Lecture 5: Bacterial and Archaeal Growth Flashcards
(90 cards)
1
Q
Before cell division, bacteria must
A
reach nutrient stage and critical mass then it elongates.
2
Q
Binary fission process
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- Cell elongates
- Septum forms as chromosomes move to opposite ends and cytoplasmic components are distributed.
- septum is synthesized completely through cell center (creating two daughter cells).
- Daughter cells completely separated.
3
Q
Budding
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begins with small bud (portion of bacteria) that enlarges and separates.
4
Q
Multiple fission
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progeny is held within parent cell until maturity.
5
Q
Multinucleoid
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Filaments that eventually divide to form uninucleoid spores.
6
Q
Streptomyces
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Filamentous bacteria that forms filaments.
- They start branching out in little segments (hypha) which become spores.
7
Q
Bacterial Cell Cycle Phases
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- period of growth after cell is born as it increases in size.
- Replication of chromosomes and partitioning.
- Cytokinesis: actual cell separation stage.
- during which a septum and daughter cells formed.
8
Q
Chromosome Replication and Partitioning process
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- Most bacteria have a single circular chromosome.
- DNA replication proceeds in both directions from origin.
- Origins move to opposite ends of cell, and rest of each chromosome follows.
9
Q
Origin of replication
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- Sequence in DNA that has info needed to trigger duplication event.
Site at which replication begins.
10
Q
Terminus
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site at which replication is terminated, located opposite of the origin.
11
Q
Replisome
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DNA synthesis machinery including necessary proteins and enzymes helping to synthesize DNA.
12
Q
Cell cycle of E. coli (3 brief steps on diagram)
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- initiation mass reached
- initiation of replication
- septum formation begins when z-ring forms
13
Q
cell cycle of E. coli in depth
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- Circular chromosome with point of origin and opposite end being the terminus.
- Replication happens in both directions. Circle moving its way in through replisome. This continues process until entire chromosome is read. Origins are starting to gravitate to one side of cell.
- Gets to a point where entire cell has been replicated.
14
Q
Components of chromosomes partitioning
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ParA protein
ParB protein
ParS region on chromosome (S is DNA)
15
Q
ParS functions
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- ParS is part of circular chromosome.
- Contains sequence that triggers replication.
- Sits near origin of replication.
- Direct segregation of two daughter chromosomes.
16
Q
Steps of Chromosome Partitioning
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- ParB forms a complex that binds to DNA or parS on both sides opposite.
- ParA draws one half of chromosome to other side of cell through diffusion that’s occurring.
- ParB gives ParA the chromosome to move it further to one side of cell as one partition complex remains at stalk pole.
17
Q
Cytokinesis and septation definitions
A
Cytokinesis: formation of 2 daughter cells after cell division.
Septation: formation of cross wall between 2 daughter cells.
18
Q
Septation steps
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- Selection of site for septum formation.
- Assembly of Z-ring (composed of protein FtsZ).
- Assembly of cell wall-synthesizing machinery.
- Constriction of cell and septum formation.
19
Q
FtsZ and Min proteins
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- FtsZ protein involved in assemly of Z-ring.
- Min proteins inhibit FtsZ if they come into contact with it.
20
Q
Z-ring formation
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- FtsZ monomers polymerize to make long chain.
- Universally spread around cell and localize to future division site.
- FtsZ move away from the Min around which makes them know the center to divide the cell.
21
Q
Importance of Z-ring timing
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Location of FtsZ polymerization must coordinate w/ timing.
* Too early, Z-ring constrict preventing proper partitioning.
22
Q
Nucleoid Occlusion
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- Coordinates chromosome movement and cell septation.
- Nucleoid has SlmA proteins that coat chromosome.
- SlmA proteins repel FtsZ.
- Z-ring can form when SlmA tagged chromosome has moved away after nucleoid separates.
23
Q
Divisome
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Made up of more than 30 proteins catalyzing peptidoglycan.
24
Q
Divisome formation
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- Z-ring is not membrane bound and attached to adaptor proteins to anchor it to membrane.
- Z-ring is a scaffold for enzymes that synthesize cell envelope.
- As the cell is pinching, the divisome is making peptidoglycan and cell wall.
25
Cellular Growth and Determination of Cell Shape
* Cell shape is strict and passed on through generations.
* Peptidoglycan synthesis is critical in shape determination as divisome builds new cell wall.
* Some microbes change shape under circumstances.
