Microorganisms Flashcards
do we know more about bacteria or archaea?
bacteria!
What are the two domains of prokaryotes?
- archaea and bacteria
What are the sizes of prokaryotes?
- very variable (0.2 - 700 micrometers)
- typically ~ 1 micrometer (high SA:V ratio)
Why is a large SA consequential for a prokaryote?
- huge amount of surface area to transport and acquire materials, and a large part of the surface is a part of the organism itself
What are two common shapes of prokaryotes?
- cocci (singular coccus) : spherical
- rods/bacilli (singular bacillus) - some rods are quire short, others are in different stages of growth: periods of elongation and then binary fission
What are some of the clusters that may form of prokaryotes?
- chain and clusters (the plane of division is not preserved)
What are some of the general features of the prokaryotic cell?
- envelope : outer covering - contains the function rich cellular membrane and typically cell wall
- other extracellular features common eg; flagella and pilli for swimming/sticking
- few internal structures/organless: simple cytoskeleton
- small compact genotype : generally one circular chromosome in nuceloid
Is the envelope of the prokaryotic cell complex or simple?
- it is generally complex
Where is the DNA found in prokaryotes? What form is it generally found in?
- in the nucleoid; small compact genome; one circular chromosome
What do prokaryotes not have?
- mitochondria or a complex endomembrane system
What forms the cellular membrane?
- the phospholipid bilayer, which is rich in membrane proteins
What are some functions of the cellular membrane?
- most functions use the membrane proteins
- functions include: selective permeability, forming the proton gradient, detecting environmental signals, protein anchor, some structural support, and attachment of chromosomes especially during cell division
What is the cellular membranes role in selective permeability?
- controls movements of most molecules in an out of cytoplasm
What does it mean when the cellular membrane forms the proton gradient?
- harnessing the proton motive force (PMF) : the tendency of protons to move into the cell
- also forms other ion channels
what is the proton motive force?
PMF: the tendency of protons to move into the cell
- cell membrane functions to make proton gradients and harness the PMF (among other ion gradients)
What types of transport across the cell membrane is there?
- active transport, facilitated diffusion, passive diffusion
Describe passive, active, and facilitated diffusion
- passive: small, uncharged molecules pass down concentration gradient
charged, larger molecules require transport proteins:
- facilitated diffusion: proteins create channel for them to pass through
active transport: moves against concentration gradient
What are 2 methods of active transport across a cell membrane?
a) coupled transport
b) ATP driven (eg: ABC transporters)
provide two examples of coupled transport? What process drives these systems?
1) Lac permease (a symporter): concentration of H+ higher on outside, ‘drags’ lactose into cell with it
2) Sodium proton antiporter: in order for H+ to move in, kicks sodium out
both processes are driven by the proton motive force (the tendency of protons to move into cells) - since this is not ATP driven!
What is a symporter and an antiporter?
-both are a form of coupled transport
- Symporter pulls both molecules into cell
- antiporter removes one cell in exchange for another one (‘replaces’)
What are the 3 components of the cellular envelope?
- cell wall (peptidoglycan - almost always present) and the cell membrane
What is the order of materials from the outside of the cell to the cytoplasm in a prokaryotic cell?
- outside, peptidoglycan cell wall, cellular membrane, cytoplasm
What is the cell wall made up of? What function does it serve?
peptidoglycan
- provides structural support (eg: resistance to osmotic pressure)
- recall example: treating a cell with lysosome in cell wall media leads to shapeless but intact cells as opposed to bursting cells
Is peptidoglycan found in both bacteria and archaea?
- NO it is found only in bacteria
What is peptidoglycan? What makes up peptidoglycan?
It is what the cell wall in most prokaryotes is made up of = Sugars and amino acids
- important for cellular strength (ie: resists osmotic pressure)
Describe the structure of peptidoglycan?
