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? AP Biology

Evolution of gene regulation Prokaryotes single-celled u evolved to grow & divide rapidly u must respond quickly to changes in external environment u exploit transient resources Gene regulation u turn genes on & off rapidly u AP Biology flexibility & reversibility adjust levels of enzymes for synthesis & digestion

Evolution of gene regulation Eukaryotes multicellular u evolved to maintain constant internal conditions while facing changing external conditions u u homeostasis regulate body as a whole growth & development w long term processes specialization w turn on & off large number of genes AP Biology must coordinate the body as a whole rather than serve the needs of individual cells

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 3. m. RNA processing 4. m. RNA transport 5. translation 6. protein processing 7. protein degradation AP Biology

1. 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 AP Biology condensed chromosome

Nucleosomes 8 histone molecules “Beads on a string” 1 st level of DNA packing u histone proteins u 8 protein molecules positively charged amino acids bind tightly to negatively charged DNA AP Biology DNA packing movie

DNA packing as gene control Degree of packing of DNA regulates transcription u tightly wrapped around histones no transcription genes turned off § heterochromatin darker DNA (H) = tightly packed § euchromatin lighter DNA (E) = loosely packed H AP Biology E

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

Histone acetylation Acetylation of histones unwinds DNA u loosely wrapped around histones u attachment of acetyl groups (–COCH 3) to histones AP Biology enables transcription genes turned on conformational change in histone proteins transcription factors have easier access to genes

Histone Modifications In histone acetylation, acetyl groups are attached to positively charged lysines in histone tails This process loosens chromatin structure, thereby promoting the initiation of transcription The addition of methyl groups (methylation) can condense chromatin; the addition of phosphate groups (phosphorylation) next to a methylated amino acid can loosen Animation: DNA Packing chromatin AP Biology

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

Model for Enhancer action Enhancer DNA sequences u Activator proteins u distant control sequences bind to enhancer sequence & stimulates transcription Silencer proteins u 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 Coactivator A E F B TFIID H RNA polymerase II Coding r egion T A Core promoter and initiation complex Initiation Complex at Promoter Site binding site of RNA polymerase AP Biology

An activator is a protein that binds to an enhancer and stimulates transcription of a gene Bound activators cause mediator proteins to interact with proteins at the promoter Animation: Initiation of Transcription AP Biology

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

4. Regulation of m. RNA degradation Life span of m. RNA determines amount of protein synthesis u m. RNA can last from hours to weeks AP Biology RNA processing movie

m. RNA Degradation The life span of m. RNA molecules in the cytoplasm is a key to determining protein synthesis Eukaryotic m. RNA is more long lived than prokaryotic m. RNA The m. RNA life span is determined in part by sequences in the leader and trailer regions Animation: m. RNA Degradation AP Biology

RNA interference NEW Small interfering RNAs (si. 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” post-transcriptional control turns off gene = no protein produced si. RNA AP Biology !

Action of si. RNA Hot … new Hot t in b opic iolog y dicer enzyme m. RNA for translation si. RNA double-stranded mi. RNA + si. RNA breakdown enzyme (RISC) m. RNA degraded AP Biology functionally turns gene off

RNA interference 1990 s | 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 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

Initiation of Translation The initiation of translation of selected m. RNAs can be blocked by regulatory proteins that bind to sequences or structures of the m. RNA Alternatively, translation of all m. RNAs in a cell may be regulated simultaneously For example, translation initiation factors are simultaneously activated in an egg following fertilization Animation: Blocking Translation AP Biology

6 -7. Protein processing & degradation Protein processing u folding, cleaving, adding sugar groups, targeting for transport Protein degradation ubiquitin tagging u proteasome degradation u AP Biology Protein processing movie

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 proteasomes Aaron Ciechanover AP Biology Israel Avram Hershko Israel Irwin Rose UC Riverside

Protein Processing and Degradation After translation, various types of protein processing, including cleavage and the addition of chemical groups, are subject to control Proteasomes are giant protein complexes that bind protein molecules and degrade them Animation: Protein Processing Animation: Protein Degradation AP Biology

Proteasome Protein-degrading “machine” cell’s waste disposer u breaks down any proteins into 7 -9 amino acid fragments u cellular recycling AP Biology play Nobel animation

6 7 Gene Regulation protein processing & degradation 1 & 2. transcription - DNA packing - transcription factors 5 4 initiation of translation m. RNA processing 3 & 4. post-transcription - m. RNA processing - splicing - 5’ cap & poly-A tail - breakdown by si. RNA 5. translation - block start of translation 1 2 initiation of transcription AP Biology m. RNA splicing 3 6 & 7. post-translation - protein processing - protein degradation 4 m. RNA protection

The other important source of developmental information is the environment around the cell, especially signals from nearby embryonic cells In the process called induction, signal molecules from embryonic cells cause transcriptional changes in nearby target cells Thus, interactions between cells induce differentiation of specialized cell types Animation: Cell Signaling AP Biology

Axis Establishment Maternal effect genes encode for cytoplasmic determinants that initially establish the axes of the body of Drosophila These maternal effect genes are also called egg-polarity genes because they control orientation of the egg and consequently the fly Animation: Development of Head-Tail Axis in Fruit Flies AP Biology

Turn your Question Genes on! AP Biology 2007 -2008

6 Gene Regulation 7 1 & 2. _________________ - ____________ 5 4 1 2 3 & 4. _________ - ____________________ 5. _________ - ____________________ AP Biology 3 4 6 & 7. _________________ - ____________