BI548 Microbial Physiology and Genetics
The Ecological, Medical and Scientific Importance of Bacteria
Microbial Taxonomy
Microbial Physiology and Genetics
Bacteria Cell Structure and Function
Murein Structure and Biosynthesis
Lipopolysaccharide: Structure, Function and Biosynthesis
Capsule: Structure, Function and Synthesis
Protein Export and Adhesins
Flagella and Chemotaxis
Bacterial DNA Organisation
Gene Expression
Biosynthesis and Fuelling
Growth Cycle
Growth Cycle II
Lac and Diauxie
Specialised Structures and Biofilms
Growth, Fuelling and Biosynthesis
Specialised Structures and Biofilms II
Cell Differentiation
Quorum Sensing: Microbial Communication
The Regulation and Control of Microbial Cells: Planktonic vs Attached Cells
Phototrophic Bacteria
Bacterial Respiration
Anaerobic Respiration
,The Ecological, Medical and Scientific Importance of Bacteria
- Approximately 5 x 10-30 cells on earth.
- > 107 different types.
- Many pathogenic bacteria are proteobacteria or gram positive.
Symbiosis
- An ecological relationship between two or more organisms living closely
together.
- There are three main types:
o Mutualism: both organisms benefit.
o Commensalism: one organism benefits while the other neither benefits
or is harmed.
o Parasitism: one organism benefits and causes harm to the other
organism.
- Chemolithotrophs: oxidise inorganic ions (NH4+, Fe2+).
- Chemoorganotrophs: oxidise organic molecules (like animals) to produce NADH
(pmf for ATP synthesis).
- Nitrogen fixing bacteria are able to generate NH3 from atmospheric N2.
Nitrogen cycle
- Plants absorb the nitrate ions from the soil by diffusion and active transport.
Nitrogen is passed through the food chain when eaten by consumers and is
also added to the soil when waste products and dead organisms are buried.
- Ammonification: this is the breakdown of proteins in dead organisms and animal
waste by decomposers, releasing NH4+ ions.
- Nitrification: nitrifying bacteria oxidise NH4+ ions to NO3- (nitrates) and then to
NO2- (nitrites).
- Denitrification: Nitrates are then reduced to nitrogen gas by denitrifying bacteria.
- Nitrogen fixation: atmospheric fixation occurs spontaneously by lightning.
Industrial fixation uses the Haber process to make nitrogen fertilisers/
- Biological fixation: nitrogen-fixing bacteria fix the majority of N2.
o This is done by Rhizobium in legumes.
Microbial Taxonomy
Domains
- Eukarya: Plants, animals humans.
- Bacteria: single-celled, no nucleus.
- Archaea: resemble bacteria but have different genes for managing and reading
DNA.
Species
- The basic taxonomic unit.
Classification systems
- Artificial
, o Based on superficial distinctions between taxa to allow for rapid
distinction.
- Phenetic
o Relationships between organisms based on their phenotypic similarity.
- Phylogenetic
o Based on evolutionary relationships, this takes into account adaptive
radiation (differences in beak sizes, etc.) and convergent evolution.
- Classification allows for organisms to be grouped and given a name. These
systems allow for identification as well as a means of understanding
evolutionary relationships between organisms
- Domain – Kingdom – Phylum – Class – Order – Family – Genus – Species
o Did King Peter Call Out For Good Singers?
- Taxonomy is the science of classification and the groups are known as taxa.
Microbial Physiology and Genetics
Phylogenetics
- Traditional methods consider the morphological or biochemical resemblances
between organisms, taking into account fossil histories.
- Newer methods make use of molecular systematics of DNA, RNA and the
relationships between them.
The study of:
- DNA (Genomics) - Proteins (Proteomics)
- RNA (Transcriptomics) - Enzyme activity (Metabolomics)
Bacteria shapes
- Spherical = cocci. - Rods = bacilli
o Staphylococci = bunch of - Spirals
spheres - Spirochete
o Streptococci = strips of - Budding and appendaged.
spheres - Filamentous
- Citrate agar tests the ability of organisms to use citrate as a carbon source. It
also includes ammonium dihydrogen phosphate as a nitrogen source, other
nutrient and bromothymol blue, which is a pH indicator.
o If the medium turns blue then the organism is citrate positive, if not then
there is no colour change.
▪ The metabolism of NH4+H2PO4 makes the medium alkaline and
causes bromothymol blue to turn royal blue.
Fatty acid methyl ester analysis (FAME)
- Identifies organisms by their lipid bilayer components.
- Bacteria are cultured, then killed by saponification, converted into methyl esters
and put through GC analysers.
- The pattern of peaks is then compared to protein databases to characterise the
bacteria.