- acts as more of a cage than a wall - glycol chains which are connected via peptides
- glycans: long linear chains of two alternating sugars: N-acetyl glucosamines (G) and N-acetyl muramic acid (M)
- connected by peptides (chains of amino acids) - cross linked to connect the glycans
What are glycans? What are peptides?
- glycans: chains of alternating sugars (Muramic acid and glucosamine) that form cell wall in bacteria
- peptides: chains of amino acids that cross link to connect glycans
How does penicillin work relative to peptidoglycan?
What are the two forms of cells envelope architecture (of bacteria)?
Gram negative and gram positive
What is the difference between gram positive and negative envelopes?
- gram positive: has a thicker peptidoglycan wall, followed by cell membrane (no outer membrane)
- gram negative has an outer membrane, a thin peptidoglycan wall, and a cellular membrane
- also has a + outer membrane and is more widespread
Which form of cell envelope of bacteria is more common?
- gram negative is more common!
In gram staining, what colour are positively charged cells?
- gram positive cells are purple
Describe, in detail, the gram positive cell envelope. What is threaded through it? How many layers are there?
- has many layers of peptidoglycan (often 20+)
- teichoic acid threaded through the peptidoglycan, some molecules attach to the cell membrane (positively charged and thus make entire cell wall positively charged)
What acid ‘threads through’ the peptidoglycan of the gram positive cell?
- teichoic acid (positively charged)
- sometimes attaches to the cell membrane (+charge)
What is the most characteristic feature of the gram negative bacterial cell envelope?
- the outer membrane (very different composition from the cell membrane)
Describe the structure of the gram negative bacterial cell envelope
Outer leaflet: mostly composed of lipopolysacharides (LSPs)
Inner leaflet: contains major lipoproteins (especially murein lipoprotein) (LPS AND LPP)
what is murein lipoprotein?
- a major lipoprotein found in the inner leaflet of the outer membrane of the gram negative bacterial cell envelope (phew!)
- chemically bonds to the peptidoglycan cell wall
Describe LSPs
- lipopolysaccharides form the majority of the outer leaflet of the outer membrane
- composed of Lipid A + polysaccharide
- the outer polysaccharide is a strain dependant O-polysaccharide - changes rapidly over evolutionary time
Describe porins
- an outer membrane protein:
- aqueous channels
- allow passage of smaller molecules through the outer membrane (eg; monosaccharides, amino acids) - NOT proteins
- outer membrane much more porous than cell membrane
- not just passive channels : many different porins with different functions
Is the outer membrane or the cell membrane more porous in the gram-negative bacterial cell?
- the outer membrane: has porins which are proteins that create aqueous channels in the outer membrane
- allows flow of smaller subunits into the cell
What is the space in between the cell membrane and the outer membrane called? What is its function?
The periplasm (the periplasmic space)
- the compartment between the cell membrane and the outer membrane
- contains important proteins (eg; enzymes involved in nutrient acquisition)
What is an example of a protein found in the periplasm?
- ABC transporter are a solute binding protein: an example of periplasmic protein
- they are ATP driven, used for active transport
- floats in periplasm and allows for active transport
Describe the extracellular layers of the gram positive bacterial cell
- common but not universal
- usually not essential for cell viability
- often only present during certain stages of life
- examples : S layer proteins and capsules
What are some examples of the extracellular layers found in the gram positive cell envelope?
- capsules and s layer proteins (some but not all)
Describe the Capsules
- a thick, diffuse layer
- typically polysaccharides
- functions: prevents desiccation, protects from virus/immune system/disease, causes adhesion (sticky)
What are external projections in prokaryotic cells?
- often extracellular, anchored to the cell membrane, outer membrane, or both
- typically made up of proteins
- examples: bacterial flagella and pili
Describe bacterial flagella
- thin, helical, flexible filaments
- present in many bacterial groups ; often only expressed under certain conditions
- main function: swimming locomotion
- many species are peritricous: many single flagella all over the cell
What does peritichrous mean?
