Topic 2 Flashcards
(151 cards)
1
Q
2 Major differences between prokaryotes and eukaryotes
A
- Prokaryotes generally a lot smaller
- Eukaryotes have organelles while prokaryotes usually don’t
2
Q
Why is a high surface area to volume ratio favoured
A
Small cells (higher ratio) can generally grow (reproduce) quicker than those with a lower ratio
Smaller size also means less time/energy to replicate cell
3
Q
Bacteria shapes
A
Cocci (spheres), Bacilli (rods), Vibrio (comma/bent rod), Helical, Spirochetes (long spirals), appendaged/budding, filamentous
4
Q
Reasons for different cell morphologies
A
Nutrient access/uptake, motility, attachment to surfaces, formation of biofilms, interactions with other microbes or eukaryotic host cells
5
Q
Morphogenesis
A
Monomorphic: one shape; observed in most pure cultures
Pleomorphoic: multiple different morphologies of same bacterium
6
Q
Example of different morphologies at different stages of growth
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Arthrobacter crystallopoietes: grows as a rod during logarithmic (fast) growth and becomes a coccus in stationary phase (slow/no growth)
7
Q
Parts of a cell envelope (structures around cytoplasm)
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Can include cytoplasmic membrane, cell wall, outer membrane, S-layers, etc.
8
Q
Functions of the cell envelope
A
Barrier against environment, protects cell from stress, transport of nutrients into cell and waste out, energy conservation/production, etc.
9
Q
Describe the cytoplasmic (cell) membrane
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- All cells have a cell membrane
- In gram negative aka inner membrane
- Primary barrier between cytoplasm and environment
- Lipid bilayer
10
Q
What makes up a cell membrane
A
Phospholipid bilayer split into a hydrophilic heads and hydrophobic tails
11
Q
What makes up a phospholipid
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Side chain (variable) , glycerol phosphate backbone, fatty acids (inc. unsaturation = inc. fluidity —> can’t pack as tightly b/c of double bonds)
12
Q
Types of proteins found in the cytoplasmic (cell) membrane
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Peripheral (loosely attached), integral (embedded) and transmembrane (type of integral that goes all the way through cell membrane)
13
Q
2 faces of the cytoplasmic (cell) membrane
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Cytoplasmic face (faces cytoplasm) vs periplasmic face (faces out)
- faces are NOT identical, certain domains face one or the other
14
Q
Gram positive cell wall (general)
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Thick cell well (thick peptidoglycan layer), no outer membrane
15
Q
Gram negative cell wall (general)
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Thin cell wall (thin peptidoglycan layer), have an outer membrane
16
Q
Describe peptidoglycan
A
aka murein (not found in archaea and eukarya)
lattice-like structure formed from chains of glycans linked together by peptide beidges
17
Q
Sugar backbone in peptidoglycan
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alternating N-Acetylglucosamine (NAG) and N-Acetylmuramic Acid (NAM) ß(1,4) linkages (glycosidic bond)
18
Q
Peptide crosslinks in peptidoglycan
A
short peptide chain (attached to NAM) covalently linked to the peptide from an adjacent chain via a peptide bond (between position 3 [DAP] and 4 [D-Ala])
19
Q
Gram negative bacteria
A
typically ~1-3 peptidoglycan layers (~2-7 nm thick)
also has an outer membrane that envelopes the thin peptidoglycan layer
20
Q
Gram postive bacteria
A
can be 15+ layers (~20-35 nm)
- has INTERBRIDGES which help connect different peptidoglycan layers, (also peptide crosslinks but extended by a few amino acids)
21
Q
Peptidoglycan peptide sequence
A
Sequence of peptide is conserved for a given bacterium (Not random)
Different (specific) sequences in different organisms
22
Q
Teichoic Acids
A
- only in gram +
- glycerol phosphate or ribitol phosphate with attached D-glucose and/or D-alanine
- covalently attached to peptidoglycan
- help trap divalent metal ions (Mg2+)
23
Q
Gram +: Wall-associated proteins
A
-serve many important functions like cell adhesion
- in gram +, proteins associate (covalently or non-covalently) with the cell wall
- some also interact with teichoic acid
24
Q
Gram staining
A
purple = positive (insoluble crystal violet-iodine)
pink = negative (safranin counterstain)
25
Why is Gram + purple and Gram - pink
+ b/c of thick layer of peptidoglycan which prevents escape of crystal violet dye
- b/c of decolorizing agent degrading the OM and thin peptido. layer allows the crystal violet dye to escape and cells stained with the safranin counterstain
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Unusual bacteria that lack a cell wall
Mycoplasma pneumoniae is a human pathogen (intracellular parasite)
- specialized cell membrane
27
Describe the cell wall
porous and dynamic
- not generally a permeability barrier except to large molecules
28
Describe the Outer Membrane (OM)
- only found in Gram - bacteria
- found outside cell wall
- comprised of LPS
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Asymmetry of the OM
Inner leaflet composed of phospholipid and Outer Leaflet composed of LPS
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Lipopolysaccharide (LPS)
main feature of OM
