Ch18 Regulation Of Gene Expression PDF

18. Regulation of Gene Expression AP Biology  Control of Prokaryotic (Bacterial) Genes AP Biology  Bacterial metabolism Bacteria need to respond quickly to changes in their environment  if they have enough of a product, need to st...

18. Regulation of Gene Expression AP Biology  Control of Prokaryotic (Bacterial) Genes AP Biology  Bacterial metabolism Bacteria need to respond quickly to changes in their environment  if they have enough of a product, need to stop production why? waste of energy to produce more STOP how? stop production of enzymes for synthesis  if they find new food/energy source, need to utilize it quickly why? metabolism, growth, reproduction GO how? start production of enzymes for digestion AP Biology  Remember Regulating Metabolism? Feedback inhibition - = inhibition  product acts as an allosteric inhibitor of 1st enzyme in tryptophan pathway  but this is wasteful production of enzymes - Oh, I remember this! AP Biology  Different way to Regulate Metabolism Gene regulation  instead of blocking - = inhibition enzyme function, block transcription of genes for all enzymes in tryptophan pathway saves energy by not wasting it on unnecessary - protein synthesis - Now, that’s a good idea from a AP Biology lowly bacterium!  Precursor Genes that encode enzymes 1, 2, and 3 Feedback trpE inhibition Enzyme 1 trpD Regulation of gene expression Enzyme 2 trpC – trpB – Enzyme 3 trpA Tryptophan (a) Regulation of enzyme (b) Regulation of enzyme activity production © 2017 Pearson Education, Inc.  Gene regulation in bacteria Cells vary amount of specific enzymes by regulating gene transcription  turn genes on or turn genes off turn genes OFF example if bacterium has enough tryptophan then it STOP doesn’t need to make enzymes used to build tryptophan turn genes ON example if bacterium encounters new sugar (energy GO source), like lactose, then it needs to start making enzymes used to digest lactose AP Biology  Bacteria group genes together Operon (P-O-G) 1. promoter = RNA polymerase binding site single promoter controls transcription of all genes in operon transcribed as one unit & a single mRNA is made 2. operator = DNA binding site of repressor protein 3. genes = grouped together with related functions example: all enzymes in a metabolic pathway AP Biology  So how can these genes be turned off? Repressor protein  binds to DNA at operator site  blocking RNA polymerase  blocks transcription AP Biology  Operon model Operon: operator, promoter & genes they control RNA polymerase serve as a model for gene regulation RNA TATA repressor polymerase gene1 gene2 gene3 gene4 DNA mRNA 1 2 3 4 enzyme1 enzyme2 enzyme3 enzyme4 promoter operator Repressor protein turns off gene by repressor = repressor protein blocking AP BiologyRNA polymerase binding site.  Repressible operon: tryptophan Synthesis pathway model RNA When excess tryptophan is present, polymerase it binds to tryp repressor protein & triggers repressor to bind to DNA  blocks (represses) transcription RNA TATA trp repressor polymerase gene1 gene2 gene3 gene4 DNA mRNA 1 2 3 4 trp trp trp trp enzyme1 enzyme2 enzyme3 enzyme4 promoter operator trp trp repressor repressor protein trp trp trp tryptophan trp conformational change in tryptophan – repressor protein AP Biologyprotein! repressor trp repressor complex  Tryptophan operon What happens when tryptophan is present? Don’t need to make tryptophan-building enzymes Tryptophan AP Biology is allosteric regulator of repressor protein Figure 18.3 trp operon DNA trp promoter Promoter Regulatory gene Genes of operon trpR trpE trpD trpC trpB trpA RNA trp operator Stop codon polymerase Start codon 3′ Polypeptide mRNA mRNA 5′ 5′ subunits that make up enzymes Inactive trp E D C B A for tryptophan Protein synthesis repressor (a) Tryptophan absent, repressor inactive, operon on. DNA trpR trpE No RNA 3′ mRNA made 5′ Protein Active trp repressor Tryptophan (corepressor) (b) Tryptophan present, repressor active, operon off. © 2017 Pearson Education, Inc.  