MICROBIOLOGY 120. Microbial Physiology Course description: Physiological processes in microorganisms including a study of structure, energy production, macromolecular biosynthesis, nutrition and growth Credits: 3 units (3 hrs of lecture per week) Prerequisite: MCB 1 and CHEM 160 Course Objectives: 1) To identify the structure, chemistry and functions of major structures in a bacterial cell; 2) To elucidate the requirements of microbial growth; 3) To identify the various metabolic pathways present in different microorganisms; 4) To understand enzyme regulation present in microbial cells; 5) To relate the principles of microbial physiology to the industrial applications of microorganisms.
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MICROBIOLOGY 120. Microbial Physiology
Course description: Physiological processes in microorganisms including a study of structure, energy production, macromolecular biosynthesis, nutrition and growth
Credits: 3 units (3 hrs of lecture per week)
Prerequisite: MCB 1 and CHEM 160
Course Objectives:1) To identify the structure, chemistry and functions of major structures in a bacterial cell;2) To elucidate the requirements of microbial growth;3) To identify the various metabolic pathways present in different
microorganisms;4) To understand enzyme regulation present in microbial cells;5) To relate the principles of microbial physiology to the industrial
applications of microorganisms.
OUTLINE
I. Introduction
II. The bacterial cell: structures and functions
1. Major cellular structures
2. Chemistry and synthesis of cellular structures
First long exam
III. Microbial Growth
1. Definition of growth2. Measurements of growth3. Growth Physiology4. Steady-state Growth and Continuous5. Factors affecting growth
1. A general make-up exam which is comprehensive in scope will be given towards theend of the semester to students who missed any of the 4 long exams due to a validreason (an official excuse slip must be presented).
2. A student who incurs at least 10 absences in the lecture will be automatically droppedfrom the course. Attendance sheets will be passed around for monitoring of thestudent's attendance in class.
If majority of the absences are excused, the student shall be given a grade of DRP.
If majority of the absences are unexcused, the student shall be given a grade of 5.0.
3. Excuse slips must be presented not later than the second class session following thestudent's return.
LECTURER’S INFORMATION
Name: DR. RINA B. OPULENCIA
MS Microbiology: University of Queensland, Australia
PhD Microbiology: University of Illinois, Urbana-Champaign, USA
Physiology- study of the functions of living organisms and their physicochemical parts and metabolic reactions
cytology (physical and chemical structures) biochemistry (enzymes and chemical reactions) nutrition genetics
Microbial Physiology- study of life processes of microorganisms
INTRODUCTION
1. Knowledge of microbial physiology can be applied toother fields.
2. Microorganisms can serve as models to understand lifeprocesses.
Importance of Studying Microbial Physiology
Importance of Prokaryotes
ubiquitous
exhibit great metabolic and genetic diversity
comprise the majority of organic matter
major environmental determinants on earth
Whitman, W. B. 1998. PNAS USA. 95: 6579
Whitman, W. B. 1998. PNAS USA. 95: 6579
White, D. 2006Whitman, W.B. 2009. J. Bacteriol. 491:2000-2005
Lipids: alcohols ether-linked toglycerol Cell Wall: variable, some havepseudo-PG Genome: eukaryotic-typehistones; DNA organized intonucleosome-like structures Transcription machinery: RNAPhas 8-10 subunits, like eukaryotes;RifR
Lipids: fatty acids ester-linkedto glycerol Cell Wall: Peptidoglycan (PG) auniversal component Genome: histone-like proteins,but not organized like nucleosomes
Transcription machinery: RNAPhas 4 subunits; is RifS
ARCHAEA vs BACTERIA
Translation machinery: Use Met as initiator amino acid;insensitive to translational inhibitorsthat affect bacteria; require EF-2like eukaryotic ribosomes
UNIQUE: Light-driven ion pumps (halophiles) Unique coenzymes (methanogens)
Translation machinery:Use f-Met as initiatoramino acid; sensitive totranslational inhibitors,e.g., Tet, Cm
ARCHAEA vs BACTERIA
MICROBIOLOGY 120. MICROBIAL PHYSIOLOGY
majority of the topics is “bacterial” physiology
studies done on Escherichia coli or Bacillus subtilis
Model organisms provide basis for understandingimportant biological principles but not all bacteria are the same.
The Prokaryotic Cell
Brock Biology of Microorganisms 10/eMadigan/Martinko/Parker
2003 Benjamin Cummings
CELL WALL
fairly rigid layer that lies outside the plasma membrane
Importance:- confers shape- protects the cell from osmotic lysis- anchors the flagellum- adds to pathogenicity of the cell- protects the cell from toxic substances and pathogens
Bacteria can be divided into two big groups based on cell wall structure.
