lecture 9 & 10: bacterial physiology Flashcards
microbial physiology
refers to the diverse metabolic and cellular functions of microorganisms across different phylogenetic lineages
bacterial physiology
knowledge about life supporting processes and functions of bacteria (how bacteria grow, metabolize and respond to their environments)
- critical for understanding their roles in ecosystems and their behaviour in microbial communities
key bacterial internal and surface structure
- internal structures
–> eg: nucleoid, ribosomes - surface structures
–> eg: flagella, pili, fimbriae, capsules
bacterial cell wall structure
- cell envelope (eg: membrane, peptidoglycan)
–> implications for immune responses and antibiotics
chemical work
synthesis of biological molecules, what happens inside the cell (need to make a protein, need to split and divide)
mechanical work
motility, movement of structures, how bacteria are to interact with the environment
transport work
take up nutrients, eliminate waste
bacterial metabolism def
focuses on chemical changes that create energy in bacteria especially during growth and development
what does an efflux pump do
it can recognise certain drug molecules or any kind of chemical that harms bacteria, and it can pump these harmful chemicals out
binary fission
asexual reproduction by a seperation of the body into two new bodies
growth phases of binary fission
lag, log, stationary, death
hydrocarbon
a carbon bound to a hydrogen
- found in fossil fuels
- high energy bonds that can be used for energy
what are the building blocks of life
- carbs (sugars)
monosaccharides to polysaccharides - lipids (fats)
saturated fats to trans fats - proteins
amino acids to peptides - nucleic acids (RNA and DNA)
where can nutrients come from
either an organic or inorganic source
metabolic pathways def
chemical reactions involved in the process of chemically processing nutrients into a useable form
metabolism is the sum of …..
all chemical reactions that occur in a cell
catabolism basic def
- break down of large molecules
- release of energy
anabolism basic def
- synthesises large molecules
- uptake of energy
- living organisms must synthesise molecules to sustain life
types of catabolic pathways
- glycolysis, Entner-Doudoroff pathway, Pentose phosphate pathway
- aerobic vs anaerobic respiration (ATP production, electron transport)
- fermentation
types of anabolic pathways
- biosynthesis of amino acids, nucleotides, lipids
- carbon fixation
- bacterial growth and survival
micronutrients
- also required by organisms
- required in small amounts
- normally part of enzymes and cofactors
- aid in the catalysis of reactions and maintenance of protein structure
- naturally found in water, soil etc
list of major macronutrients
- carbon
- nitrogen
- hydrogen
- oxygen
- sulphur
- phosphorous
- k, ca, mg, fe
examples of micronutrients or trace elements
Mn, Zn, Co, Ni, Cu
what are the major external sources for carbon
CO2 (inorganic), simple and complex sugars (organic)
what are the major external sources for nitrogen
NH4+, NO3-, N2 (inorganic)
proteins, amino acids, urea (organic)
what are the major external sources for hydrogen
organic compound H2O
what are the major external sources for oxygen
H2O, CO2, O2
what are the major external sources for sulphur
SO4 (inorganic) cysteine, methionine (organic)
what are the major external sources for phosphorous
PO4
what are the major external sources for K, Ca, Mg, Fe
as ions in solution
what are the major external sources for micronutrients
as ions in solution
what does it mean by ATP is the energy currencu of all cells
- the molecule is not the energy itself, it is the molecule stored in its chemical bond
- stored chemical energy will be released into mechanical energy used to drive most cellular processes
what happens to released energy
it is captured and used to drive reactions to completion, from anabolism , to transport and mechanical work
cellular respiration
- the process by which microbes obtain energy from carbs
- if energy is not needed, it will be combined with phosphate ions to form ATP where carbon dioxide is given off as a waste product
what is the energy source used to generate ATP in aerobic respiration
glucose
processes involved in cellular respiration
- glycolysis
- krebs cycle
- electron transport chain
glycolysis
breakdown of glucose, resulting in the formation of ATP
what are krebs cycle intermediates used for
to synthesize important ceullular molecules including amino acid or nucleotides
electron transport chain
- exists in the plasma membrane in prokaryotic cells
- ATP generated in known as oxidative phosphorylation (final step in cellular respiration)
processes in anaerobic cellular respiration
glycolysis and fermentation
obligate aerobes
prokaryotes that require oxygen for metabolism
obligate anaerobes
prokaryotes that do not need oxygen (or cannot be exposed to oxygen) only undergo anaerobic metabolism
metabolic reprogramming/flexibility
facultative anaerobic bacteria are able to switch
metabolic regulation
process by which metabolic pathways are regulated
- bacteria control the expression of genes involved in their metabolism based on the availability of nutrients in their environment
the lac operon
- necessary for the utilization of lactose as a carbon source (acquire and process lactose from environment)
- to use lactose, bacteria must express the lac operon genes, which encode key enzymes for lactose uptake and metabolism
the use of glucose vs lactose
glucose requires fewer steps and less energy to break down than lactose. however if lactose is the only sugar available, bacteria will use it as an energy source
lacY (beta galactoside permease)
transport protein that pumps lactose into the cell
key genes in lac operon
- lacY
- lacZ
- lacA
lacZ (beta galactosidase) = bi functional enzyme
- cleaves lactose into glucose and galactose
- isomerization of lactose to allolactose
lacA (beta galactoside transacetylase)
