive charged lysines AP Biology enables transcription genes turned on Neutralized (+) charged tails no longer bind to neighboring nucleosomes transcription factors have easier access to genes Acetylated histones Unacetylated histones (b) Acetylation of histone tails promotes loose chromatin structure that permits transcription DNA methylation Methylation of DNA blocks transcription factors no transcription genes turned off attachment of methyl groups (–CH3) to cytosine C = cytosine nearly permanent inactivation of genes ex. inactivated mammalian X chromosome = Barr body Ex. Epigenetic inheritance Inheritance of traits by mechanisms not involving the nucleotide sequence AP Biology Regulation of Transcription Initiation Chromatin-modifying enzymes provide initial control of gene expression By making a region of DNA either more or less able to bind the transcription machinery AP Biology 2. Transcription initiation Noncoding control regions on DNA AP Biology promoter nearby control sequence on DNA binding of RNA polymerase & transcription factors proximal control elements UTR located close to the promoter enhancer distant control sequences on DNA binding of activator proteins “enhanced” rate (high level) of transcription Organization of a Typical Eukaryotic Gene Enhancer (distal control elements) Poly-A signal sequence Proximal control elements Exon Intron Exon Intron Termination region Exon DNA Downstream Upstream Promoter Chromatin changes Transcription Exon Primary RNA transcript 5 (pre-mRNA) Intron Exon Intron RNA RNA processing mRNA G P 5 Figure 19.5 AP Biology Cleared 3 end of primary transport Coding segment Translation Protein processing and degradation Exon RNA processing: Cap and tail added; introns excised and exons spliced together Transcription mRNA degradation Intron Poly-A signal P P Cap 5 UTR (untranslated region) Start codon Stop codon Poly-A 3 UTR (untranslated tail region) Model for Enhancer action Enhancer DNA sequences Activator proteins distant control sequences bind to enhancer sequence & stimulates transcription Silencer (repressor) proteins bind to enhancer sequence & block gene transcription AP Biology Turning on Gene movie Transcription complex Activator Proteins • regulatory proteins bind to DNA at Enhancer Sites distant enhancer sites • increase the rate of transcription regulatory sites on DNA distant from gene Enhancer Activator Activator Activator Coactivator A E F B TFIID RNA polymerase II H Core promoter and initiation complex Initiation Complex at Promoter Site binding site of RNA polymerase AP Biology Combinatorial Control of Gene Activation Enhancer A particular combination of control elements Albumin gene Control elements Crystallin gene Liver cell nucleus Will be able to activate transcription only when the appropriate activator proteins are present AP Biology Promoter Lens cell nucleus Available activators Available activators Albumin gene not expressed Albumin gene expressed Crystallin gene not expressed (a) Liver cell Crystallin gene expressed (b) Lens cell Coordinately Controlled Genes Unlike the genes of a prokaryotic operon Coordinately controlled eukaryotic genes each have a promoter and control elements The same regulatory sequences Are common to all the genes of a group, enabling recognition by the same specific transcription factors AP Biology 3. Post-transcriptional control Alternative RNA splicing Different mRNA molecules produced from the same primary transcript Depends on which RNA segments are treated as introns and exons AP Biology 4. Regulation of mRNA degradation Life span of mRNA determines amount of protein synthesis mRNA can last from hours to weeks Ex. Long lived hemoglobin & short lived growth factor Determined by sequences towards the 3’ end UTR Enzymatic shortening of poly A tail removal of 5’ cap nuclease degrades mRNA AP Biology RNA processing movie RNA interference Small interfering RNAs (siRNA) short segments of RNA (21-28 bases) bind to mRNA create sections of double-stranded mRNA “death” tag for mRNA triggers degradation of mRNA cause gene “silencing” post-transcriptional control turns off gene = no protein produced siRNA AP Biology RNA interference by single-stranded microRNAs (miRNAs) Can lead to degradation of an mRNA or block its translation 1 The microRNA (miRNA) precursor folds back on itself, held together by hydrogen bonds. An enzyme 22 called Dicer moves along the doublestranded RNA, cutting it into shorter segments. One strand of 3 each short doublestranded RNA is degraded; the other strand (miRNA) then associates with a complex of proteins. 4 The bound miRNA can base-pair with any target mRNA that contains the complementary sequence. 