Ch. 18 Notes - Gene Regulation (Annotated PDF)

## **CH. 18- REGULATION OF GENE EXPRESSION** - when, how, & why genes get turned on/off - genes expressed in developing wing of a fly - **INTRODUCTION TO EPIGENETICS** - TED Talks: Epigenetic Transformation- You Are What Your Grandparents Ate- Pamela Peeke (21:14) - outside the genome-it's...

## **CH. 18- REGULATION OF GENE EXPRESSION** - when, how, & why genes get turned on/off - genes expressed in developing wing of a fly - **INTRODUCTION TO EPIGENETICS** - TED Talks: Epigenetic Transformation- You Are What Your Grandparents Ate- Pamela Peeke (21:14) - outside the genome-it's not just the sequence of DNA that counts ## **PROKARYOTIC GENE EXPRESSION** - **Concept 18.1** - Individual bacteria respond to environmental change by regulating their gene expression - ex. *E. coli* - lives in colon - Can tune its metabolism to the changing environment & food sources - Conservation of resources/energy - don't need the products = don't make it - can activate or shutdown pathway - use as few genes as possible - **OPERONS: THE BASIC CONCEPT** - Related genes are under coordinated control of an *operon*, which includes: - **promoter:** sequence upstream of genes - **operator:** "on-off" switch - Part of the promoter = controls access to promoter - Used as a binding site to block access of RNA pol - Repressor proteins bind here - do the blocking = related pathways - controls a set of genes - all on or all off - McGraw Hill Animation: Regulatory Proteins (2 min) - Ex. *E. coli*- 5 genes under one promoter (transcription unit) ## **REPRESSIBLE OPERONS** - Ex. Trp Operon - Synthesis - Typical of anabolic pathways - Default: genes are ON - Repressor/corepressor binds and turns genes off - ex trp repressor- made by regulatory gene *trpR* - 5 genes under control of one promoter - when we have too much product - repress the gene - trp repressor binds at allosteric site - activation - blocks RNA pol - no transcription! ## **INDUCIBLE OPERONS** - Ex. Lac Operon - digestion - Typical of catabolic pathways (hydrolysis) - Default: gens are OFF - Activator protein (or inducer) binds to repressor and inactivates it - turns genes on - when inducer is present - food! - Ex. Lactose - for repressor protein - gene for B-galactosidase: Lactose -> Glucose + Galactose - no food = no inducer OR if glucose is present (preferred source) - regul. gene - operator - lacz - transcription ## **NEGATIVE GENE REGULATION** - Regulation of the *trp* and *lac* operons involves negative control of genes - Operons are switched OFF by the active form of the repressor ## **POSITIVE GENE REGULATION** - **Involves stimulatory proteins** - Activators of transcription - ex. catabolite activator protein (CAP) in *lac* operon - When glucose is low, CAP is activated by binding with cyclic AMP - Activated CAP attaches to the promoter of the *lac* operon and increases affinity of RNA pol - When glucose is high, CAP detaches, and transcription returns to normal rate - fast transcription of *lac* operon genes - **↓ glucose ↑ cAMP** - **cAMP activates CAP** - **CAP binds DNA & allows RNA pol better access to promoter** - **↑ glucose ↓ cAMP** - **YouTube Video: Lac Operon Animation- Negative & Positive Regulation (6 min)** ## **EUKARYOTIC GENE REGULATION** - **Concept 18.2** - Each gene has separate control - no operons; each gene has its own switch - genomic equivalence - Specialized cells & differential gene expression - Diseases and cancer - turning off the wrong gene: ex. p53 tumor suppressor - only 20% of genes expressed at once - **same DNA in every somatic cell** - **Stem Cells** ## **INCLUDES:** - Chromatin Modification - Transcriptional Control - RNA Processing Control - RNA Transport Control - Translational Control - destroy/deactivate protein - **histone acetyl & transcription factors** - **differential splicing** - **mRNA never leaves nucleus** ## **REGULATION OF CHROMATIN STRUCTURE** - **Mutations are permanent but this can be reversed, ex. folic acid - diet & lifestyle choices** - **pushes apart beads (nucleosomes)** - Genes within packed heterochromatin - usually not expressed - Histone tail modifications: acetylation & phosphorylation - loosens; methylation (CH3)- condenses - Epigenetic inheritance - **imprinting - gene silencing; which autosome you get a gene from matters - egg or sperm?