HEukarya - Eukaryotic Gene Expression Eukaryotic Genomes...

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Unformatted text preview: Eukaryotic Gene Expression Eukaryotic Genomes & Gene Expression Eukaryotic Cells Have Multiple Chromosomes • Eukaryotic cells have 5 –20x more DNA per cell than do bacteria. • Divided into linear dsDNA + proteins : chromosomes • Typical chromosome averages ~1.5x10 8 nucleotide pairs. – If straight strands would be ~ 4 cm long. • Humans have 46 different chromosomes – So collectively amounts to ~ 2 m long dsDNA packed into each cell nucleus! (4 m after replication!) Plant cell just before division Stages in gene expression that can be regulated in eukaryotic cells Chromatin: nondividing cells Signal DNA RNA NUCLEUS Chromatin Chromatin modification: DNA unpacking involving histone acetylation and DNA demethlation Gene available for transcription Gene Transcription Exon Primary transcript Intron RNA processing Tail Cap • DNA is coiled to pack into nucleus mRNA in nucleus Transport to cytoplasm CYTOPLASM mRNA in cytoplasm Degradation of mRNA • Different degrees of coiling and packing Translation Polypetide Cleavage Chemical modification Transport to cellular destination Active protein Degradation of protein Degraded protein Figure 19.3 Levels of chromatin packing Histone tails and the effect of acetylation 1. Transcription factors may catalyze histone acetylation 2. Acetylated histone tails may recruit transcription factors 2 nm DNA double helix Histones Histone tails Histone H1 Beads of eight histone proteins 10 nm DNA double helix Linker DNA (“string ”) Nucleosome (“bead ”) chromatin (a) Nucleosomes (10-nm fiber) 30 nm Amino acids on tails available for chemical modification (a) Histone tails protrude outward from a nucleosome Dense regions of heterochromatin Unacetylated histones Nucleosome DNA remains coiled around histone “beads ” except during replication. Figure 19.2 Heyer Histone tails Less dense regions of euchromatin Acetylated histones (b) Acetylation of histone tails promotes loose chromatin structure that permits transcription Figure 19.4 1 Eukaryotic Gene Expression DNA in a eukaryotic chromosome from a developing salamander egg During cell division • chromatin condenses into visible chromosomes • Tightly wound chromosomes segregate without tangling together More loosely coiled loops are available for transcription and gene expression. Levels of chromatin packing Cell Differentiation in Multicellular Organisms Differential Gene Expression • Even though every cell has the same genome, each cell type only uses a small subset of genes. 30 nm Nucleosome – – – – chromatin (b) 30-nm fiber Protein scaffold Loops 300 nm Scaffold (c) Looped domains (300-nm fiber) ~200 cell types in mammals Each uses only ~20% of total genes Fewer in more specialized cells Unused genes may be permanently inactivated • Histone modification – 700 nm chromosome Methylation of histone residues may condense associated DNA into non- transcribable heterochromatin • DNA methylation – – 1,400 nm Methylation of cytosines related to gene inactivation Methylated DNA may attract/bind histone deacetylation enzymes Epigenic inheritance — patterns of methylation passed on to daughter cells – (d) Metaphase chromosome Figure 47.7 Blastulation Figure 19.2 A eukaryotic gene and its transcript Processing of “primary transcript” RNA [Review Gene Expression slides!] Enhancer (distal control elements) Proximal control elements Exon Intron Exon Poly-A signal Termination sequence region Intron Exon DNA 50 to 250 adenine nucleotides added to the 3 ¢ end by poly-A synthetase using ATPs A modified methyl-guanine nucleotide added to the 5 ¢ end Upstream Chromatin changes 5¢ Protein-coding segment G PPP 5¢ Cap Polyadenylation signal AAUAAA 5¢ UTR Start codon Stop codon 3¢ UTR 3¢ Exon Intron Exon Transcription AAA…AAA Poly-A tail RNA processing mRNA degradation Figure 17.9 Intron RNA Coding segment Translation Protein processing and degradation •Cap & tail protect mRNA from rapid degradation in the cytoplasm. •Eukaryotic mRNA stay active for hours, or even days, in the cytoplasm. •Prokaryotes lack cap & tail; mRNA only lasts for minutes. Heyer Downstream Poly-A signal Cleared 3 ¢ end Intron Exon of primary RNA processing: transport Cap and tail added; introns excised and exons spliced together Transcription Promoter Primary RNA transcript 5¢ (pre-mRNA) Figure 19.5 mRNA G P P P 5¢ Cap 5¢ UTR (untranslated region) Start codon Stop codon 3¢ UTR Poly-A tail (untranslated region) • Enhancer sequences may be several kb upstream or downstream of the gene, or within an intron . • One gene may have several enhancers. 