Inducible operon: lactose lac lac Digestive pathway model lac RNA lac When lactose is present, binds to polymerase lac lac repressor protein & triggers lac repressor to release DNA lac  induces transcription RNA TATAlac repressor polymerase gene1 gene2 gene3 gene4 DNA mRNA 1 2 3 4 enzyme1 enzyme2 enzyme3 enzyme4 promoter operator repressor repressor protein lac lactose conformational change in lactose – repressor protein AP Biologyprotein! lac repressor repressor complex  Lactose operon What happens when lactose is present? Need to make lactose-digesting enzymes Lactose is allosteric regulator of repressor protein AP Biology Figure 18.4 Regulatory Promoter DNA gene Operator lacI lacZ No RNA 3′ made mRNA 5′ RNA polymerase Protein Active repressor (a) Lactose absent, repressor active, operon off. lac operon DNA lacI lacZ lacY lacA RNA polymerase Start codon Stop codon 3′ mRNA 5′ mRNA 5′ Protein β-Galactosidase Permease Transacetylase Inactive lac Allolactose repressor Enzymes for using lactose (inducer) (b) Lactose present, repressor inactive, operon on. © 2017 Pearson Education, Inc.  Operon summary Repressible operon (trp operon)  Default ON  usually functions in anabolic pathways synthesizing end products  when end product is present in excess, cell allocates resources to other uses Inducible operon (lac operon)  Default OFF  usually functions in catabolic pathways, digesting nutrients to simpler molecules  produce enzymes only when nutrient is available cell avoids making proteins that have nothing to do, cell allocates resources to other uses AP Biology AP Biology  Gene Regulation: Positive vs. Negative Control  Negative control: Operons are switched on/off by active form of repressor or inducer protein Eg. trp operon, lac operon  Positive control: Regulatory protein interacts directly with genome to increase rate of transcription Eg. cAMP and CAP (catabolite activator protein) AP Biology AP Biology  Two types of Negative Gene Regulation AP Biology  Positive Gene Regulation Glucose is preferred food source over lactose, why?? When lactose is present, and glucose is low  cAMP activates CAP  increases rate of transcription When lactose and glucose are both present  cAMP level is low  CAP detaches  transcription back to AP Biology normal rate  Don’t be repressed! How can I induce you to ask Questions? AP Biology  Control of Eukaryotic Genes AP Biology  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  Points of control The control of gene expression can occur at any step in the pathway from gene to functional protein 1. Chromatin modification 2. Transcription 3. RNA processing 4. RNA transport 5. Translation 6. Protein processing 7. Protein transport AP Biology  Chromatin Structure: Tightly bound DNA  less accessible for transcription DNA methylation: methyl groups added to DNA; tightly packed;  transcription Histone acetylation: acetyl groups added to histones; loosened;  transcription AP Biology  DNA packing as gene control Degree of packing of DNA regulates transcription  tightly wrapped around histones no transcription genes turned off  heterochromatin darker DNA (H) = tightly packed  euchromatin lighter DNA (E) = loosely packed H E AP Biology  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 AP Biology  Histone acetylation Acetylation of histones unwinds DNA  loosely wrapped around histones enables transcription genes turned on  attachment of acetyl groups (–COCH 3) to histones conformational change in histone proteins transcription factors have easier access to genes AP Biology AP Biology AP Biology  Epigenetic Inheritance Modifications on chromatin can be passed on to future generations Unlike DNA mutations, these changes to chromatin can be reversed (de- methylation of DNA) Explains differences between identical twins Eg. DNA methylation (gene silencing), histone acetylation, X chromosome inactivation, heterochromatin (silent chromatin) AP Biology  https://learn.genetics.utah.edu/content/epigenetics/intro/ https://learn.genetics.utah.edu/content/epigenetics/ AP Biology  https://learn.genetics.utah.edu/content/epigenetics/twins/ https://learn.genetics.utah.edu/content/epigenetics/ AP Biology  Transcription Initiation: Specific transcription factors (activators or repressors) bind to control elements (enhancer region) Activators: increase transcription Repressors: decrease transcription AP Biology Figure 18.8b_3 Proximal Transcription Poly-A signal control elements start site sequence Exon Intron Exon Intron Exon DNA Promoter Transcription Poly-A signal Cleaved 3′ Primary RNA Exon Intron Exon Intron Exon 5′ end of transcript primary (pre-mRNA) RNA processing transcript Intron RNA Coding segment mRNA G P P P AAA···AAA 3′ 5′ Cap 5′ UTR Start Stop 3′ UTR Poly-A codon codon tail © 2017 Pearson Education, Inc.  