Mesoplasma florum:Physiology: Difference between revisions
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* Protein quality control through chaperones, protein folding catalysts and ATP-dependent proteases | * 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 | * 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 | * 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 | * 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== | ==Organizational ideas== | ||
Line 202: | Line 264: | ||
** Protein production | ** Protein production | ||
** Cell division | ** Cell division | ||
[[Category:Mesoplasma florum]] |
Latest revision as of 13:13, 8 May 2007
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