Module 2: Bacteria (Part 1) Flashcards
What are the four main morphologies of bacteria?
1) Cocci
2) Bacilli
3) Vibrio
4) Spirilia
What is the determinant of bacterial morphology?
Cell wall organization
Cocci
Spherical
Bacilli
Rod-shaped
Vibrio
Curved-Rod (comma shape)
Spirila
Spiral Shaped
Why is morphology NOT enough for conclusive bacterial identification?
1) Many bacteria have the same morphology
2) Environmental stressors can alter morphology
Bacteria with variable morphology
Pleiomorphic
What are the main multicellular arrangements bacteria form?
1) Hyphae
2) Mycelia
3) Trichomes (mainly in cyanobacteria)
Hyphae
Irregularly branching filaments made of bacterial chains
Mycelia
3D network of hyphae
–> Hyphae go below or rise above the substrate (surface)
Trichomes
Smooth, unbranched chains of bacterial cells
(that may have a polysaccharide coating over the chain)
IN CYANOBACTERIA
What is the size range of most bacteria?
0.5um - 5um (LENGTH)
At what size is it too hard to see a structure with the naked eye?
<100um
What is needed to view bacteria?
Why?
A light microscope
Because most bacteria are less than 100um big
What is the size of the smallest eukaryal cell?
5um
Bacterial Size Exception:
What is the name and size of the biggest bacteria we know of?
Thiomargarito namibiensis
–> Typically ~100-300um (BUT can get up to 750um)
Bacterial size exception:
What is the name and size of the smallest bacteria we know of?
Mycoplasmas (a number of different kinds)
Usually ~0.2um in diameter
(Mycoplasma galicepticum = smallest known organism)
What is the morphology of mycoplasmas?
They have no cell wall so they are ultra-small, PLEIOMORPHIC bacteria
Cytoplasm
Aqueous environment enclosed within the plasma membrane
Nucleoid
The nuclear region; area of bacterial cells that contains the chromosomal DNA
Structure of bacterial DNA
Bacteria tend to have ONE big circular chromosome that gets bunched together into the nucleoid
What is the largest structure in the cytoplasm?
The nucleoid
Other than DNA what is also found in the nucleoid region?
1) Many proteins involved in DNA replication and transcription
2) Proteins involved in DNA condensing (Topoisomerase)
3) Cations (that also aid in DNA condensing)
What is the composition of the cytoplasm (in %)
80% water
20% Proteins, carbs., lipids, ions
Cytoplasm = “Macromolecule stew”
Ribosomes
Organelles made up of rRNA and proteins that acts at the PROTEIN SYNTHESIS MACHINE
Plasmid
Small DNA molecule (usually double stranded and circular) that is physically separate from the chromosomal DNA
Inclusion Bodies
Aggregates of stable substances (usually for storage of extra: carbon, nitrogen, sulfur, and phosphorus)
A STORAGE VESSEL
What do inclusion bodies appear as under the light microscope?
Granules
What are 3 specialized structures (organelles) of bacteria?
1) Magnetosome
2) Gas Vesicles
3) Carboxysomes
Gas Vesicle
Typical Shape? Function?
Protein structure filled with gas
Shape = tube with conical endcaps
Function =
1) Provide BUOYANCY to the cell!
2) Regulate a cell’s position in water in response to light/nutrient levels
In what microorganisms are gas vesicles usually found?
Micro-planktonic organisms
Carboxysomes
Function? Organism?
A polyhedral protein shell filled with RuBisCo
Function = Used for RuBisCo sequestering; primary site for calvin cycle (carbon fixation)
Organism = CYANOBACTERIA (photosynthetic bacteria)
RuBisCo
Ribulose Biphosphate Carboxylase
(Main enzyme for the Calvin Cycle)
Magnetosome
Function? Shape?
Membrane enclosed organelle containing magnetic material (magnetite)
Function = Acts as a “cellular compass”
–> Associated with direction finding that aids in locating the preferred microaerophilic environs (low O2)
What organisms have magnetosomes?
