Mesoplasma florum:Physiology

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Contents

From White

  • Structure and function
  • Growth and cell division
  • Membrane bioenergetics: the proton potential
  • Electron transport
  • Regulation of the metabolic pathways
  • Bioenergetics in the cytosol
  • Central metabolic pathways
  • Metabolism of lipids
  • Metabolism of Nucleotides
  • Metabolism of amino acieds
  • DNA synthesis
  • RNA synthesis
  • Protein synthesis
  • Inorganic metabolism
  • Fermentation
  • Homeostasis
  • Membrane transport
  • Protein transport
  • Physiologic response to environment and stress


From Neidhardt

  • Composition and organization of the bacterial cell
  • Structure and function of the bacterrial cell parts
  • assembly and polymerization: the bacterial interior
  • Assembly and polymerization: the bacterial envelope
  • Biosynthesis and fueling
  • Quest for food
  • Growth of cells and populations
  • Effects of temperature, pressure and pH
  • Genetic adaptation: the genome and its plasticity
  • Genetic adaptation: genetic exchange and recombination
  • Coordination of metabolic reactions
  • Regulation of gene expression: individual operons
  • Regulation of gene expression: multigene systems and global regulation
  • Cell cycle
  • Growth rate as a variable


From Schumann

  • Structure of a bacterial cell
    • cytoplasm compartment
    • cytoplasmic membrane compartment
    • extracellular matrices
    • appendages


  • Organization of the bacterial chromosome
    • structure of the chromosome
    • principles to compact the bacterial chromosome
    • superhelicity
    • histone like proteins in E. coli
    • ogranization of the bacterial chromosome into genes and repetitive sequences
    • genes
    • repetitive sequences
    • large rearrangements within the chromosome
    • duplications
    • deletions
    • inversions


  • The bacterial cell cycle: Replication of the chromosome, partitioning, and cell divison
    • replication of circular chromosomes
    • partitioning of daughter chromosomes
    • cell division


  • Recombination
    • homologous recombination
    • the RecBCD pathway of homologous recombination
    • The RecF pathway of homologous recombination
    • additional homologous recombination functions
    • recovery of replication at a blocking DNA lesion
    • sequence specific recombination
    • integration/excision systems
    • resolvase systems
    • inversion systems
    • shufflons
    • integrons
    • homing endonucleases
    • illegitimate recombination
    • insertion sequence elements
    • transposons
    • transposing bacteriophages
    • mechanisms of transposition
    • conjugative and integrative elements
    • nonhomologous endjoining (NHEJ)
  • Origin of Mutations and Repair of DNA lesions
    • Classes of mutations
    • Origin of mutations
    • Spontaneous mutations
    • Induced mutations
    • Detection systems for mutations
    • Adaptive mutations
    • Repeair of DNA lesions
    • The methyl-mediated mismatch repair system
    • Very short patch repair
    • The nucleotide excision repair systems
    • Pathways of base excision repair
    • Repair of oxidized nucleotides
    • Photoreactivation of cyclobutane dimers
    • Transcription coupled nucleotide excision repair
    • The adaptive response
    • The SOS response
    • Replication and repair
    • Repair of interstrand crosslinks in DNA
    • Deinococcus radiodurans


  • Principles of Gene Regulation
    • Regulation at the level of DNA
    • Alterations of the structure of the DNA
    • GATC methylation and gene expression
    • Programmed DNA rearrangements within the chromoosome
    • Transcriptional silencing and cryptic genes
    • Regulation at the level of transcription
    • The DNA dependent RNA polymerase
    • Regions of the promoter
    • Initiation of transcription
    • Elongation of transcription
    • Termination of transcription
    • Anti-sigma factors
    • Anti-termination/Attenuation of termination
    • Regulatiors of the DNA dependent RNA polymerase
    • Post-transcriptional regulation
    • Protein mediated regulation
    • Riboregulation
    • Riboswitches
    • mRNA decay
    • Introns
    • RNA binding proteins
    • Rgulation at the level of translation
    • Initiation of translation
    • Elongation of translation
    • Termination of translation
    • Ribosome recycling
    • Translational control
    • The 21 and 22 amino acids selenocysteine and pyrrolysine
    • Mechanisms to create multiple gene products from a single cistron
    • Post-translational regulation
    • Proteolysis
    • Protein splicing
    • Protein glycosylation
    • Circular polypeptides


  • Protein quality control through chaperones, protein folding catalysts and ATP-dependent proteases
    • Introduction
    • Molecular chaparones
    • Folder chaparones
    • Holder chaparones
    • Disaggregating chaparones
    • Intramolecular chaparones
    • Folding of nascent polypeptide chains
    • Protein-folding catalysis
    • Peptidyl-prolyl isomerases
    • Disulfide bond formation
    • Proteases
    • ATP-dependent proteases
    • ATP-independent proteases


  • Secretion of proteins
    • Introduction
    • Protein sorting signals for subcellular localization
    • Cytosolic targeting factors
    • Translocases move mewly made proteins into or across membranes
    • The Sec pathway of protein translocation through the inner membrane
    • The Tat pathway of secretion proteins through the inner membrane
    • Insertion proteins into the inner membrane
    • Anchoring of lipoproteins into the outer membranes
    • Protein translocation pathways through both membranes of gram-negative bacteria
    • The type I secretion pathway
    • The type II secretion pathway
    • The type III secretion pathway
    • The type IV secretion pathway
    • The type V secretion pathway (Autotransporter)
    • Vesicle-mediated export
    • Cell wal anchored surface proteins
    • S-layers


  • Stress genes and their regulation
    • The stress response pathway
    • The heat shock response
    • The cold shock response
    • The osmotic shock response
    • The hyperosmotic shock response
    • The hyposomotic shock response
    • The oxidative shock response
    • The OxyR regulon
    • The SoxRS regulon
    • pH regulated genes
    • Acid stress
    • Alkaline stress
    • Metabolic stress: the stringent response
    • Nutrient limitations (starvation stress)
    • Envelope stress response


  • Exchange of genes: transformation, conjugation and transduction
    • Transformation
    • Transformation of gram-positive bacteria
    • Transformation of gram-negative bacteria
    • Cojugation
    • Gram-negative bacteria
    • Gram-positive bacteria
    • Conjugative transposons
    • Transduction
    • Generalized transduction
    • Specialized transduction
    • Horizontal gene transfer

Organizational ideas

  • Structure & composition
  • Information and control
  • Transport systems
  • Degradation pathways
  • Fermentation and energy production
  • Synthetic pathways
    • DNA replication
    • RNA transcription
    • Protein production
    • Cell division
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