26
Peptidoglycan Synthesis
1. NAG and NAM are bound to bactoprenol (lipid carrier found inside membrane).
2. MurJ flips carrier-bound building block outside of a cell to face peptidoglycan cell wall.
- some enzymes come in to help attach MurJ.
3. Glycotransferases (Gtases) insert NAG-NAM into peptidoglycan strand.
4. Transpeptidases (TP) cross-link strands by connecting MurJ to existing cell walls.
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Transpeptidases (TP) and penicillin
- This is the enzyme that penicillin acts on.
- It inhibits this like putting bricks together without cement which weakens it.
- penicillin is an antibiotic
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Cell shape determination is by
Cellular location of peptidoglycan synthesis.
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Coccus cell shape is characterized by
Peptidoglycan only forms at central septum.
* FtsZ localization placement involved.
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Rod cell shape is charcaterized by
- MreB creates filaments along cytoplasmic face of plasma membrane.
- growth occurs in many bands around cell not at poles.
- Instead of FtsZ, the protein used is MreB.
- Elongasome is a rod complex used.
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Curved cell shape is characterized by
crescentin localizes to one side of cell.
resulting in asymmetric cell wall and vibroid shape.
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Archaeal Cell Cycle
Similar to eukaryal cell cycles except in segregation of chromosomes.
* Growth phase (G1)
* DNA replication (S phase)
* G2 phase
* segregation of chromosomes
* cytokinesis.
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Segregation of chromosomes in archaea
Segregation occurs via use of SegA/SegB protein system similar to bacterial partitioning systems.
* SegA similar in structure and function to ParA.
* SegB unique to archaea, but function similarly to ParB.
- ParS not yet found in archaea.
34
Archaeal cytokinesis
Similar to eukaryotes occurs via cell division (Cdv) proteins.
* CdvA: Bind membrane/form noncontractile ring at midcell
* CdvB: Ring constricts to separate the daughter cells.
* CdvC:Recruited with CdvB to the site of division.
* FtsZ: Z-ring associates with new S-layer instead of PG.
35
Growth
increase in cellular constituents that may result in an increase in cell number and cell size.
36
Microbial growth curve
Observed when microorganisms are cultivated in liquid (broth) culture.
usually plotted as logarithm of cell number versus time.
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Batch culture
microorganisms incubated in a closed vessel with a single batch of medium that is fixed from the start and is not renewable.
38
Lag Phase
- Colony takes time to adapt to new surroundings.
- Cell synthesizes new components.
- Replenish spent materials (ribosomes and ATP).
- Synthesizes new enzymes to adapt to medium.
- Cells replicate their DNA, increase in mass (less division).
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Exponential Phase
- Rate of growth and division is constant and maximal.
- Population is most uniform in terms of chemical and physiological properties of each cell.
- Most cells are on the same wavelength and undergoing division.
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rate of growth in exponential phase is dependent on:
Nutrient availability.
- Final net growth increases with initial amount of limiting nutrient present.
- Growth rate increases with nutrient concentration but it saturates.
- Plateau because of saturation of nutrient transport proteins.
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Stationary phase
In a closed system, growth eventually ceases because no nutrient is added.
- Total number of viable cells remains constant.
- Balance between cell division and cell death
- Some sense change in nutrient availability and stop undergoing division but remain metabolically active.
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Reasons for stationary phase:
- Nutrient limitation
- Limited oxygen availability
- Toxic waste accumulation (ex. acid from sugar fermentation which is how bacteria turn sugar to energy).
- Critical population density reached as no space available.
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Death Phase
- Number of viable cells declines exponentially with cells dying at a constant rate.
- Nutrient deprivation and buildup of toxic wastes causes irreparable harm to cells.
- Some cells may adjust and undergo sporulation to form endospores that can be vegetative cells when nutrients are available again.
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Long-term Stationary Phase
Bacterial population continually evolves.
- Genetic variants that can withstand the toxic environment survive and grow a little.
- Process marked by successive waves of genetically distinct variants.
- Can use nutrients released by dying bacteria and tolerate waste products.
- Natural selection occurs within a single culture.
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Generation (doubling) time
- Time required for population to double in size.
- Number of cells in the culture = N(0) x 2^n
- n is generation number.
- Constant doubling due to binary fission.
- Varies depending on species of microorganisms and environment.
- E.coli are popular for cell cloning purposes because generation time is only 0.35 hours.
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Extremophiles
- Grow under harsh conditions that would kill other organisms.
- Eg. Bacillus infernus
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Infleunce of environmental factors on growth
- All microbes must respond to changes in their environment.