- has 3 parts: lipid A (within membrane), core polysaccharide (middle of the 2), O-specific polysaccharide (outermost)
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Describe Lipid A
Very different from phospholipids
- anchored in OM by its hydrophobic tails
- aka endotoxin and is sensed by the immune system
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Describe O-specific polysaccharide (O antigen)
- polysacc. comprised of diverse sugar subunits
- usually conserved within a strain but highly variable from lineage to lineage
- can use specific antibodies to detect O antigen
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How is the OM anchored to the Cell wall
Braun's lipoprotein connects OM to cell wall (very abundant in Gram -)
- other end of protein covalently attached to peptidoglycan
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Describe Porins (specific/non-specific)
OM is generally impermeable to large molecules but is permeable to many small molecules due to porins
- protein channels that serve as channels for entrance/exit (specific or nonspecific)
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Functions of the OM
provides mechanical strength to cell - ionic bonds between LPS via divalent metal ions
- more permeable than cell membrane, but still an important barrier and for antibiotic sensitivity
- enables a larger periplasmic space
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Describe the periplasm
mostly in gram - bacteria, the space between inner/outer membranes
- smaller periplasmic space in gram +
- buffer b/w environment and cell
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Periplasm functions
- break down macromolecules for uptake as nutrients
- high affinity binding protein for nutrients
- detoxify harmful compounds
- protein folding (disulfide bond formation)
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What does the periplasm do in Gram + bacteria
Function/importance less clear; smaller space between cell membrane and cell wall
39
Describe S-layers
- some bacteria produce S-layers
- rigid/permeable monolayer of protein or glycoprotein - self-organized into a repeating struture
- always the outermost layer of the cell
- protective layer
40
Describe Capsules and slime layers
-some bacteria produce them (coats of polysaccharides around the cell surface
Capsules are organized into a matrix and attached to the cell whereas slime layers are looseley attached, less organized
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Functions of Capsules and Slime layers
can include: adhering to surfaces, protection from host immune cells & protection from water loss
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Describe Pili & Fimbriae
- pili are protein filaments that extend fromt he surface of a cell
- most bacteria (Gram - specially) produce these
- different types of pili (e.g conjugative)
- Fimbria (considered a type of pili) mediates attachment to a surface or another cell (shorter and more #)
43
What can move freely across the cytoplasmic (cell) membrane
small uncharged, non-polar molecules e.g. dissolved O2, dissolved CO2, small alcohols/ fatty acids
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What molecules can move across the cell membrane at a hindered rate
H2O, glycerol, some amino acids
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What is the cell membrane essentially impermeable to
Large and/or charged molecules, Na+, K+
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How do molecules enter bacterial cells
Passive Transport: requires no energy (Simple and Facilitated diffusion)
Active Transport: requires energy [against conc. gradient] (simple transport, ABC transporters, group transport)
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What is Diffusion
The net movement of a chemical down it's concentration gradient (high to low conc.) (entropically favoured)
- no energy required
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What is Osmosis
The diffusion of water through a selectively permeable membrane
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What is Facilitated Diffusion
Diffusion of molecules across a membrane via a membrane protein e.g. Porins in the OM
- can be specific (carrier proteins) or nonspecific (channel proteins)
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What is Active Transport
- molecules transported against its concentration gradient (needs energy)
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Where does the energy for Active Transport come from
Stored chemical energy (e.g. ATP hydrolysis) or dissipation of another concentration gradient (couple another molecule moving down its conc. gradient)
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What is Simple Transport
- symporters and antiporters use energy from chemical gradients (e.g. the proton motive force) to power the transport of a different molecule against its conc. gradient
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What is a symport
Both molecules travel in the same direction
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What is an antiport
One molecule goes in and the other goes out (travels in opposite "anti" directions)
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What is the Sodium Proton antiporter
- maintains pH (and Na+) homeostasis!