The Ecological, Medical and Scientific Importance of Bacteria
Microbial Taxonomy
Microbial Physiology and Genetics
Bacteria Cell Structure and Function
Murein Structure and Biosynthesis
Lipopolysaccharide: Structure, Function and Biosynthesis
Capsule: Structure, Function and Synthesis
Protein Export and Adhesins
Flagella and Chemotaxis
Bacterial DNA Organisation
Gene Expression
Biosynthesis and Fuelling
Growth Cycle
Growth Cycle II
Lac and Diauxie
Specialised Structures and Biofilms
Growth, Fuelling and Biosynthesis
Specialised Structures and Biofilms II
Cell Differentiation
Quorum Sensing: Microbial Communication
The Regulation and Control of Microbial Cells: Planktonic vs Attached Cells
Phototrophic Bacteria
Bacterial Respiration
Anaerobic Respiration
,The Ecological, Medical and Scientific Importance of Bacteria
- Approximately 5 x 10-30 cells on earth.
- > 107 different types.
- Many pathogenic bacteria are proteobacteria or gram positive.
Symbiosis
- An ecological relationship between two or more organisms living closely
together.
- There are three main types:
o Mutualism: both organisms benefit.
o Commensalism: one organism benefits while the other neither benefits
or is harmed.
o Parasitism: one organism benefits and causes harm to the other
organism.
- Chemolithotrophs: oxidise inorganic ions (NH4+, Fe2+).
- Chemoorganotrophs: oxidise organic molecules (like animals) to produce NADH
(pmf for ATP synthesis).
- Nitrogen fixing bacteria are able to generate NH3 from atmospheric N2.
Nitrogen cycle
- Plants absorb the nitrate ions from the soil by diffusion and active transport.
Nitrogen is passed through the food chain when eaten by consumers and is
also added to the soil when waste products and dead organisms are buried.
- Ammonification: this is the breakdown of proteins in dead organisms and animal
waste by decomposers, releasing NH4+ ions.
- Nitrification: nitrifying bacteria oxidise NH4+ ions to NO3- (nitrates) and then to
NO2- (nitrites).
- Denitrification: Nitrates are then reduced to nitrogen gas by denitrifying bacteria.
- Nitrogen fixation: atmospheric fixation occurs spontaneously by lightning.
Industrial fixation uses the Haber process to make nitrogen fertilisers/
- Biological fixation: nitrogen-fixing bacteria fix the majority of N2.
o This is done by Rhizobium in legumes.
Microbial Taxonomy
Domains
- Eukarya: Plants, animals humans.
- Bacteria: single-celled, no nucleus.
- Archaea: resemble bacteria but have different genes for managing and reading
DNA.
Species
- The basic taxonomic unit.
Classification systems
- Artificial
, o Based on superficial distinctions between taxa to allow for rapid
distinction.
- Phenetic
o Relationships between organisms based on their phenotypic similarity.
- Phylogenetic
o Based on evolutionary relationships, this takes into account adaptive
radiation (differences in beak sizes, etc.) and convergent evolution.
- Classification allows for organisms to be grouped and given a name. These
systems allow for identification as well as a means of understanding
evolutionary relationships between organisms
- Domain – Kingdom – Phylum – Class – Order – Family – Genus – Species
o Did King Peter Call Out For Good Singers?
- Taxonomy is the science of classification and the groups are known as taxa.
Microbial Physiology and Genetics
Phylogenetics
- Traditional methods consider the morphological or biochemical resemblances
between organisms, taking into account fossil histories.
- Newer methods make use of molecular systematics of DNA, RNA and the
relationships between them.
The study of:
- DNA (Genomics) - Proteins (Proteomics)
- RNA (Transcriptomics) - Enzyme activity (Metabolomics)
Bacteria shapes
- Spherical = cocci. - Rods = bacilli
o Staphylococci = bunch of - Spirals
spheres - Spirochete
o Streptococci = strips of - Budding and appendaged.
spheres - Filamentous
- Citrate agar tests the ability of organisms to use citrate as a carbon source. It
also includes ammonium dihydrogen phosphate as a nitrogen source, other
nutrient and bromothymol blue, which is a pH indicator.
o If the medium turns blue then the organism is citrate positive, if not then
there is no colour change.
▪ The metabolism of NH4+H2PO4 makes the medium alkaline and
causes bromothymol blue to turn royal blue.
Fatty acid methyl ester analysis (FAME)
- Identifies organisms by their lipid bilayer components.
- Bacteria are cultured, then killed by saponification, converted into methyl esters
and put through GC analysers.
- The pattern of peaks is then compared to protein databases to characterise the
bacteria.