- Microbes have an optimal range of environmental factors for best growth.
- anything below or above that decreases growth significantly.
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Osmosis and osmolarity
- Movement of water across membrane from area of high water activity to low water activity.
Osmolarity: Ability of solutions to induce water to cross a membrane (it's all about water here).
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Osmotic pressure and Semi permeable membrane
- A force arising due to tendency of water to move by osmosis.
- Allows some molecules to cross while restricting others.
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How do solutes impose osmotic pressure?
Addition of solutes forces water to enter to increase the water in the gaps between the solutes.
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Tonicity
The ability of a solution to alter cell volume (when we talk about what happens to the cell).
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Isotonic solution
Solute concentration is balanced in and outside cell with no change in cell volume.
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Urea
A penetrating molecule that passes through cell membrane. If introduced to solution with salt, it won't change cell volume. If introduced alone to cell, then it will penetrate cell membrane and equilibrate on both sides. Urea will add to existing solutes trapped on both sides creating hyper-osmotic environment and cell will swell.
54
Hypotonic solution
- Lower solute concentration outside the cell than inside.
- Water enters the cell and may burst.
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Hypertonic solution
- Higher solute concentration outside cell than inside.
- Water leaves the cell and membrane shrinks
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How do microbes adapt to changes in osmotic concentrations?
- Most microbes live in hypotonic environments.
- Protected by cell wall, preventing over-expansion of plasma membrane.
- Mechanisms to lower solute concentration in cytoplasm:
- Mechanosensitive (MS) channels are ion channels that allow certain solutions to leave or enter cell in plasma membrane.
- Protists use contractile vacuoles to expel excess water.
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Osmophiles
A type of microbes adapted to extreme hypertonic environments.
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Halophiles
- Live in salty environments.
- Require NaCl at a concentration above 0.2 M.
- Extreme halophiles: salt concentration is 3-6.2 M.
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Two ways halophiles adjust:
Salt-in: Go with the flow and allow salt to enter into cell. Allow ions (K and Cl) into cytoplasm. Bacteria modified their proteins to need these high salt levels.
Salt-out: cell spends amount of resources on keeping salt ions out. They synthesize solutes less destructive than salt that don't interfere with growth. There will be balance of solutes inside and outside. Example is amino acids like proline and glutamic acid.
60
Water Activity (a_w)
- Measure of degree of water availability.
- When solutes are in water, water molecules interact with solutes that make them not free to use.
- Most microorganisms grow well at a_w around 0.98.
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Osmotolerant
Organisms that can grow over a wide range of water activity but optimally at higher levels.
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Xerotolerant
microbes that withstand high solute concentrations and dry environments (desert regions).
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pH and how it's measured
- A measure of relative acidity of a solution.
- Negative logarithm of hydrogen ion concentration.
- The lower the hydrogen ions, the higher the pH.
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Acidophiles
Organisms that grow best between pH 0 and 5.5.
Most fungi prefer pH 4-6.
Photosynthetic protists prefer slightly acidic.
Some archea are acidophiles.
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Alkaliphiles
- Organisms that grow best between pH 8 and 11.5
- Distributed among all three domains of life.
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Neutrophiles
most bacteria and protists grow best at pH 5.5-8.0.
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Changes to internal pH affects:
ionization of proteins and lipids and would affect the way these subunits work.
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How do the three types respond to changes in external pH?
Microorganisms use mechanisms that maintain a neutral cytoplasmic pH.
- Neutrophiles: exchange potassium for protons.
- Acidophiles: pump protons (H+) out of cell to keep environement more acidic and have highly impermeable membrane.
- Alkaliphiles: Exchange internal Na+ for external protons.
69
Temperature effect on microorganisms
- Microbes cannot regulate their internal temperature.
- Enzymes have optimal temperature at which they function optimally.
- Below optimum temperature, enzyme is not catalytic.
- High temperatures may inhibit enzyme functioning and be
lethal.
70
Five types of microorganisms and their optimal temperature
Psychro-philes: 0-20 C
Psychro-trophs: 0-35 C
Meso-philes: 20-45 C
Thermo-philes: 45-85 C
Hyperthermo-philes: 85-100 C
71
How thermophiles adapt to extreme environments:
- Heat-stable enzymes and protein synthesis that function at high temperatures.
Protein structure stabilized by
1. more hydrogen bonds.
2. more proline amino acid, less flexible peptides (rigid cyclic side chains).