- many single flagella all over the cell
Where are bacterial flagella found?
- the external cell projections of prokaryotic cells
What is the flagellum’s structure?
- Filament
- has a basal body:
ring of motor proteins in cell membrane around the rotor - flagellum rotates (powers by proton motive force) and drives the rotor
How does the flagellum move?
- flagellum can rotate clockwise or counter clockwise
- most peritrichous cells:
CCW: forms a flagellar bundle, straight line ‘run’
+1 CW: fails to form bundle, random ‘tumble
What does it mean for the flagellum to be swimming?
- alternating runs and random tumble turns
- a random walk through space
How does the cell learn to ‘swim with purpose’
- random walks can be biased by altering the frequency of random tumbles in response to a que
ie: chemotaxis: moving towards a chemical attractant
What is chemotaxis? Where does it apply?
Chemotaxis is the process of moving towards a chemical attractant
- in flagella, they increase the frequency of random tumbles to get to where they want to go
What are pili?
another form of external cell projection
- many different kinds
- made up of rods / tubes of protein
- main roles: adhesion and locomotion
Describe the cytoplasm in prokaryotes
- (as in eukaryotes)
- site of many enzymatic reactions
- pools of small molecules (amino acids, ATP, ions, etc, etc)
- site of protein synthesis
Do prokaryotes always have simple intermolecular structures?
- no, some prokaryotes do have some complex internal structures (extreme case of complexity in prokaryotic cells)
What are storage granules? provide some examples?
- for energy/nutrient reserves
- examples: poly B hydroxybutyric acid (PHB) granules
- fatty acid polymers
energy store: made under ‘excess-carbon’ conditions
What are the major shape determining proteins of the bacterial cytoskeleton?
- “z-ring” - includes FtsZ
- division plane
MreB : needed for elongation (growth) of rod shaped cells
- guides cell wall synthesis
Describe the prokaryotic DNA
- usually a single, circular chromosome but often with extrachromosomal plasmids
- found in the nuceloid, not a separate nucleus : compaction via supercoiling, plus DNA-binding proteins
Describe the prokaryotic chromosomes
- densely packed with information
- most (~90%) of the DNA encodes proteins
-intervening sequences (introns) nearly absent - many genes in co-transcribed groups (operons)
How much of the DNA in prokaryotes encodes proteins?
~90% encodes proteins
What does it mean for genes to be co-transcribed?
- forming a single mRNA molecule encoding all of the genes
What is coupled transcription and translation? Where and why might it occur?
- when the ribosomes begin translating the mRNA before the DNA is even finished being transcribed
- occurs in prokaryotic cells where there is no sharp separation between nucleoid and cytoplasm
What are plasmids?
- extrachromosomal genetic elements
- usually encode functions that change properties of the host cell, but not required for cell viability
Are plasmids required for cell viability?
- plasmids encode functions that change properties of the host cell, but are not required for viability
How does the cytoplasm in bacterial prokaryotic cells resemble eukaryotic cytoplasm?
- pools of small chemicals
- site of enzymatic reactions
- site of protein synthesis
Describe prokaryotic DNA
- generally a single, condensed circular chromosome - often has extrachromosomal plasmids
- condensed via supercoiling and DNA binding proteins
How is DNA condensed in prokaryotic cells?
- in the nucleoids, DNA is condensed via supercoiling as well as DNA binding protiens (NOT histones in bacteria)
What is a co-transcribed group?
Forming a single mRNA molecules encoding multiple genes
Describe the ratio of operons to introns in prokaryotic chromosomes
- very few introns, majority of co- transcribed groups (operons)
What is coupled transcription and translation? Where does it occur?
- this occurs in the prokaryotic cells, since there is no division between the cytoplasm and the nucleoid mRNA strands begin to get translated before the DNA is even done being transcribed
Is a prokaryotic cell that does not have plasmids considered viable?