Magnetotactic Bacteria
Cytoskeleton
Network of microfilaments and intermediate filaments that provide structure and direct movement
What are some key cytoskeletal structures/systems of bacteria? (3)
1) FtsZ (Z Ring)
2) MreB (helical bands)
3) ParMRC System (plasmid segregation during cell division)
Z-Ring
(+ Its composition)
Filamentous ring that forms along the inside of the PM
–> Individual filaments are made up of polymerized monomers of FtsZ proteins
–> The FtsZ filaments then bundle together to form the Z-Ring
What is the purpose of the Z-Ring?
3 main functions:
1) Acts as a scaffold for division proteins recruitment (scaffold for the division machinery)
2) Guides the synthesis of septal peptidoglycan (formation of new cell wall)
3) Contracts (pinches in) through the removal of FtsZ monomers from the filaments leading to the constriction of the dividing cell into two
What is FtsZ?
A protein (evolutionarily related to TUBULIN) that is a monomer for filaments making up the Z-ring)
What is MreB?
A protein (evolutionarily related to ACTIN) that is a monomer of actin-like filaments which form helical bands in non-spherical bacteria
Purpose of MreB Helical Bands
Believed to help direct the growth of non-spherical bacteria into their respective shapes (elongated cylinders rather than spheres)
In what organisms are MreB helical bands found?
Almost in ALL non-spherical bacteria;
very very rarely found in cocci (spherical)
What is the ParMRC system?
A mechanism for segregating plasmids to opposite ends of bacterial cells during cellular division
Consists of 3 components:
ParM
ParR
ParC
ParM
Protein that polymerizes to form actin-like filaments that are responsible for PUSHING plasmids to opposite ends during cell division
ParC
A plasmid DNA sequence that is a binding site for ParR
ParR
A DNA binding adapter protein that binds to both ParC and ParM, connecting the plasmid to the “segregation machinery” (ParM)
What is the process of the ParMRC system?
1) Search. ParM monomers search for ParR by rapidly forming and disassembling short, dynamic filaments throughout the cytoplasm
2) Capture. When ParM “finds” a ParR protein (bound to ParC), it binds to ParR! –> Creates a ParR-C CAP on the ParM filament, stabilizing the filament and preventing its disassembly
–> This ParM then attaches at the other end to ANOTHER ParR-C complex
3) Elongation. ParM monomers (bound to ATP) add onto the growing ParM filament causing elongation of the filament that PUSHES the ParR-C endcaps towards opposite ends!
4) Depolymerization. Right before cell division, ParM filament depolymerizes –> Following this the cell splits into two
What is the purpose of ParMRC?
Ensures that plasmids are faithfully passed down to ever daughter cell of bacterial division
Why are plasmids important to bacteria?
Plasmids may contain genes that provide bacteria with significant advantages such as antibiotic resistance
Plasma Membrane
A semi-permeable bilayer enclosing the cytoplasm that mainly consists of phospholipids
How can plasma membrane phospholipids differ?
1) Length of the fatty acid (hydrocarbon) chains (tails)
2) Chemical groups in the polar head (side grps. connected to the phosphate group)
3) # of double bonds in the tails (level of saturation)
What do bacterial plasma membranes lack that WE have?
Sterol Lipids (Ex: Cholesterol)
Hopanoids
Pentacyclic compounds (sterol-like) found in bacterial cell membranes
What is the bacterial alternative to sterol lipids?
Hopanoids
What is the function of hopanoids?
1) Regulation of membrane rigidity and permeability ( > amount of hopanoids = greater rigidity)
2) Stabilize bacterial membranes across temperature and pH ranges (Ex: preventing excessive fluidity of membranes at high temperatures)
How many bacteria have hopanoids?
Only about 10% of bacteria produce hopanoids
Integral Proteins
Proteins that span the width of the plasma membrane; embedded IN the PM
Domains:
–> 2 hydrophilic (1 facing ECF + 1 facing cytoplasm)
–> 1 hydrophobic (within the PM)
How much of the plasma membrane is protein?
~50% of the PM is proteins!!! (not just a lipid structure!)
Peripheral Protein
Proteins associated with the surface of the PM (NOT embedded)
What are the main functions of PM proteins? (4)
1) Control of movement of materials into and out of cytoplasm
2) Capture/storage of energy (respiration + photosynthesis)
3) Maintenance of chemical + electrical gradients
4) Environmental sensing (signal transduction w/ receptors)
What are freely permeable to the PM?