Transcription Initiation Complex Activators bind to enhancer regions + other proteins + RNA polymerase AP Biology  Cell type-specific transcription AP Biology  Transcription initiation Control regions on DNA  promoter nearby control sequence on DNA binding of RNA polymerase & transcription factors “base” rate of transcription  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  distant control sequences Activator proteins  bind to enhancer sequence & stimulates transcription Silencer proteins  bind to enhancer sequence & block gene transcription AP Biology Turning on Gene movie  Post-transcriptional control Alternative RNA splicing  variable processing of exons creates a family of proteins AP Biology Figure 18.13 Exons DNA 1 2 3 4 5 Troponin T gene Primary RNA 1 2 3 4 5 transcript RNA splicing mRNA 1 2 3 5 OR 1 2 4 5 © 2017 Pearson Education, Inc.  Regulation of mRNA degradation Life span of mRNA determines amount of protein synthesis  mRNA can last from hours to weeks AP Biology  RNA degradation Regulation of mRNA: micro RNAs (miRNAs) and small interfering RNAs (siRNAs) can bind to mRNA and degrade it or block translation AP Biology  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 AP Biology  Control of translation Block initiation of translation stage  regulatory proteins attach to 5' end of mRNA prevent attachment of ribosomal subunits & initiator tRNA block translation of mRNA to protein AP Biology  Protein processing & degradation Protein processing  folding, cleaving, adding sugar groups, targeting for transport Protein degradation  ubiquitin tagging  proteasome degradation AP Biology Protein processing movie  Proteasome Protein-degrading “machine”  cell’s waste disposer  breaks down any proteins into 7-9 amino acid fragments cellular recycling AP Biology  Summary of Eukaryotic Gene Regulation AP Biology AP Biology AP Biology AP Biology  18.4 EMBRYONIC DEVELOPMENT OF MULTICELLULAR ORGANISMS AP Biology AP Biology  Embryonic Development: Zygote  Organism 1. Cell Division: large # identical cells through mitosis 2. Cell Differentiation: cells become specialized in structure & function 3. Morphogenesis: “creation of form” – organism’s shape AP Biology  Determination: irreversible series of events that lead to cell differentiation AP Biology  Cytoplasmic determinants:  maternal substances in egg distributed unevenly in early cells of embryo  Include mRNA, proteins, chemicals, and organelles  Sets up gradients that determines “head” side vs. “tail” side AP Biology AP Biology  Induction: cells triggered to differentiate Cell-Cell Signals: molecules produced by one cell influences neighboring cells  Eg. Growth factors AP Biology AP Biology AP Biology  Pattern formation: setting up the body plan (head, tail, L/R, back, front) AP Biology  Morphogens: substances that establish an embryo’s axes AP Biology  Bicoid anterior mutations AP Biology  Homeotic genes: master control genes that control pattern formation (eg. Hox genes) AP Biology  HHMI Short Film EVOLVING SWITCHES, EVOLVING BODIES AP Biology  Pitx1 Gene = Homeotic/Hox Gene Stickleback Fish Humans Development of pelvic Development of anterior bone structures, brain, structure of hindlimb Mutation may cause clubfoot, polydactyly (extra fingers/toes), upper limb deformities AP Biology  Role of Apoptosis Most of the embryonic cells are produced in excess Cells will undergo apoptosis (programmed cell death) to sculpture organs and tissues Carried out by caspase proteins AP Biology  18.5: CANCER RESULTS FROM GENETIC CHANGES THAT AFFECT CELL CYCLE CONTROL AP Biology  Control of Cell Cycle: Proto-oncogene = stimulates cell division Tumor-suppressor gene = inhibits