2 Eukaryotic Gene Expression A model for the action of enhancers and transcription activators Distal control element Cell type–specific transcription Enhancer Promoter Promoter Activators Gene Enhancer TATA box 1 Activator proteins bind to distal control elements grouped as an enhancer in the DNA. This enhancer has three binding sites. DNA-bending protein Available activators Group of Mediator proteins Available activators RNA Polymerase II Albumin gene not expressed Albumin gene expressed Chromatin changes 3 The activators bind to certain general transcription factors and mediator proteins, helping them form an active transcription initiation complex on the promoter. Crystallin gene Lens cell nucleus Liver cell nucleus General transcription factors 2 A DNA-bending protein brings the bound activators closer to the promoter. Other transcription factors, mediator proteins, and RNA polymerase are nearby. Albumin gene Control elements Transcription RNA processing mRNA degradation RNA Polymerase II Translation Crystallin gene Crystallin gene not expressed expressed (a) Liver cell (b) Lens cell Protein processing and degradation Transcription Initiation complex RNA synthesis Figure 19.6 Alternative RNA splicing Regulation of gene expression by microRNAs (miRNAs) 1 The microRNA ( miRNA) precursor folds back on itself, held together by hydrogen bonds. Chromatin changes Transcription RNA processing 2 An enzyme called Dicer moves along the doublestranded RNA, cutting it into shorter segments. 3 One strand of 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. 5 The miRNA -protein complex prevents gene expression either by degrading the target mRNA or by blocking its translation. Translation Chromatin changes Transcription Protein processing and degradation RNA processing Exons mRNA degradation DNA Dicer Primary RNA transcript Degradation of mRNA OR miRNA or Blockage of translation Hydrogen bond Figure 19.8 Figure 19.9 Protein entering a proteasome Protein fragments (peptides) Figure 19.10 Heyer Degraded protein Polypetide Cleavage Chemical modification Transport to cellular destination Translation CYTOPLASM mRNA in nucleus Transport to cytoplasm Tail Primary transcript RNA processing Exon Intron mRNA in cytoplasm Degradation of mRNA Ubiquinated protein Cap Signal Protein to be degraded RNA Proteasome Gene Proteasome and ubiquitin to be recycled Ubiquitin Translation Protein processing and degradation DNA mRNA degradation Gene available for transcription Transcription RNA processing Transcription 2 Enzymatic components of the proteasome cut the protein into small peptides, which can be further degraded by other enzymes in the cytosol. NUCLEUS 2 The ubiquitin -tagged protein is recognized by a proteasome, which unfolds the protein and sequesters it within a central cavity. Chromatin 1 Multiple ubiquitin molecules are attached to a protein by enzymes in the cytosol. Stages in gene expression that can be regulated in eukaryotic cells Chromatin modification: DNA unpacking involving histone acetylation and DNA demethlation Degradation of a protein by a proteasome Active protein RNA splicing Target mRNA mRNA Chromatin changes Translation Protein processing and degradation Protein complex Degradation of protein mRNA degradation Figure 19.7 Figure 19.3 3 Eukaryotic Gene Expression Movement of eukaryotic transposable elements The effect of transposable elements on corn kernel color New copy of transposon Transposon DNA of genome Transposon is copied Insertion Mobile transposon (a) Transposon movement ( “copy-and-paste ” mechanism) New copy of Retrotransposon retrotransposon DNA of genome RNA Reverse transcriptase Insertion (b) Retrotransposon movement Figure 19.16 Figure 19.15 Types of DNA sequences in the human genome Exons (regions of genes coding for protein, rRNA , tRNA) (1.5%) Repetitive DNA that includes transposable elements and related sequences (44%) Introns a nd regulatory sequences (24%) Repetitive DNA unrelated to transposable elements (about 15%) Alu elements (10%) Simple sequence DNA (3%) Unique noncoding DNA (15%) Large-segment duplications (5 –6%) Figure 19.14 Heyer 4 ...
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