BACTERIAL CELL WALL
Brock Biology of Microorganisms 10/eMadigan/Martinko/Parker
2003 Benjamin Cummings
GRAM POSITIVE CELL WALL
Characteristics
A. Thick layer of peptidoglycan (murein; mucopeptide)
•• a polymer of disaccharide linked by polypeptidea polymer of disaccharide linked by polypeptide
•• insoluble, porous, big polymerinsoluble, porous, big polymer
•• > 50% of the cell wall> 50% of the cell wall’’s dry weight; 15 - 40 nm thicks dry weight; 15 - 40 nm thick
•• isolatable as murein sacculusisolatable as murein sacculus
Peptidoglycan Subunit
Brock Biology of Microorganisms 10/eMadigan/Martinko/Parker
2003 Benjamin Cummings
Peptidoglycan Interbridge
Type I. Direct D-alanyl-R3 peptide bond - found in E. coli and other gram negative bacteria - also found in many bacilli
Type II. Pentaglycine or Other L- or D- amino acid sequences - varies from organism to organism
Type III. A bridge composed of one to several peptides, each having the same amino acid sequence as the peptide unit attached to muramic acid
Type IV. A bridge extending between carboxyl groups belonging to either D-alanine or D-glutamic acid and a diamino acid residue or a diamino acid containing short peptide
Peptidoglycan Interbridge
Brock Biology of Microorganisms 10/e
Madigan/Martinko/Parker
2003 Benjamin Cummings
Peptidoglycan Interbridge
Peptidoglycan Polymer
Brock Biology of Microorganisms 10/e by Madigan/Martinko/Parker
Synthesis of peptidoglycanoccurs in three phases:assembly of precursor in thecytoplasm, transport acrossthe inner membrane, andpolymerization. The lipid-linked muropeptide (lipid I)is generated in thecytoplasm from amino acidsand UDP-MurNAc (MurNAcis depicted by orangesquares). Transfer of N-acetylglucosamine (bluesquares) from UDP-GlcNAccompletes formation of theprecursor lipid II.Translocation across theinner membrane occurs,and subsequently, the chainpolymerizes while attachedto the lipid carrier. The unitis then transferred toexisting peptidoglycan.(PEP)Phosphoenolpyruvate; (m-DAP) meso-diaminopimelicacid.
Diffusion channel for small moleculesReceptor for phages Tula, T2
OmpF (1.2 nm)
Diffusion channel for small moleculesReceptor for phages Tulb, T4
OmpC (1.1 nm)
Diffusion channel for various metabolites includingmaltose
OmpB
Physiological RoleProtein Porin
Outer membrane proteins (OMPs) of Gram Negative Bacteria
- A separate compartment between the cell membrane and outer membrane in Gram (-) bacteria
- Seen in electron micrographs as space but should be considered an aqueous compartment
- Activites: redox reactions osmotic regulation solute transport protein secretion hydrolysis
PERIPLASM
PERIPLASM:
COMPONENTS AND FUNCTIONS1. Oligosaccharides – thought to be involved in the osmotic regulation
of the periplasm because their amounts decrease when thecells are grown in media of high osmolarity
2. Solute binding proteins – bind to solutes and deliver solutes to specific transporters in the membrane
3. Cytochrome – cyt c
4. Hydrolytic enzymes –degrade nutrients to smaller molecules thatcan be transported across the membrane by specifictransporter
5. Detoxifying agents – e.g. β-lactamase
6. TonB protein – required for the uptake of several solutes (iron siderophores, vit B12) that do not diffuse through the porin
PERIPLASM: ACTIVITIES
• Protein transport
• Nutrient acquisition
• Protein folding
• Disulfide bond formation
PERIPLASM IN GRAM POSITIVE CELLS?
Evidences:
• release of putative periplasmic proteins (distinctnucleases) in protoplasts of Bacillus subtilis • area outside the cell membrane of B. subtilis isbipartite (cryo-TEM)
Archaeal Cell Walls
- Lacks peptidoglycan
- May contain polysaccharide, protein (S layer) orpseudopeptidoglycan
Archaeal Cell Walls: Polysaccharide
• cell wall composed of glucose, glucuronic acid, acetate and galactosamine
• found in Methanosarcina spp.
Archaeal Cell Walls: S-layer
- protein subunits arranged in a regular array on the cell surface
- found in extreme halophiles, methanogens and hyperthermophiles
Albers et al. Nature Reviews Microbiology advance online publication;published online 06 June 2006 | doi:10.1038/nrmicro1440