cell division Mutations in these genes can lead to cancer AP Biology  Genes involved in cancer: Ras gene: stimulates cell cycle (proto- oncogene)  Mutations of ras occurs in 30% of cancers p53 gene: tumor-suppresor gene  Functions: halt cell cycle for DNA repair, turn on DNA repair, activate apoptosis (cell death)  Mutations of p53 in 50+% of cancers AP Biology  Proto-Oncogene Oncogene Gene that stimulates  Mutation in proto- normal cell growth & oncogene division  Cancer-causing gene Effects:  Increase product of proto-oncogene  Increase activity of each protein molecule produced by gene AP Biology  Proto-oncogene  Oncogene AP Biology Figure 18.24 1 Growth factor 3 G protein P P NUCLEUS 6 Protein that P P Ras P P stimulates GTP 5 Transcription the cell cycle factor (activator) 2 Receptor 4 Protein kinases Normal cell division (a) Normal cell cycle–stimulating pathway. MUTATION Ras Overexpression of protein GTP NUCLEUS Transcription factor (activator) Ras protein active with or without growth factor. Increased cell division (b) Mutant cell cycle–stimulating pathway. © 2017 Pearson Education, Inc. Figure 18.25 2 Protein kinases 5 Protein that Damaged DNA inhibits the is not replicated. NUCLEUS cell cycle UV light 1 DNA damage 3 Active form 4 Transcription in genome of p53 No cell division (a) Normal cell cycle–inhibiting pathway Cell cycle is Inhibitory not inhibited. protein Defective or absent UV missing light MUTATION transcription factor DNA damage in genome Increased cell division (b) Mutant cell cycle–inhibiting pathway © 2017 Pearson Education, Inc.  Cancer results when mutations accumulate (5-7 changes in DNA) Active oncogenes + loss of tumor-suppressor genes The longer we live, the more likely that cancer might develop AP Biology Figure 18.26a 1 Loss of tumor- Colon wall suppressor gene APC (or other) Normal colon Small benign epithelial cells growth (polyp) 2 Activation of 4 Loss of ras oncogene tumor-suppressor gene p53 3 Loss of 5 Additional tumor-suppressor mutations gene SMAD4 Larger benign Malignant tumor growth (adenoma) (carcinoma) © 2017 Pearson Education, Inc. Figure 18.27 MAKE CONNECTIONS: Genomics, Cell Signaling, and Cancer Luminal A Luminal B Basal-like ERα PR ERα− PR− HER2− ERα++ 15–20% of breast cancers ERα+++ PR++ More aggressive; poorer PR++ prognosis than other subtypes HER2− (shown here); HER2– some HER2++ 40% of breast cancers 15–20% of breast cancers Best prognosis Poorer prognosis than luminal A subtype A research scientist examines DNA sequencing data from breast cancer samples. HER2 HER2 ERα− Normal Breast Cells in a Milk Duct PR− In a normal breast cell, the three signal receptors HER2++ HER2 10–15% of breast are at normal levels (indicated by +): receptor cancers ERα+ Duct Dimer Poorer prognosis PR+ interior than luminal HER2+ A subtype Estrogen Milk receptor duct alpha (ERα) Signaling molecule Progesterone receptor (PR) P P P P Response P P ATP ADP (cell division) HER2 Mammary Epithelial receptor Treatment with Herceptin for the HER2 subtype gland milk-secreting lobule Herceptin molecule cell Support Extracellular cell matrix HER2 receptors © 2017 Pearson Education, Inc. Figure 18.27d MAKE CONNECTIONS: Genomics, Cell Signaling, and Cancer HER2 HER2 ERα− PR− HER2++ 10–15% of breast cancers Poorer prognosis than luminal A subtype Signaling HER2 molecule receptor Dimer P P P P Response ATP ADP P P (cell division) Treatment with Herceptin for the HER2 subtype Herceptin molecule HER2 receptors © 2017 Pearson Education, Inc.  Summary Embryonic development occurs when gene regulation proceeds correctly Cancer occurs when gene regulation goes awry AP Biology  7 6 protein processing & Gene degradation Regulation 1 & 2. transcription - DNA packing - transcription factors 5 initiation of 4 3 & 4. post-transcription translation - mRNA processing mRNA processing - splicing - 5’ cap & poly-A tail - breakdown by siRNA 1 2 5. translation initiation of - block start of transcription translation 6 & 7. post-translation - protein processing - protein transport mRNA AP Biology mRNA splicing 4 protection 3  Turn your Question Genes on! 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