Mesoplasma florum:Physiology

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