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Regulation of Metabolism

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Last revised: Thursday, March 16, 2000
Ch. 12 (p. 237-250) in Prescott et al, Microbiology, 4th Ed.
Note: These notes are provided as a guide to topics the instructor hopes to cover during lecture. Actual coverage will always differ somewhat from what is printed here. These notes are not a substitute for the actual lecture!
Copyright 2000. Thomas M. Terry

Metabolic Channeling

Regulation of enzyme activity

Regulation of gene expression in prokaryotes

Many genes occur in operons

Transcription & Translation are coupled

Some genes are expressed constitutively

Some genes are inducible: transcribed only in presence of inducer

Some genes are repressible; transcription is shut down in presence of repressor

Levels of regulation

  1. Negative control
    • Discussed above: both inducible and repressible genes are examples of negative control
  2. Positive control
    • So far, assumed RNA polymerase always able to transcribe unless blocked by repressor protein (negative control).
    • But many genes are not transcribed unless some protein binds to DNA, facilitates RNA Polymerase activity. This is Positive control (nothing happens unless you say "Yes".)
    • View animation of positive control from Cornell University. (Requires shockwave plug-in).
  3. Global Regulation
    1. Catabolite Repression.
      • Synthesis of variety of different enzymes involved in catabolism are inhibited if glucose is present. (Can also be called "glucose effect"). Flagellar synthesis also controlled by catabolite repression.
      • View animation of catabolite repression from Cornell University (requires schockwave plug-in)
      • Diauxic growth curve illustrates the effect

      • How does it work? combination of positive & negative control.
      • Already saw negative control system: need inducer to get rid of repressor
      • BUT also need activator protein (called Catabolite Activator Protein, or CAP)
      • CAP is allosteric protein, only binds to DNA if cAMP is present. cAMP is made from ATP by enzyme adenyl cyclase, but is inhibited by glucose.
      • Cell signal: glucose high, no cAMP. CAP doesn't bind, not positive control for dozens of operons. But if glucose conc. falls low, cAMP produced, CAP binds, now many operons can be used (depending on other inducers & repressors).
      • View CAP protein bound to DNA, from Cornell University.

      Group Practice
    2. Alternative Sigma factors
      • In E. coli most promoters recognized by sigma70. But if cells experience severe temp. shock (e.g. heat), new set of genes turned on to "rescue" cells from disaster.
      • New sigma factor is made, recognizes different set of genes with different promoters.

Gene organization in Prokaryotes vs. Eukaryotes

Regulation in prokaryotes and eukaryotes
DNA geometry
  • single circular molecule
  • multiple linear molecules
  • Replication origin (ori)
  • one per DNA molecule
  • many per chromosome
  • DNA replication rate
  • 750-1000 bp/sec
  • 50-100 bp/sec.
  • Rate is 10x times slower than bacteria. However, since eucaryotic chromosomes have many ori sites, overall time required for DNA replication can actually be less than for bacteria (which are limited to one ori site).
  • Cell's use of DNA
  • almost all DNA codes for protein
  • large regions of noncoding DNA
  • Gene organization
  • many operons (one promoter + several structural genes)
  • genes lack introns; DNA is colinear with polypeptide (rare exceptions)
  • no operons (one promoter + one structural gene)
  • genes contain introns; must be removed in nucleus before mRNA is formed
  • some large polypeptides cleaved into multiple active proteins
  • RNA polymerase
  • 4 subunits in single "core enzyme", plus sigma or rho factors
  • Archaea have 8-10 subunits, single enzyme
  • 10-12 subunits, 3 different enzymes
  • mRNA organization
  • many mRNAs have multiple "start" and "stop" signals; code for multiple proteins (polycistronic)
  • mRNAs have one "start" and "stop" signal; code for one protein (monocistronic)
  • Control of RNA synthesis
  • some genes constitutive
  • some genes inducible
  • some genes repressible
  • some genes cryptic
  • some genes constitutive
  • inducible genes regulated by complex set of activator proteins
  • Fate of RNA
  • translated immediately (coupled transcription-translation
  • short half-life
  • not translated immediately
  • 5' methyl Guanosine "cap" and 3' poly-A "tail"capped" are added to new RNA
  • processed in nucleus to remove introns
  • splicing is catalyzed by RNA (ribozyme) rather than protein enzyme
  • exported from nucleus to cytoplasm
  • long half-life
  • Protein synthetic rate
  • 350-400 amino acids/min
  • 70S ribosomes; 30S + 50S subunits
  • 50 amino acids/min
  • 80S ribosomes; 40S + 60S subunits
  • "Start" amino acid (AUG codon)
  • N-formyl-methionine
  • (but methionine in Archaea)
  • methionine
  • antibiotic effects

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