- exchanges protons for Na+ ions
- expels Na+ under high [salt]
- lowers pH of cell under alkaline (basic) conditions
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What is the Lac permease symporter
Proton motive Force (PMF) used to drive the uptake of lactose (& other disaccharides)
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How does the uptake of Lactose be used for energy/nutrients
Lactose hydrolysis has higher energy produced than the energy needed to bring it in
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What is Group translocation
- type of Active transport
- transported substance is bound by a transporter and is chemically modified during transformed
e.g. glucose uptake via phosphotransferase system
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Where does Group translocation get its energy from
Energy provided by hydrolysis of high energy bond in Phosphoenolpyruvate (PEP)
- phosphorylates sugar (glucose) is helpful metabolically
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What is the ABC transporters
- type of active transport
- ATP Binding Cassette (ABC) uses ATP
- one of the largest/oldest gene families (found in all phyla)
- wide range of molecules transported by diff ABC
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What makes up the ABC transporters
- 2 ATPase domains (a dimer) provides energy
- Transmembrane domain(s) (a selective channel)
- Substrate binding protein (binds molecule with high affinity)
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What are Substrate (periplasmic) binding proteins
Prokaryotic ABC transporters best studied in Gram - (captures ligand within the periplasm)
In archaea and Gram + (no OM) substrate binding protein is often tethered to the cell membrane
63
Explain the Uptake of Vitamin B12 (large, complicated, rare molecule)
- example of an ABC transporter
- can't diffuse through porins
- OM barrel protein BtuB binds B12 with high affinity, transports it across the OM using energy from TonB complex (via PMF)
- BtuCD-F = ABC transporter for uptake across cell membrane
64
What is the actual ABC transporter in the uptake of Vitamin B12
BtuCD-F is the actual ABC transporter (spans the cell/cytoplasmic membrane)
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What is BtuF used for
It is a periplasmic binding protein that has very high affinity for Vitamin B12
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What is BtuB
It bind B12 with high affinity and transports it across the OM
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What is the TonB complex
It harnesses energy from the proton motive force (PMF) and in turn gives this energy to BtuB
68
What's an example of a bacteria that isn't motile
Yersinia pestis (caused the plague)
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What is the flagella (general)
large, complex, multi-protein
~50 different proteins
- long, thin filament that acts like a propeller
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What is swarming
multiple bacteria coming together like a raft and moving across a solid surface
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What is Peritrichous
- many flagella across pole/body
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What is monotrichous (polar)
- 1 flagellum at a single pole
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What is lophotrichous
- many flagella, all at one pole
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What is amphitrichous
- 2 flagella, one at each pole
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What is atrichous
- no flagella at all
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How does petritrichous flagella move
Longer runs (counterclockwise) and short tumbles (clockwise) (one or more flagella start to rotate CW and disrupts the bundle from moving CCW)
- switching from CCW to CW dictates direction
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How do monotrichous flagellum move
they have a reversible flagellum (switches directions)
or
they have a unidirectional flagella (rotation stops/starts and the random movement during stops changes directions)
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What are the 3 segments of the flagellum
Filament (long, thin propeller)
Hook (adaptor that connects filament to basal body)
Basal Body (core of the structure; powers rotation of filament)
79
Describe the flagellar motor
>20 proteins anchored in cell membrane and cell wall
- uses the proton motive force
- Central rod passes through a series of rings (MS, C, P and L)
- Stator couples the flow of protons to rotation of the MS ring
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Describe the MS ring (cytoplasmic membrane)
- rotates the rod and ultimately hook and filament
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Describe the L (outer membrane) / P (peptidoglycan) rings