** ## **TRANSCRIPTIONAL CONTROL** - **Fig. 18-9-3** - Activators bind - Control elements - segments of noncoding DNA, regulate transcription initiation - Virtual Cell Animation: Regulated Eukaryotic Transcription (4 min) - DNA bending protein brings activators close to promoter - Activators bind to form an active transcription initiation complex - **controls binding of transcription factors** - **RNA PROCESSING** - **"post-transcriptional"** - **↓# of genes** - **spliceosome cuts out diff. regions** - diff. mRNAs made from same primary transcript, depends on which RNA segments are treated as exons ## **PROTEIN PROCESSING & DEGRADATION** - Proteasomes - giant protein complexes that bind protein molecules and degrade them - recognize ubiquitin tags - "little chambers of horror" - HHMI Animation: Proteosome (2 min) - **processing: phosphorylation, sugar tags, chaperonins, cleavage of polypeptides** ## **NONCODING RNAS** - **Concept 18.3** - MicroRNAs (miRNAs)- small single-stranded RNA molecules that can bid to mRNA, degrade mRNA, or block its translation - reg. full complementarity - degradation - block ribosome - block translation ## **RNA INTERFERENCE (RNAi)** - RNA interference (RNAi)- inhibition of gene expression by RNA molecules - caused by small interfering RNAs (siRNAs) - play a role in heterochromatin formation - block large regions of the chromosome - block transcription of specific genes - similar to miRNA (diff. precursor) - YouTube Video: RNA Interference (RNAi) (3 min) - **reg. at translational level** - Fig. 18-13 - activated by p53 - hairpin loops generate miRNA - YouTube Video: Gene Silencing by MicroRNA (5 min) - dSRNA - enzyme cuts hairpins ## **CRISPR/CAS9** - CRISPR: clustered Regularly Interspaced Short Palindromic Repeats - Cas9: RNA guided nuclease - Heritable, precise insertions & deletions into eukaryotic genome - identifies & cuts specific sections of DNA - **CRISPR/Cas9** - YouTube Video: CRISPR: Gene Editing & Beyond (5 min) - **"gene-knock-out"** ## **18.4- EMBRYONIC DEVELOPMENT** - A fertilized egg gives rise to different cell types - results from cell division, cell differentiation, and morphogenesis - textbook pgs. 102.5-1027 - shape & size - **HHMI Animation: Human Developement (2 min)** - **Blastocyst** - **Zygote** - **Inner Cell Mass** - **Trophoblast** - **Blastocoele** - **endoderm-inner** - **mesoderm-middle** - **ectoderm-outer ** ## **PATTERN FORMATION & BODY PLAN** - **Pattern formation:** spatial organization of tissues and organs - major axes - **Positional information:** molecular cues tell a cell its location relative to body axes and neighboring cells - **Cytoplasmic determinants** - **Inductive signals** - **paracrine signaling** - **from nearby embryonic cells** - **maternal cytoplasm** - **uneven distribution** - **diff. gene expression** - **migration patterns** - **changes in transcription** - **differentiation** ## **SUMMARY** - **Chromation modification** - Genes in highly compacted chromatin are generally not transcribed - Histone acetylation seems to loosen chromatin structure, enhancing transcription - DNA methylation generally reduces transcription - **Transcription** - Regulation of transcription initiation: DNA control elements bind specific transcription factors - Bending of the DNA enables activators to contact proteins at the promoter, initiating transcription - Coordinate regulation: enhancer for liver-specific genes; enhancer for lens-specific genes - **RNA Processing** - Alternative RNA splicing: primary RNA transcript -> mRNA - mRNA degradation: each mRNA has a characteristic life span, determined in part by sequences in the 5' and 3' UTRs - **Translation** - Initiation of translation can be controlled via regulation of initiation factors. - **Protein processing & degradation** - Protein processing and degradation by proteasomes are subject to regulation. ## **OTHER HELPFUL VIDEOS** - YouTube Video: Bozeman Science- Gene Regulation (10 min) - YouTube Video: Bozeman Science- The Lac Operon (10 min) - YouTube Video: Bozeman Science- Developmental Timing & Coordination (14 min)