Chapter 19 Control of Eukaryotic Genome AP Biology

Chapter 19. Control of Eukaryotic Genome AP Biology 2005 -2006

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? AP Biology 2005 -2006

Prokaryote vs. eukaryote genome Prokaryotes u u small size of genome circular molecule of naked DNA u most of DNA codes for protein or RNA AP Biology DNA is readily available to RNA polymerase control of transcription by regulatory proteins w operon system no introns, small amount of non-coding DNA w regulatory sequences: promoters, operators 2005 -2006

Prokaryote vs. eukaryote genome Eukaryotes u much greater size of genome u DNA packaged in chromatin fibers u need to turn on & off large numbers of genes most of DNA does not code for protein AP Biology regulates access to DNA by RNA polymerase cell specialization u how does all that DNA fit into nucleus? 97% “junk DNA” in humans 2005 -2006

Points of control The control of gene expression can occur at any step in the pathway from gene to functional protein u unpacking DNA u transcription u m. RNA processing u m. RNA transport u u u AP Biology out of nucleus through cytoplasm protection from degradation translation protein processing protein degradation 2005 -2006

Why turn genes on & off? Specialization u each cell of a multicellular eukaryote expresses only a small fraction of its genes Development u different genes needed at different points in life cycle of an organism afterwards need to be turned off permanently Responding to organism’s needs u u AP Biology homeostasis cells of multicellular organisms must continually turn certain genes on & off in response to signals from their external & internal environment 2005 -2006

DNA packing How do you fit all that DNA into nucleus? u DNA coiling & folding double helix nucleosomes chromatin fiber looped domains chromosome from DNA double helix to condensed chromosome AP Biology 2005 -2006

Nucleosomes 8 histone molecules “Beads on a string” 1 st level of DNA packing u histone proteins u 8 protein molecules many positively charged amino acids w arginine & lysine bind tightly to negatively charged DNA AP Biology DNA packing movie 2005 -2006

DNA packing Degree of packing of DNA regulates transcription u u tightly packed = no transcription = genes turned off darker DNA (H) = tightly packed lighter DNA (E) = loosely packed AP Biology 2005 -2006

DNA methylation Methylation of DNA blocks transcription factors u u no transcription = genes turned off attachment of methyl groups (–CH 3) to cytosine u nearly permanent inactivation of genes AP Biology C = cytosine ex. inactivated mammalian X chromosome 2005 -2006

Histone acetylation Acetylation of histones unwinds DNA u u loosely packed = transcription = genes turned on AP Biology attachment of acetyl groups (–COCH 3) to histones w conformational change in histone proteins w transcription factors have easier access to genes 2005 -2006

Transcription initiation Control regions on DNA u promoter nearby control sequence on DNA binding of RNA polymerase & transcription factors “base” rate of transcription u enhancers distant control sequences on DNA binding of activator proteins “enhanced” rate (high level) of transcription AP Biology 2005 -2006

Model for Enhancer action Enhancer DNA sequences u Activator proteins u distant control sequences bind to enhancer sequence & stimulates transcription Silencer proteins bind to enhancer sequence & block gene transcription AP Biology Turning on Gene movie u 2005 -2006

Post-transcriptional control Alternative RNA splicing u AP Biology variable processing of exons creates a family of proteins 2005 -2006

Regulation of m. RNA degradation Life span of m. RNA determines pattern of protein synthesis u m. RNA can last from hours to weeks AP Biology RNA processing movie 2005 -2006

RNA interference NEW ! Small RNAs (s. RNA) u short segments of RNA (21 -28 bases) bind to m. RNA create sections of double-stranded m. RNA “death” tag for m. RNA w triggers degradation of m. RNA u cause gene “silencing” even though post-transcriptional control, still turns off a gene si. RNA AP Biology 2005 -2006

Hott new est topic in bi olog y RNA interference Small RNAs m. RNA double-stranded RNA s. RNA + m. RNA degraded functionally turns gene off AP Biology 2005 -2006

Control of translation Block initiation stage u regulatory proteins attach to 5’ end of m. RNA prevent attachment of ribosomal subunits & initiator t. RNA block translation of m. RNA to protein AP Biology Control of translation movie 2005 -2006

Protein processing & degradation Protein processing u folding, cleaving, adding sugar groups, targeting for transport Protein degradation ubiquitin tagging u proteosome degradation u AP Biology Protein processing movie 2005 -2006