55 The miRNA-protein complex prevents gene expression either by degrading the target mRNA or by blocking its translation. Chromatin changes Transcription RNA processing mRNA degradation Translation Protein processing and degradation Protein complex Dicer Degradation of mRNA OR miRNA Target mRNA Figure 19.9 AP Biology Hydrogen bond Blockage of translation RNA interference 1990s | 2006 “for their discovery of RNA interference — gene silencing by double-stranded RNA” Andrew Fire AP Biology Stanford Craig Mello U Mass 5. Control of translation Block initiation of translation stage regulatory proteins attach to 5' end of UTR of mRNA prevent attachment of ribosomal subunits & initiator tRNA block translation of mRNA to protein AP Biology Control of translation movie 6-7. Protein processing & degradation Protein processing folding, cleaving, adding sugar groups, targeting for transport Protein degradation ubiquitin tagging proteasome degradation AP Biology Protein processing movie 1980s | 2004 Ubiquitin “Death tag” mark unwanted proteins with a label 76 amino acid polypeptide, ubiquitin labeled proteins are broken down rapidly in "waste disposers" AP proteasomes Aaron Ciechanover Biology Israel Avram Hershko Israel Irwin Rose UC Riverside Proteasome Protein-degrading “machine” cell’s waste disposer breaks down any proteins into 7-9 amino acid fragments cellular recycling AP Biology play Nobel animation Proteasomes Are giant protein complexes that bind protein molecules and degrade them 3 Enzymatic components of the 1 Chromatin changes Multiple ubiquitin molecules are attached to a protein by enzymes in the cytosol. The ubiquitin-tagged protein 2 is recognized by a proteasome, which unfolds the protein and sequesters it within a central cavity. proteasome cut the protein into small peptides, which can be further degraded by other enzymes in the cytosol. Transcription RNA processing mRNA degradation Proteasome and ubiquitin to be recycled Ubiquitin Translation Proteasome Protein processing and degradation Protein to be degraded Ubiquinated protein Protein entering a proteasome Figure 19.10 AP Biology Protein fragments (peptides) Duplications, rearrangements, and mutations of DNA contribute to genome evolution The basis of change at the genomic level is mutation Accidents in cell division AP Biology Can lead to extra copies of all or part of a genome, which may then diverge if one set accumulates sequence changes Duplication and Divergence of DNA Segments Unequal crossing over during prophase I of meiosis Can result in one chromosome with a deletion and another with a duplication of a particular gene Transposable element Gene Nonsister chromatids Crossover Incorrect pairing of two homologues during meiosis and AP Biology Evolution of Genes with Related Functions: The Human Globin Genes The genes encoding the various globin proteins Evolved from one common ancestral globin gene, which duplicated and diverged Ancestral globin gene Duplication of ancestral gene Mutation in both copies Transposition to different chromosomes Further duplications and mutations 2 1 2 -Globin gene family on chromosome 16 AP Biology 1 G A -Globin gene family on chromosome 11 Evolution of Genes with Related Functions: The Human Globin Genes Subsequent duplications of these genes and random mutations Gave rise to the present globin genes, all of which code for oxygen-binding proteins Ancestral globin gene Duplication of ancestral gene Mutation in both copies Transposition to different chromosomes Further duplications and mutations 2 AP Biology 1 2 -Globin gene family on chromosome 16 1 G A -Globin gene family on chromosome 11 Evolution of Genes with Novel Functions • The copies of some duplicated genes ▫ Have diverged so much during evolutionary time that the functions of their encoded proteins are now substantially different ▫ Ex: similar amino acid sequence in lactalbumin and lysozyme enzyme AP Biology Rearrangements of Parts of Genes: Exon Duplication and Exon Shuffling A particular exon within a gene Could be duplicated on one chromosome and deleted from the homologous chromosome AP Biology In exon shuffling Errors in meiotic recombination lead to the occasional mixing and matching of different exons either within a gene or between two nonallelic genes EGF EGF EGF EGF Epidermal growth factor gene with multiple EGF exons (green) Exon shuffling F F F Fibronectin gene with multiple “finger” exons (orange) Exon duplication F F EGF K K Plasminogen gene with a “kfingle” exon (blue) Figure 19.20 Portions of ancestral genes AP Biology Exon shuffling TPA gene as it exists today K How Transposable Elements Contribute to Genome Evolution Movement of transposable elements or recombination between copies of the same element Occasionally generates new sequence combinations that are beneficial to the organism Some mechanisms Can alter the functions of genes or their patterns of expression and regulation AP Biology