Yes! plasmids may encode for functions that change the properties of the cell but they are not required for cell viability
What does it mean when a plasmid is ‘promiscuous’ ?
many plasmids are readily exchanged between individual cells, however some can be transferred between different species (promiscuous)
What is the advantage of a plasmid being ‘promiscuous’?
May encode multiple antibiotic resistance genes
Describe chromosome replication?
- usually one origin of replication
- bidirectional: 2 replication forks
- complete when forks meet (at termination site)
- overlapping replication cycles when cell generation time shorter than DNA replication cycle
Describe growth and reproduction?
- typically cell grows then divides evenly in two (binary fission)
- division includes: replication of chromosomes, formation of septum (separation) at Z ring (Ftsz)
Describe bacterial population growth
- some species can undergo binary fission 20-30 minutes under optimal conditions (will vary hugely between different species)
Nt = No x 2^n
Describe the growth curve stages
- log phase, stationary phase, death phase
- log phase: period of exponential growth : nutrient limitation or toxic buildup -culture enters stationary phase
What is differentiation in prokaryotes?
- different cell types in a few colonial forms
- heterocysts in some cyanobacteria
- one cell can have different forms, often triggered by environmental stressors adapting to local conditions
–> more common: alternate cell forms specialized for dormancy and/or dispersal
What are some examples of differentiation?
- akinetes: some cyanobacteria
- spores: some actinobacteria
- endospores: some firmicutes
What is catabolism and anabolism?
- catabolism: break into smaller pieces for energy
- anabolism: build organic molecules, sticking them together: biosynthesis
What are photoautotrophs? Chemoautotrophs? photoheterotrophs? Chemoheterotrophs?
- photo autotroph: plants, microorganisms - energy from light, creates own energy
- chemoautotroph: energy from performing chemical reactions but can also use that energy to fix CO2
- photoheterotrophs: gets energy from sunlight, but to grow need source of organic molecules from its environment (cannot fix Co2, gets from others)
- chemoheterotrophs: animals, many microbes
What are organotrophs? What are lithographs?
- Organotrophs: catabolism of organic molecules
- lithotrophs: energy from oxidizing inorganic molecules (litho = rock)
What is an aerobe? What are the two kinds of aerobes?
Aerobes rely on oxygen as an electron acceptor
- obligate aerobes need O2 for growth
- micro aerophiles prefer lower levels of oxygen
What are anaerobes? What are the two kinds?
- anaerobes do not use O2
- aerotolerant anaerobes: tolerate but do not use O2
- strict/obligate anaerobes: need very little O2 to live, it is toxic to them
What are facultative anaerobes?
- can survive with or without molecular oxygen
What kind of organism is Lilly and all her friends?
- an aerobic chemo-organo-heterotroph
- oxygen dependent, require chemical reactions for energy - specifically organic chemicals - and needs existing carbon to make new biomass
What is oxidative phosphorylation?
- electron transport linked to ATP synthesis by proton motive force
- forms around 30 ATP molecules
Describe the variety of energy generating pathways in prokaryotes
- huge variety of energy generating pathways in prokaryotes (- entire doudoroff pathway is oftenn used instead of classical glycolysis)
- components that make up electron transport systems vary substantially
Describe metabolic diversity in prokaryotes
- much of the metabolic diversity we see is when oxygen/ organic carbon is limited
- we look at: fermentation, anaerobic respiration, lithography
Describe fermentations
- ~organotrophy, without external electron acceptor
- substrates and products in redox balance: no use of the electron transport system
- often under anaerobic conditions
- low energy yields per molecule of substrates: large amount of substrate converted = large amounts of end products created
- eg lactic (homolactic) fermentation
there are many different microbial fermentations
Are fermentation end products always depleted in energy?
- No! Many fermentation end products are still energy rich: potential substrates (food) for other organisms
- Co2 makes things fizzy, some fermentation make H2
Describe the different levels of reduction potential
High electron potential: really good electron acceptor, gets reduced
Low electron potential: strong electron donor: gets oxidized
How do we calculate the energy available from a reaction?