3. More chaperons aid in folding and keep proteins in their proper shape (example: heat shock proteins).
Lipid membrane stabilized by being
1. more saturated, more branched, and higher molecular weight resulting in low fluidity.
2. Ether linkages which are resistant to hydrolysis.
72
What does growth in presence of difference oxygen concentrations depend on?
Depends on microbe's metabolic processes, electron transport chains (ETC), terminal electron acceptor used.
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Five types of relationships to oxygen:
Obligate aerobe: requires oxygen.
Obligate anaerobe: killed in presence of oxygen.
Microaerophile: requires 2 to 10% oxygen.
Facultative aerobe: don't require oxygen but grow better in it.
Aerotolerant anaerobes: grow with or without oxygen.
74
Why are there oxygen sensitivities?
Reactive oxygen species (ROS) are toxic derivatives of oxygen metabolism which cause cellular damage.
They have one available oxygen atom that bind in ways they're not supposed to bind.
- Superoxide radical
- Hydrogen peroxide
- Hydroxyl radical
75
How do microorganisms protect themselves form ROS?
Aerobes produce protective enzymes:
1. Superoxide dismutase (SOD)
2. Catalase
3. Peroxidase
Enzymes reduce or degrade ROS so they can't bind or cause damage to molecules (such as binding to DNA causing mutations).
76
Barotolerant
Adversely affected by increased pressure, but not as severely as non-tolerant organisms.
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Peizophilic (barophilic)
- Require high pressure for growth.
- Change membrane fatty acids to adapt to increasing pressure.
- Lipids become more unsaturated and shorter to increase fluidity.
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Harmful radiation causes
- Disrupts chemical structure of molecules.
- Causes atoms to lose electrons making it bind to things they're not supposed to bind to.
- Breaks H-bonds and destroys ring structures.
- cause mutations that indirectly result in death.
79
What are resistant to ionizing radiation?
Bacterial endospores and deinococcus radiodurans are extremely resistant to ionizing radiaiton from x-rays, gamma-rays and ultraviolet.
80
What wavelength is most harmful and how?
- UV radiation of 260 nm is absorbed by DNA.
- DNA damage can be repaired by several repair mechanisms.
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How does visible light cause radiation damage?
- At high intensities generates singlet oxygen, a
powerful oxidizing agent.
- Carotenoid pigments protect many light-exposed
microorganisms from photooxidation.
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Oligotrophic and Eutrophic
oligotrophic: low nutrient environment.
eutrophic: nutrient rich environment.
Most microbes live in oligotrophic environments.
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How do microbes adapt to starvation and environmental stress?
- Endospore formation.
- have numerous proteins that help.
- Growth arrest: enter stationary phase.
- Viable (metabolically active) but not culturable (dividing) state.
- use cellular components as nutrients.
- Persisters: under growth arrest state, they are not synthesizing new proteins making them resistant to antibiotics while targets are inactive.
- resume growth once nutrient return
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Sessile and planktonic microbes
Most microbes grow attached to surfaces (sessile) rather than free floating (planktonic).
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Biofilm
Complex, slime enclosed communities of microbes.
- Allow microbes to survive.
- Ubiquitous found everywhere in nature in water.
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Biofilm formation steps
1. Surface preconditioning by ambient molecules
2. Cell deposition
3. Cell absorption
4. Cell desorption if they dont like it
5. cell-to-cell signaling that triggers production of exopolymers.
6. Convective and diffusive transport of O2 and nutrients into biofilm.
7. Replication and growth
8. Secretion of polysaccharide matrix
9. Detachment, erosion, and sloughing
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Extracellular polymeric substance
The glue that keeps the biofilm together. It's made of polysaccharides, proteins, and DNA.
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Emerging properties and relation to biofilms
Properties couldn't be predicted from studying single cell.
- Physiological changes and EPS protect microbes from harmful UV rays.
- When formed on medical devices, antibiotic treatment fails.
- Chunks of biofilm can be sloughed off which can contaminate a drinking water system.
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Quorom sensing
- Bacterial cells communicate via small molecules that diffuse in the environment.
- Quorom is the minimum number of cells needed for a community.
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Quorom Sensing process
1. Autoinducer AHL is synthesized and diffuses (moves across plasma membrane from cytoplasm to outside of cell).
2. The population grows in number.
3. Extracellular AHL concentration increases as population increases.
4. AHL starts diffusing into the cell by binding to its receptor which induces gene expression.
5. Triggers signaling networks that initiate cooperative processes.