acts like bearings to help rotation
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Describe the C ring (cytoplasm)
- generates torque, switch motor direction, flagellin secretion
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What rings are present in Gram positive bacteria
Only C and MS rings are present; lack P and L rings (since Gram + bacteria has no OM and a thick peptidoglycan)
84
Describe the Flagellar filament (flagellin)
- long filament that drives movement
- made of 1000s of copies of a single protein called flagellin
~5-10 µM long, ~20 nm wide
- free at one end (enviro) and connected to motor (via rod, hook)
- often used in serotyping (H antigen)
- rigid, helical and hollow
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How is the flagellum made
- structure built from inside out (inside built first)
- flagellin grows from outside (produced in cytoplasm & secreted through flagellum via hollow filament)
- new subunit assembles at end (outside cell) with help of cap proteins
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What is the Type III secretion system
it is used to export flagellin: a related system is used as a protein toxin injection system by certain pathogens
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What are some variations in flagellar motility
- some bacteria have motors that use Na+ gradient instead of PMF
- spirochetes flagellum
- flagellar motility is often highly regulated
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How are spirochetes flagellum unique
- spirochetes have a flagellum (axial filament) that resides in periplasm - rotation = corkscrew motion of entire bacterium
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Describe Taxis
Taxis is the directed movement of bacteria (think of telling a taxi where you wanna go)
- accomplished using a bias random walk
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Describe Chemotaxis
movement in the direction of gradients of increasing or decreasing concentration to particular chemicals (towards chemicals)
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How do bacteria move towards a desirable nutrient
longer runs, less frequent tumbles
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If bacteria are moving away from a desirable nutrient
shorter runs, more frequent tumbles (when they orient to a new direction)
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What is phototaxis
Movement toward/away from light
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What is Aerotaxis
Directed motility in response to O2 (usually towards?)
- similar to chemotaxis
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Describe Carbon Storage polymers
Bacteria (and other microbes) store carbon when times are good (for periods of starvation)
- store carbon as lipids -- most common is poly-ß-hydroxybutric acid (PHB)
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What is Twitching motility
(non-flageller motility)
Type IV pilus attaches to surface and retracts
- acts like a grappling hook
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What are cell inclusions
Prokaryotic cells can contain inclusions -- bodies or aggregates within the cell
- often related to storage of a substance
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What are microcompartments
Bacterial cells can have microcompoartments -- polyhedral protein shells that encase specific enzymes/metabolites/cofactors
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When is poly-ß-hydroxybutryic acid (PHB) made
This polymer is produced when there is an excess of carbon/energy and it aggregates and form large granules
- broken down when needed
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What are some other storage granules
- Inorganic phosphate stored in polyphosphate granules and is broken down to form nucleic acids/ phospholipids
- Sulfur storage granules (by bacteria that oxidized reduced sulfur compounds for energy)
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Describe Gas vesicles
- used in bacteria/archaea that can float
- protein structures that keep water/solutes out, but allow gas in
- buoyant! to bring microbes to favourable enviro. e.g. more light
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What are Carboxysomes
a microcompartment that concentrates enzymes invovled in CO2 fixation - increases efficiency and reduces unwanted side reactions
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Another purpose of microcompartments
Protect cell against toxic/reactive intermediates or biproducts
- e.g. propionaldehyde, a toxic intermediate
- encapsulates toxics
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Describe Endospores (kinda like cryogenically freezing yourself)
highly differentiated, dormant cells (survive starvation and very harsh enviro.)
