The Eukaryotic Genome and Its Expression. The Eukaryotic Genome and Its Expression. A. The Eukaryotic Genome. Lecture Series 11

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1 The Eukaryotic Genome and Its Expression Lecture Series 11 The Eukaryotic Genome and Its Expression A. The Eukaryotic Genome B. Repetitive Sequences (rem: teleomeres) C. The Structures of Protein-Coding Genes E. Posttranscriptional and Posttranslational Control A. The Eukaryotic Genome Although eukaryotes have more in their genomes than prokaryotes, in some cases there is NO apparent relationship between genome size and organism complexity. Amoeba dubia is the big winner at 670 Billion base pairs per cell and an uncertain phylogeny! 1

2 A. The Eukaryotic Genome Unlike prokaryotic, eukaryotic is separated from the cytoplasm by being contained within a nucleus. The initial mrna transcript of the may be modified before it is exported from the cytoplasm. A. The Eukaryotic Genome The genome of the single-celled budding yeast contains genes for the same metabolic machinery as bacteria, as well as genes for protein targeting in the cell. A. The Eukaryotic Genome The genome of the multicellular roundworm Caenorhabditis elegans contains genes required for intercellular interactions. The genome of the fruit fly has fewer genes than that of the roundworm. Many of its sequences are homologs of sequences on roundworm and mammalian genes. 2

3 Chromatin in a developing salamander ovum Levels of chromatin packing Chromatin Chromatin, detail B. Repetitive Sequences B. Repetitive Sequences Highly repetitive is present in up to millions of copies of short sequences. It is not transcribed. Its role is unknown. Rem: : Some moderately repetitive sequences, such as telomeric is found at the ends of chromosomes. Some moderately repetitive sequences, such as those coding for ribosomal RNA s, are transcribed. Three rrnas result, two go to the large subunit and one goes to the small subunit. 3

4 Moderately repetitive sequences Part of a family of identical genes for ribosomal RNA B. Repetitive Sequences Some moderately repetitive sequences are transposable, or able to move about the genome. These are known as Transposons. Transposons in corn Types of sequences in the human genome Exons (regions of genes coding for protein, rrna, trna) (1.5%) Repetitive that includes transposable elements and related sequences (44%) Introns and regulatory sequences (24%) Alu elements (10%) Repetitive unrelated to transposable elements (about 15%) Unique noncoding (15%) Simple sequence (3%) Large-segment duplications (5 6%) 4

5 C. The Structures of Protein- Coding Genes A typical protein-coding gene has noncoding internal sequences (introns( introns) ) as well as flanking sequences that are involved in the machinery of transcription and translation in addition to its exons or coding regions. These are usually single copy genes. C. The Structures of Protein- Coding Genes Some eukaryotic genes form families of related genes that have similar sequences and code for similar proteins. These related proteins may be made at different times and in different tissues. Some sequences in gene families are pseudogenes,, which code for nonfunctional mrna s s or proteins. Gene Families Pseudogenes C. The Structures of Protein- Coding Genes Differential expression of different genes in the β-globin family ensures important physiological changes during human development. 5

6 The evolution of human α-globin and β-globin gene families Stages in gene expression that can be regulated in eukaryotic cells Signal NUCLEUS Chromatin Eukaryotic gene expression can be controlled at the transcriptional, posttranscriptional, translational, and posttranslational levels. Cap RNA Chromatin modification: unpacking involving histone acetylation and demethlation Gene available for transcription Gene Exon Primary transcript Intron Tail mrna in nucleus Transport to cytoplasm Degradation of mrna CYTOPLASM mrna in cytoplasm Translation Polypetide Cleavage Chemical modification Transport to cellular destination Active protein Degradation of protein Degraded protein The major method of control of eukaryotic gene expression is selective transcription, which results from specific proteins binding to regulatory regions on. A series of transcription factors must bind to the promoter before RNA polymerase can bind. Whether RNA polymerase will initiate transcription also depends on the binding of regulatory proteins, activator proteins, and repressor proteins. 6

7 Chromatin changes mrna degradation Translation Protein processing and degradation A eukaryotic gene and its transcript A model for the action of enhancers and transcription activators Enhancer (distal control elements) Proximal control elements Poly-A signal sequence Termination region Distal control element Activators Promoter Gene Upstream Chromatin changes mrna Translation degradation Exon Intron Exon Intron Exon Promoter Poly-A signal Primary RNA Exon Intron Exon Intron Exon transcript 5 (pre-mrna) : Cap and tail added; introns excised and Intron RNA exons spliced together Coding segment Downstream Cleared 3 end of primary transport Enhancer 1 Activator proteins bind to distal control elements grouped as an enhancer in the. This enhancer has three binding sites. 2 A -bending protein brings the bound activators closer to the promoter. Other transcription factors, mediator proteins, and RNA polymerase are nearby. TATA box -bending protein General transcription factors Group of Mediator proteins RNA Polymerase II Protein processing and degradation mrna G P P P 5 Cap 5 UTR (untranslated region) Start codon Stop codon 3 UTR Poly-A (untranslated tail region) 3 The activators bind to certain general transcription factors and mediator proteins, helping them form an active transcription initiation complex on the promoter. Initiation complex RNA Polymerase II RNA synthesis Three of the major types of -binding domains in transcription factors The -binding domains of most - binding proteins have one of four structural motifs: helix-turn turn-helix, zinc finger, leucine zipper, or helix-loop loop-helix. A simple model of histone tails and the effect of histone acetylation Chromatin changes Acetylation of histone tails promotes loose chromatin structure that permits transcription to more readily occur. mrna Translation degradation Protein processing and degradation Histone tails double helix Amino acids available for chemical modification (a) Histone tails protrude outward from a nucleosome Unacetylated histones Acetylated histones (b) Acetylation of histone tails promotes loose chromatin structure that permits transcription 7

8 E. Posttranscriptional Control Alternative RNA splicing Chromatin changes Because eukaryotic genes have several exons,, alterative mrnas can be generated from the same RNA transcript. This alternate splicing can be used to produce different proteins. The stability of mrna in the cytoplasm can be regulated by the binding of proteins. mrna Translation degradation Protein processing and degradation Primary RNA transcript Exons RNA splicing or mrna E. Posttranslational Control Degradation of a protein by a proteasome Proteasomes degrade proteins targeted for breakdown. Proteasomes 8