- the energy of the acceptor - the energy of the donor
- large positive value: lots of energy available
- large negative value: reaction requires a lot of energy to proceed
In principle, many other molecules could be used as electron acceptors when oxygen is not available. Provide an example.
Ecoli is a facultative anaerobe: works with and without oxygen
- aerobic respiration: 6 protons pumped across cell membrane
- under anoxia (all O2 used up): nitrate reduction: only 4 protons pumped across cell membrane (less energy)
What is denitrification?
- anaerobic respiration with nitrate as terminal electron acceptor, but reduced to N2
- a major cause of loss of available nitrogen form ecosystems
What is lithotrophy in one sentence?
- when an inorganic molecule is used as the original electron donor (ie: food)
What is lithotrophy in detail?
- needs a source of reduced inorganic compounds (in a form that can give up electrons) = metal/metal ions/sulfur, nitrogen, hydrogen gas
How are reduced inorganic compounds produced?
- through geological processes or through other organisms (anaerobic respiration, fermentation)
- and: reduced sulfur compounds (eg;H2S) as electron donors = example of lithography
Where can sulfur/sulfure oxidizers be found?
- often at the interface between sulfide rich anoxic layers and overlaying aerobic zone
Describe nitrogen in lithotrophy?
- strongly negative reduction potential: therefore energy rich food
- sources: geological (eg; hydrothermal vents), waste product of some fermentations
- eg; mixed fermentation, various acids, ethanol, CO2, H2
What is biosynthesis?
- making new biomass
- raw materials for biosynthesis:
- organotrophs growing in compost: lots of lipids as sources of energy
- sulfur oxidising lithotroph in a 90 C acidic hot spring: limited organic material, takes Co2 from environment to make organic material
What is autrophy?
- fixation of organic carbon (usually CO2) to form organic carbon: ie: reduction of CO2
- most phototrophs and most lithographs are capable of autotrophy
- requires energy (generated via autotrophy or lithography) including reducing power (ie: NADH)
What is carboxysomes?
- crystalline aggregations of rubisco: the signature Calvin cycle enzyme
- some ecosystems are based on lithoautotrophy
Describe nitrogen
- for biosynthesis of amino acids, nucleotides, vitamins, etc
- most prokaryotes can assimilate ammonium (NH4+)
- many also assimilate nitrate (No3—> Nh4+)
- a very few require organic N (eg; amino acids)
- some prokaryotes capable of nitrogen fixation (atmospheric N2 –> NH4+)
Describe prokaryotic species
- animal and plants; ideal of biological species concept based on infertility but in prokaryotes there is no true sexual process
- instead species are based on operational criteria
- 15,000 names
Why are there so few prokaryotes named?
- 1) demanding rules to name a species (eg; must be cultured)
2) prokaryotic species may contain much more genetic diversity than animal or plant species
What are the patterns of prokaryote evolution?
Some groups distinguished by major cellular or physiological traits ;
- eg; bacteria vs. archaea
- eg; spirochetes (periplasmic flagella)
–> but many major traits appear in very distantly related organisms
- much due to horizontal (lateral) gene transfer
Describe the significance of Bacillus and bacillus
→ remember: genus names always Capitalised and italicised: ‘Bacillus’ is genus, ‘bacillus’ is shape (referred to as rods)
Which groups of bacteria are examined?
- firmicutes, actinobacteria, proteobacteria, cyanobacteria, spirchetes, briefly others
What are firmicutes (Bacillota)?
- strong skin bacteria, refers to thick cell walls (think cuticle)
- includes: main models for the gram positive envelope
- most are organotrophs
- range from obligate aerobes to obligate anaerobes
–> most common in soil, sediments
- many live on animals and/or pathogenic
what are some examples of firmicutes?
- lactic acid bacteria
- endospore formers (eg; bacillus, clodistrium)