- only produced by some members of the phylum Firmicutes (Gram +)
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Describe Endospore formation
Vegetative cell -> developing endospore inside sporulating cell -> mature endospore -> back to vegitative state when enviro is more favourable
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Describe Vegitative cells
- they are metabolically active, growing/dividing cells
- differentiate into endospores upon nutrient deprivation (initiates endospore formation)
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Features of Endospores that make them resistance
- High Calcium content, and dipicolinic acid is present
- low water content, and small acid-soluble spore proteins present
- metabolism is shut off
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How important is the dehydration of the core for endospores
KEY! - water goes from >80% to <25%,
- resistant to dessication, heat, chemicals
- inactivates (withiout denaturing) cell's enzymes
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Describe Dipicolinic Acid (DPA)
- unique to spores
- complexed with Ca2+
- important for dehydration process
- binds/stabilizes DNA
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Describe Small Acid Soluble Proteins (SASPs)
- only made during sporulation
- Bind DNA (makes it compact and protect from damage: UV, heat, denaturation, mutation)
- carbon/energy source during germination/outgrowth
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Desribe Endospore structure
Core (DNA/ribosomes)
Cortex (peptidoglycan layer)
2 membranes ("OM" - not like Gram -, no LPS)
Coat (outside of OM, protective protein layer)
SOME have another protein layer called exosporium
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Sporulation Stages
Assymetric Cell division
Engulfment
Late sporulation
maturation
Mother cell Lysis
Germination
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Vegetative cycle
Growth and Cell division
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What happens in Assymetric cell division of sporulation
commitment to sporulation! (can't go back duh)
- septum forms (separates mother cell and forespore)
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What hapens in Engulfment stage of sporulation
Outer spore membrane formed
- septium turns into 2 membranes?
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What happens in Late sporulation stage
cortex and spore coat formed
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What happens in Maturation stage of sporulation
dehydration of spore, Ca2+ uptake, SASPs, dipicolinc acid
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What happens during Mother cell lysis stage of sporulation
The endospore is freed and could stay here for 20 mins or 20 years (needs favourable conditions)
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When does the free endospore enter germination
When environmental conditions are favourable
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Does Archaea share a more recent common ancestor with Eukarya or Bacteria
Eukarya!
- Archaea have more DNA related biology/processes
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What are some unique components of Archaea cell membranes
Ether-linked instead of Ester
isoprenoid isntead of fatty acids
contain side branches and rings
lipid monolayer
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Describe the Lipid monolayer in Archaea
The lipid tails are joined
- diglycerol tetraethers instead of glycerol diether
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Describe Archaea cell walls
- variation of cell wall depending on environment
- proteinaceous S-layers act as cell wall (majority)
- some have carbohydrate structures
- few archaea lack a cell wall
- rare few have a second membrane
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Describe Pseudomurein in Archaeal cell walls
- small subset of Archaea cell walls
-murein = peptido.
- pseudo = fake
- Lacks D-amino acids, diff sugar linkages, NAM replaced with NAT
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What's the differences between Pseudomurein and Peptidoglycan
Pseudo has:
- β (1-3) linkages -> immune to lysozyme
- NAT instead of NAM
- No D isomers
Peptido has:
- β (1,4) linkages -> can be lysed
- NAM
- D isomers
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Describe the Hamus
- unique archaea appendage that fix cells to a surface or to other cells
- proteinaceous "grappling hook"
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Describe the Archaellum
- like the flagellum but in arachaea (but functionally/evolutionarily distinct)
- simpler (less proteins) than flagella (but uses ATP hydrolysis not PMF)
- Filament built from inside out (opposite of flagellum)
- Archaea generally swim slower
126
Describe Haloquadratum walsbyi
- extreme halophile found in hyper-saline lakes (4x salt in seawater)
- very unique morphology (thin squares - high SA to Volume ratio)
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Describe the endosymbiotic theory
alpha-proteobacterium (aerobic) swalleowed by a large anaerobic bacteria
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Describe Asgard Archaea
- superphylum of archaea (lokiarchaeota discovered first)
- closer related to eukarya
- found in anaerobic marine sediments
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What are some genomic components of Asgard archaea?