transfers acetyl groups from acetyl-CoA to beta-galactosides
lac repressor (Lacl)
a DNA-binding protein that inhibits the expression of genes involved in the metabolism of lactose
- sits upstream from the lac operon
- lac genes are repressed when lactose is absent (save energy)
catabolic activator protein (CAP)
- also known as cAMP receptor protein (CRP)
- when glucose levels decrease
–> potential starvation = get more sugar
–> cAMP (second messenger molecule) start to accumulate - intracellular signalling - cAMP activates CAP and the complex binds to DNA
–> increases expression of genes
what is the role of CAP in DNA binding
- binds DNA upstream of RNA polymerase binding sites
- binds to major grooves on DNA
- opens DNA to allow RNA polymerase to bind
- activates transcription through interaction with the RNA polymerase
metabolic regulation - quorum sensing
- coordinate gene regulation system that controls bacterial social behaviours, including virulence, motility, biofilm formation, toxin production in response to cell density
- mediated via acyl-homoserine lactone (AHL)
- controls nutrient acquisition and help maintain homeostatic metabolism
- QS restricts glucose uptake and slows primary metabolism in crowded conditions
metabolic regulation - stress response
- regulation occurs at transcriptional, translational, and post translational levels
- leading to gene expression changes, protein activity and cellular metabolism
- mediate resistance to stresses and repair of cellular damage
upregultion of stress response
- increased energy production within the cell = causes an imbalance, as energy production is meant for making new building blocks but in this case it is rewired to deal with the stress and all the other processes are neglected, so after a while it will kill the bacterial cell
impact of bactericidal antibiotics
stimulates cell metabolism, including upregulating stress response networks and electron chain and TCA cycle activity
impact of bacteriostatic antibiotics
- decrease cellular respiration
- inhibits cell growth by down regulating key cell processes, including the glycolysis pathway and the TCA cycle
- macromolecular biosynthesis and protein translation processes may also be limited resulting in a build-up of energy
how does antibiotics interact with the metabolic state of bacteria
- antibiotics alter the metabolic state of bacteria
- metabolic state influences susceptibility to antibiotics
- antibiotic efficacy can be enhanced by altering the metabolic state
stationary phase
resource exhaustion, repressed metabolic activity and tolerance to antibiotics
bacterial cells in biofilms
- impaired drug permeability through biofilm matrix and decreased metabolic activity
- essentially a house around bacteria, slows down diffusion of antibiotics, so bacteria deep in the biofilm will likely survive
how to survive starvation (general)
- morphological changes ( endospores and nucleoid condensation)
- starvation proteins
- formation of persister cells
- biofilms
how do endospores help to survive starvation
- they are difficult to treat
- metabolically dormant
- resistant to heat, and other stress
- dormancy in bacteria
how does nucleoid condensation help survive starvation
- nucleoid associated proteins (NAPs)
- change in transcription
- stress response pathways
- growth arrest/slow growth
- when cells are happy they often elongate, as soon as they start getting stressed they start to shrink due to nucleoid condensation
- expression of NAPs changes throughout growth
- chromosome compaction level is higher in stationary phase than in exponential phase
- induce topological and/or structural changes in the chromosomal DNA
–> alter RNA polymerase (RNAP) or transcription factor (TF) binding
starvation proteins
- transpeptidases
–> peptidoglycan cross linking surrounding the cell membrane
–> thickening of cell wall - 1-3 layers of gram negative
- 10-20 layers gram-positive
- carbapenem antibiotics can inhibit transpeptidases - antibiotics target transpeptidases so they can’t link the peptidoglycan, can overcome this by shrinking so antibiotics can’t penetrate through the peptidoglycan layer so it can’t target transpeptidases
what cells are harder to kill
- starved cells are hard to kill
- can survive for years/can become more virulent
formation of persister cells
- small subset of cells
–> spontaneously dormant (non-growing) - even with nutrients
–> prepare for harsh conditions - starvation trigger
–> nutrient depletion, stress adaptation - allows bacterial cells to escape the effects of environmental stressors without undergoing genetic change
significance of persister cells
- survive antibiotic pressure
–> do not harbour antibiotic resistance genes
–> antibiotic tolerant phenotype
–> tolerant to the immune system - important because they are difficult to eradicate
how do persister cells survive with the help of biofilms
- bactericidal antibiotic (kill bacteria)
–> non-growing persister cells survive - termination of treatment
–> replenish population - biofilm environment
–> facilitates persister cells
biofilms
thin layer of microorganisms (like bacteria, fungi, or algae) that stick to a surface and form a protective coating
- microbial communities
–> individual or polymicrobial (eg: bacteria, fungi)
- attach to surface or themselves
biofilm development
- initial attachment phase
- reversible attachment
- irreversible attachment - primary colonization phase (maturation)
- climax community phase (maturation and dispersion)
medical application of bacterial metabolism
- bacterial metabolism is a key factor in how bacteria cause infection and disease
- evade the immune system (i.e. killing by neutrophils/macrophages)
- host releases metalloproteinases to degrade matrix components
- bacteria bind to degraded matrix components
–> facilitate colonization and proliferation - modulate immune response and promote bacterial survival
- the host immune system and pathogen act together for the benefit of the bacteria