Small + UNCHARGED molecules can diffuse freely across the bilayer
(Ex: CO2 + O2)
How does water get across the PM?
Through AQUAPORINS (facilitated diffusion; moves up solute gradient)
Aquaporins
Protein CHANNELS that facilitate the passage of water across a membrane
–> Water moves by osmosis (NOT pumped)
Osmosis
The flow of water from LOW solute concentration to HIGH solute concentration (Moves UP solute gradient)
Hypotonic
ECF is LESS (hypo) concentrated than cell
–> Cell is more concentrated
–> SO water flows INTO cell
What happens to a cell in hypotonic solution?
Cell swells as it fills with water; can eventually lead to lysis
Hypertonic
ECF is MORE (hyper) concentrated than cell
–> ECF is more concentrated
–> SO water flows OUT OF cell
What happens to a cell in hypertonic solution?
The cell shrinks!
What in bacteria protects against potentially damaging osmotic effects?
The cell wall; provides stability, preventing structural collapse under various osmotic conditions
–> In Hypotonic Soln: Provides a rigid structure that resists excessive swelling
How do nutrients and other molecules transport across membrane?
Through transport proteins
Types of Transport Proteins
1) Channel Proteins
2) Symporters
3) Antiporters
4) ATPases (ATP-dependent transporters)
Protein Channels
Form hydrophilic (aqueous) passageways for specific substances to pass through
–> Facilitated diffusion!
–> Acts like a molecular door
–> Exhibit a range of selectivity depending on the protein
Active Transport
PM proteins that require energy expenditure to move materials AGAINST their gradients
Two types:
1) Primary
2) Secondary
Secondary Active Transport
CO-TRANSPORT
–> Movement of a molecule AGAINST its concentration gradient by COUPLING its transport to another molecule moving down its concentration gradient
–> Uses the energy of electrochemical gradient of another molecule (usually generated somewhere else by primary active transport)
Symporter
Protein that facilitates the coupled transport of one substance to another that are moving in the SAME direction
Antiporter
Protein that facilitates the coupled transport of one substance to another in OPPOSITE directions
Co-transporters
1) Symporters
2) Antiporters
Primary Active Transport
DIRECTLY uses ATP energy for molecular transport
Two main primary active transport proteins:
1) P-TYPE ATPase
2) ABC-Transporter
P-Type ATPase vs ABC Transporter
P-Type –> The transporter itself gets phosphorylated (Phosphorylation triggers conformation change)
ABC –> No phosphorylation!!!! (Binding ATP triggers conformation change)
BOTH involve ATP hydrolysis!!
P-Type ATPase Process
1) Pump open to one side of the membrane (not phosphorylated) and allowing substrate in to bind
2) ATP bound to the pump is hydrolyzed, phosphorylating a specific AA of the pump itself
3) Phosphorylation triggers conformational change in the pump causing it to open to the other side of the membrane (while closing on the previously open side)
4) The bound substrates release and exit the pump into the “new side”
–> While the substrates release, another type of substrate may enter (depending on what pump it is) and bind to the pump
5) The phosphate group leaves (dephosphorylation) the protein pump causing the pump to snap back to its original state (open to the original side)
Starts all over again
ABC Transporter Process
Example of P-Type ATPase
Na+/K+ - ATPase
Ca2+ - ATPase
H+ - ATPase
How much energy does sodium-potassium pump use?
30% of body’s total ATP
What molecules are moved in the sodium-potassium pump?
3 Na+ OUT
2K+ IN
What does ABC transporter stand for?
ATP Binding Casette Transporter
How many domains are a part of the ABC transporter? What are they?
2 Nucleotide Binding Domains (ATP Binds) = NBDs
2 Transmembrane Domains (where substrate interacts and is transported through) = TMDs
Overview (short summary) of ABC transporter mechanism
Substrate-substrate BP complex interacts with the transmembrane domain causing the substrate to be up-taken by the transmembrane domain
ATP binds to the nucleotide binding domain, ATP is hydrolyzed, the NBDs dissociate, pulling the TMDs apart with them = opens TMD to other side and substrate passes through
ABC Transporter Full Process
1) Substrate binds to specific solute binding protein (BP) forming a substrate complex
2) The substrate complex interacts with the TMD triggering a conformational change in which the substrate “enters” the TMD
3) 2 ATP bind to the NBDs
4) ATPs are hydrolyzed (releasing aphosphate grp.) triggering the two NBDs to dissociate (move apart)
5) As NBDs move apart, they pull them their associated TMDs with them causing an opening to form between the TMDs
6) Substrate moves through the opening, crossing the PM
7) ADP is released from NBD and the domains go back to their original conformations
How is the PM involved with energy capture?
