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do now
Do Now:

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.

gene control

Gene Control

Prokaryotes vs. Eukaryotes

slide3

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

quick review in metabolic regulation
Quick Review in Metabolic regulation
  • Allosteric inhibitors – provide feedback inhibition (enzyme regulators)
  • Product of pathwaysignals continuation ofpath to STOP
  • Making all these enzymes is wasteful
alternative method
Alternative Method…
  • Gene regulation
  • Block transcription of genes for ALL enzymes in a pathway,not just enzyme function
  • Energy efficient
more on gene regulation
More 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
the operon model
The Operon Model
  • 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!

ex repressible operon tryptophan

trp

RNA

polymerase

RNA

polymerase

repressor

repressor

repressor

enzyme1

1

enzyme2

2

enzyme3

3

enzyme4

4

promoter

repressor protein

operator

tryptophan

trp

trp

trp

trp

trp

trp

trp

trp

trp

tryptophan – repressor protein

complex

Ex: Repressible operon: tryptophan
  • Excess tryptophan present, binds to tryp repressor proteintriggering repressor to bind to DNA
    • blocks (represses) transcription
    • tend to be anabolic pathways

gene1

gene2

gene3

gene4

TATA

DNA

mRNA

trp

conformational change in repressor protein!

trp

ex inducible operon lactose

RNA

polymerase

RNA

polymerase

repressor

repressor

repressor

enzyme1

1

enzyme2

2

enzyme3

3

enzyme4

4

promoter

repressor protein

operator

lactose

lac

lac

lac

lac

lac

lac

lac

lactose – repressor protein

complex

Ex: Inducibleoperon: lactose

Lactose present, binds to lac repressor protein & triggers repressor to release DNA

  • induces transcription
  • catabolic pathways

lac

gene1

gene2

gene3

gene4

TATA

DNA

mRNA

lac

conformational change in repressor protein!

lac

slide10

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

when does gene control occur
When does gene control occur???
  • Packing/unpacking DNA
  • Transcription
  • mRNA processing
  • Translation
  • Protein processing
  • Protein degradation
1 dna packing
1. DNA Packing

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
A little more about nucleosomes…
  • “Beads on a string”
    • 1st level of DNA packing
    • histone proteins
      • 8 protein molecules
      • positively charged amino acids
      • bind tightly to negatively charged DNA
slide14

Degree of packing regulates transcription

    • Tightly packed = no transcription = genes OFF
      • Heterochromatin – “dark” DNA = tight
      • Euchromatin – “light” DNA = loose
slide15

Methylation of DNA (adding -CH3’s) blocks transcription factors  no transcription  genes OFF!

  • Acetylation of histones(adding –COCH3’s) unwinds DNA  coils loosen  transcription  genes ON!
2 transcription initiation
2. Transcription Initiation
  • Control regions on DNA
    • Promoter
      • nearby control sequence – “standard” rate
      • bind RNA pol
      • bind transcription factors
    • Enhancer
      • distant control sequence – “enhanced” rate
      • bind activator proteins
transcription complex
Transcription complex…

Activator Proteins

• regulatory proteins bind to DNA at distant enhancer sites

• increase the rate of transcription

Enhancer Sites

regulatory sites on DNA distant from gene

Activator

Activator

Activator

Coactivator

E

F

B

RNA polymerase II

H

TFIID

A

Coding region

T A T A

Core promoter

and initiation complex

Initiation Complex at Promoter binding site of RNA pol

3 post transcriptional control
3. Post-transcriptional control
  • Alternate splicing pattern
    • ↑ variation in protein family
4 regulation of mrna degradation
4. Regulation of mRNA degradation
  • Lifespan of mRNA controls amt of protein synthesized
    • Review: which component on mRNA determines lifespan?
    • mRNA can last from hrs to weeks!
what if degradation is interfered with
What 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
action of sirna
Action of siRNA

dicerenzyme

mRNA for translation

siRNA

double-stranded miRNA + siRNA

breakdownenzyme

(RISC)

mRNA degraded

functionally turns gene off

5 control of translation
5. Control of Translation
  • Block initiation of translation
    • Regulatory proteins attach to 5’ end
      • Prevent attachment of ribosome & initiator tRNA
      • Synthesis turned OFF
6 7 protein processing degradation
6/7. Protein Processing & Degradation
  • Protein processing
    • Folding, cleaving, adding sugar groups, targeting for transport
  • Protein degradation
    • Ubiquitin – (76 aa’s) “death tag”
    • Proteasome – degradation machinery