1980 s | 2004 Ubiquitin “Death tag” mark unwanted proteins with a label u 76 amino acid polypeptide, ubiquitin u labeled proteins are broken down rapidly in "waste disposers" u AP proteasomes Aaron Ciechanover Biology Israel Avram Hershko Israel Irwin Rose UC Riverside 2005 -2006

Proteasome Protein-degrading “machine” cell’s waste disposer u can breakdown all proteins into 7 -9 amino acid fragments u AP Biology play Nobel animation 2005 -2006

6 1. transcription -DNA packing -transcription factors posttranslation 2. m. RNA processing -splicing 4 5 translation m. RNA transport 4. m. RNA transport in cytoplasm -protection by 3’ cap & poly-A tail 1 5. translation -factors which block start of translation transcription 6. post-translation m. RNA transport -protein processing 2005 -2006 -protein degradation out of nucleus 3 2 m. RNA processing AP Biology 3. m. RNA transport out of nucleus -breakdown by s. RNA

Structure of the Eukaryotic Genome AP Biology 2005 -2006

How many genes? Genes only ~3% of human genome u protein-coding sequences u u 1% of human genome non-protein coding genes 2% of human genome t. RNA ribosomal RNAs si. RNAs AP Biology 2005 -2006

What about the rest of the DNA? Non-coding DNA sequences u regulatory sequences promoters, enhancers terminators u “junk” DNA introns repetitive DNA w centromeres w telomeres w tandem & interspersed repeats transposons & retrotransposons w Alu in humans AP Biology 2005 -2006

Repetitive DNA & other non-coding sequences account for most of eukaryotic DNA AP Biology 2005 -2006

Genetic disorders of repeats Fragile X syndrome most common form of inherited mental retardation u defect in X chromosome u mutation of FMR 1 gene causing many repeats of CGG triplet in promoter region w 200+ copies w normal = 6 -40 CGG repeats FMR 1 gene not expressed & protein (FMRP) not produced w function of FMR 1 protein unknown w binds RNA AP Biology 2005 -2006

Fragile X syndrome The more triplet repeats there are on the X chromosome, the more severely affected the individual will be u AP Biology mutation causes increased number of repeats (expansion) with each generation 2005 -2006

Huntington’s Disease Rare autosomal dominant degenerative neurological disease 1 st described in 1872 by Dr. Huntington u most common in white Europeans u 1 st symptoms at age 30 -50 u death comes ~12 years after onset Mutation on chromosome 4 u CAG repeats 40 -100+ copies normal = 11 -30 CAG repeats CAG codes for glutamine amino acid AP Biology 2005 -2006

Huntington’s disease Abnormal (huntingtin) protein produced chain of charged glutamines in protein u bonds tightly to brain protein, HAP-1 u Woody Guthrie AP Biology 2005 -2006

Families of genes Human globin gene family u evolved from duplication of common ancestral globin gene Different versions are expressed at different times in development allowing hemoglobin to function throughout life of developing animal AP Biology 2005 -2006

Hemoglobin differential expression of different beta globin genes ensures important physiological changes during human development AP Biology 2005 -2006

Interspersed repetitive DNA Repetitive DNA is spread throughout genome interspersed repetitive DNA make up 25 -40% of mammalian genome u in humans, at least 5% of genome is made of a family of similar sequences called, Alu elements u 300 bases long Alu is an example of a "jumping gene" – a transposon DNA sequence that "reproduces" by copying itself & inserting into new chromosome locations AP Biology 2005 -2006

Rearrangements in the genome Transposons u transposable genetic element piece of DNA that can move from one location to another in cell’s genome One gene of an insertion sequence codes for transposase, which catalyzes the transposon’s movement. The inverted repeats, about 20 to 40 nucleotide pairs long, are backward, upside-down versions of each oth. In transposition, transposase molecules bind to the inverted repeats & catalyze the cutting & resealing of DNA required for AP Biology 2005 -2006 insertion of the transposon at a target site.

Transposons Insertion of transposon sequence in new position in genome insertion sequences cause mutations when they happen to land within the coding sequence of a gene or within a DNA region that regulates gene expression AP Biology 2005 -2006

Transposons 1947|1983 Barbara Mc. Clintock u AP Biology discovered 1 st transposons in Zea mays (corn) in 1947 2005 -2006

AP Biology 2005 -2006

Retrotransposons Transposons actually make up over 50% of the corn (maize) genome & 10% of the human genome. Most of these transposons are retrotransposons, transposable elements that move within a genome by means of RNA intermediate, transcript of the retrotransposon DNA AP Biology 2005 -2006