- contain eukaryote-specific genes
- genes related to the cytoskeleton and vesicular trafficking
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Eukaryotic Components: Nucleus
where DNA is contained
- transcription/ translation uncoupled (coupled in bacteria)
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Eukaryotic Components: Mitochondria
- almost universal in all eukaryotes
- vary in number & shape depending on type of cell
- energy center of the cell (respiration & ATP synth)
- contains its own genomes, ribosomes
- evloved from alphaproteobacterium
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Eukaryotic Compartments: Golgi comples & endoplasmic reticulum
- modifying & sorting proteins (& lipids) to be secreted from cell or to other parts of the cell
- where glycosylation takes place (sugars added)
- proteins and other molecules packaged into vesicles
133
Describe the cytoskeleton (eukaryotes)
dynamic protein filament network (actin, IF and MT) invovled in cell shape, transport within cell and cell movement
134
Describe Vacuoles (eukaryotes)
- membrane bound compartment
- store nutrients and/or waste
- lysosomes (specialized vacuole): enzymes to break down incoming nutrients
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Descibe Chloroplasts (eukaryotes: phototrophs)
- contain the machinery for photosynthesis
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Describe Vesicles (eukaryotes)
small, membrane vound compartments used to traffic materials around the cell, into/out of cells and b/w organelles
- "vehicles" for materials
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Describe the Cell Wall (eukaryotes)
- found in plants and fungi, not in animals
- much diversity
138
Describe an example of Eukaryotic microbe
(saccharomyces cerevisiae)
- model yeast organism
- small/simple eukaryote (has comparmentalization)
- ~20x largger than E. coli
139
What is the LECA
Last eukaryotic common ancestor
- ancestor of all eukaryotes
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What are the 5 supergroups of Eukarya
Acrhaeplastida
SAR clade (not a plant or animal, not tested)
Exacavates
Amoebozoa
Opisthokonta
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What is the secondary endosymbiosis
Chloroplast uptake after the mitochondria
142
Describe Algae
- definition is highly variable (photosynthetic organisms that aren't plants)
- includes microbes (micro algae) and non-microbes (macro algae)
- 10 000s - 100 000s of species (many are single-celled eukaryotes)
143
Describe Fungi
kingdom of life that includes both microbes (e.g. yeast) and non-microbes (e.g. mushrooms)
- microbial group most-closely related to animals
- mostly non-motile
- Chitin cell walls
144
What kingdom has Chitin (polysaccharide) cell walls
defining features in fungi
145
Describe Candida albicans
- opportunistic fungal pathogen
- common in healthy individuals
- most common cause of yeast infections in women
146
Describe Yeast
- single-celled fungi (S. cerevisiae)
- model system for eukaryote genetics and cell biology
- converts carbohydrates to CO2 + alcohol via fermentation
- used in baking & brewing
147
Describe Amoeba
- single-celled eukaryotes
- use pseudopods for locomotion
- live in many enviro (e.g fresh water and soil)
148
What are Pseudopods
- in Amoebas
- temporary projections that stick out from cell - use these as "arms" to crawl across surfaces
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Some "P" words that can relate to eukaryote microbes
Protist/protozoa (eukaryote that isn't a plant, animal or fungus
Plankton (Drifters)
Parasite (specific symbiotic relationship & a generic term for some eukaryotic microbe pathogens)
