D O N OW : Review: how can you distinguish between pro/eukaryotes? Structurally? Environmentally? Both types of organisms seek efficiency, so genes often can be turned on and off. What kinds of “switches” might control whether genes are on and off for each of these? Do you think they are the same? What about the response? Explain your response.

G ENE C ONTROL Prokaryotes vs. Eukaryotes

What kind of environment do bacteria live in? How do you think this impacts the way genes get regulated, if at all? Quick response needed Have enough? New stimuli (food?) introduced Utilize it fast!!! STOP

Q UICK R EVIEW IN M ETABOLIC REGULATION Allosteric inhibitors – provide feedback inhibition (enzyme regulators) Product of pathway signals continuation of path to STOP Making all these enzymes is wasteful

A LTERNATIVE M ETHOD … Gene regulation Block transcription of genes for ALL enzymes in a pathway, not just enzyme function Energy efficient

M ORE ON GENE REGULATION Turning genes ON & OFF regulates amt of enzymes present in cell Example: OFF Enough tryptophan present, bacteria turns off genes coding for enzymes used to build it Example: ON Sugar lactose enters cell, genes coding for enzymes to break sugar down turned on

T HE O PERON M ODEL Operon – group of genes with related functions Genes – code for specific proteins Promoter – RNA pol binding site controls transcription of ALL genes in operon Single mRNA produced Operator – binding site of repressor protein (turns off gene) These 3 make up an operon!

mRNA enzyme 1 enzyme 2 enzyme 3 enzyme 4 operatorpromoter E X : R EPRESSIBLE OPERON : TRYPTOPHAN DNATATA RNA polymerase tryptophan repressor repressor protein repressor tryptophan – repressor protein complex Excess tryptophan present, binds to tryp repressor protein triggering repressor to bind to DNA blocks (represses) transcription tend to be anabolic pathways gene 1 gene 2 gene 3 gene 4 conformational change in repressor protein! 1234 repressor trp RNA polymerase trp

mRNA enzyme 1 enzyme 2 enzyme 3 enzyme 4 operatorpromoter E X : I NDUCIBLE OPERON : LACTOSE LACTOSE DNATATA RNA polymerase repressor repressor protein repressor lactose – repressor protein complex lactose lac repressor gene 1 gene 2 gene 3 gene 4 Lactose present, binds to lac repressor protein & triggers repressor to release DNA induces transcription catabolic pathways RNA polymerase 1234 lac conformational change in repressor protein! lac

What about Eukaryotes? How are they different? What might the process have to accommodate for? How might it do this? Eukaryotes often multicellular Must maintain homeostasis Coordinate body as a whole Differentiated & specialized cells Battle changing environment

W HEN DOES GENE CONTROL OCCUR ??? 1. Packing/unpacking DNA 2. Transcription 3. mRNA processing 4. Translation 5. Protein processing 6. Protein degradation

1. DNA P ACKING If all 46 of your chromosomes were lined up in a row, your DNA would be over 3 feet long. How can your cells contain this large amount of material when cells are microscopic? Coils & Folds Double helix Nucleosomes Chromatin fiber Looped domains Chromosomes from DNA double helix to condensed chromosome

A LITTLE MORE ABOUT NUCLEOSOMES … “Beads on a string” 1 st level of DNA packing histone proteins 8 protein molecules positively charged amino acids bind tightly to negatively charged DNA

Degree of packing regulates transcription Tightly packed = no transcription = genes OFF Heterochromatin – “dark” DNA = tight Euchromatin – “light” DNA = loose

Methylation of DNA (adding -CH 3 ’s) blocks transcription factors  no transcription  genes OFF! Acetylation of histones (adding –COCH 3 ’s) unwinds DNA  coils loosen  transcription  genes ON!

2. T RANSCRIPTION I NITIATION Control regions on DNA Promoter nearby control sequence – “standard” rate bind RNA pol bind transcription factors Enhancer distant control sequence – “enhanced” rate b ind activator proteins

T RANSCRIPTION COMPLEX … Activator Coactivator RNA polymerase II A B F E H TFIID Core promoter and initiation complex Activator Proteins regulatory proteins bind to DNA at distant enhancer sites increase the rate of transcription Coding region T A Enhancer Sites regulatory sites on DNA distant from gene Initiation Complex at Promoter binding site of RNA pol

3. P OST - TRANSCRIPTIONAL CONTROL Alternate splicing pattern ↑ variation in protein family

4. R EGULATION OF M RNA DEGRADATION Lifespan of mRNA controls amt of protein synthesized Review: w hich component on mRNA determines lifespan? mRNA can last from hrs to weeks!

W HAT IF DEGRADATION IS INTERFERED WITH ??? 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 gene “silencing” post-transcriptional control turns off gene = no protein

A CTION OF SI RNA siRNA double-stranded miRNA + siRNA mRNA degraded functionally turns gene off mRNA for translation breakdown enzyme (RISC) dicer enzyme

5. C ONTROL OF T RANSLATION Block initiation of translation Regulatory proteins attach to 5’ end Prevent attachment of ribosome & initiator tRNA Synthesis turned OFF

6/7. P ROTEIN P ROCESSING & D EGRADATION Protein processing Folding, cleaving, adding sugar groups, targeting for transport Protein degradation Ubiquitin – (76 aa’s) “death tag” Proteasome – degradation machinery

W HAT D ARWIN N EVER K NEW … VideoVideo – 39:57