PM hosts many proteins associated with electron transport systems!
–> Such systems generate a proton gradient (electrochemical) that generate proton motive force
What is the Proton Motive Force (PMF)?
Potential energy stored across a biological membrane due to a proton gradient
What uses PMF?
1) Respiration (powers ATP synthase)
2) Photosynthesis
3) Flagellar motor (powers rotor)
How is the PM involved in protein secretion?
It hosts numerous proteins that make up the General Secretory Pathway (GSP) which allows for the transmembrane movement of cytoplasmic proteins to the OUTSIDE of the cell
What are the main proteins involved in the general secretory pathway?
SecB
SecA
SecYEG Complex (SecY, SecE, SecG)
General Secretory Pathway Process
1) Protein is synthesized in the ribosome and marked with a signal polypeptide at its end (N-terminal)
2) SecB binds to the nascent-marked-polypeptide (as it is still coming out) = Protein folding is blocked
3) SecA binds to SecB (that is bound to polypeptide) and associates it with the SecYEG channel in the PM
4) SecA hydrolyzes ATP and uses this energy to direct (PUSH) the polypeptide through the SecYEG channel
5) SecB dissociates from the protein as it moves through the channel
6) Upon entry into the cytoplasm, the signal peptide is cleaved by a signal peptidase
7) The polypeptide finally folds into its functional form (in the cytoplasm)
SecB
Protein that binds to secretory polypeptides to prevent their folding and direct them for transport out of the cell
SecA
An ATPase the uses ATP energy to direct (push) SecB-bound protein through the SecYEG channel
How does the PM contribute to sensory systems?
PM hosts numerous receptor proteins that sense the extracellular environment and transduce signals to cytoplasmic response systems
–> Usually causes some change in gene expression that alters protein synthesis
Sulfur Globules
Storage of elemental sulfur within bacteria
Why are sulfur globules important?
In anaerobic bacteria, elemental sulfur (S2) acts as the final electron acceptor in the ETC (allowing ATP to be produced without O2) present
THUS, sulfur globules allow for there to be a store of S2 ready to be used for anaerobic respiration
Other than acting as an electron acceptor, what can bacteria do with elemental sulfur?
They can oxidize it to turn it into SO4- and in doing so release energy
What is topoisomerase in bacteria? Its function?
Histone like proteins!!!
Enzymes that aid in DNA coiling and packaging to compact the bacterial chromosome (so it all fits in the cell)
Reduce the torsional strain associated with DNA supercoiling (by making little cuts in the DNA)
Supercoiling
The twisting of DNA to form a compact chromosome
What is PHB?
(In some cases it can account for how much of the bacterial dry weight?)
Polyhydroxybutyrate
–> A lipid polymer used for carbon storage in bacteria
–> Can sometimes account for 50% of a cell’s dry weight
How do bacteria condense their chromosome into the nucleoid region?
1) Utilizing cations (Mg2+, K+, and Na+) which attach to the (-) sugar-phosphate backbone of DNA, reducing the repulsion between DNA strands and allowing them to compact closer together
2) Positively charged proteins that maintain the condensed form of the nucleoid
3) Topoisomerases which encourage DNA supercoiling
What is the role of cations in the nucleoid?
Cations such as Mg2+, K+, and Na+ bind to the NEGATIVE sugar-phosphate backbone of DNA, shielding the (-) charges of the backbone and allowing the strands of DNA to fold closer to each other (allowing for greater condensation!!!)
What is the smallest a structure can be and still be seen using a LIGHT microscope?
0.2 um
What is the smallest a structure can be and still be seen using an ELECTRON microscope?
0.005um
Staphyloccocus vs Streptococcus
Staphylococcus = CLUSTER of cocci
Streptococcus = CHAIN of cocci
